Mercurial > repos > bgruening > flexynesis
changeset 3:525c661a7fdc draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
| author | bgruening |
|---|---|
| date | Tue, 24 Jun 2025 05:55:40 +0000 |
| parents | 902e26dc8e81 |
| children | |
| files | fetch_cbioportal_data.py flexynesis.xml flexynesis_plot.py flexynesis_utils.py macros.xml test-data/embeddings.csv test-data/labels.csv test-data/labels_pr.csv test-data/labels_scatter.csv test-data/loc.sample test-data/mut.tabular test-data/test/clin test-data/train/clin tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 15 files changed, 21041 insertions(+), 2032 deletions(-) [+] |
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--- a/fetch_cbioportal_data.py Wed May 14 06:46:42 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -#!/usr/bin/env python - -import argparse -import os - -from flexynesis.utils import CBioPortalData - - -def main(): - parser = argparse.ArgumentParser(description="Fetch and prepare cBioPortal data for Flexynesis.") - parser.add_argument("--study_id", required=True, help="cBioPortal study ID (e.g., 'brca_tcga')") - parser.add_argument("--data_types", required=True, help="Comma-separated list of data types (e.g., 'clin,mut,omics')") - parser.add_argument("--mapped_files", default=None, help="Comma-separated list of .txt files to map to data_types (optional)") - parser.add_argument("--split_ratio", type=float, default=0.7, help="Training/test split ratio (0.0 to 1.0)") - parser.add_argument("--output_dir", required=True, help="Output directory for datasets") - - args = parser.parse_args() - - data_types = args.data_types.split(",") - if "clin" not in data_types: - raise ValueError("Clinical data ('clin') is required for splitting the dataset.") - - file_mapping = { - "clin": "data_clinical_patient.txt", # can be any with 'clinical' in file name - "mut": "data_mutations.txt", # any with 'mutations' in file name - "omics": "data_cna.txt", - "other": None - } - - if args.mapped_files: - mapped_files = args.mapped_files.split(",") - if len(mapped_files) != len(data_types): - raise ValueError(f"Number of mapped files ({len(mapped_files)}) must match number of data types ({len(data_types)}).") - files_to_fetch = {dt: mf for dt, mf in zip(data_types, mapped_files)} - for mf in mapped_files: - if not mf.endswith(".txt"): - raise ValueError(f"Mapped file '{mf}' must end with '.txt'.") - else: - files_to_fetch = {dt: file_mapping[dt] for dt in data_types if dt in file_mapping} - - invalid_types = set(data_types) - set(file_mapping.keys()) - if invalid_types: - raise ValueError(f"Invalid data types: {invalid_types}. Supported types: {list(file_mapping.keys())}") - - cbioportal = CBioPortalData(study_id=args.study_id) - cbioportal.get_cbioportal_data(study_id=args.study_id, files=files_to_fetch) - dataset = cbioportal.split_data(ratio=args.split_ratio) - - os.makedirs(args.output_dir, exist_ok=True) - - for data_type in data_types: - if data_type in dataset['train']: - train_file = os.path.join(args.output_dir, f"{data_type}_train.csv") - dataset['train'][data_type].to_csv(train_file, index=True) - if data_type in dataset['test']: - test_file = os.path.join(args.output_dir, f"{data_type}_test.csv") - dataset['test'][data_type].to_csv(test_file, index=True) - - -if __name__ == "__main__": - main()
--- a/flexynesis.xml Wed May 14 06:46:42 2025 +0000 +++ b/flexynesis.xml Tue Jun 24 05:55:40 2025 +0000 @@ -5,6 +5,9 @@ </macros> <expand macro="edam"/> <expand macro="requirements"/> + <required_files> + <include path="flexynesis_plot.py" /> + </required_files> <command detect_errors="exit_code"><![CDATA[ @CHECK_NON_COMMERCIAL_USE@ mkdir -p input/test input/train output && @@ -15,7 +18,7 @@ #set $name = str($assay_main.replace(" ", "_")) ln -s '$train_omics_main' input/train/${name}.csv && ln -s '$test_omics_main' input/test/${name}.csv && - #set $data_names = [$name] + #set $data_names = [$name] #else ln -s '$train_omics_main' input/train/main.csv && ln -s '$test_omics_main' input/test/main.csv && @@ -47,52 +50,179 @@ #end if #end if #end for - flexynesis - --data_path 'input' - --outdir 'output' - --model_class $model_class - #if str($model_class) == 'GNN': - --gnn_conv_type $gnn_conv_type - --string_organism $string_organism - --string_node_name $string_node_name - #end if - #if str($training_type.model) == 's_train': - #if str($target_variables) != '': - --target_variables $target_variables - #end if - #if str($surv_event_var) != '': - --surv_event_var $surv_event_var - --surv_time_var $surv_time_var - #end if + flexynesis + --data_path input + --outdir output + --model_class $model_class + #if str($model_class) == 'GNN': + --gnn_conv_type $gnn_conv_type + --string_organism $string_organism + --string_node_name $string_node_name + #end if + #if str($training_type.model) == 's_train': + #if str($target_variables) != '': + --target_variables $target_variables + #end if + #if str($surv_event_var) != '': + --surv_event_var $surv_event_var + --surv_time_var $surv_time_var + #end if + #end if + #if str($training_type.model) == 'cm_train': + --input_layers $str(",".join($input_layers)) + --output_layers $str(",".join($output_layers)) + #end if + --fusion_type $fusion_type + --hpo_iter $hpo_iter + --val_size $val_size + --finetuning_samples $finetuning_samples + --variance_threshold $variance_threshold + --correlation_threshold $correlation_threshold + --subsample $subsample + --features_min $features_min + --features_top_percentile $features_top_percentile + --data_types $str(",".join($data_names)) + --early_stop_patience $early_stop_patience + --hpo_patience $hpo_patience + $log_transform + $use_loss_weighting + $use_cv + $evaluate_baseline_performance + --feature_importance_method $feature_importance_method + \${GALAXY_FLEXYNESIS_EXTRA_ARGUMENTS} + #if str($plot.plot_embeddings_conditional.plot_embeddings) == 'yes': + && python $__tool_directory__/flexynesis_plot.py + --plot_type dimred + --embeddings output/job.embeddings_test.csv + --labels output/job.predicted_labels.csv + --method $plot.plot_embeddings_conditional.method + --target_variables $target_variables + --output_dir plots + --format $plot.plot_embeddings_conditional.format + --dpi $plot.plot_embeddings_conditional.dpi + #end if + #if str($plot.plot_km_conditional.plot_km) == 'yes': + #if str($surv_event_var) == '' or str($surv_time_var) == '': + && echo "Survival event and time variables must be specified for Kaplan-Meier plots." + && exit 1 + #else + && python $__tool_directory__/flexynesis_plot.py + --plot_type kaplan_meier + --labels output/job.predicted_labels.csv + --survival_data input/test/clin.csv + --surv_event_var $surv_event_var + --surv_time_var $surv_time_var + --event_value $plot.plot_km_conditional.event_value + --output_dir plots + --format $plot.plot_km_conditional.format + --dpi $plot.plot_km_conditional.dpi + #end if + #end if + #if str($plot.plot_cox_conditional.plot_cox) == 'yes': + #if str($surv_event_var) == '' or str($surv_time_var) == '': + && echo "Survival event and time variables must be specified for cox plots." + && exit 1 + #else + && python $__tool_directory__/flexynesis_plot.py + --plot_type cox + --model output/job.final_model.pth + --clinical_train input/train/clin.csv + --clinical_test input/test/clin.csv + #if str($plot.plot_cox_conditional.omics_name) != '': + #set $name = str($plot.plot_cox_conditional.omics_name.replace(" ", "_")) + --omics_train input/train/${name}.csv + --omics_test input/test/${name}.csv + #else + --omics_train input/train/main.csv + --omics_test input/test/main.csv #end if - #if str($training_type.model) == 'cm_train': - --input_layers $str(",".join($input_layers)) - --output_layers $str(",".join($output_layers)) + --surv_time_var $surv_time_var + --surv_event_var $surv_event_var + #if str($plot.plot_cox_conditional.clinical_variables) != '': + --clinical_variables $str($plot.plot_cox_conditional.clinical_variables) + #end if + --top_features $plot.plot_cox_conditional.top_features + --event_value $plot.plot_cox_conditional.event_value + #if str($plot.plot_cox_conditional.crossval_conditional.crossval) == 'yes': + --crossval + #end if + #if str($plot.plot_cox_conditional.crossval_conditional.crossval) == 'yes': + --n_splits $plot.plot_cox_conditional.crossval_conditional.n_splits #end if - --fusion_type $fusion_type - --hpo_iter $hpo_iter - --val_size $val_size - --finetuning_samples $finetuning_samples - --variance_threshold $variance_threshold - --correlation_threshold $correlation_threshold - --subsample $subsample - --features_min $features_min - --features_top_percentile $features_top_percentile - --data_types $str(",".join($data_names)) - --early_stop_patience $early_stop_patience - --hpo_patience $hpo_patience - $log_transform - $use_loss_weighting - $use_cv - $evaluate_baseline_performance - --feature_importance_method $feature_importance_method - $disable_marker_finding - \${GALAXY_FLEXYNESIS_EXTRA_ARGUMENTS} + --random_state 42 + --output_dir plots + --format $plot.plot_cox_conditional.format + --dpi $plot.plot_cox_conditional.dpi + #end if + #end if + #if str($plot.plot_scatter_conditional.plot_scatter) == 'yes': + && python $__tool_directory__/flexynesis_plot.py + --plot_type scatter + --labels output/job.predicted_labels.csv + #if str($surv_event_var) != '': + --target_value $target_variables,$surv_event_var + #else + --target_value $target_variables + #end if + --output_dir plots + --format $plot.plot_scatter_conditional.format + --dpi $plot.plot_scatter_conditional.dpi + #end if + #if str($plot.plot_concordance_conditional.plot_concordance) == 'yes': + && python $__tool_directory__/flexynesis_plot.py + --plot_type concordance_heatmap + --labels output/job.predicted_labels.csv + #if str($surv_event_var) != '': + --target_value $target_variables,$surv_event_var + #else + --target_value $target_variables + #end if + --output_dir plots + --format $plot.plot_concordance_conditional.format + --dpi $plot.plot_concordance_conditional.dpi + #end if + #if str($plot.plot_pr_curves_conditional.plot_pr_curves) == 'yes': + && python $__tool_directory__/flexynesis_plot.py + --plot_type pr_curve + --labels output/job.predicted_labels.csv + #if str($surv_event_var) != '': + --target_value $target_variables,$surv_event_var + #else + --target_value $target_variables + #end if + --output_dir plots + --format $plot.plot_pr_curves_conditional.format + --dpi $plot.plot_pr_curves_conditional.dpi + #end if + #if str($plot.plot_roc_curves_conditional.plot_roc_curves) == 'yes': + && python $__tool_directory__/flexynesis_plot.py + --plot_type roc_curve + --labels output/job.predicted_labels.csv + #if str($surv_event_var) != '': + --target_value $target_variables,$surv_event_var + #else + --target_value $target_variables + #end if + --output_dir plots + --format $plot.plot_roc_curves_conditional.format + --dpi $plot.plot_roc_curves_conditional.dpi + #end if + #if str($plot.plot_boxplot_conditional.plot_boxplot) == 'yes': + && python $__tool_directory__/flexynesis_plot.py + --plot_type box_plot + --labels output/job.predicted_labels.csv + #if str($surv_event_var) != '': + --target_value $target_variables,$surv_event_var + #else + --target_value $target_variables + #end if + --output_dir plots + --format $plot.plot_boxplot_conditional.format + --dpi $plot.plot_boxplot_conditional.dpi + #end if ]]></command> <inputs> - <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> - <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> - </param> + <expand macro="commercial_use_param"/> <conditional name="training_type"> <param name="model" type="select" label="Type of Analysis" > <option value="s_train">Supervised training</option> @@ -139,19 +269,13 @@ <when value="XGBoost"/> </conditional> <param argument="--target_variables" type="text" label="Target variables" help="Which variables in 'clin.csv' to use for predictions, comma-separated if multiple."> - <sanitizer invalid_char=""> - <valid initial="string.printable"></valid> - </sanitizer> + <expand macro="sanitizer_printable"/> </param> <param argument="--surv_event_var" type="text" label="Survival event" help="Which column in 'clin.csv' to use as event/status indicator for survival modeling."> - <sanitizer invalid_char=""> - <valid initial="string.printable"></valid> - </sanitizer> + <expand macro="sanitizer_printable"/> </param> <param argument="--surv_time_var" type="text" label="Survival time" help="Which column in 'clin.csv' to use as time/duration indicator for survival modeling."> - <sanitizer invalid_char=""> - <valid initial="string.printable"></valid> - </sanitizer> + <expand macro="sanitizer_printable"/> </param> <expand macro="advanced"/> </when> @@ -182,16 +306,138 @@ <option value="CrossModalPred">CrossModalPred</option> </param> <expand macro="advanced"/> - </when> + </when> </conditional> + <section name="plot" title="Visualization"> + <conditional name="plot_embeddings_conditional"> + <param name="plot_embeddings" type="select" label="Generate embeddings plot?" help="Generate PCA or UMAP plot of the test dataset"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="method" type="select" label="Transformation method"> + <option value="pca" selected="true">PCA</option> + <option value="umap">UMAP</option> + </param> + <expand macro="plots_common_param"/> + </when> + </conditional> + <conditional name="plot_km_conditional"> + <param name="plot_km" type="select" label="Generate kaplan meier curves plot?" help="Generate KM curves plot of risk subtype based on predicted events probabilities"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="event_value" type="text" label="Event value" optional="false" help="The value in the event column that indicates an event (e.g. death) has occurred."> + <expand macro="sanitizer_printable"/> + </param> + <expand macro="plots_common_param"/> + </when> + </conditional> + <conditional name="plot_cox_conditional"> + <param name="plot_cox" type="select" label="Generate hazard ratio plot?" help="Performs Cox regression on data based on top features and selected clinical covariates."> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="omics_name" type="text" label="Omics layer to use for cox input" optional="false" help="If not specified, the first omics layer will be used."> + <expand macro="sanitizer_printable"/> + </param> + <param name="clinical_variables" type="text" label="Clinical covariates" optional="true" help="Comma-separated list of clinical covariates to include in the Cox model (e.g SEX, AGE, ...)."> + <expand macro="sanitizer_printable"/> + </param> + <param argument="--top_features" type="integer" min="1" value="20" label="Number of top important features to include in Cox model"/> + <param name="event_value" type="text" label="Event value" optional="false" help="The value in the event column that indicates an event (e.g. death) has occurred."> + <expand macro="sanitizer_printable"/> + </param> + <conditional name="crossval_conditional"> + <param name="crossval" type="select" label="Performs K-fold cross-validation?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <param name="n_splits" type="integer" min="2" value="5" label="Number of folds for cross-validation"/> + </when> + <when value="no"/> + </conditional> + <expand macro="plots_common_param"/> + </when> + </conditional> + <conditional name="plot_scatter_conditional"> + <param name="plot_scatter" type="select" label="Generate scatter plot?" help="Generates a scatter plot of numeric true and predicted labels for all available targets."> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <expand macro="plots_common_param"/> + </when> + </conditional> + <conditional name="plot_concordance_conditional"> + <param name="plot_concordance" type="select" label="Generate concordance heatmap plot?" help="Generates a plot showing the concordance between true and predicted labels for all targets."> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <expand macro="plots_common_param"/> + </when> + </conditional> + <conditional name="plot_pr_curves_conditional"> + <param name="plot_pr_curves" type="select" label="Generate precision-recall curves plot?" help="Generates precision-recall curves for all available targets."> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <expand macro="plots_common_param"/> + </when> + </conditional> + <conditional name="plot_roc_curves_conditional"> + <param name="plot_roc_curves" type="select" label="Generate ROC curves plot?" help="Generates ROC curves for all available targets."> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <expand macro="plots_common_param"/> + </when> + </conditional> + <conditional name="plot_boxplot_conditional"> + <param name="plot_boxplot" type="select" label="Generate boxplot?" help="Generates a boxplot for all available targets."> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <expand macro="plots_common_param"/> + </when> + </conditional> + </section> </inputs> <outputs> <collection name="results" type="list" label="${tool.name} on ${on_string}: results"> <discover_datasets pattern="(?P<name>.+)\.csv$" format="csv" directory="output"/> </collection> + <collection name="plots" type="list" label="${tool.name} on ${on_string}: embeddings plots"> + <discover_datasets pattern="__name_and_ext__" directory="plots"/> + <filter>plot['plot_embeddings_conditional']['plot_embeddings'] == 'yes' or plot['plot_km_conditional']['plot_km'] == 'yes' or plot['plot_cox_conditional']['plot_cox'] == 'yes' or plot['plot_scatter_conditional']['plot_scatter'] == 'yes' or plot['plot_concordance_conditional']['plot_concordance'] == 'yes' or plot['plot_pr_curves_conditional']['plot_pr_curves'] == 'yes' or plot['plot_roc_curves_conditional']['plot_roc_curves'] == 'yes' or plot['plot_boxplot_conditional']['plot_boxplot'] == 'yes'</filter> + </collection> </outputs> <tests> - <test> + <!-- test 1: Supervised training with GEX and CNV data, DirectPred model, Erlotinib target --> + <test expect_num_outputs="1"> <param name="non_commercial_use" value="True"/> <conditional name="training_type"> <param name="model" value="s_train"/> @@ -263,7 +509,8 @@ </element> </output_collection> </test> - <test> + <!-- test 2: Supervised training with GEX data, DirectPred model, Erlotinib target --> + <test expect_num_outputs="1"> <param name="non_commercial_use" value="True"/> <conditional name="training_type"> <param name="model" value="s_train"/> @@ -325,7 +572,8 @@ </element> </output_collection> </test> - <test> + <!-- test 3: Supervised training with GEX and CNV data, DirectPred model, Irinotecan target --> + <test expect_num_outputs="1"> <param name="non_commercial_use" value="True"/> <conditional name="training_type"> <param name="model" value="s_train"/> @@ -397,7 +645,8 @@ </element> </output_collection> </test> - <test> + <!-- test 4: Un-supervised training with GEX and CNV data, supervised_vae model --> + <test expect_num_outputs="1"> <param name="non_commercial_use" value="True"/> <conditional name="training_type"> <param name="model" value="us_train"/> @@ -439,7 +688,8 @@ </element> </output_collection> </test> - <test> + <!-- test 5: Cross-modality training with GEX and CNV data, CrossModalPred model --> + <test expect_num_outputs="1"> <param name="non_commercial_use" value="True"/> <conditional name="training_type"> <param name="model" value="cm_train"/> @@ -493,7 +743,8 @@ </element> </output_collection> </test> - <test> + <!-- test 6: Supervised training with GEX and CNV data, GNN model, Erlotinib target --> + <test expect_num_outputs="1"> <param name="non_commercial_use" value="True"/> <conditional name="training_type"> <param name="model" value="s_train"/> @@ -568,7 +819,8 @@ </element> </output_collection> </test> - <test> + <!-- test 7: test 4 + checking whitespace in assay name --> + <test expect_num_outputs="1"> <param name="non_commercial_use" value="True"/> <conditional name="training_type"> <param name="model" value="us_train"/> @@ -610,7 +862,8 @@ </element> </output_collection> </test> - <test> + <!-- test 8: Supervised training with GEX and CNV data, XGBoost model, Erlotinib target --> + <test expect_num_outputs="1"> <param name="non_commercial_use" value="True"/> <conditional name="training_type"> <param name="model" value="s_train"/> @@ -642,7 +895,8 @@ </element> </output_collection> </test> - <test> + <!-- test 9: test 1 + checking IntegratedGradients method --> + <test expect_num_outputs="1"> <param name="non_commercial_use" value="True"/> <conditional name="training_type"> <param name="model" value="s_train"/> @@ -708,20 +962,312 @@ </element> </output_collection> </test> + <!-- test 10: dimred plot --> + <test expect_num_outputs="2"> + <param name="non_commercial_use" value="True"/> + <conditional name="training_type"> + <param name="model" value="s_train"/> + <param name="train_clin" value="train/clin" ftype="csv"/> + <param name="test_clin" value="test/clin" ftype="csv"/> + <param name="train_omics_main" value="train/gex" ftype="csv"/> + <param name="test_omics_main" value="test/gex" ftype="csv"/> + <param name="assay_main" value="bar"/> + <repeat name="omics"> + <param name="train_omics" value="train/cnv" ftype="csv"/> + <param name="test_omics" value="test/cnv" ftype="csv"/> + <param name="assay" value="foo"/> + </repeat> + <conditional name="model_class"> + <param name="model_class" value="DirectPred"/> + </conditional> + <param name="target_variables" value="Erlotinib"/> + <section name="advanced"> + <param name="hpo_iter" value="1"/> + </section> + </conditional> + <section name="plot"> + <conditional name="plot_embeddings_conditional"> + <param name="plot_embeddings" value="yes"/> + <param name="method" value="pca"/> + <param name="format" value="jpg"/> + <param name="dpi" value="300"/> + </conditional> + </section> + <output_collection name="results" type="list"> + <element name="job.embeddings_test"> + <assert_contents> + <has_n_lines n="50"/> + </assert_contents> + </element> + <element name="job.embeddings_train"> + <assert_contents> + <has_n_lines n="50"/> + </assert_contents> + </element> + <element name="job.feature_importance.GradientShap"> + <assert_contents> + <has_text_matching expression="Erlotinib,0,,bar,A2M,"/> + <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/> + <has_text_matching expression="GradientShap"/> + </assert_contents> + </element> + <element name="job.feature_importance.IntegratedGradients"> + <assert_contents> + <has_text_matching expression="Erlotinib,0,,bar,A2M,"/> + <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/> + <has_text_matching expression="IntegratedGradients"/> + </assert_contents> + </element> + <element name="job.feature_logs.bar"> + <assert_contents> + <has_n_lines n="25"/> + </assert_contents> + </element> + <element name="job.feature_logs.omics_foo"> + <assert_contents> + <has_n_lines n="25"/> + </assert_contents> + </element> + <element name="job.predicted_labels"> + <assert_contents> + <has_text_matching expression="source_dataset:A-704,Erlotinib,"/> + <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/> + </assert_contents> + </element> + <element name="job.stats"> + <assert_contents> + <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/> + <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/> + <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="plots" type="list"> + <element name="job.embeddings_test_pca_Erlotinib_known"> + <assert_contents> + <has_image_center_of_mass center_of_mass="962,732" eps="5"/> + <has_image_channels channels="3"/> + <has_image_height height="1461"/> + <has_image_width width="1941"/> + </assert_contents> + </element> + <element name="job.embeddings_test_pca_Erlotinib_predicted"> + <assert_contents> + <has_image_center_of_mass center_of_mass="959.5,732.5" eps="5"/> + <has_image_channels channels="3"/> + <has_image_height height="1461"/> + <has_image_width width="1941"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- test 11: km plot --> + <test expect_num_outputs="2"> + <expand macro="common_test"> + <section name="plot"> + <conditional name="plot_km_conditional"> + <param name="plot_km" value="yes"/> + <param name="event_value" value="1:DECEASED"/> + <param name="format" value="jpg"/> + <param name="dpi" value="300"/> + </conditional> + </section> + </expand> + <output_collection name="plots" type="list"> + <element name="clin_km_km_risk_subtypes"> + <assert_contents> + <has_image_center_of_mass center_of_mass="971,732" eps="5"/> + <has_image_channels channels="3"/> + <has_image_height height="1461"/> + <has_image_width width="1941"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- test 12: cox plot --> + <test expect_num_outputs="2"> + <expand macro="common_test"> + <section name="plot"> + <conditional name="plot_cox_conditional"> + <param name="plot_cox" value="yes"/> + <param name="omics_name" value="bar"/> + <param name="clinical_variables" value="Crizotinib, Erlotinib"/> + <param name="top_features" value="10"/> + <param name="event_value" value="1:DECEASED"/> + <param name="format" value="jpg"/> + <param name="dpi" value="300"/> + </conditional> + </section> + </expand> + <output_collection name="plots" type="list"> + <element name="job.final_model_cox_hazard_ratios"> + <assert_contents> + <has_image_center_of_mass center_of_mass="972,737" eps="5"/> + <has_image_channels channels="3"/> + <has_image_height height="1461"/> + <has_image_width width="1941"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- test 13: scatter plot --> + <test expect_num_outputs="2"> + <expand macro="common_test"> + <section name="plot"> + <conditional name="plot_scatter_conditional"> + <param name="plot_scatter" value="yes"/> + <param name="format" value="jpg"/> + <param name="dpi" value="300"/> + </conditional> + </section> + </expand> + <output_collection name="plots" type="list"> + <element name="job.predicted_labels_scatter_Erlotinib"> + <assert_contents> + <has_image_center_of_mass center_of_mass="969,735" eps="5"/> + <has_image_channels channels="3"/> + <has_image_height height="1461"/> + <has_image_width width="1940"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- test 14: concordance plot --> + <test expect_num_outputs="2"> + <expand macro="common_test"> + <section name="plot"> + <conditional name="plot_concordance_conditional"> + <param name="plot_concordance" value="yes"/> + <param name="format" value="jpg"/> + <param name="dpi" value="300"/> + </conditional> + </section> + </expand> + <output_collection name="plots" type="list"> + <element name="job.predicted_labels_concordance_Erlotinib"> + <assert_contents> + <has_image_center_of_mass center_of_mass="1547,1620" eps="30"/> + <has_image_channels channels="3"/> + <has_image_height height="3060" delta="50"/> + <has_image_width width="3192" delta="50"/> + </assert_contents> + </element> + <element name="job.predicted_labels_concordance_OS_STATUS"> + <assert_contents> + <has_image_channels channels="3"/> + <has_image_height height="2558" delta="50"/> + <has_image_width width="2794" delta="50"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- test 15: pr curve plot --> + <test expect_num_outputs="2"> + <expand macro="common_test"> + <section name="plot"> + <conditional name="plot_pr_curves_conditional"> + <param name="plot_pr_curves" value="yes"/> + <param name="format" value="jpg"/> + <param name="dpi" value="300"/> + </conditional> + </section> + </expand> + <output_collection name="plots" type="list"> + <element name="job.predicted_labels_pr_curves_OS_STATUS"> + <assert_contents> + <has_image_center_of_mass center_of_mass="975,732" eps="20"/> + <has_image_channels channels="3"/> + <has_image_height height="1461" delta="20"/> + <has_image_width width="1941" delta="20"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- test 16: roc curve plot --> + <test expect_num_outputs="2"> + <expand macro="common_test"> + <section name="plot"> + <conditional name="plot_roc_curves_conditional"> + <param name="plot_roc_curves" value="yes"/> + <param name="format" value="jpg"/> + <param name="dpi" value="300"/> + </conditional> + </section> + </expand> + <output_collection name="plots" type="list"> + <element name="job.predicted_labels_roc_curves_OS_STATUS"> + <assert_contents> + <has_image_center_of_mass center_of_mass="970,730" eps="20"/> + <has_image_channels channels="3"/> + <has_image_height height="1461" delta="20"/> + <has_image_width width="1941" delta="20"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- test 17: boxplot plot --> + <test expect_num_outputs="2"> + <expand macro="common_test"> + <section name="plot"> + <conditional name="plot_boxplot_conditional"> + <param name="plot_boxplot" value="yes"/> + <param name="format" value="jpg"/> + <param name="dpi" value="300"/> + </conditional> + </section> + </expand> + <output_collection name="plots" type="list"> + <element name="job.predicted_labels_box_plot_OS_STATUS_0_LIVING"> + <assert_contents> + <has_image_center_of_mass center_of_mass="1485,882" eps="20"/> + <has_image_channels channels="3"/> + <has_image_height height="1783" delta="20"/> + <has_image_width width="2967" delta="20"/> + </assert_contents> + </element> + <element name="job.predicted_labels_box_plot_OS_STATUS_1_DECEASED"> + <assert_contents> + <has_image_center_of_mass center_of_mass="1485,882" eps="20"/> + <has_image_channels channels="3"/> + <has_image_height height="1765" delta="20"/> + <has_image_width width="2967" delta="20"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- test 18: cox plot with multiple clinical variables + crossvar--> + <test expect_num_outputs="2"> + <expand macro="common_test"> + <section name="plot"> + <conditional name="plot_cox_conditional"> + <param name="plot_cox" value="yes"/> + <param name="omics_name" value="bar"/> + <param name="clinical_variables" value="Crizotinib, Erlotinib"/> + <param name="top_features" value="10"/> + <param name="event_value" value="1:DECEASED"/> + <conditional name="crossval_conditional"> + <param name="crossval" value="yes"/> + <param name="n_splits" value="5"/> + </conditional> + <param name="format" value="jpg"/> + <param name="dpi" value="300"/> + </conditional> + </section> + </expand> + <output_collection name="plots" type="list"> + <element name="job.final_model_cox_hazard_ratios"> + <assert_contents> + <has_image_center_of_mass center_of_mass="972,737" eps="5"/> + <has_image_channels channels="3"/> + <has_image_height height="1461"/> + <has_image_width width="1941"/> + </assert_contents> + </element> + </output_collection> + </test> </tests> - <help> -.. class:: warningmark - -**WARNING: This tool is only available for NON-COMMERCIAL use. Permission is only granted for academic, research, and educational purposes. Before using, be sure to review, agree, and comply with the license.** - -Flexynesis is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. -The package includes multiple types of deep learning architectures such as simple fully connected networks, supervised variational autoencoders, graph convolutional networks, multi-triplet networks different options of data layer fusion, and automates feature selection and hyperparameter optimisation. - -For more information, please check the Documentation_ : - -For commercial use, please review the license_ and contact the `copyright holders`_ . - ------ + <help><![CDATA[ +@COMMON_HELP@ .. image:: https://raw.githubusercontent.com/BIMSBbioinfo/flexynesis/c4634d97f84e51f569dcfdab2caf42c9be453ef6/img/graphical_abstract.jpg :width: 600 @@ -732,27 +1278,27 @@ **clin.csv** -clin.csv contains the sample metadata. The first column contains unique sample identifiers. The other columns contain sample-associated clinical variables. NA values are allowed in the clinical variables. +clin.csv contains the sample metadata. The first column contains unique sample identifiers. The other columns contain sample-associated clinical variables. NA values are allowed in the clinical variables. The format might look like so: -======== === === === +======== === === === , v1 v2 ... -------- --- --- --- sample1 a b ... -------- --- --- --- sample2 c d ... -------- --- --- --- -sample3 e f ... +sample3 e f ... -------- --- --- --- -... ... ... ... +... ... ... ... ======== === === === . **omics.csv** -The first column of the feature tables must be unique feature identifiers (e.g. gene names). The column names must be sample identifiers that should overlap with those in the clin.csv. They don't have to be completely identical or in the same order. Samples from the clin.csv that are not represented in the omics table will be dropped. +The first column of the feature tables must be unique feature identifiers (e.g. gene names). The column names must be sample identifiers that should overlap with those in the clin.csv. They don't have to be completely identical or in the same order. Samples from the clin.csv that are not represented in the omics table will be dropped. The format might look like so: @@ -774,7 +1320,7 @@ **Concordance between train/test splits:** -The corresponding omics files in train/test splits must contain overlapping feature names (they don't have to be identical or in the same order). The clin.csv files in train/test must contain matching clinical variables. +The corresponding omics files in train/test splits must contain overlapping feature names (they don't have to be identical or in the same order). The clin.csv files in train/test must contain matching clinical variables. ----- @@ -783,10 +1329,10 @@ **Minimum requirements** * clin.csv and omics.csv files for training and testing -* Selection of a tool/model +* Selection of a tool/model * One target variable which can be numerical or categorical for regression/classification tasks. -Flexynesis supports both single-task and multi-task training. We can provide one or more target variables and optionally survival variables as input and Flexynesis will build the appropriate model architecture. If the selected variable is numerical, a Multi-Layered-Perceptron (MLP) with MSE loss will be used. If a categorical variable is provided, an MLP with cross-entropy-loss will be utilized. If survival variables are provided, an MLP with Cox-Proportional-Hazards loss will be attached to the model. +Flexynesis supports both single-task and multi-task training. We can provide one or more target variables and optionally survival variables as input and Flexynesis will build the appropriate model architecture. If the selected variable is numerical, a Multi-Layered-Perceptron (MLP) with MSE loss will be used. If a categorical variable is provided, an MLP with cross-entropy-loss will be utilized. If survival variables are provided, an MLP with Cox-Proportional-Hazards loss will be attached to the model. **Regression:** @@ -802,15 +1348,15 @@ If your target variable is survival data, Flexynesis will build a survival analysis model. -For survival analysis, two separate variables are required, where the first variable is a numeric event variable (consisting of 0's or 1's, where 1 means an event such as disease progression or death has occurred). The second variable is also a numeric time variable, which indicates how much time it took since last patient follow-up. +For survival analysis, two separate variables are required, where the first variable is a numeric event variable (consisting of 0's or 1's, where 1 means an event such as disease progression or death has occurred). The second variable is also a numeric time variable, which indicates how much time it took since last patient follow-up. .. class:: infomark -**Note:** Flexynesis can be trained with multiple target variables, which can be a mixture of regression/classification/survival tasks. +**Note:** Flexynesis can be trained with multiple target variables, which can be a mixture of regression/classification/survival tasks. .. class:: infomark -**Note:** For the supervised tasks, the user can easily switch between different model architectures. +**Note:** For the supervised tasks, the user can easily switch between different model architectures. .. class:: infomark @@ -828,13 +1374,13 @@ **Unsupervised Training** -In the absence of any target variables or survival variables, you can use a VAE architecture to carry out unsupervised training. +In the absence of any target variables or survival variables, you can use a VAE architecture to carry out unsupervised training. ----- **Cross-modality Training** -We have implemented a special case of VAEs where the input data layers and output data layers can be set to different data modalities. The purpose of a cross-modality encoder is to learn embeddings that can translate from one data modality to another. Crossmodality encoder we implemented supports both single/multiple input layers and also one or more target/survival variables can be added to the model. +We have implemented a special case of VAEs where the input data layers and output data layers can be set to different data modalities. The purpose of a cross-modality encoder is to learn embeddings that can translate from one data modality to another. Crossmodality encoder we implemented supports both single/multiple input layers and also one or more target/survival variables can be added to the model. .. class:: infomark @@ -844,14 +1390,13 @@ .. class:: infomark -**Modality fusion:** +**Modality fusion:** -Flexynesis currently supports two main ways of fusing different omics data modalities: 1. Early fusion: The input data matrices are initially concatenated and pushed through the networks 2. Intermediate fusion: The input data matrices are initially pushed through the networks to obtain a modality-specific embedding space, which then gets concatenated to serve as input for the supervisor MLPs. +Flexynesis currently supports two main ways of fusing different omics data modalities: 1. Early fusion: The input data matrices are initially concatenated and pushed through the networks 2. Intermediate fusion: The input data matrices are initially pushed through the networks to obtain a modality-specific embedding space, which then gets concatenated to serve as input for the supervisor MLPs. -.. _license: https://github.com/BIMSBbioinfo/flexynesis/blob/main/LICENSE .. _Documentation: https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/site/ .. _copyright holders: https://github.com/BIMSBbioinfo/flexynesis - </help> - - <expand macro="citations" /> + ]]></help> + <expand macro="creator"/> + <expand macro="citations"/> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexynesis_plot.py Tue Jun 24 05:55:40 2025 +0000 @@ -0,0 +1,1282 @@ +#!/usr/bin/env python +"""Generate plots using flexynesis +This script generates dimensionality reduction plots, Kaplan-Meier survival curves, +and Cox proportional hazards models from data processed by flexynesis.""" + +import argparse +import os +from pathlib import Path + +import matplotlib.pyplot as plt +import numpy as np +import pandas as pd +import seaborn as sns +import torch +from flexynesis import ( + build_cox_model, + get_important_features, + plot_dim_reduced, + plot_hazard_ratios, + plot_kaplan_meier_curves, + plot_pr_curves, + plot_roc_curves, + plot_scatter +) +from scipy.stats import kruskal, mannwhitneyu + + +def load_embeddings(embeddings_path): + """Load embeddings from a file""" + try: + # Determine file extension + file_ext = Path(embeddings_path).suffix.lower() + + if file_ext == '.csv': + df = pd.read_csv(embeddings_path, index_col=0) + elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']: + df = pd.read_csv(embeddings_path, sep='\t', index_col=0) + else: + raise ValueError(f"Unsupported file extension: {file_ext}") + + return df, df.index.tolist() + + except Exception as e: + raise ValueError(f"Error loading embeddings from {embeddings_path}: {e}") from e + + +def load_labels(labels_input): + """Load predicted labels from flexynesis""" + try: + # Determine file extension + file_ext = Path(labels_input).suffix.lower() + + if file_ext == '.csv': + df = pd.read_csv(labels_input) + elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']: + df = pd.read_csv(labels_input, sep='\t') + + # Check if this is the specific format with sample_id, known_label, predicted_label + required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label'] + if all(col in df.columns for col in required_cols): + return df + else: + raise ValueError(f"Labels file {labels_input} does not contain required columns: {required_cols}") + + except Exception as e: + raise ValueError(f"Error loading labels from {labels_input}: {e}") from e + + +def load_survival_data(survival_path): + """Load survival data from a file. First column should be sample_id""" + try: + # Determine file extension + file_ext = Path(survival_path).suffix.lower() + + if file_ext == '.csv': + df = pd.read_csv(survival_path, index_col=0) + elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']: + df = pd.read_csv(survival_path, sep='\t', index_col=0) + else: + raise ValueError(f"Unsupported file extension: {file_ext}") + return df + + except Exception as e: + raise ValueError(f"Error loading survival data from {survival_path}: {e}") from e + + +def load_omics(omics_path): + """Load omics data from a file. First column should be features""" + try: + # Determine file extension + file_ext = Path(omics_path).suffix.lower() + + if file_ext == '.csv': + df = pd.read_csv(omics_path, index_col=0) + elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']: + df = pd.read_csv(omics_path, sep='\t', index_col=0) + else: + raise ValueError(f"Unsupported file extension: {file_ext}") + return df + + except Exception as e: + raise ValueError(f"Error loading omics data from {omics_path}: {e}") from e + + +def load_model(model_path): + """Load flexynesis model from pickle file""" + try: + with open(model_path, 'rb') as f: + model = torch.load(f, weights_only=False) + return model + except Exception as e: + raise ValueError(f"Error loading model from {model_path}: {e}") from e + + +def match_samples_to_embeddings(sample_names, label_data): + """Filter label data to match sample names in the embeddings""" + df_matched = label_data[label_data['sample_id'].isin(sample_names)] + return df_matched + + +def detect_color_type(labels_series): + """Auto-detect whether target variables should be treated as categorical or numerical""" + # Remove NaN + clean_labels = labels_series.dropna() + + if clean_labels.empty: + return 'categorical' # default output if no labels + + # Check if all values can be converted to numbers + try: + numeric_labels = pd.to_numeric(clean_labels, errors='coerce') + + # If conversion failed -> categorical + if numeric_labels.isna().any(): + return 'categorical' + + # Check number of unique values + unique_count = len(clean_labels.unique()) + total_count = len(clean_labels) + + # If few unique values relative to total -> categorical + # Threshold: if unique values < 10 OR unique/total < 0.1 + if unique_count < 10 or (unique_count / total_count) < 0.1: + return 'categorical' + else: + return 'numerical' + + except Exception: + return 'categorical' + + +def plot_label_concordance_heatmap(labels1, labels2, figsize=(12, 10)): + """ + Plot a heatmap reflecting the concordance between two sets of labels using pandas crosstab. + + Parameters: + - labels1: The first set of labels. + - labels2: The second set of labels. + """ + # Compute the cross-tabulation + ct = pd.crosstab(pd.Series(labels1, name='Labels Set 1'), pd.Series(labels2, name='Labels Set 2')) + # Normalize the cross-tabulation matrix column-wise + ct_normalized = ct.div(ct.sum(axis=1), axis=0) + + # Plot the heatmap + plt.figure(figsize=figsize) + sns.heatmap(ct_normalized, annot=True, cmap='viridis', linewidths=.5) # col_cluster=False) + plt.title('Concordance between label groups') + + return plt.gcf() + + +def plot_boxplot(categorical_x, numerical_y, title_x='Categories', title_y='Values', figsize=(10, 6), jittersize=4): + """ + Create a boxplot with to visualize the distribution of predicted probabilities across different categories. + the x axis represents the true labels, and the y axis represents the predicted probabilities for specific categories. + """ + df = pd.DataFrame({title_x: categorical_x, title_y: numerical_y}) + + # Compute p-value + groups = df[title_x].unique() + if len(groups) == 2: + group1 = df[df[title_x] == groups[0]][title_y] + group2 = df[df[title_x] == groups[1]][title_y] + stat, p = mannwhitneyu(group1, group2, alternative='two-sided') + test_name = "Mann-Whitney U" + else: + group_data = [df[df[title_x] == group][title_y] for group in groups] + stat, p = kruskal(*group_data) + test_name = "Kruskal-Wallis" + + # Create a boxplot with jittered points + plt.figure(figsize=figsize) + sns.boxplot(x=title_x, y=title_y, hue=title_x, data=df, palette='Set2', legend=False, fill=False) + sns.stripplot(x=title_x, y=title_y, data=df, color='black', size=jittersize, jitter=True, dodge=True, alpha=0.4) + + # Labels and p-value annotation + plt.xlabel(title_x) + plt.ylabel(title_y) + plt.text( + x=-0.4, + y=plt.ylim()[1], + s=f'{test_name} p = {p:.3e}', + verticalalignment='top', + horizontalalignment='left', + fontsize=12, + bbox=dict(boxstyle='round,pad=0.3', facecolor='white', edgecolor='gray') + ) + + plt.tight_layout() + return plt.gcf() + + +def generate_dimred_plots(embeddings, matched_labels, args, output_dir, output_name_base): + """Generate dimensionality reduction plots""" + + # Parse target variables + target_vars = [var.strip() for var in args.target_variables.split(',')] + + print(f"Generating {args.method.upper()} plots for {len(target_vars)} target variable(s): {', '.join(target_vars)}") + + # Check variables + available_vars = matched_labels['variable'].unique() + missing_vars = [var for var in target_vars if var not in available_vars] + + if missing_vars: + print(f"Warning: The following target variables were not found in the data: {', '.join(missing_vars)}") + print(f"Available variables: {', '.join(available_vars)}") + + # Filter to only process available variables + valid_vars = [var for var in target_vars if var in available_vars] + + if not valid_vars: + raise ValueError(f"None of the specified target variables were found in the data. Available: {', '.join(available_vars)}") + + # Generate plots for each valid target variable + for var in valid_vars: + print(f"\nPlotting variable: {var}") + + # Filter matched labels for current variable + var_labels = matched_labels[matched_labels['variable'] == var].copy() + var_labels = var_labels.drop_duplicates(subset='sample_id') + + if var_labels.empty: + print(f"Warning: No data found for variable '{var}', skipping...") + continue + + # Auto-detect color type + known_color_type = detect_color_type(var_labels['known_label']) + predicted_color_type = detect_color_type(var_labels['predicted_label']) + + print(f" Auto-detected color types - Known: {known_color_type}, Predicted: {predicted_color_type}") + + try: + # Plot 1: Known labels + print(f" Creating known labels plot for {var}...") + fig_known = plot_dim_reduced( + matrix=embeddings, + labels=var_labels['known_label'], + method=args.method, + color_type=known_color_type + ) + + output_path_known = output_dir / f"{output_name_base}_{var}_known.{args.format}" + print(f" Saving known labels plot to: {output_path_known.name}") + fig_known.save(output_path_known, dpi=args.dpi, bbox_inches='tight') + + # Plot 2: Predicted labels + print(f" Creating predicted labels plot for {var}...") + fig_predicted = plot_dim_reduced( + matrix=embeddings, + labels=var_labels['predicted_label'], + method=args.method, + color_type=predicted_color_type + ) + + output_path_predicted = output_dir / f"{output_name_base}_{var}_predicted.{args.format}" + print(f" Saving predicted labels plot to: {output_path_predicted.name}") + fig_predicted.save(output_path_predicted, dpi=args.dpi, bbox_inches='tight') + + print(f" ✓ Successfully created plots for variable '{var}'") + + except Exception as e: + print(f" ✗ Error creating plots for variable '{var}': {e}") + continue + + print(f"\nDimensionality reduction plots completed for {len(valid_vars)} variable(s)!") + + +def generate_km_plots(survival_data, label_data, args, output_dir, output_name_base): + """Generate Kaplan-Meier plots""" + print("Generating Kaplan-Meier curves of risk subtypes...") + + # Reset index and rename the index column to sample_id + survival_data = survival_data.reset_index() + if survival_data.columns[0] != 'sample_id': + survival_data = survival_data.rename(columns={survival_data.columns[0]: 'sample_id'}) + + # Convert survival event column to binary (0/1) based on event_value + # Check if the event column exists + if args.surv_event_var not in survival_data.columns: + raise ValueError(f"Column '{args.surv_event_var}' not found in survival data") + + # Convert to string for comparison to handle mixed types + survival_data[args.surv_event_var] = survival_data[args.surv_event_var].astype(str) + event_value_str = str(args.event_value) + + # Create binary event column (1 if matches event_value, 0 otherwise) + survival_data[f'{args.surv_event_var}_binary'] = ( + survival_data[args.surv_event_var] == event_value_str + ).astype(int) + + # Filter for survival category and class_label == '1:DECEASED' + label_data['class_label'] = label_data['class_label'].astype(str) + + label_data = label_data[(label_data['variable'] == args.surv_event_var) & (label_data['class_label'] == event_value_str)] + + # check survival data + for col in [args.surv_time_var, args.surv_event_var]: + if col not in survival_data.columns: + raise ValueError(f"Column '{col}' not found in survival data") + + # Merge survival data with labels + df_deceased = pd.merge(survival_data, label_data, on='sample_id', how='inner') + + if df_deceased.empty: + raise ValueError("No matching samples found after merging survival and label data.") + + # Get risk scores + risk_scores = df_deceased['probability'].values + + # Compute groups (e.g., median split) + quantiles = np.quantile(risk_scores, [0.5]) + groups = np.digitize(risk_scores, quantiles) + group_labels = ['low_risk' if g == 0 else 'high_risk' for g in groups] + + fig_known = plot_kaplan_meier_curves( + durations=df_deceased[args.surv_time_var], + events=df_deceased[f'{args.surv_event_var}_binary'], + categorical_variable=group_labels + ) + + output_path_known = output_dir / f"{output_name_base}_km_risk_subtypes.{args.format}" + print(f"Saving Kaplan-Meier plot to: {output_path_known.absolute()}") + fig_known.save(output_path_known, dpi=args.dpi, bbox_inches='tight') + + print("Kaplan-Meier plot saved successfully!") + + +def generate_cox_plots(model, clinical_train, clinical_test, omics_train, omics_test, args, output_dir, output_name_base): + """Generate Cox proportional hazards plots""" + print("Generating Cox proportional hazards analysis...") + + # Parse clinical variables + clinical_vars = [var.strip() for var in args.clinical_variables.split(',')] + + # Validate that survival variables are included + required_vars = [args.surv_time_var, args.surv_event_var] + for var in required_vars: + if var not in clinical_vars: + clinical_vars.append(var) + + print(f"Using clinical variables: {', '.join(clinical_vars)}") + + # filter datasets for clinical variables + if all(var in clinical_train.columns and var in clinical_test.columns for var in clinical_vars): + df_clin_train = clinical_train[clinical_vars] + df_clin_test = clinical_test[clinical_vars] + # Drop rows with NaN in clinical variables + df_clin_train = df_clin_train.dropna(subset=clinical_vars) + df_clin_test = df_clin_test.dropna(subset=clinical_vars) + else: + raise ValueError(f"Not all clinical variables found in datasets. Available in train dataset: {clinical_train.columns.tolist()}, Available in test dataset: {clinical_test.columns.tolist()}") + + # Combine + df_clin = pd.concat([df_clin_train, df_clin_test], axis=0) + + # Get top survival markers + print(f"Extracting top {args.top_features} important features for {args.surv_event_var}...") + try: + imp = get_important_features(model, + var=args.surv_event_var, + top=args.top_features + )['name'].unique().tolist() + print(f"Top features: {', '.join(imp)}") + except Exception as e: + raise ValueError(f"Error getting important features: {e}") + + # Extract feature data from omics datasets + try: + omics_test = omics_test.loc[omics_test.index.isin(imp)] + omics_train = omics_train.loc[omics_train.index.isin(imp)] + # Drop rows with NaN in omics datasets + omics_test = omics_test.dropna(subset=omics_test.columns) + omics_train = omics_train.dropna(subset=omics_train.columns) + + df_imp = pd.concat([omics_train, omics_test], axis=1) + df_imp = df_imp.T # Transpose to have samples as rows + + print(f"Feature data shape: {df_imp.shape}") + except Exception as e: + raise ValueError(f"Error extracting feature subset: {e}") + + # Combine markers with clinical variables + df = pd.merge(df_imp, df_clin, left_index=True, right_index=True) + print(f"Combined data shape: {df.shape}") + + # Remove samples without survival endpoints + initial_samples = len(df) + df = df[df[args.surv_event_var].notna()] + final_samples = len(df) + print(f"Removed {initial_samples - final_samples} samples without survival data") + + if df.empty: + raise ValueError("No samples remain after filtering for survival data") + + # Convert survival event column to binary (0/1) based on event_value + # Convert to string for comparison to handle mixed types + df[args.surv_event_var] = df[args.surv_event_var].astype(str) + event_value_str = str(args.event_value) + + df[f'{args.surv_event_var}'] = ( + df[args.surv_event_var] == event_value_str + ).astype(int) + + # Build Cox model + print(f"Building Cox model with time variable: {args.surv_time_var}, event variable: {args.surv_event_var}") + try: + coxm = build_cox_model(df, + duration_col=args.surv_time_var, + event_col=args.surv_event_var, + crossval=args.crossval, + n_splits=args.n_splits, + random_state=args.random_state) + print("Cox model built successfully") + except Exception as e: + raise ValueError(f"Error building Cox model: {e}") + + # Generate hazard ratios plot + try: + print("Generating hazard ratios plot...") + fig = plot_hazard_ratios(coxm) + + output_path = output_dir / f"{output_name_base}_hazard_ratios.{args.format}" + print(f"Saving hazard ratios plot to: {output_path.absolute()}") + fig.save(output_path, dpi=args.dpi, bbox_inches='tight') + + print("Cox proportional hazards analysis completed successfully!") + + except Exception as e: + raise ValueError(f"Error generating hazard ratios plot: {e}") + + +def generate_plot_scatter(labels, args, output_dir, output_name_base): + """Generate scatter plot of known vs predicted labels""" + print("Generating scatter plots of known vs predicted labels...") + + # Parse target values from comma-separated string + if args.target_value: + target_values = [val.strip() for val in args.target_value.split(',')] + else: + # If no target values specified, use all unique variables + target_values = labels['variable'].unique().tolist() + + print(f"Processing target values: {target_values}") + + successful_plots = 0 + skipped_plots = 0 + + for target_value in target_values: + print(f"\nProcessing target value: '{target_value}'") + + # Filter labels for the current target value + target_labels = labels[labels['variable'] == target_value] + + if target_labels.empty: + print(f" Warning: No data found for target value '{target_value}' - skipping") + skipped_plots += 1 + continue + + # Check if labels are numeric and convert + true_values = pd.to_numeric(target_labels['known_label'], errors='coerce') + predicted_values = pd.to_numeric(target_labels['predicted_label'], errors='coerce') + + if true_values.isna().all() or predicted_values.isna().all(): + print(f"No valid numeric values found for known or predicted labels in '{target_value}'") + skipped_plots += 1 + continue + + try: + print(f" Generating scatter plot for '{target_value}'...") + fig = plot_scatter(true_values, predicted_values) + + # Create output filename with target value + safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_') + if len(target_values) > 1: + output_filename = f"{output_name_base}_{safe_target_name}.{args.format}" + else: + output_filename = f"{output_name_base}.{args.format}" + + output_path = output_dir / output_filename + print(f" Saving scatter plot to: {output_path.absolute()}") + fig.save(output_path, dpi=args.dpi, bbox_inches='tight') + + successful_plots += 1 + print(f" Scatter plot for '{target_value}' generated successfully!") + + except Exception as e: + print(f" Error generating plot for '{target_value}': {str(e)}") + skipped_plots += 1 + + # Summary + print(" Summary:") + print(f" Successfully generated: {successful_plots} plots") + print(f" Skipped: {skipped_plots} plots") + + if successful_plots == 0: + raise ValueError("No scatter plots could be generated. Check your data and target values.") + + print("Scatter plot generation completed!") + + +def generate_label_concordance_heatmap(labels, args, output_dir, output_name_base): + """Generate label concordance heatmap""" + print("Generating label concordance heatmaps...") + + # Parse target values from comma-separated string + if args.target_value: + target_values = [val.strip() for val in args.target_value.split(',')] + else: + # If no target values specified, use all unique variables + target_values = labels['variable'].unique().tolist() + + print(f"Processing target values: {target_values}") + + for target_value in target_values: + print(f"\nProcessing target value: '{target_value}'") + + # Filter labels for the current target value + target_labels = labels[labels['variable'] == target_value] + + if target_labels.empty: + print(f" Warning: No data found for target value '{target_value}' - skipping") + continue + + true_values = target_labels['known_label'].tolist() + predicted_values = target_labels['predicted_label'].tolist() + + try: + print(f" Generating heatmap for '{target_value}'...") + fig = plot_label_concordance_heatmap(true_values, predicted_values) + plt.close(fig) + + # Create output filename with target value + safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_') + if len(target_values) > 1: + output_filename = f"{output_name_base}_{safe_target_name}.{args.format}" + else: + output_filename = f"{output_name_base}.{args.format}" + + output_path = output_dir / output_filename + print(f" Saving heatmap to: {output_path.absolute()}") + fig.savefig(output_path, dpi=args.dpi, bbox_inches='tight') + + except Exception as e: + print(f" Error generating heatmap for '{target_value}': {str(e)}") + continue + + print("Label concordance heatmap generated successfully!") + + +def generate_pr_curves(labels, args, output_dir, output_name_base): + """Generate precision-recall curves""" + print("Generating precision-recall curves...") + + # Parse target values from comma-separated string + if args.target_value: + target_values = [val.strip() for val in args.target_value.split(',')] + else: + # If no target values specified, use all unique variables + target_values = labels['variable'].unique().tolist() + + print(f"Processing target values: {target_values}") + + for target_value in target_values: + print(f"\nProcessing target value: '{target_value}'") + + # Filter labels for the current target value + target_labels = labels[labels['variable'] == target_value] + + # Check if this is a regression problem (no class probabilities) + prob_columns = target_labels['class_label'].unique() + non_na_probs = target_labels['probability'].notna().sum() + + print(f" Class labels found: {list(prob_columns)}") + print(f" Non-NaN probabilities: {non_na_probs}/{len(target_labels)}") + + # If most probabilities are NaN, this is likely a regression problem + if non_na_probs < len(target_labels) * 0.1: # Less than 10% valid probabilities + print(" Detected regression problem - precision-recall curves not applicable") + print(f" Skipping '{target_value}' (use regression evaluation metrics instead)") + continue + + # Debug: Check data quality + total_rows = len(target_labels) + missing_labels = target_labels['known_label'].isna().sum() + missing_probs = target_labels['probability'].isna().sum() + unique_samples = target_labels['sample_id'].nunique() + unique_classes = target_labels['class_label'].nunique() + + print(f" Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes") + print(f" Missing data: {missing_labels} missing known_label, {missing_probs} missing probability") + + if missing_labels > 0: + print(f" Warning: Found {missing_labels} missing known_label values") + missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5] + print(f" Sample IDs with missing known_label: {list(missing_samples)}") + + # Remove rows with missing known_label + target_labels = target_labels.dropna(subset=['known_label']) + if target_labels.empty: + print(f" Error: No valid known_label data remaining for '{target_value}' - skipping") + continue + + # 1. Pivot to wide format + prob_df = target_labels.pivot(index='sample_id', columns='class_label', values='probability') + + print(f" After pivot: {prob_df.shape[0]} samples x {prob_df.shape[1]} classes") + print(f" Class columns: {list(prob_df.columns)}") + + # Check for NaN values in probability data + nan_counts = prob_df.isna().sum() + if nan_counts.any(): + print(f" NaN counts per class: {dict(nan_counts)}") + print(f" Samples with any NaN: {prob_df.isna().any(axis=1).sum()}/{len(prob_df)}") + + # Drop only rows where ALL probabilities are NaN + all_nan_rows = prob_df.isna().all(axis=1) + if all_nan_rows.any(): + print(f" Dropping {all_nan_rows.sum()} samples with all NaN probabilities") + prob_df = prob_df[~all_nan_rows] + + remaining_nans = prob_df.isna().sum().sum() + if remaining_nans > 0: + print(f" Warning: {remaining_nans} individual NaN values remain - filling with 0") + prob_df = prob_df.fillna(0) + + if prob_df.empty: + print(f" Error: No valid probability data remaining for '{target_value}' - skipping") + continue + + # 2. Get true labels + true_labels_df = target_labels.drop_duplicates('sample_id')[['sample_id', 'known_label']].set_index('sample_id') + + # 3. Align indices - only keep samples that exist in both datasets + common_indices = prob_df.index.intersection(true_labels_df.index) + if len(common_indices) == 0: + print(f" Error: No common sample_ids between probability and true label data for '{target_value}' - skipping") + continue + + print(f" Found {len(common_indices)} samples with both probability and true label data") + + # Filter both datasets to common indices + prob_df_aligned = prob_df.loc[common_indices] + y_true = true_labels_df.loc[common_indices]['known_label'] + + # 4. Final check for NaN values + if y_true.isna().any(): + print(f" Error: True labels still contain NaN after alignment for '{target_value}' - skipping") + continue + + if prob_df_aligned.isna().any().any(): + print(f" Error: Probability data still contains NaN after alignment for '{target_value}' - skipping") + continue + + # 5. Convert categorical labels to integer labels + # Create a mapping from class names to integers + class_names = list(prob_df_aligned.columns) + class_to_int = {class_name: i for i, class_name in enumerate(class_names)} + + print(f" Class mapping: {class_to_int}") + + # Convert true labels to integers + y_true_np = y_true.map(class_to_int).to_numpy() + y_probs_np = prob_df_aligned.to_numpy() + + print(f" Data shape: y_true={y_true_np.shape}, y_probs={y_probs_np.shape}") + print(f" Unique true labels (integers): {set(y_true_np)}") + print(f" Class labels (columns): {class_names}") + print(f" Label distribution: {dict(zip(*np.unique(y_true_np, return_counts=True)))}") + + # Check for any unmapped labels (will be NaN) + if pd.isna(y_true_np).any(): + print(" Error: Some true labels could not be mapped to class columns") + unmapped_labels = set(y_true[y_true.map(class_to_int).isna()]) + print(f" Unmapped labels: {unmapped_labels}") + print(f" Available classes: {class_names}") + continue + + try: + print(f" Generating precision-recall curve for '{target_value}'...") + fig = plot_pr_curves(y_true_np, y_probs_np) + + # Create output filename with target value + safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_') + if len(target_values) > 1: + output_filename = f"{output_name_base}_{safe_target_name}.{args.format}" + else: + output_filename = f"{output_name_base}.{args.format}" + + output_path = output_dir / output_filename + print(f" Saving precision-recall curve to: {output_path.absolute()}") + fig.save(output_path, dpi=args.dpi, bbox_inches='tight') + + except Exception as e: + print(f" Error generating precision-recall curve for '{target_value}': {str(e)}") + print(f" Debug info - y_true type: {type(y_true_np)}, contains NaN: {pd.isna(y_true_np).any()}") + print(f" Debug info - y_probs type: {type(y_probs_np)}, contains NaN: {pd.isna(y_probs_np).any()}") + continue + + print("Precision-recall curves generated successfully!") + + +def generate_roc_curves(labels, args, output_dir, output_name_base): + """Generate ROC curves""" + print("Generating ROC curves...") + + # Parse target values from comma-separated string + if args.target_value: + target_values = [val.strip() for val in args.target_value.split(',')] + else: + # If no target values specified, use all unique variables + target_values = labels['variable'].unique().tolist() + + print(f"Processing target values: {target_values}") + + for target_value in target_values: + print(f"\nProcessing target value: '{target_value}'") + + # Filter labels for the current target value + target_labels = labels[labels['variable'] == target_value] + + # Check if this is a regression problem (no class probabilities) + prob_columns = target_labels['class_label'].unique() + non_na_probs = target_labels['probability'].notna().sum() + + print(f" Class labels found: {list(prob_columns)}") + print(f" Non-NaN probabilities: {non_na_probs}/{len(target_labels)}") + + # If most probabilities are NaN, this is likely a regression problem + if non_na_probs < len(target_labels) * 0.1: # Less than 10% valid probabilities + print(" Detected regression problem - ROC curves not applicable") + print(f" Skipping '{target_value}' (use regression evaluation metrics instead)") + continue + + # Debug: Check data quality + total_rows = len(target_labels) + missing_labels = target_labels['known_label'].isna().sum() + missing_probs = target_labels['probability'].isna().sum() + unique_samples = target_labels['sample_id'].nunique() + unique_classes = target_labels['class_label'].nunique() + + print(f" Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes") + print(f" Missing data: {missing_labels} missing known_label, {missing_probs} missing probability") + + if missing_labels > 0: + print(f" Warning: Found {missing_labels} missing known_label values") + missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5] + print(f" Sample IDs with missing known_label: {list(missing_samples)}") + + # Remove rows with missing known_label + target_labels = target_labels.dropna(subset=['known_label']) + if target_labels.empty: + print(f" Error: No valid known_label data remaining for '{target_value}' - skipping") + continue + + # 1. Pivot to wide format + prob_df = target_labels.pivot(index='sample_id', columns='class_label', values='probability') + + print(f" After pivot: {prob_df.shape[0]} samples x {prob_df.shape[1]} classes") + print(f" Class columns: {list(prob_df.columns)}") + + # Check for NaN values in probability data + nan_counts = prob_df.isna().sum() + if nan_counts.any(): + print(f" NaN counts per class: {dict(nan_counts)}") + print(f" Samples with any NaN: {prob_df.isna().any(axis=1).sum()}/{len(prob_df)}") + + # Drop only rows where ALL probabilities are NaN + all_nan_rows = prob_df.isna().all(axis=1) + if all_nan_rows.any(): + print(f" Dropping {all_nan_rows.sum()} samples with all NaN probabilities") + prob_df = prob_df[~all_nan_rows] + + remaining_nans = prob_df.isna().sum().sum() + if remaining_nans > 0: + print(f" Warning: {remaining_nans} individual NaN values remain - filling with 0") + prob_df = prob_df.fillna(0) + + if prob_df.empty: + print(f" Error: No valid probability data remaining for '{target_value}' - skipping") + continue + + # 2. Get true labels + true_labels_df = target_labels.drop_duplicates('sample_id')[['sample_id', 'known_label']].set_index('sample_id') + + # 3. Align indices - only keep samples that exist in both datasets + common_indices = prob_df.index.intersection(true_labels_df.index) + if len(common_indices) == 0: + print(f" Error: No common sample_ids between probability and true label data for '{target_value}' - skipping") + continue + + print(f" Found {len(common_indices)} samples with both probability and true label data") + + # Filter both datasets to common indices + prob_df_aligned = prob_df.loc[common_indices] + y_true = true_labels_df.loc[common_indices]['known_label'] + + # 4. Final check for NaN values + if y_true.isna().any(): + print(f" Error: True labels still contain NaN after alignment for '{target_value}' - skipping") + continue + + if prob_df_aligned.isna().any().any(): + print(f" Error: Probability data still contains NaN after alignment for '{target_value}' - skipping") + continue + + # 5. Convert categorical labels to integer labels + # Create a mapping from class names to integers + class_names = list(prob_df_aligned.columns) + class_to_int = {class_name: i for i, class_name in enumerate(class_names)} + + print(f" Class mapping: {class_to_int}") + + # Convert true labels to integers + y_true_np = y_true.map(class_to_int).to_numpy() + y_probs_np = prob_df_aligned.to_numpy() + + print(f" Data shape: y_true={y_true_np.shape}, y_probs={y_probs_np.shape}") + print(f" Unique true labels (integers): {set(y_true_np)}") + print(f" Class labels (columns): {class_names}") + print(f" Label distribution: {dict(zip(*np.unique(y_true_np, return_counts=True)))}") + + # Check for any unmapped labels (will be NaN) + if pd.isna(y_true_np).any(): + print(" Error: Some true labels could not be mapped to class columns") + unmapped_labels = set(y_true[y_true.map(class_to_int).isna()]) + print(f" Unmapped labels: {unmapped_labels}") + print(f" Available classes: {class_names}") + continue + + try: + print(f" Generating ROC curve for '{target_value}'...") + fig = plot_roc_curves(y_true_np, y_probs_np) + + # Create output filename with target value + safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_') + if len(target_values) > 1: + output_filename = f"{output_name_base}_{safe_target_name}.{args.format}" + else: + output_filename = f"{output_name_base}.{args.format}" + + output_path = output_dir / output_filename + print(f" Saving ROC curve to: {output_path.absolute()}") + fig.save(output_path, dpi=args.dpi, bbox_inches='tight') + + except Exception as e: + print(f" Error generating ROC curve for '{target_value}': {str(e)}") + print(f" Debug info - y_true type: {type(y_true_np)}, contains NaN: {pd.isna(y_true_np).any()}") + print(f" Debug info - y_probs type: {type(y_probs_np)}, contains NaN: {pd.isna(y_probs_np).any()}") + continue + + print("ROC curves generated successfully!") + + +def generate_box_plots(labels, args, output_dir, output_name_base): + """Generate box plots for model predictions""" + + print("Generating box plots...") + + # Parse target values from comma-separated string + if args.target_value: + target_values = [val.strip() for val in args.target_value.split(',')] + else: + # If no target values specified, use all unique variables + target_values = labels['variable'].unique().tolist() + + print(f"Processing target values: {target_values}") + + for target_value in target_values: + print(f"\nProcessing target value: '{target_value}'") + + # Filter labels for the current target value + target_labels = labels[labels['variable'] == target_value] + + if target_labels.empty: + print(f" Warning: No data found for target value '{target_value}' - skipping") + continue + + # Check if this is a classification problem (has probabilities) + prob_columns = target_labels['class_label'].unique() + non_na_probs = target_labels['probability'].notna().sum() + + print(f" Class labels found: {list(prob_columns)}") + print(f" Non-NaN probabilities: {non_na_probs}/{len(target_labels)}") + + # If most probabilities are NaN, this is likely a regression problem + if non_na_probs < len(target_labels) * 0.1: # Less than 10% valid probabilities + print(" Detected regression problem - precision-recall curves not applicable") + print(f" Skipping '{target_value}' (use regression evaluation metrics instead)") + continue + + # Debug: Check data quality + total_rows = len(target_labels) + missing_labels = target_labels['known_label'].isna().sum() + missing_probs = target_labels['probability'].isna().sum() + unique_samples = target_labels['sample_id'].nunique() + unique_classes = target_labels['class_label'].nunique() + + print(f" Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes") + print(f" Missing data: {missing_labels} missing known_label, {missing_probs} missing probability") + + if missing_labels > 0: + print(f" Warning: Found {missing_labels} missing known_label values") + missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5] + print(f" Sample IDs with missing known_label: {list(missing_samples)}") + + # Remove rows with missing known_label + target_labels = target_labels.dropna(subset=['known_label']) + if target_labels.empty: + print(f" Error: No valid known_label data remaining for '{target_value}' - skipping") + continue + + # Remove rows with missing data + clean_data = target_labels.dropna(subset=['known_label', 'probability']) + + if clean_data.empty: + print(" No valid data after cleaning - skipping") + continue + + # Get unique classes + classes = clean_data['class_label'].unique() + + for class_label in classes: + print(f" Generating box plot for class: {class_label}") + + # Filter for current class + class_data = clean_data[clean_data['class_label'] == class_label] + + try: + # Create the box plot + fig = plot_boxplot( + categorical_x=class_data['known_label'], + numerical_y=class_data['probability'], + title_x='True Label', + title_y=f'Predicted Probability ({class_label})', + ) + + # Save the plot + safe_class_name = str(class_label).replace('/', '_').replace('\\', '_').replace(' ', '_').replace(':', '_') + safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_') + output_filename = f"{output_name_base}_{safe_target_name}_{safe_class_name}.{args.format}" + output_path = output_dir / output_filename + + print(f" Saving box plot to: {output_path.absolute()}") + fig.savefig(output_path, dpi=args.dpi, bbox_inches='tight') + plt.close(fig) + + except Exception as e: + print(f" Error generating box plot for class '{class_label}': {str(e)}") + continue + + +def main(): + """Main function to parse arguments and generate plots""" + parser = argparse.ArgumentParser(description="Generate plots using flexynesis") + + # Required arguments + parser.add_argument("--labels", type=str, required=False, + help="Path to labels file generated by flexynesis") + + # Plot type + parser.add_argument("--plot_type", type=str, required=True, + choices=['dimred', 'kaplan_meier', 'cox', 'scatter', 'concordance_heatmap', 'pr_curve', 'roc_curve', 'box_plot'], + help="Type of plot to generate: 'dimred' for dimensionality reduction, 'kaplan_meier' for survival analysis, 'cox' for Cox proportional hazards analysis, 'scatter' for scatter plots, 'concordance_heatmap' for label concordance heatmaps, 'pr_curve' for precision-recall curves, 'roc_curve' for ROC curves, or 'box_plot' for box plots.") + + # Arguments for dimensionality reduction + parser.add_argument("--embeddings", type=str, + help="Path to input data embeddings file (CSV or tabular format). Required for dimred plots.") + parser.add_argument("--method", type=str, default='pca', choices=['pca', 'umap'], + help="Transformation method ('pca' or 'umap'). Default is 'pca'. Used for dimred plots.") + parser.add_argument("--target_variables", type=str, required=False, + help="Comma-separated list of target variables to plot.") + + # Arguments for Kaplan-Meier + parser.add_argument("--survival_data", type=str, + help="Path to survival data file with columns: duration and event. Required for kaplan_meier plots.") + parser.add_argument("--surv_time_var", type=str, required=False, + help="Column name for survival time") + parser.add_argument("--surv_event_var", type=str, required=False, + help="Column name for survival event") + parser.add_argument("--event_value", type=str, required=False, + help="Value in event column that represents an event (e.g., 'DECEASED')") + + # Arguments for Cox analysis + parser.add_argument("--model", type=str, + help="Path to trained flexynesis model (pickle file). Required for cox plots.") + parser.add_argument("--clinical_train", type=str, + help="Path to training dataset (pickle file). Required for cox plots.") + parser.add_argument("--clinical_test", type=str, + help="Path to test dataset (pickle file). Required for cox plots.") + parser.add_argument("--omics_train", type=str, default=None, + help="Path to training omics dataset. Optional for cox plots.") + parser.add_argument("--omics_test", type=str, default=None, + help="Path to test omics dataset. Optional for cox plots.") + parser.add_argument("--clinical_variables", type=str, + help="Comma-separated list of clinical variables to include in Cox model (e.g., 'AGE,SEX,HISTOLOGICAL_DIAGNOSIS,STUDY')") + parser.add_argument("--top_features", type=int, default=20, + help="Number of top important features to include in Cox model. Default is 5") + parser.add_argument("--crossval", action='store_true', + help="If True, performs K-fold cross-validation and returns average C-index. Default is False") + parser.add_argument("--n_splits", type=int, default=5, + help="Number of folds for cross-validation. Default is 5") + parser.add_argument("--random_state", type=int, default=42, + help="Random seed for reproducibility. Default is 42") + + # Arguments for scatter plot, heatmap, PR curves, ROC curves, and box plots + parser.add_argument("--target_value", type=str, default=None, + help="Target value for scatter plot.") + + # Common arguments + parser.add_argument("--output_dir", type=str, default='output', + help="Output directory. Default is 'output'") + parser.add_argument("--output_name", type=str, default=None, + help="Output filename base") + parser.add_argument("--format", type=str, default='jpg', choices=['png', 'pdf', 'svg', 'jpg'], + help="Output format for the plot. Default is 'jpg'") + parser.add_argument("--dpi", type=int, default=300, + help="DPI for the output image. Default is 300") + + args = parser.parse_args() + + try: + # validate plot type + if not args.plot_type: + raise ValueError("Please specify a plot type using --plot_type") + if args.plot_type not in ['dimred', 'kaplan_meier', 'cox', 'scatter', 'concordance_heatmap', 'pr_curve', 'roc_curve', 'box_plot']: + raise ValueError(f"Invalid plot type: {args.plot_type}. Must be one of: 'dimred', 'kaplan_meier', 'cox', 'scatter', 'concordance_heatmap', 'pr_curve', 'roc_curve', 'box_plot'") + + # Validate plot type requirements + if args.plot_type in ['dimred']: + if not args.embeddings: + raise ValueError("--embeddings is required when plot_type is 'dimred'") + if not os.path.isfile(args.embeddings): + raise FileNotFoundError(f"embeddings file not found: {args.embeddings}") + if not args.labels: + raise ValueError("--labels is required for dimensionality reduction plots") + if not args.method: + raise ValueError("--method is required for dimensionality reduction plots") + if not args.target_variables: + raise ValueError("--target_variables is required for dimensionality reduction plots") + + if args.plot_type in ['kaplan_meier']: + if not args.survival_data: + raise ValueError("--survival_data is required when plot_type is 'kaplan_meier'") + if not os.path.isfile(args.survival_data): + raise FileNotFoundError(f"Survival data file not found: {args.survival_data}") + if not args.labels: + raise ValueError("--labels is required for dimensionality reduction plots") + if not args.method: + raise ValueError("--method is required for dimensionality reduction plots") + if not args.surv_time_var: + raise ValueError("--surv_time_var is required for Kaplan-Meier plots") + if not args.surv_event_var: + raise ValueError("--surv_event_var is required for Kaplan-Meier plots") + if not args.event_value: + raise ValueError("--event_value is required for Kaplan-Meier plots") + + if args.plot_type in ['cox']: + if not args.model: + raise ValueError("--model is required when plot_type is 'cox'") + if not os.path.isfile(args.model): + raise FileNotFoundError(f"Model file not found: {args.model}") + if not args.clinical_train: + raise ValueError("--clinical_train is required when plot_type is 'cox'") + if not os.path.isfile(args.clinical_train): + raise FileNotFoundError(f"Training dataset file not found: {args.clinical_train}") + if not args.clinical_test: + raise ValueError("--clinical_test is required when plot_type is 'cox'") + if not os.path.isfile(args.clinical_test): + raise FileNotFoundError(f"Test dataset file not found: {args.clinical_test}") + if not args.omics_train: + raise ValueError("--omics_train is required when plot_type is 'cox'") + if not os.path.isfile(args.omics_train): + raise FileNotFoundError(f"Training omics dataset file not found: {args.omics_train}") + if not args.omics_test: + raise ValueError("--omics_test is required when plot_type is 'cox'") + if not os.path.isfile(args.omics_test): + raise FileNotFoundError(f"Test omics dataset file not found: {args.omics_test}") + if not args.surv_time_var: + raise ValueError("--surv_time_var is required for Cox plots") + if not args.surv_event_var: + raise ValueError("--surv_event_var is required for Cox plots") + if not args.clinical_variables: + raise ValueError("--clinical_variables is required for Cox plots") + if not isinstance(args.top_features, int) or args.top_features <= 0: + raise ValueError("--top_features must be a positive integer") + if not args.event_value: + raise ValueError("--event_value is required for Kaplan-Meier plots") + if not args.crossval: + args.crossval = False + if not isinstance(args.n_splits, int) or args.n_splits <= 0: + raise ValueError("--n_splits must be a positive integer") + if not isinstance(args.random_state, int): + raise ValueError("--random_state must be an integer") + + if args.plot_type in ['scatter']: + if not args.labels: + raise ValueError("--labels is required for scatter plots") + if not args.target_value: + print("--target_value is not specified, using all unique variables from labels") + if not os.path.isfile(args.labels): + raise FileNotFoundError(f"Labels file not found: {args.labels}") + + if args.plot_type in ['concordance_heatmap']: + if not args.labels: + raise ValueError("--labels is required for concordance heatmap") + if not args.target_value: + print("--target_value is not specified, using all unique variables from labels") + if not os.path.isfile(args.labels): + raise FileNotFoundError(f"Labels file not found: {args.labels}") + + if args.plot_type in ['pr_curve']: + if not args.labels: + raise ValueError("--labels is required for precision-recall curves") + if not args.target_value: + print("--target_value is not specified, using all unique variables from labels") + if not os.path.isfile(args.labels): + raise FileNotFoundError(f"Labels file not found: {args.labels}") + + if args.plot_type in ['roc_curve']: + if not args.labels: + raise ValueError("--labels is required for ROC curves") + if not args.target_value: + print("--target_value is not specified, using all unique variables from labels") + if not os.path.isfile(args.labels): + raise FileNotFoundError(f"Labels file not found: {args.labels}") + + if args.plot_type in ['box_plot']: + if not args.labels: + raise ValueError("--labels is required for box plots") + if not args.target_value: + print("--target_value is not specified, using all unique variables from labels") + if not os.path.isfile(args.labels): + raise FileNotFoundError(f"Labels file not found: {args.labels}") + + # Validate other arguments + if args.method not in ['pca', 'umap']: + raise ValueError("Method must be 'pca' or 'umap'") + + # Create output directory + output_dir = Path(args.output_dir) + output_dir.mkdir(parents=True, exist_ok=True) + print(f"Output directory: {output_dir.absolute()}") + + # Generate output filename base + if args.output_name: + output_name_base = args.output_name + else: + if args.plot_type == 'dimred': + embeddings_name = Path(args.embeddings).stem + output_name_base = f"{embeddings_name}_{args.method}" + elif args.plot_type == 'kaplan_meier': + survival_name = Path(args.survival_data).stem + output_name_base = f"{survival_name}_km" + elif args.plot_type == 'cox': + model_name = Path(args.model).stem + output_name_base = f"{model_name}_cox" + elif args.plot_type == 'scatter': + labels_name = Path(args.labels).stem + output_name_base = f"{labels_name}_scatter" + elif args.plot_type == 'concordance_heatmap': + labels_name = Path(args.labels).stem + output_name_base = f"{labels_name}_concordance" + elif args.plot_type == 'pr_curve': + labels_name = Path(args.labels).stem + output_name_base = f"{labels_name}_pr_curves" + elif args.plot_type == 'roc_curve': + labels_name = Path(args.labels).stem + output_name_base = f"{labels_name}_roc_curves" + elif args.plot_type == 'box_plot': + labels_name = Path(args.labels).stem + output_name_base = f"{labels_name}_box_plot" + + # Generate plots based on type + if args.plot_type in ['dimred']: + # Load labels + print(f"Loading labels from: {args.labels}") + label_data = load_labels(args.labels) + # Load embeddings data + print(f"Loading embeddings from: {args.embeddings}") + embeddings, sample_names = load_embeddings(args.embeddings) + print(f"embeddings shape: {embeddings.shape}") + + # Match samples to embeddings + matched_labels = match_samples_to_embeddings(sample_names, label_data) + print(f"Successfully matched {len(matched_labels)} samples for dimensionality reduction") + + generate_dimred_plots(embeddings, matched_labels, args, output_dir, output_name_base) + + elif args.plot_type in ['kaplan_meier']: + # Load labels + print(f"Loading labels from: {args.labels}") + label_data = load_labels(args.labels) + # Load survival data + print(f"Loading survival data from: {args.survival_data}") + survival_data = load_survival_data(args.survival_data) + print(f"Survival data shape: {survival_data.shape}") + + generate_km_plots(survival_data, label_data, args, output_dir, output_name_base) + + elif args.plot_type in ['cox']: + # Load model and datasets + print(f"Loading model from: {args.model}") + model = load_model(args.model) + print(f"Loading training dataset from: {args.clinical_train}") + clinical_train = load_omics(args.clinical_train) + print(f"Loading test dataset from: {args.clinical_test}") + clinical_test = load_omics(args.clinical_test) + print(f"Loading training omics dataset from: {args.omics_train}") + omics_train = load_omics(args.omics_train) + print(f"Loading test omics dataset from: {args.omics_test}") + omics_test = load_omics(args.omics_test) + + generate_cox_plots(model, clinical_train, clinical_test, omics_test, omics_train, args, output_dir, output_name_base) + + elif args.plot_type in ['scatter']: + # Load labels + print(f"Loading labels from: {args.labels}") + label_data = load_labels(args.labels) + + generate_plot_scatter(label_data, args, output_dir, output_name_base) + + elif args.plot_type in ['concordance_heatmap']: + # Load labels + print(f"Loading labels from: {args.labels}") + label_data = load_labels(args.labels) + + generate_label_concordance_heatmap(label_data, args, output_dir, output_name_base) + + elif args.plot_type in ['pr_curve']: + # Load labels + print(f"Loading labels from: {args.labels}") + label_data = load_labels(args.labels) + + generate_pr_curves(label_data, args, output_dir, output_name_base) + + elif args.plot_type in ['roc_curve']: + # Load labels + print(f"Loading labels from: {args.labels}") + label_data = load_labels(args.labels) + + generate_roc_curves(label_data, args, output_dir, output_name_base) + + elif args.plot_type in ['box_plot']: + # Load labels + print(f"Loading labels from: {args.labels}") + label_data = load_labels(args.labels) + + generate_box_plots(label_data, args, output_dir, output_name_base) + + print("All plots generated successfully!") + + except (FileNotFoundError, ValueError, pd.errors.ParserError) as e: + print(f"Error: {e}") + return 1 + + return 0 + + +if __name__ == "__main__": + exit(main())
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexynesis_utils.py Tue Jun 24 05:55:40 2025 +0000 @@ -0,0 +1,257 @@ +#!/usr/bin/env python + +import argparse +import os +import sys +from pathlib import Path + +import pandas as pd + + +def read_data(data_input, index=False): + """Load CSV or TSV data file.""" + try: + file_ext = Path(data_input).suffix.lower() + sep = ',' if file_ext == '.csv' else '\t' + index_col = 0 if index else None + + if file_ext in ['.csv', '.tsv', '.txt', '.tab', '.tabular']: + return pd.read_csv(data_input, sep=sep, index_col=index_col) + else: + raise ValueError(f"Unsupported file extension: {file_ext}") + except Exception as e: + raise ValueError(f"Error loading data from {data_input}: {e}") from e + + +def binarize_mutations(df, gene_idx=1, sample_idx=2): + """ + Binarize mutation data by creating a matrix of gene x sample with 1/0 values. + """ + # galaxy index is 1-based, convert to zero-based + gene_idx -= 1 + sample_idx -= 1 + # check idx + if gene_idx >= len(df.columns) or sample_idx >= len(df.columns): + raise ValueError(f"Column indices out of bounds. DataFrame has {len(df.columns)} columns, " + f"but requested indices are {gene_idx} and {sample_idx}") + if gene_idx == sample_idx: + raise ValueError("Gene and sample column indices must be different") + + # Get column names by index + gene_col = df.columns[gene_idx] + print(f"Using gene column: {gene_col} (index {gene_idx})") + sample_col = df.columns[sample_idx] + print(f"Using sample column: {sample_col} (index {sample_idx})") + + # Check if columns contain data + if df[gene_col].isna().all(): + raise ValueError(f"Gene column (index {gene_idx}) contains only NaN values.") + if df[sample_col].isna().all(): + raise ValueError(f"Sample column (index {sample_idx}) contains only NaN values.") + + # Group by gene and sample, count mutations + mutation_counts = df.groupby([gene_col, sample_col]).size().reset_index(name='count') + + # Create pivot table + mutation_matrix = mutation_counts.pivot(index=gene_col, columns=sample_col, values='count').fillna(0) + + # Binarize: convert any count > 0 to 1 + mutation_matrix[mutation_matrix > 0] = 1 + + return mutation_matrix + + +def make_data_dict(clin_path, omics_paths): + """Read clinical and omics data files into a dictionary.""" + data = {} + + # Read clinical data + print(f"Reading clinical data from {clin_path}") + try: + clin = read_data(clin_path, index=True) + + if clin.empty: + raise ValueError(f"Clinical file {clin_path} is empty") + data['clin'] = clin + print(f"Loaded clinical data: {clin.shape[0]} samples, {clin.shape[1]} features") + except Exception as e: + raise ValueError(f"Error reading clinical file {clin_path}: {e}") + + # Read omics data + print(f"Reading omics data from {', '.join(omics_paths)}") + for path in omics_paths: + try: + name = os.path.splitext(os.path.basename(path))[0] + df = read_data(path, index=True) + if df.empty: + print(f"Warning: Omics file {path} is empty, skipping") + continue + data[name] = df + print(f"Loaded {name}: {df.shape[0]} features, {df.shape[1]} samples") + except Exception as e: + print(f"Warning: Error reading omics file {path}: {e}") + continue + + if len(data) == 1: # Only clinical data loaded + raise ValueError("No omics data was successfully loaded") + + return data + + +def validate_data_consistency(data): + """Validate that clinical and omics data have consistent samples.""" + clin_samples = set(data['clin'].index) + + for name, df in data.items(): + if name == 'clin': + continue + + omics_samples = set(df.columns) + + # Check for sample overlap + common_samples = clin_samples.intersection(omics_samples) + if len(common_samples) == 0: + raise ValueError(f"No common samples between clinical data and {name}") + + missing_in_omics = clin_samples - omics_samples + missing_in_clin = omics_samples - clin_samples + + if missing_in_omics: + print(f"Warning: {len(missing_in_omics)} clinical samples not found in {name}") + if missing_in_clin: + print(f"Warning: {len(missing_in_clin)} samples in {name} not found in clinical data") + + return True + + +def split_and_save_data(data, ratio=0.7, output_dir='.'): + """Split data into train/test sets and save to files.""" + # Validate data consistency first + validate_data_consistency(data) + + samples = data['clin'].index.tolist() + + train_samples = list(pd.Series(samples).sample(frac=ratio, random_state=42)) + test_samples = list(set(samples) - set(train_samples)) + + train_data = {} + test_data = {} + + for key, df in data.items(): + try: + if key == 'clin': + train_data[key] = df.loc[df.index.intersection(train_samples)] + test_data[key] = df.loc[df.index.intersection(test_samples)] + else: + train_data[key] = df.loc[:, df.columns.intersection(train_samples)] + test_data[key] = df.loc[:, df.columns.intersection(test_samples)] + except Exception as e: + print(f"Error splitting data {key}: {e}") + continue + + # Create output directories + os.makedirs(os.path.join(output_dir, 'train'), exist_ok=True) + os.makedirs(os.path.join(output_dir, 'test'), exist_ok=True) + + # Save train and test data + for key in data.keys(): + try: + train_data[key].to_csv(os.path.join(output_dir, 'train', f'{key}.csv')) + test_data[key].to_csv(os.path.join(output_dir, 'test', f'{key}.csv')) + except Exception as e: + print(f"Error saving {key}: {e}") + continue + + +def main(): + parser = argparse.ArgumentParser(description='Flexynesis extra utilities') + + parser.add_argument("--util", type=str, required=True, + choices=['split', 'binarize'], + help="Utility function: 'split' for spiting data to train and test, 'binarize' for creating a binarized matrix from a mutation data") + + # Arguments for split + parser.add_argument('--clin', required=False, + help='Path to clinical data CSV file (samples in rows)') + parser.add_argument('--omics', required=False, + help='Comma-separated list of omics CSV files (samples in columns)') + parser.add_argument('--split', type=float, default=0.7, + help='Train split ratio (default: 0.7)') + + # Arguments for binarize + parser.add_argument('--mutations', type=str, required=False, + help='Path to mutation data CSV file (samples in rows, genes in columns)') + parser.add_argument('--gene_idx', type=int, default=0, + help='Column index for genes in mutation data (default: 0)') + parser.add_argument('--sample_idx', type=int, default=1, + help='Column index for samples in mutation data (default: 1)') + + # common arguments + parser.add_argument('--out', default='.', + help='Output directory (default: current directory)') + + args = parser.parse_args() + + try: + # validate utility function + if not args.util: + raise ValueError("Utility function must be specified") + if args.util not in ['split', 'binarize']: + raise ValueError(f"Invalid utility function: {args.util}") + + if args.util == 'split': + # Validate inputs + if not args.clin: + raise ValueError("Clinical data file must be provided") + if not args.omics: + raise ValueError("At least one omics file must be provided") + if not os.path.isfile(args.clin): + raise FileNotFoundError(f"Clinical file not found: {args.clin}") + # Validate split ratio + if not 0 < args.split < 1: + raise ValueError(f"Split ratio must be between 0 and 1, got {args.split}") + + elif args.util == 'binarize': + # Validate mutation data file + if not args.mutations: + raise ValueError("Mutation data file must be provided") + if not os.path.isfile(args.mutations): + raise FileNotFoundError(f"Mutation data file not found: {args.mutations}") + # Validate gene and sample indices + if args.gene_idx < 0 or args.sample_idx < 0: + raise ValueError("Gene and sample indices must be non-negative integers") + + # Create output directory if it doesn't exist + if not os.path.exists(args.out): + os.makedirs(args.out) + + if args.util == 'split': + # Parse omics files + omics_files = [f.strip() for f in args.omics.split(',') if f.strip()] + if not omics_files: + raise ValueError("At least one omics file must be provided") + # Check omics files exist + for f in omics_files: + if not os.path.isfile(f): + raise FileNotFoundError(f"Omics file not found: {f}") + data = make_data_dict(args.clin, omics_files) + split_and_save_data(data, ratio=args.split, output_dir=args.out) + + elif args.util == 'binarize': + mutations_df = read_data(args.mutations, index=False) + if mutations_df.empty: + raise ValueError("Mutation data file is empty") + + binarized_matrix = binarize_mutations(mutations_df, gene_idx=args.gene_idx, sample_idx=args.sample_idx) + # Save binarized matrix + output_file = os.path.join(args.out, 'binarized_mutations.csv') + binarized_matrix.to_csv(output_file) + print(f"Binarized mutation matrix saved to {output_file}") + + except Exception as e: + print(f"Error: {e}", file=sys.stderr) + sys.exit(1) + + +if __name__ == "__main__": + main()
--- a/macros.xml Wed May 14 06:46:42 2025 +0000 +++ b/macros.xml Tue Jun 24 05:55:40 2025 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.2.18</token> + <token name="@TOOL_VERSION@">0.2.20</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">24.1</token> <xml name="requirements"> @@ -20,34 +20,48 @@ <edam_operation>operation_2426</edam_operation> </edam_operations> </xml> + <xml name="sanitizer_printable"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value="'"/> + <remove value='"'/> + <remove value=" "/> + <yield/> + </valid> + </sanitizer> + </xml> + <xml name="sanitizer_letters"> + <sanitizer invalid_char=" "> + <valid initial="string.letters"> + <add value="_"/> + </valid> + </sanitizer> + </xml> <token name="@CHECK_NON_COMMERCIAL_USE@"><![CDATA[ #if not $non_commercial_use >&2 echo "this tool is only available for non commercial use"; exit 1; #end if ]]></token> + <xml name="commercial_use_param"> + <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> + <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> + </param> + </xml> <xml name="main_inputs"> <param name="train_clin" type="data" format="csv" label="Training clinical data"/> <param name="test_clin" type="data" format="csv" label="Test clinical data"/> <param name="train_omics_main" type="data" format="csv" label="Training omics data"/> <param name="test_omics_main" type="data" format="csv" label="Test omics data"/> <param name="assay_main" type="text" optional="true" label="What type of assay is your input?" help="This would be used as output name."> - <sanitizer invalid_char=" "> - <valid initial="string.letters"> - <add value="_" /> - </valid> - </sanitizer> + <expand macro="sanitizer_letters"/> </param> </xml> <xml name="extra_inputs"> <param name="train_omics" type="data" optional="true" format="csv" label="Training omics data"/> <param name="test_omics" type="data" optional="true" format="csv" label="Test omics data"/> <param name="assay" type="text" optional="true" label="What type of assay is your input?" help="This would be used as output name." > - <sanitizer invalid_char=" "> - <valid initial="string.letters"> - <add value="_" /> - </valid> - </sanitizer> + <expand macro="sanitizer_letters"/> </param> </xml> <xml name="advanced"> @@ -56,28 +70,247 @@ <option value="intermediate">intermediate</option> <option value="early">early</option> </param> - <param argument="--finetuning_samples" type="integer" min="0" value="0" label="Number of samples from the test dataset to use for fine-tuning the model." help="Set to 0 to disable fine-tuning." /> - <param argument="--variance_threshold" type="float" min="0" max="100" value="1" label="Variance threshold (as percentile) to drop low variance features." help="Set to 0 for no variance filtering." /> - <param argument="--correlation_threshold" type="float" min="0" max="1" value="0.8" label="Correlation threshold to drop highly redundant features." help="Set to 1 for no redundancy filtering." /> - <param argument="--subsample" type="integer" min="0" value="0" label="Downsample training set to randomly drawn N samples for training." /> - <param argument="--features_min" type="integer" min="0" value="500" label="Minimum number of features to retain after feature selection." /> - <param argument="--features_top_percentile" type="float" min="0" max="100" value="20" label="Top percentile features (among the features remaining after variance filtering and data cleanup) to retain after feature selection." /> - <param argument="--log_transform" type="boolean" truevalue="--log_transform True" falsevalue="" checked="false" label="Whether to apply log-transformation to input data matrices" /> - <param argument="--early_stop_patience" type="integer" min="-1" value="10" label="How many epochs to wait when no improvements in validation loss are observed." help="Set to -1 to disable early stopping." /> - <param argument="--hpo_iter" type="integer" min="1" value="100" label="Number of iterations for hyperparameter optimisation." /> + <param argument="--finetuning_samples" type="integer" min="0" value="0" label="Number of samples from the test dataset to use for fine-tuning the model." help="Set to 0 to disable fine-tuning."/> + <param argument="--variance_threshold" type="float" min="0" max="100" value="1" label="Variance threshold (as percentile) to drop low variance features." help="Set to 0 for no variance filtering."/> + <param argument="--correlation_threshold" type="float" min="0" max="1" value="0.8" label="Correlation threshold to drop highly redundant features." help="Set to 1 for no redundancy filtering."/> + <param argument="--subsample" type="integer" min="0" value="0" label="Downsample training set to randomly drawn N samples for training."/> + <param argument="--features_min" type="integer" min="0" value="500" label="Minimum number of features to retain after feature selection."/> + <param argument="--features_top_percentile" type="float" min="0" max="100" value="20" label="Top percentile features (among the features remaining after variance filtering and data cleanup) to retain after feature selection."/> + <param argument="--log_transform" type="boolean" truevalue="--log_transform True" falsevalue="" checked="false" label="Whether to apply log-transformation to input data matrices"/> + <param argument="--early_stop_patience" type="integer" min="-1" value="10" label="How many epochs to wait when no improvements in validation loss are observed." help="Set to -1 to disable early stopping."/> + <param argument="--hpo_iter" type="integer" min="1" value="100" label="Number of iterations for hyperparameter optimization."/> <param argument="--val_size" type="float" min="0.0" max="1" value="0.2" label="Proportion of training data to be used as validation split"/> - <param argument="--hpo_patience" type="integer" min="0" value="10" label="How many hyperparameter optimisation iterations to wait for when no improvements are observed." help="Set to 0 to disable early stopping." /> - <param argument="--use_cv" type="boolean" truevalue="--use_cv" falsevalue="" checked="false" label="Cross validation" help="If set, a 5-fold cross-validation training will be done. Otherwise, a single training on 80 percent of the dataset is done. " /> - <param argument="--use_loss_weighting" type="boolean" truevalue="--use_loss_weighting True" falsevalue="" checked="true" label="Whether to apply loss-balancing using uncertainty weights method." /> - <param argument="--evaluate_baseline_performance" type="boolean" truevalue="--evaluate_baseline_performance" falsevalue="" checked="false" label="Enable modeling also with Random Forest + SVMs to see the performance of off-the-shelf tools on the same dataset." /> + <param argument="--hpo_patience" type="integer" min="0" value="10" label="How many hyperparameter optimization iterations to wait for when no improvements are observed." help="Set to 0 to disable early stopping."/> + <param argument="--use_cv" type="boolean" truevalue="--use_cv" falsevalue="" checked="false" label="Cross validation" help="If set, a 5-fold cross-validation training will be done. Otherwise, a single training on 80 percent of the dataset is done. "/> + <param argument="--use_loss_weighting" type="boolean" truevalue="--use_loss_weighting True" falsevalue="" checked="true" label="Whether to apply loss-balancing using uncertainty weights method."/> + <param argument="--evaluate_baseline_performance" type="boolean" truevalue="--evaluate_baseline_performance" falsevalue="" checked="false" label="Enable modeling also with Random Forest + SVMs to see the performance of off-the-shelf tools on the same dataset."/> <param argument="--feature_importance_method" type="select" label="which method(s) to use to compute feature importance scores."> <option value="Both" selected="true">Both</option> <option value="IntegratedGradients">IntegratedGradients</option> <option value="GradientShap">GradientShap</option> </param> - <param argument="--disable_marker_finding" type="boolean" truevalue="--disable_marker_finding" falsevalue="" checked="false" label="Disable marker discovery after model training." /> </section> </xml> + <xml name="plots_common_param"> + <yield/> + <param name="format" type="select" label="Output format"> + <option value="jpg" selected="true">jpg</option> + <option value="png">png</option> + <option value="pdf">pdf</option> + <option value="svg">svg</option> + </param> + <param name="dpi" type="integer" min="0" max="1200" value="300" label="DPI"/> + </xml> + <xml name="plots_common_input"> + <yield/> + <param argument="--labels" type="data" format="tabular,csv" label="Predicted labels" help="Generated by flexynesis"/> + </xml> + <token name="@PLOT_COMMON_CONFIG@"><![CDATA[ +label_data = load_labels('inputs/$plot_conditional.labels.element_identifier.$plot_conditional.labels.ext') + ]]></token> + <token name="@PR_ROC_BOX_CONFIG@"><![CDATA[ +@PLOT_COMMON_CONFIG@ + +# Check if this is a regression problem (no class probabilities) +non_na_probs = label_data['probability'].notna().sum() + +print(f" Non-NaN probabilities: {non_na_probs}/{len(label_data)}") + +# If most probabilities are NaN, this is likely a regression problem +if non_na_probs < len(label_data) * 0.1: # Less than 10% valid probabilities + raise ValueError(" Detected regression problem - precision-recall curves not applicable") + +# Debug: Check data quality +total_rows = len(label_data) +missing_labels = label_data['known_label'].isna().sum() +missing_probs = label_data['probability'].isna().sum() +unique_samples = label_data['sample_id'].nunique() +unique_classes = label_data['class_label'].nunique() + +print(f" Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes") +print(f" Missing data: {missing_labels} missing known_label, {missing_probs} missing probability") + +if missing_labels > 0: + print(f" Warning: Found {missing_labels} missing known_label values") + missing_samples = label_data[label_data['known_label'].isna()]['sample_id'].unique()[:5] + print(f" Sample IDs with missing known_label: {list(missing_samples)}") + + # Remove rows with missing known_label + label_data = label_data.dropna(subset=['known_label']) + if label_data.empty: + raise ValueError("Error: No valid known_label data remaining") + + ]]></token> + <token name="@PR_ROC_CONFIG@"><![CDATA[ +@PR_ROC_BOX_CONFIG@ + +# 1. Pivot to wide format +prob_df = label_data.pivot(index='sample_id', columns='class_label', values='probability') + +print(f" After pivot: {prob_df.shape[0]} samples x {prob_df.shape[1]} classes") +print(f" Class columns: {list(prob_df.columns)}") + +# Check for NaN values in probability data +nan_counts = prob_df.isna().sum() +if nan_counts.any(): + print(f" NaN counts per class: {dict(nan_counts)}") + print(f" Samples with any NaN: {prob_df.isna().any(axis=1).sum()}/{len(prob_df)}") + + # Drop only rows where ALL probabilities are NaN + all_nan_rows = prob_df.isna().all(axis=1) + if all_nan_rows.any(): + print(f" Dropping {all_nan_rows.sum()} samples with all NaN probabilities") + prob_df = prob_df[~all_nan_rows] + + remaining_nans = prob_df.isna().sum().sum() + if remaining_nans > 0: + print(f" Warning: {remaining_nans} individual NaN values remain - filling with 0") + prob_df = prob_df.fillna(0) + + if prob_df.empty: + raise ValueError(f" Error: No valid probability data remaining for") + +# 2. Get true labels +true_labels_df = label_data.drop_duplicates('sample_id')[['sample_id', 'known_label']].set_index('sample_id') + +# 3. Align indices - only keep samples that exist in both datasets +common_indices = prob_df.index.intersection(true_labels_df.index) +if len(common_indices) == 0: + raise ValueError(f" Error: No common sample_ids between probability and true label data") + +print(f" Found {len(common_indices)} samples with both probability and true label data") + +# Filter both datasets to common indices +prob_df_aligned = prob_df.loc[common_indices] +y_true = true_labels_df.loc[common_indices]['known_label'] + +# 4. Final check for NaN values +if y_true.isna().any(): + raise ValueError(f" Error: True labels still contain NaN after alignment") + +if prob_df_aligned.isna().any().any(): + raise ValueError(f" Error: Probability data still contains NaN after alignment") + +# 5. Convert categorical labels to integer labels +# Create a mapping from class names to integers +class_names = list(prob_df_aligned.columns) +class_to_int = {class_name: i for i, class_name in enumerate(class_names)} + +print(f" Class mapping: {class_to_int}") + +# Convert true labels to integers +y_true_np = y_true.map(class_to_int).to_numpy() +y_probs_np = prob_df_aligned.to_numpy() + +print(f" Data shape: y_true={y_true_np.shape}, y_probs={y_probs_np.shape}") +print(f" Unique true labels (integers): {set(y_true_np)}") +print(f" Class labels (columns): {class_names}") +print(f" Label distribution: {dict(zip(*np.unique(y_true_np, return_counts=True)))}") + +# Check for any unmapped labels (will be NaN) +if pd.isna(y_true_np).any(): + raise ValueError(" Error: Some true labels could not be mapped to class columns") + + ]]></token> + <xml name="common_test"> + <param name="non_commercial_use" value="True"/> + <conditional name="training_type"> + <param name="model" value="s_train"/> + <param name="train_clin" value="train/clin" ftype="csv"/> + <param name="test_clin" value="test/clin" ftype="csv"/> + <param name="train_omics_main" value="train/gex" ftype="csv"/> + <param name="test_omics_main" value="test/gex" ftype="csv"/> + <param name="assay_main" value="bar"/> + <repeat name="omics"> + <param name="train_omics" value="train/cnv" ftype="csv"/> + <param name="test_omics" value="test/cnv" ftype="csv"/> + <param name="assay" value="foo"/> + </repeat> + <conditional name="model_class"> + <param name="model_class" value="DirectPred"/> + </conditional> + <param name="target_variables" value="Erlotinib"/> + <param name="surv_event_var" value="OS_STATUS"/> + <param name="surv_time_var" value="OS_MONTHS"/> + <section name="advanced"> + <param name="hpo_iter" value="1"/> + </section> + </conditional> + <yield/> + <output_collection name="results" type="list"> + <element name="job.embeddings_test"> + <assert_contents> + <has_n_lines n="50"/> + </assert_contents> + </element> + <element name="job.embeddings_train"> + <assert_contents> + <has_n_lines n="50"/> + </assert_contents> + </element> + <element name="job.feature_importance.GradientShap"> + <assert_contents> + <has_text_matching expression="Erlotinib,0,,bar,A2M,"/> + <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/> + <has_text_matching expression="GradientShap"/> + </assert_contents> + </element> + <element name="job.feature_importance.IntegratedGradients"> + <assert_contents> + <has_text_matching expression="Erlotinib,0,,bar,A2M,"/> + <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/> + <has_text_matching expression="IntegratedGradients"/> + </assert_contents> + </element> + <element name="job.feature_logs.bar"> + <assert_contents> + <has_n_lines n="25"/> + </assert_contents> + </element> + <element name="job.feature_logs.omics_foo"> + <assert_contents> + <has_n_lines n="25"/> + </assert_contents> + </element> + <element name="job.predicted_labels"> + <assert_contents> + <has_text_matching expression="source_dataset:A-704,Erlotinib,"/> + <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/> + </assert_contents> + </element> + <element name="job.stats"> + <assert_contents> + <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/> + <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/> + <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/> + </assert_contents> + </element> + </output_collection> + </xml> + <token name="@COMMON_HELP@"> + +.. class:: warningmark + +**WARNING: This tool is only available for NON-COMMERCIAL use. Permission is only granted for academic, research, and educational purposes. Before using, be sure to review, agree, and comply with the license.** + +Flexynesis is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. +The package includes multiple types of deep learning architectures such as simple fully connected networks, supervised variational autoencoders, graph convolutional networks, multi-triplet networks different options of data layer fusion, and automates feature selection and hyperparameter optimization. + +For more information, please check the Documentation_ : + +For commercial use, please review the flexynesis license on GitHub and contact the `copyright holders`_ . + +----- + + </token> + <xml name="creator"> + <creator> + <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/"/> + <person givenName="Amirhossein" familyName="Naghsh Nilchi" email="nilchia@informatik.uni-freiburg.de"/> + <yield/> + <person givenName="Björn" familyName="Grüning" email="gruening@informatik.uni-freiburg.de"/> + </creator> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1101/2024.07.16.603606</citation>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/embeddings.csv Tue Jun 24 05:55:40 2025 +0000 @@ -0,0 +1,561 @@ +sample_id,E0,E1,E2,E3,E4,E5,E6,E7,E8,E9,E10,E11,E12,E13,E14,E15,E16,E17,E18 +MB-0177,-1.1295899,0.7271579,1.4129219,1.3045986,-1.5297145,-0.12802456,1.2583072,2.5505233,-1.0879718,2.4856799,1.4740374,1.2774653,1.3727989,-2.2527804,-0.36677012,-0.1789978,-0.38056374,2.2817554,-0.6288571 +MB-5115,0.35240406,5.8083305,-3.4783957,-0.1466259,0.39060318,4.274947,-4.4099383,-8.144719,-3.7266977,-6.1133585,0.7837595,-3.908979,0.063239194,7.383131,2.1164417,12.265211,1.6705978,0.29005942,-1.8743639 +MB-3781,0.07074807,1.1994786,1.0994637,0.16382095,0.18301679,0.17052262,0.63744575,0.5536389,0.3689339,0.7740066,-1.376791,-0.88482296,0.5070692,-1.1155727,0.4058765,-1.3321368,-0.3261943,2.1462286,0.5076201 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/labels.csv Tue Jun 24 05:55:40 2025 +0000 @@ -0,0 +1,561 @@ +sample_id,variable,class_label,probability,known_label,predicted_label,split +MB-0177,CLAUDIN_SUBTYPE,Basal,0.00065193686,LumA,LumA,test +MB-5115,CLAUDIN_SUBTYPE,Basal,0.996806,Basal,Basal,test +MB-3781,CLAUDIN_SUBTYPE,Basal,0.002550664,LumA,LumA,test +MB-5271,CLAUDIN_SUBTYPE,Basal,0.019927176,LumB,LumB,test +MB-6179,CLAUDIN_SUBTYPE,Basal,0.027884316,LumA,LumB,test +MB-0492,CLAUDIN_SUBTYPE,Basal,0.018194975,LumB,LumB,test +MB-5135,CLAUDIN_SUBTYPE,Basal,0.9942643,Basal,Basal,test +MB-5079,CLAUDIN_SUBTYPE,Basal,0.00039439273,LumA,LumA,test +MB-5243,CLAUDIN_SUBTYPE,Basal,0.040594183,LumB,LumA,test +MB-2984,CLAUDIN_SUBTYPE,Basal,0.004155519,LumB,LumB,test +MB-4017,CLAUDIN_SUBTYPE,Basal,0.005148993,LumB,LumB,test +MB-5447,CLAUDIN_SUBTYPE,Basal,0.019656463,LumB,LumB,test +MB-5616,CLAUDIN_SUBTYPE,Basal,0.17296688,claudin-low,claudin-low,test +MB-3021,CLAUDIN_SUBTYPE,Basal,0.0047936346,LumA,LumA,test +MB-0872,CLAUDIN_SUBTYPE,Basal,0.008130632,Normal,Normal,test +MB-3386,CLAUDIN_SUBTYPE,Basal,0.012321706,Her2,Her2,test +MB-7080,CLAUDIN_SUBTYPE,Basal,0.00022694626,LumA,LumA,test +MB-5405,CLAUDIN_SUBTYPE,Basal,0.068026006,claudin-low,claudin-low,test +MB-4357,CLAUDIN_SUBTYPE,Basal,0.06376728,LumA,Her2,test +MB-6286,CLAUDIN_SUBTYPE,Basal,0.00011293625,LumA,LumA,test +MB-5134,CLAUDIN_SUBTYPE,Basal,0.000034737288,LumA,LumA,test +MB-4942,CLAUDIN_SUBTYPE,Basal,0.0806648,claudin-low,claudin-low,test +MB-6238,CLAUDIN_SUBTYPE,Basal,0.004182132,LumA,LumA,test +MB-0127,CLAUDIN_SUBTYPE,Basal,0.14812747,Normal,Her2,test +MB-7277,CLAUDIN_SUBTYPE,Basal,0.00010833181,LumA,LumA,test +MB-0060,CLAUDIN_SUBTYPE,Basal,0.42745838,LumB,LumB,test +MB-4721,CLAUDIN_SUBTYPE,Basal,0.0001352974,LumA,LumA,test +MB-0882,CLAUDIN_SUBTYPE,Basal,0.004198095,LumB,LumB,test +MB-3271,CLAUDIN_SUBTYPE,Basal,0.7585569,claudin-low,Basal,test +MB-4746,CLAUDIN_SUBTYPE,Basal,0.023426726,Normal,LumA,test +MB-6069,CLAUDIN_SUBTYPE,Basal,0.011962601,LumA,LumA,test +MB-6044,CLAUDIN_SUBTYPE,Basal,0.091202796,Her2,LumA,test +MB-0601,CLAUDIN_SUBTYPE,Basal,0.09948703,LumB,LumB,test +MB-4887,CLAUDIN_SUBTYPE,Basal,0.045928933,Normal,Normal,test +MB-7111,CLAUDIN_SUBTYPE,Basal,0.68688107,Basal,Basal,test +MB-7174,CLAUDIN_SUBTYPE,Basal,0.037639856,LumB,LumB,test +MB-0317,CLAUDIN_SUBTYPE,Basal,0.0013807476,LumA,LumA,test +MB-4712,CLAUDIN_SUBTYPE,Basal,0.04694011,Normal,Her2,test +MB-7263,CLAUDIN_SUBTYPE,Basal,0.008590267,LumB,LumB,test +MB-5582,CLAUDIN_SUBTYPE,Basal,0.00032956575,LumA,LumA,test +MB-5420,CLAUDIN_SUBTYPE,Basal,0.14000916,Basal,Normal,test +MB-2718,CLAUDIN_SUBTYPE,Basal,0.9568239,Basal,Basal,test +MB-5268,CLAUDIN_SUBTYPE,Basal,0.00022492505,LumA,LumA,test +MB-5514,CLAUDIN_SUBTYPE,Basal,0.011733811,LumA,LumA,test +MB-7053,CLAUDIN_SUBTYPE,Basal,0.054197155,LumA,LumA,test +MB-5348,CLAUDIN_SUBTYPE,Basal,0.31805244,claudin-low,claudin-low,test +MB-0901,CLAUDIN_SUBTYPE,Basal,0.91394204,Basal,Basal,test +MB-5381,CLAUDIN_SUBTYPE,Basal,0.14966057,Her2,Her2,test +MB-3153,CLAUDIN_SUBTYPE,Basal,0.54439086,Basal,Basal,test +MB-5366,CLAUDIN_SUBTYPE,Basal,0.03821787,Her2,Her2,test +MB-7107,CLAUDIN_SUBTYPE,Basal,0.011886511,LumA,LumB,test +MB-4697,CLAUDIN_SUBTYPE,Basal,0.02601451,NC,LumA,test +MB-5070,CLAUDIN_SUBTYPE,Basal,0.55893034,Basal,Basal,test +MB-0598,CLAUDIN_SUBTYPE,Basal,0.025924109,LumB,LumB,test +MB-4374,CLAUDIN_SUBTYPE,Basal,0.00005950361,LumA,LumA,test +MB-0264,CLAUDIN_SUBTYPE,Basal,0.064288855,Her2,LumA,test +MB-4688,CLAUDIN_SUBTYPE,Basal,0.020050965,LumB,LumB,test +MB-7003,CLAUDIN_SUBTYPE,Basal,0.0070154336,Normal,LumA,test +MB-2964,CLAUDIN_SUBTYPE,Basal,0.22110376,Her2,Normal,test +MB-6237,CLAUDIN_SUBTYPE,Basal,0.79525214,Basal,Basal,test +MB-4977,CLAUDIN_SUBTYPE,Basal,0.008476745,LumA,LumB,test +MB-4329,CLAUDIN_SUBTYPE,Basal,0.0005693444,LumA,LumA,test +MB-4001,CLAUDIN_SUBTYPE,Basal,0.040497895,LumA,LumA,test +MB-6163,CLAUDIN_SUBTYPE,Basal,0.01724588,LumA,LumA,test +MB-7151,CLAUDIN_SUBTYPE,Basal,0.99036413,Basal,Basal,test +MB-3341,CLAUDIN_SUBTYPE,Basal,0.00052954024,LumA,LumA,test +MB-5378,CLAUDIN_SUBTYPE,Basal,0.99011266,Basal,Basal,test +MB-0458,CLAUDIN_SUBTYPE,Basal,0.023540689,Normal,Normal,test +MB-0197,CLAUDIN_SUBTYPE,Basal,0.011809357,LumB,LumB,test +MB-3002,CLAUDIN_SUBTYPE,Basal,0.004542802,LumA,LumA,test +MB-0411,CLAUDIN_SUBTYPE,Basal,0.033319343,LumA,LumA,test +MB-0230,CLAUDIN_SUBTYPE,Basal,0.0413835,Her2,Her2,test +MB-0188,CLAUDIN_SUBTYPE,Basal,0.04173352,Her2,LumB,test +MB-4911,CLAUDIN_SUBTYPE,Basal,0.99012136,Basal,Basal,test +MB-0428,CLAUDIN_SUBTYPE,Basal,0.089249864,LumA,LumA,test +MB-5068,CLAUDIN_SUBTYPE,Basal,0.0002629537,LumA,LumA,test +MB-5518,CLAUDIN_SUBTYPE,Basal,0.017793423,LumB,LumB,test +MB-5185,CLAUDIN_SUBTYPE,Basal,0.008536392,LumA,LumA,test +MB-4836,CLAUDIN_SUBTYPE,Basal,0.25713205,Her2,Her2,test +MB-6125,CLAUDIN_SUBTYPE,Basal,0.042460058,Normal,LumA,test +MB-2932,CLAUDIN_SUBTYPE,Basal,0.010055175,LumB,LumB,test +MB-0095,CLAUDIN_SUBTYPE,Basal,0.0011303613,LumB,LumB,test +MB-2564,CLAUDIN_SUBTYPE,Basal,0.00018593732,LumA,LumA,test +MB-7155,CLAUDIN_SUBTYPE,Basal,0.90355,Basal,Basal,test +MB-4603,CLAUDIN_SUBTYPE,Basal,0.0017825573,Normal,LumA,test +MB-4173,CLAUDIN_SUBTYPE,Basal,0.00006163649,LumA,LumA,test +MB-0578,CLAUDIN_SUBTYPE,Basal,0.013469911,Normal,Normal,test +MB-3272,CLAUDIN_SUBTYPE,Basal,0.033196483,LumB,LumB,test +MB-4695,CLAUDIN_SUBTYPE,Basal,0.0014625929,Normal,LumA,test +MB-0455,CLAUDIN_SUBTYPE,Basal,0.12362967,LumB,claudin-low,test +MB-2863,CLAUDIN_SUBTYPE,Basal,0.00010688343,LumA,LumA,test +MB-0346,CLAUDIN_SUBTYPE,Basal,0.010869512,Her2,Her2,test +MB-4709,CLAUDIN_SUBTYPE,Basal,0.00011124542,LumA,LumA,test +MB-5057,CLAUDIN_SUBTYPE,Basal,0.82365197,Basal,Basal,test +MB-4724,CLAUDIN_SUBTYPE,Basal,0.02104304,Her2,Her2,test +MB-6217,CLAUDIN_SUBTYPE,Basal,0.01368638,LumB,LumB,test +MB-7160,CLAUDIN_SUBTYPE,Basal,0.63306177,Her2,Basal,test +MB-4548,CLAUDIN_SUBTYPE,Basal,0.7617707,Her2,Basal,test +MB-5222,CLAUDIN_SUBTYPE,Basal,0.040132806,claudin-low,claudin-low,test +MB-5422,CLAUDIN_SUBTYPE,Basal,0.00061716465,LumA,LumA,test +MB-0384,CLAUDIN_SUBTYPE,Basal,0.008731177,LumB,LumA,test +MB-5335,CLAUDIN_SUBTYPE,Basal,0.98229927,Basal,Basal,test +MB-0157,CLAUDIN_SUBTYPE,Basal,0.021822063,claudin-low,claudin-low,test +MB-5324,CLAUDIN_SUBTYPE,Basal,0.00030340505,LumA,LumA,test +MB-5150,CLAUDIN_SUBTYPE,Basal,0.0014000323,Normal,LumA,test +MB-7073,CLAUDIN_SUBTYPE,Basal,0.8283376,Basal,Basal,test +MB-0136,CLAUDIN_SUBTYPE,Basal,0.006129607,LumA,LumA,test +MB-0163,CLAUDIN_SUBTYPE,Basal,0.99020535,Basal,Basal,test +MB-4834,CLAUDIN_SUBTYPE,Basal,0.0062780203,LumB,LumB,test +MB-5465,CLAUDIN_SUBTYPE,Basal,0.8397852,Basal,Basal,test +MB-5330,CLAUDIN_SUBTYPE,Basal,0.0018246461,LumA,LumA,test +MB-0489,CLAUDIN_SUBTYPE,Basal,0.0018973575,claudin-low,claudin-low,test +MB-0107,CLAUDIN_SUBTYPE,Basal,0.019695183,LumB,LumB,test +MB-5593,CLAUDIN_SUBTYPE,Basal,0.019911716,Her2,Her2,test +MB-6245,CLAUDIN_SUBTYPE,Basal,0.97986525,Basal,Basal,test +MB-5329,CLAUDIN_SUBTYPE,Basal,0.062605105,LumA,Normal,test +MB-6346,CLAUDIN_SUBTYPE,Basal,0.0035589235,LumB,LumA,test +MB-0200,CLAUDIN_SUBTYPE,Basal,0.99442106,Basal,Basal,test +MB-0354,CLAUDIN_SUBTYPE,Basal,0.005794085,claudin-low,claudin-low,test +MB-5474,CLAUDIN_SUBTYPE,Basal,0.59014565,claudin-low,Basal,test +MB-3328,CLAUDIN_SUBTYPE,Basal,0.0009819119,LumA,LumA,test +MB-6018,CLAUDIN_SUBTYPE,Basal,0.0031151162,LumA,LumA,test +MB-0599,CLAUDIN_SUBTYPE,Basal,0.03173055,LumA,Normal,test +MB-4591,CLAUDIN_SUBTYPE,Basal,0.006855861,LumB,LumB,test +MB-0378,CLAUDIN_SUBTYPE,Basal,0.05696687,Her2,Her2,test +MB-3548,CLAUDIN_SUBTYPE,Basal,0.00068786135,LumA,LumA,test +MB-0226,CLAUDIN_SUBTYPE,Basal,0.0013146834,LumA,LumA,test +MB-7193,CLAUDIN_SUBTYPE,Basal,0.0012215632,LumB,LumB,test +MB-5622,CLAUDIN_SUBTYPE,Basal,0.0045035863,LumB,LumB,test +MB-0171,CLAUDIN_SUBTYPE,Basal,0.014331588,Normal,Normal,test +MB-7286,CLAUDIN_SUBTYPE,Basal,0.0062232437,LumB,LumB,test +MB-4974,CLAUDIN_SUBTYPE,Basal,0.12730515,Basal,claudin-low,test +MB-0452,CLAUDIN_SUBTYPE,Basal,0.0023872657,LumB,LumB,test +MB-2846,CLAUDIN_SUBTYPE,Basal,0.110638395,Basal,Normal,test +MB-5195,CLAUDIN_SUBTYPE,Basal,0.029660814,LumA,LumB,test +MB-0302,CLAUDIN_SUBTYPE,Basal,0.10346622,LumA,LumA,test +MB-2712,CLAUDIN_SUBTYPE,Basal,0.0008071044,LumA,LumA,test +MB-4896,CLAUDIN_SUBTYPE,Basal,0.31161806,Basal,Her2,test +MB-7084,CLAUDIN_SUBTYPE,Basal,0.9638875,Basal,Basal,test +MB-2772,CLAUDIN_SUBTYPE,Basal,0.08007874,LumB,LumB,test +MB-5221,CLAUDIN_SUBTYPE,Basal,0.0001289943,LumA,LumA,test +MB-5572,CLAUDIN_SUBTYPE,Basal,0.012371493,claudin-low,claudin-low,test +MB-5045,CLAUDIN_SUBTYPE,Basal,0.14420292,LumA,Normal,test +MB-5093,CLAUDIN_SUBTYPE,Basal,0.008165335,Her2,LumB,test +MB-5044,CLAUDIN_SUBTYPE,Basal,0.018178718,LumB,LumB,test +MB-3028,CLAUDIN_SUBTYPE,Basal,0.08454357,LumB,LumB,test +MB-0658,CLAUDIN_SUBTYPE,Basal,0.230179,claudin-low,claudin-low,test +MB-7005,CLAUDIN_SUBTYPE,Basal,0.008641446,LumB,LumB,test +MB-5228,CLAUDIN_SUBTYPE,Basal,0.054715365,LumB,LumB,test +MB-0314,CLAUDIN_SUBTYPE,Basal,0.048630077,Her2,Her2,test +MB-7293,CLAUDIN_SUBTYPE,Basal,0.000700282,LumA,LumA,test +MB-5602,CLAUDIN_SUBTYPE,Basal,0.5253072,Basal,Basal,test +MB-5406,CLAUDIN_SUBTYPE,Basal,0.02733475,LumB,LumB,test +MB-0884,CLAUDIN_SUBTYPE,Basal,0.0040842826,LumB,LumB,test +MB-7112,CLAUDIN_SUBTYPE,Basal,0.038913336,LumB,LumA,test +MB-2939,CLAUDIN_SUBTYPE,Basal,0.0050817286,LumB,LumB,test +MB-0541,CLAUDIN_SUBTYPE,Basal,0.018826589,LumA,LumB,test +MB-7186,CLAUDIN_SUBTYPE,Basal,0.005265429,LumB,LumB,test +MB-5230,CLAUDIN_SUBTYPE,Basal,0.00295254,LumA,LumA,test +MB-5059,CLAUDIN_SUBTYPE,Basal,0.00003445285,LumA,LumA,test +MB-0656,CLAUDIN_SUBTYPE,Basal,0.59791833,claudin-low,Basal,test +MB-6059,CLAUDIN_SUBTYPE,Basal,0.10510234,Normal,LumB,test +MB-3062,CLAUDIN_SUBTYPE,Basal,0.010768656,claudin-low,claudin-low,test +MB-0393,CLAUDIN_SUBTYPE,Basal,0.116923705,claudin-low,LumA,test +MB-3379,CLAUDIN_SUBTYPE,Basal,0.0040908083,LumA,LumA,test +MB-4601,CLAUDIN_SUBTYPE,Basal,0.28315553,Basal,Her2,test +MB-5310,CLAUDIN_SUBTYPE,Basal,0.018802995,LumA,LumA,test +MB-0412,CLAUDIN_SUBTYPE,Basal,0.0015564469,LumB,LumB,test +MB-5527,CLAUDIN_SUBTYPE,Basal,0.027947528,claudin-low,claudin-low,test +MB-3007,CLAUDIN_SUBTYPE,Basal,0.011360846,LumB,LumB,test +MB-2951,CLAUDIN_SUBTYPE,Basal,0.005496098,LumA,LumA,test +MB-7027,CLAUDIN_SUBTYPE,Basal,0.18513304,Her2,claudin-low,test +MB-0500,CLAUDIN_SUBTYPE,Basal,0.99305624,Basal,Basal,test +MB-3064,CLAUDIN_SUBTYPE,Basal,0.09197106,LumA,Normal,test +MB-2792,CLAUDIN_SUBTYPE,Basal,0.035945714,Her2,LumA,test +MB-4375,CLAUDIN_SUBTYPE,Basal,0.005555877,Normal,Normal,test +MB-4908,CLAUDIN_SUBTYPE,Basal,0.003958556,LumB,LumB,test +MB-5628,CLAUDIN_SUBTYPE,Basal,0.012981304,LumB,LumB,test +MB-3381,CLAUDIN_SUBTYPE,Basal,0.0020334984,LumA,LumA,test +MB-7011,CLAUDIN_SUBTYPE,Basal,0.0033411589,LumB,LumB,test +MB-4640,CLAUDIN_SUBTYPE,Basal,0.045325782,Her2,Her2,test +MB-0666,CLAUDIN_SUBTYPE,Basal,0.021183776,LumA,LumB,test +MB-4059,CLAUDIN_SUBTYPE,Basal,0.003601682,Normal,LumA,test +MB-7150,CLAUDIN_SUBTYPE,Basal,0.0064166198,LumB,LumB,test +MB-7262,CLAUDIN_SUBTYPE,Basal,0.013179999,Her2,Her2,test +MB-0133,CLAUDIN_SUBTYPE,Basal,0.00045371466,LumA,LumA,test +MB-4343,CLAUDIN_SUBTYPE,Basal,0.47470322,Her2,Basal,test +MB-4015,CLAUDIN_SUBTYPE,Basal,0.010890819,Her2,Her2,test +MB-2708,CLAUDIN_SUBTYPE,Basal,0.0040587,LumB,LumA,test +MB-3462,CLAUDIN_SUBTYPE,Basal,0.0016569006,LumA,LumA,test +MB-5383,CLAUDIN_SUBTYPE,Basal,0.026178962,LumA,LumB,test +MB-7294,CLAUDIN_SUBTYPE,Basal,0.013935004,LumB,LumB,test +MB-2833,CLAUDIN_SUBTYPE,Basal,0.016667495,claudin-low,claudin-low,test +MB-0419,CLAUDIN_SUBTYPE,Basal,0.0048514134,LumA,LumA,test +MB-6050,CLAUDIN_SUBTYPE,Basal,0.0017174709,LumA,LumA,test +MB-7092,CLAUDIN_SUBTYPE,Basal,0.09593538,Her2,LumB,test +MB-0114,CLAUDIN_SUBTYPE,Basal,0.0022584063,LumA,LumA,test +MB-7079,CLAUDIN_SUBTYPE,Basal,0.0065553426,claudin-low,claudin-low,test +MB-0425,CLAUDIN_SUBTYPE,Basal,0.0048174113,LumA,LumA,test +MB-0285,CLAUDIN_SUBTYPE,Basal,0.015996402,claudin-low,claudin-low,test +MB-7164,CLAUDIN_SUBTYPE,Basal,0.0008814891,LumA,LumA,test +MB-2786,CLAUDIN_SUBTYPE,Basal,0.02980681,LumA,LumB,test +MB-4322,CLAUDIN_SUBTYPE,Basal,0.0022297003,LumA,LumA,test +MB-4929,CLAUDIN_SUBTYPE,Basal,0.036082525,Her2,LumA,test +MB-3049,CLAUDIN_SUBTYPE,Basal,0.009222006,LumA,LumA,test +MB-4797,CLAUDIN_SUBTYPE,Basal,0.006543896,LumA,LumA,test +MB-0324,CLAUDIN_SUBTYPE,Basal,0.01106631,LumA,LumB,test +MB-4701,CLAUDIN_SUBTYPE,Basal,0.000017004955,LumA,LumA,test +MB-0244,CLAUDIN_SUBTYPE,Basal,0.016717277,Normal,LumA,test +MB-4681,CLAUDIN_SUBTYPE,Basal,0.00028730012,LumA,LumA,test +MB-7201,CLAUDIN_SUBTYPE,Basal,0.13286604,claudin-low,claudin-low,test +MB-2556,CLAUDIN_SUBTYPE,Basal,0.019965198,claudin-low,claudin-low,test +MB-5451,CLAUDIN_SUBTYPE,Basal,0.00019718484,LumA,LumA,test +MB-6071,CLAUDIN_SUBTYPE,Basal,0.0063935183,LumA,LumA,test +MB-7121,CLAUDIN_SUBTYPE,Basal,0.28942513,claudin-low,claudin-low,test +MB-4691,CLAUDIN_SUBTYPE,Basal,0.0004175498,LumA,LumA,test +MB-0234,CLAUDIN_SUBTYPE,Basal,0.013009974,LumB,LumB,test +MB-6017,CLAUDIN_SUBTYPE,Basal,0.00013364745,LumA,LumA,test +MB-4008,CLAUDIN_SUBTYPE,Basal,0.00715301,LumB,LumB,test +MB-0542,CLAUDIN_SUBTYPE,Basal,0.18582183,Normal,LumA,test +MB-5563,CLAUDIN_SUBTYPE,Basal,0.000028127823,LumA,LumA,test +MB-4945,CLAUDIN_SUBTYPE,Basal,0.92402095,Basal,Basal,test +MB-0081,CLAUDIN_SUBTYPE,Basal,0.26086026,claudin-low,claudin-low,test +MB-0106,CLAUDIN_SUBTYPE,Basal,0.0007867359,LumA,LumA,test +MB-5049,CLAUDIN_SUBTYPE,Basal,0.008915669,LumB,LumA,test +MB-0442,CLAUDIN_SUBTYPE,Basal,0.018254837,claudin-low,claudin-low,test +MB-0534,CLAUDIN_SUBTYPE,Basal,0.035875645,claudin-low,Normal,test +MB-2721,CLAUDIN_SUBTYPE,Basal,0.0027118893,LumA,LumA,test +MB-7088,CLAUDIN_SUBTYPE,Basal,0.11950952,Her2,LumB,test +MB-6019,CLAUDIN_SUBTYPE,Basal,0.17273197,Normal,Her2,test +MB-0377,CLAUDIN_SUBTYPE,Basal,0.097247094,LumA,Normal,test +MB-7145,CLAUDIN_SUBTYPE,Basal,0.9859118,Basal,Basal,test +MB-4362,CLAUDIN_SUBTYPE,Basal,0.000048199137,Normal,LumA,test +MB-3001,CLAUDIN_SUBTYPE,Basal,0.8703276,claudin-low,Basal,test +MB-5364,CLAUDIN_SUBTYPE,Basal,0.017264724,Normal,LumA,test +MB-4292,CLAUDIN_SUBTYPE,Basal,0.002748507,LumA,LumA,test +MB-0294,CLAUDIN_SUBTYPE,Basal,0.080543205,Normal,claudin-low,test +MB-4395,CLAUDIN_SUBTYPE,Basal,0.048069697,Her2,LumB,test +MB-3707,CLAUDIN_SUBTYPE,Basal,0.028681524,claudin-low,claudin-low,test +MB-0606,CLAUDIN_SUBTYPE,Basal,0.007836574,LumB,LumB,test +MB-5360,CLAUDIN_SUBTYPE,Basal,0.0031488223,LumA,LumA,test +MB-3300,CLAUDIN_SUBTYPE,Basal,0.026190653,LumB,LumB,test +MB-3748,CLAUDIN_SUBTYPE,Basal,0.0010757027,LumA,LumA,test +MB-4665,CLAUDIN_SUBTYPE,Basal,0.0040027923,LumA,LumA,test +MB-3702,CLAUDIN_SUBTYPE,Basal,0.41824463,claudin-low,Basal,test +MB-4770,CLAUDIN_SUBTYPE,Basal,0.3075867,Her2,Her2,test +MB-5175,CLAUDIN_SUBTYPE,Basal,0.086505786,claudin-low,claudin-low,test +MB-6231,CLAUDIN_SUBTYPE,Basal,0.015856754,Normal,LumA,test +MB-2735,CLAUDIN_SUBTYPE,Basal,0.027673326,LumB,LumB,test +MB-4894,CLAUDIN_SUBTYPE,Basal,0.008146837,LumA,LumB,test +MB-3292,CLAUDIN_SUBTYPE,Basal,0.12310144,claudin-low,claudin-low,test +MB-4872,CLAUDIN_SUBTYPE,Basal,0.03850913,LumA,LumA,test +MB-4266,CLAUDIN_SUBTYPE,Basal,0.20300272,LumA,LumB,test +MB-0536,CLAUDIN_SUBTYPE,Basal,0.07104641,LumB,LumB,test +MB-7057,CLAUDIN_SUBTYPE,Basal,0.033891283,Normal,Normal,test +MB-6055,CLAUDIN_SUBTYPE,Basal,0.10617896,claudin-low,claudin-low,test +MB-5116,CLAUDIN_SUBTYPE,Basal,0.0019858023,LumB,LumB,test +MB-5264,CLAUDIN_SUBTYPE,Basal,0.00009177315,LumA,LumA,test +MB-6232,CLAUDIN_SUBTYPE,Basal,0.0003516687,LumA,LumA,test +MB-0586,CLAUDIN_SUBTYPE,Basal,0.00016750579,LumA,LumA,test +MB-3079,CLAUDIN_SUBTYPE,Basal,0.0012705416,LumA,LumA,test +MB-7046,CLAUDIN_SUBTYPE,Basal,0.020394996,Her2,LumB,test +MB-0609,CLAUDIN_SUBTYPE,Basal,0.0038115378,LumA,LumA,test +MB-5642,CLAUDIN_SUBTYPE,Basal,0.000386987,LumA,LumA,test +MB-2536,CLAUDIN_SUBTYPE,Basal,0.000158365,LumA,LumA,test +MB-4849,CLAUDIN_SUBTYPE,Basal,0.014060427,LumA,LumA,test +MB-5481,CLAUDIN_SUBTYPE,Basal,0.04727273,LumB,LumB,test +MB-2904,CLAUDIN_SUBTYPE,Basal,0.820908,claudin-low,Basal,test +MB-5345,CLAUDIN_SUBTYPE,Basal,0.0003942885,Normal,LumA,test +MB-5256,CLAUDIN_SUBTYPE,Basal,0.0052847103,LumA,LumA,test +MB-3329,CLAUDIN_SUBTYPE,Basal,0.46680883,Her2,Basal,test +MB-2725,CLAUDIN_SUBTYPE,Basal,0.0114249615,LumA,Normal,test +MB-6192,CLAUDIN_SUBTYPE,Basal,0.020725993,LumB,LumB,test +MB-6007,CLAUDIN_SUBTYPE,Basal,0.15368254,Her2,LumB,test +MB-5440,CLAUDIN_SUBTYPE,Basal,0.018648334,claudin-low,claudin-low,test +MB-2617,CLAUDIN_SUBTYPE,Basal,0.0055856854,LumB,LumA,test +MB-0517,CLAUDIN_SUBTYPE,Basal,0.0005509023,LumA,LumA,test +MB-6257,CLAUDIN_SUBTYPE,Basal,0.00825107,LumB,LumB,test +MB-5463,CLAUDIN_SUBTYPE,Basal,0.10012772,LumB,Her2,test +MB-4704,CLAUDIN_SUBTYPE,Basal,0.0030723102,LumA,LumA,test +MB-5019,CLAUDIN_SUBTYPE,Basal,0.1187088,Normal,Her2,test +MB-2705,CLAUDIN_SUBTYPE,Basal,0.0049891807,LumB,LumB,test +MB-7207,CLAUDIN_SUBTYPE,Basal,0.022932222,Her2,Her2,test +MB-0223,CLAUDIN_SUBTYPE,Basal,0.0013372044,LumA,LumA,test +MB-6224,CLAUDIN_SUBTYPE,Basal,0.19748071,Her2,claudin-low,test +MB-3058,CLAUDIN_SUBTYPE,Basal,0.43238187,Basal,Basal,test +MB-0427,CLAUDIN_SUBTYPE,Basal,0.13718928,LumA,claudin-low,test +MB-5176,CLAUDIN_SUBTYPE,Basal,0.16037229,claudin-low,claudin-low,test +MB-5491,CLAUDIN_SUBTYPE,Basal,0.02443612,LumB,LumB,test +MB-7225,CLAUDIN_SUBTYPE,Basal,0.99748164,Basal,Basal,test +MB-5533,CLAUDIN_SUBTYPE,Basal,0.0533677,Normal,Normal,test +MB-0010,CLAUDIN_SUBTYPE,Basal,0.00858182,LumB,LumB,test +MB-0366,CLAUDIN_SUBTYPE,Basal,0.0043867035,LumA,LumA,test +MB-4000,CLAUDIN_SUBTYPE,Basal,0.0070070336,LumA,LumA,test +MB-0131,CLAUDIN_SUBTYPE,Basal,0.010145989,LumA,LumA,test +MB-6107,CLAUDIN_SUBTYPE,Basal,0.11152945,Normal,Normal,test +MB-5613,CLAUDIN_SUBTYPE,Basal,0.040446434,LumB,LumB,test +MB-0467,CLAUDIN_SUBTYPE,Basal,0.086296946,Her2,Her2,test +MB-3525,CLAUDIN_SUBTYPE,Basal,0.005030327,LumB,LumB,test +MB-5532,CLAUDIN_SUBTYPE,Basal,0.011970935,LumA,LumB,test +MB-5201,CLAUDIN_SUBTYPE,Basal,0.000013542817,LumA,LumA,test +MB-5041,CLAUDIN_SUBTYPE,Basal,0.059350874,claudin-low,claudin-low,test +MB-7251,CLAUDIN_SUBTYPE,Basal,0.04400487,Her2,Her2,test +MB-5632,CLAUDIN_SUBTYPE,Basal,0.02690288,LumB,LumB,test +MB-7008,CLAUDIN_SUBTYPE,Basal,0.14291425,claudin-low,claudin-low,test +MB-5174,CLAUDIN_SUBTYPE,Basal,0.47107643,Her2,Basal,test +MB-5305,CLAUDIN_SUBTYPE,Basal,0.00010249849,LumA,LumA,test +MB-5407,CLAUDIN_SUBTYPE,Basal,0.0011000666,LumA,LumA,test +MB-0256,CLAUDIN_SUBTYPE,Basal,0.0016889563,LumA,LumA,test +MB-5166,CLAUDIN_SUBTYPE,Basal,0.036223304,LumB,LumB,test +MB-5377,CLAUDIN_SUBTYPE,Basal,0.017830601,LumB,LumB,test +MB-0464,CLAUDIN_SUBTYPE,Basal,0.7071817,Basal,Basal,test +MB-4949,CLAUDIN_SUBTYPE,Basal,0.047740042,LumB,LumB,test +MB-5162,CLAUDIN_SUBTYPE,Basal,0.0034282694,claudin-low,claudin-low,test +MB-7158,CLAUDIN_SUBTYPE,Basal,0.05165293,claudin-low,claudin-low,test +MB-3303,CLAUDIN_SUBTYPE,Basal,0.037725344,LumB,LumB,test +MB-4686,CLAUDIN_SUBTYPE,Basal,0.0104456,LumA,LumA,test +MB-0211,CLAUDIN_SUBTYPE,Basal,0.074217185,claudin-low,claudin-low,test +MB-4623,CLAUDIN_SUBTYPE,Basal,0.031749863,LumA,LumA,test +MB-7051,CLAUDIN_SUBTYPE,Basal,0.019793851,Her2,LumB,test +MB-7102,CLAUDIN_SUBTYPE,Basal,0.015069642,LumB,LumB,test +MB-5328,CLAUDIN_SUBTYPE,Basal,0.01695427,LumB,LumB,test +MB-5327,CLAUDIN_SUBTYPE,Basal,0.029235683,Her2,Her2,test +MB-6021,CLAUDIN_SUBTYPE,Basal,0.00018965527,LumA,LumA,test +MB-5261,CLAUDIN_SUBTYPE,Basal,0.01641713,LumB,LumB,test +MB-0282,CLAUDIN_SUBTYPE,Basal,0.068172865,claudin-low,Normal,test +MB-0266,CLAUDIN_SUBTYPE,Basal,0.0015670573,LumA,LumA,test +MB-6256,CLAUDIN_SUBTYPE,Basal,0.052125204,LumA,LumA,test +MB-4333,CLAUDIN_SUBTYPE,Basal,0.0033138813,LumA,LumA,test +MB-0313,CLAUDIN_SUBTYPE,Basal,0.05912761,LumB,LumB,test +MB-5510,CLAUDIN_SUBTYPE,Basal,0.00012463347,LumA,LumA,test +MB-5393,CLAUDIN_SUBTYPE,Basal,0.0005118491,LumB,LumA,test +MB-6308,CLAUDIN_SUBTYPE,Basal,0.00013780262,LumA,LumA,test +MB-7115,CLAUDIN_SUBTYPE,Basal,0.008631562,Her2,Her2,test +MB-3388,CLAUDIN_SUBTYPE,Basal,0.005404918,LumB,LumB,test +MB-0654,CLAUDIN_SUBTYPE,Basal,0.00018675308,LumA,LumA,test +MB-0236,CLAUDIN_SUBTYPE,Basal,0.009044096,LumA,LumA,test +MB-0154,CLAUDIN_SUBTYPE,Basal,0.00007889601,LumA,LumA,test +MB-0257,CLAUDIN_SUBTYPE,Basal,0.008032525,LumA,LumA,test +MB-4878,CLAUDIN_SUBTYPE,Basal,0.019948626,LumA,LumA,test +MB-7298,CLAUDIN_SUBTYPE,Basal,0.0045288745,LumB,LumB,test +MB-3254,CLAUDIN_SUBTYPE,Basal,0.00022470046,LumA,LumA,test +MB-7109,CLAUDIN_SUBTYPE,Basal,0.00033619878,LumB,LumB,test +MB-2517,CLAUDIN_SUBTYPE,Basal,0.046940178,Her2,LumA,test +MB-0125,CLAUDIN_SUBTYPE,Basal,0.0001302165,LumB,LumA,test +MB-6319,CLAUDIN_SUBTYPE,Basal,0.0036058899,Normal,LumA,test +MB-4952,CLAUDIN_SUBTYPE,Basal,0.11574637,Her2,claudin-low,test +MB-4602,CLAUDIN_SUBTYPE,Basal,0.0030722558,LumB,LumB,test +MB-5382,CLAUDIN_SUBTYPE,Basal,0.0065480038,LumA,LumA,test +MB-3222,CLAUDIN_SUBTYPE,Basal,0.042421207,LumA,LumA,test +MB-4351,CLAUDIN_SUBTYPE,Basal,0.39117947,Her2,Her2,test +MB-2801,CLAUDIN_SUBTYPE,Basal,0.0105636865,LumA,LumB,test +MB-6336,CLAUDIN_SUBTYPE,Basal,0.9780357,Basal,Basal,test +MB-0238,CLAUDIN_SUBTYPE,Basal,0.4415894,claudin-low,claudin-low,test +MB-6051,CLAUDIN_SUBTYPE,Basal,0.0000783062,LumA,LumA,test +MB-0035,CLAUDIN_SUBTYPE,Basal,0.04660786,Her2,Her2,test +MB-0258,CLAUDIN_SUBTYPE,Basal,0.01340173,LumA,LumB,test +MB-7196,CLAUDIN_SUBTYPE,Basal,0.014710226,Her2,LumB,test +MB-7010,CLAUDIN_SUBTYPE,Basal,0.0014947575,LumA,LumA,test +MB-0507,CLAUDIN_SUBTYPE,Basal,0.014943987,LumA,LumA,test +MB-3033,CLAUDIN_SUBTYPE,Basal,0.00007264832,LumA,LumA,test +MB-6225,CLAUDIN_SUBTYPE,Basal,0.0036495982,LumA,LumA,test +MB-2917,CLAUDIN_SUBTYPE,Basal,0.9463504,Basal,Basal,test +MB-4250,CLAUDIN_SUBTYPE,Basal,0.0023491702,LumA,LumA,test +MB-0897,CLAUDIN_SUBTYPE,Basal,0.0013110188,Normal,LumA,test +MB-5039,CLAUDIN_SUBTYPE,Basal,0.0922615,LumB,LumB,test +MB-7017,CLAUDIN_SUBTYPE,Basal,0.40332106,claudin-low,claudin-low,test +MB-5014,CLAUDIN_SUBTYPE,Basal,0.025201658,LumB,LumB,test +MB-4318,CLAUDIN_SUBTYPE,Basal,0.0012839211,LumB,LumB,test +MB-2744,CLAUDIN_SUBTYPE,Basal,0.013939582,Normal,Normal,test +MB-7131,CLAUDIN_SUBTYPE,Basal,0.018158045,LumB,LumB,test +MB-7163,CLAUDIN_SUBTYPE,Basal,0.00030775947,LumA,LumA,test +MB-7095,CLAUDIN_SUBTYPE,Basal,0.0032390642,LumA,LumA,test +MB-5110,CLAUDIN_SUBTYPE,Basal,0.044399105,Normal,Normal,test +MB-5191,CLAUDIN_SUBTYPE,Basal,0.010420343,LumA,LumA,test +MB-5052,CLAUDIN_SUBTYPE,Basal,0.017237134,claudin-low,claudin-low,test +MB-5078,CLAUDIN_SUBTYPE,Basal,0.24473657,LumB,Her2,test +MB-7078,CLAUDIN_SUBTYPE,Basal,0.01774906,claudin-low,claudin-low,test +MB-7279,CLAUDIN_SUBTYPE,Basal,0.10951925,Her2,Her2,test +MB-5172,CLAUDIN_SUBTYPE,Basal,0.017404724,Her2,Her2,test +MB-5138,CLAUDIN_SUBTYPE,Basal,0.96672106,Basal,Basal,test +MB-0512,CLAUDIN_SUBTYPE,Basal,0.023697501,LumA,LumB,test +MB-7173,CLAUDIN_SUBTYPE,Basal,0.01869835,LumA,LumB,test +MB-0288,CLAUDIN_SUBTYPE,Basal,0.0023877192,Normal,LumA,test +MB-5651,CLAUDIN_SUBTYPE,Basal,0.1600857,claudin-low,claudin-low,test +MB-4706,CLAUDIN_SUBTYPE,Basal,0.0035911708,LumA,LumA,test +MB-0229,CLAUDIN_SUBTYPE,Basal,0.0027642664,LumA,LumA,test +MB-5173,CLAUDIN_SUBTYPE,Basal,0.843011,Basal,Basal,test +MB-6273,CLAUDIN_SUBTYPE,Basal,0.0009950558,LumA,LumA,test +MB-2927,CLAUDIN_SUBTYPE,Basal,0.046562012,LumA,LumA,test +MB-0227,CLAUDIN_SUBTYPE,Basal,0.0040115644,LumA,LumA,test +MB-6168,CLAUDIN_SUBTYPE,Basal,0.002689905,LumA,LumA,test +MB-4843,CLAUDIN_SUBTYPE,Basal,0.0002493313,LumA,LumA,test +MB-7171,CLAUDIN_SUBTYPE,Basal,0.057506997,LumB,LumB,test +MB-4722,CLAUDIN_SUBTYPE,Basal,0.0013486504,LumA,LumA,test +MB-4825,CLAUDIN_SUBTYPE,Basal,0.010020296,LumA,LumA,test +MB-7270,CLAUDIN_SUBTYPE,Basal,0.4941126,Basal,Basal,test +MB-0503,CLAUDIN_SUBTYPE,Basal,0.0030855036,LumA,LumA,test +MB-3123,CLAUDIN_SUBTYPE,Basal,0.9821264,Basal,Basal,test +MB-4323,CLAUDIN_SUBTYPE,Basal,0.0014945951,LumA,LumA,test +MB-3371,CLAUDIN_SUBTYPE,Basal,0.00894019,LumB,LumB,test +MB-6122,CLAUDIN_SUBTYPE,Basal,0.48250183,Basal,Basal,test +MB-4702,CLAUDIN_SUBTYPE,Basal,0.028206088,LumB,LumB,test +MB-5596,CLAUDIN_SUBTYPE,Basal,0.000033043274,LumA,LumA,test +MB-0471,CLAUDIN_SUBTYPE,Basal,0.011027864,LumA,LumB,test +MB-5384,CLAUDIN_SUBTYPE,Basal,0.120825455,LumA,LumB,test +MB-4779,CLAUDIN_SUBTYPE,Basal,0.000060203776,LumA,LumA,test +MB-5396,CLAUDIN_SUBTYPE,Basal,0.0028882464,LumB,LumB,test +MB-5638,CLAUDIN_SUBTYPE,Basal,0.057065018,LumA,LumA,test +MB-0573,CLAUDIN_SUBTYPE,Basal,0.08095056,claudin-low,claudin-low,test +MB-4679,CLAUDIN_SUBTYPE,Basal,0.98210365,Basal,Basal,test +MB-5645,CLAUDIN_SUBTYPE,Basal,0.015252581,LumA,LumA,test +MB-0389,CLAUDIN_SUBTYPE,Basal,0.012667824,LumB,LumB,test +MB-0484,CLAUDIN_SUBTYPE,Basal,0.05460147,Her2,LumB,test +MB-4992,CLAUDIN_SUBTYPE,Basal,0.013725633,LumA,LumA,test +MB-0224,CLAUDIN_SUBTYPE,Basal,0.0020582175,LumA,LumA,test +MB-7235,CLAUDIN_SUBTYPE,Basal,0.0020686353,LumA,LumA,test +MB-3355,CLAUDIN_SUBTYPE,Basal,0.29062548,Her2,Her2,test +MB-7217,CLAUDIN_SUBTYPE,Basal,0.057230562,LumA,LumA,test +MB-2754,CLAUDIN_SUBTYPE,Basal,0.13703783,Normal,Normal,test +MB-5478,CLAUDIN_SUBTYPE,Basal,0.0038339214,LumA,LumA,test +MB-3363,CLAUDIN_SUBTYPE,Basal,0.9548865,Basal,Basal,test +MB-7250,CLAUDIN_SUBTYPE,Basal,0.008389959,Her2,Her2,test +MB-3466,CLAUDIN_SUBTYPE,Basal,0.0054750456,Her2,LumB,test +MB-5063,CLAUDIN_SUBTYPE,Basal,0.24830134,Her2,Her2,test +MB-6190,CLAUDIN_SUBTYPE,Basal,0.010308503,LumA,LumA,test +MB-5155,CLAUDIN_SUBTYPE,Basal,0.000935166,Normal,LumA,test +MB-4341,CLAUDIN_SUBTYPE,Basal,0.06784694,Her2,Her2,test +MB-0311,CLAUDIN_SUBTYPE,Basal,0.019236883,LumB,LumB,test +MB-0417,CLAUDIN_SUBTYPE,Basal,0.00608791,Her2,LumA,test +MB-0495,CLAUDIN_SUBTYPE,Basal,0.0354971,claudin-low,claudin-low,test +MB-4350,CLAUDIN_SUBTYPE,Basal,0.66395986,Her2,Basal,test +MB-3487,CLAUDIN_SUBTYPE,Basal,0.0041024117,LumB,LumB,test +MB-4212,CLAUDIN_SUBTYPE,Basal,0.000009000377,LumA,LumA,test +MB-6344,CLAUDIN_SUBTYPE,Basal,0.00653923,LumB,LumB,test +MB-0899,CLAUDIN_SUBTYPE,Basal,0.0056963847,LumA,LumA,test +MB-7019,CLAUDIN_SUBTYPE,Basal,0.0104463,LumB,LumA,test +MB-5551,CLAUDIN_SUBTYPE,Basal,0.9833264,Basal,Basal,test +MB-0143,CLAUDIN_SUBTYPE,Basal,0.00506314,LumA,LumB,test +MB-7137,CLAUDIN_SUBTYPE,Basal,0.00010265978,LumA,LumA,test +MB-2774,CLAUDIN_SUBTYPE,Basal,0.051009756,LumB,LumB,test +MB-4621,CLAUDIN_SUBTYPE,Basal,0.98992467,Basal,Basal,test +MB-5008,CLAUDIN_SUBTYPE,Basal,0.34858075,Her2,Her2,test +MB-7097,CLAUDIN_SUBTYPE,Basal,0.021539504,LumB,LumA,test +MB-3092,CLAUDIN_SUBTYPE,Basal,0.022655169,LumB,LumB,test +MB-0522,CLAUDIN_SUBTYPE,Basal,0.04810809,Her2,Her2,test +MB-7253,CLAUDIN_SUBTYPE,Basal,0.0071902177,LumB,LumB,test +MB-5213,CLAUDIN_SUBTYPE,Basal,0.11381865,Her2,Her2,test +MB-0491,CLAUDIN_SUBTYPE,Basal,0.04346168,LumA,LumA,test +MB-6280,CLAUDIN_SUBTYPE,Basal,0.9459036,Basal,Basal,test +MB-0650,CLAUDIN_SUBTYPE,Basal,0.0016324744,LumA,LumA,test +MB-7297,CLAUDIN_SUBTYPE,Basal,0.0016908284,LumB,LumB,test +MB-7031,CLAUDIN_SUBTYPE,Basal,0.99211204,Basal,Basal,test +MB-5020,CLAUDIN_SUBTYPE,Basal,0.003316274,LumA,LumA,test +MB-5468,CLAUDIN_SUBTYPE,Basal,0.9622314,Basal,Basal,test +MB-6147,CLAUDIN_SUBTYPE,Basal,0.08704209,claudin-low,Normal,test +MB-0406,CLAUDIN_SUBTYPE,Basal,0.0028475868,LumB,LumB,test +MB-0504,CLAUDIN_SUBTYPE,Basal,0.0009693012,LumA,LumA,test +MB-6330,CLAUDIN_SUBTYPE,Basal,0.026411599,Her2,Her2,test +MB-6135,CLAUDIN_SUBTYPE,Basal,0.01622039,LumB,LumB,test +MB-4838,CLAUDIN_SUBTYPE,Basal,0.0027385608,LumB,LumB,test +MB-0235,CLAUDIN_SUBTYPE,Basal,0.00012883723,LumA,LumA,test +MB-0349,CLAUDIN_SUBTYPE,Basal,0.004910741,LumB,LumA,test +MB-3013,CLAUDIN_SUBTYPE,Basal,0.008502817,claudin-low,LumA,test +MB-0559,CLAUDIN_SUBTYPE,Basal,0.014843292,LumA,LumB,test +MB-5227,CLAUDIN_SUBTYPE,Basal,0.012661014,LumA,LumA,test +MB-5084,CLAUDIN_SUBTYPE,Basal,0.00004069903,LumA,LumA,test +MB-4234,CLAUDIN_SUBTYPE,Basal,0.0006037344,LumA,LumA,test +MB-4641,CLAUDIN_SUBTYPE,Basal,0.00005447803,LumA,LumA,test +MB-0286,CLAUDIN_SUBTYPE,Basal,0.045152564,claudin-low,claudin-low,test +MB-3014,CLAUDIN_SUBTYPE,Basal,0.9668346,Basal,Basal,test +MB-2796,CLAUDIN_SUBTYPE,Basal,0.0099408,claudin-low,LumA,test +MB-7058,CLAUDIN_SUBTYPE,Basal,0.004823737,Normal,LumA,test +MB-5287,CLAUDIN_SUBTYPE,Basal,0.00011211436,LumA,LumA,test +MB-7281,CLAUDIN_SUBTYPE,Basal,0.13046472,Her2,Her2,test +MB-4011,CLAUDIN_SUBTYPE,Basal,0.013587133,LumA,LumA,test +MB-3102,CLAUDIN_SUBTYPE,Basal,0.006243442,LumA,LumB,test +MB-6194,CLAUDIN_SUBTYPE,Basal,0.23802574,Normal,Normal,test +MB-3026,CLAUDIN_SUBTYPE,Basal,0.008249727,LumA,LumA,test +MB-7052,CLAUDIN_SUBTYPE,Basal,0.58712304,claudin-low,Basal,test +MB-5291,CLAUDIN_SUBTYPE,Basal,0.005792461,LumB,LumB,test +MB-4767,CLAUDIN_SUBTYPE,Basal,0.11165398,LumB,LumB,test +MB-7043,CLAUDIN_SUBTYPE,Basal,0.115664475,claudin-low,claudin-low,test +MB-0472,CLAUDIN_SUBTYPE,Basal,0.0007786848,LumB,LumA,test +MB-5338,CLAUDIN_SUBTYPE,Basal,0.030729877,LumB,LumB,test +MB-2966,CLAUDIN_SUBTYPE,Basal,0.0031380653,LumA,LumA,test +MB-0551,CLAUDIN_SUBTYPE,Basal,0.016118636,Normal,Normal,test +MB-5404,CLAUDIN_SUBTYPE,Basal,0.0011252166,LumA,LumA,test +MB-5540,CLAUDIN_SUBTYPE,Basal,0.003374003,LumB,LumB,test +MB-0644,CLAUDIN_SUBTYPE,Basal,0.061044354,claudin-low,claudin-low,test +MB-0618,CLAUDIN_SUBTYPE,Basal,0.008935495,LumB,LumA,test +MB-3439,CLAUDIN_SUBTYPE,Basal,0.00030271732,LumA,LumA,test +MB-3797,CLAUDIN_SUBTYPE,Basal,0.0017444948,LumA,LumA,test +MB-2929,CLAUDIN_SUBTYPE,Basal,0.04076907,Her2,Her2,test +MB-5182,CLAUDIN_SUBTYPE,Basal,0.00003222719,LumA,LumA,test +MB-0642,CLAUDIN_SUBTYPE,Basal,0.00073901145,LumA,LumA,test +MB-4738,CLAUDIN_SUBTYPE,Basal,0.0006314964,Normal,LumA,test 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+MB-6047,CLAUDIN_SUBTYPE,Basal,0.005496206,Her2,Her2,train +MB-6047,CLAUDIN_SUBTYPE,Her2,0.9864028,Her2,Her2,train +MB-6047,CLAUDIN_SUBTYPE,LumA,9.449862e-05,Her2,Her2,train +MB-6047,CLAUDIN_SUBTYPE,LumB,0.002123127,Her2,Her2,train +MB-6047,CLAUDIN_SUBTYPE,NC,0.00028473616,Her2,Her2,train +MB-6047,CLAUDIN_SUBTYPE,Normal,0.005091633,Her2,Her2,train +MB-6047,CLAUDIN_SUBTYPE,claudin-low,0.0005070798,Her2,Her2,train +MB-0328,CLAUDIN_SUBTYPE,Basal,0.0064487713,LumB,LumB,train +MB-0328,CLAUDIN_SUBTYPE,Her2,0.0003459218,LumB,LumB,train +MB-0328,CLAUDIN_SUBTYPE,LumA,0.004037428,LumB,LumB,train +MB-0328,CLAUDIN_SUBTYPE,LumB,0.987248,LumB,LumB,train +MB-0328,CLAUDIN_SUBTYPE,NC,0.0011023093,LumB,LumB,train +MB-0328,CLAUDIN_SUBTYPE,Normal,0.00046134234,LumB,LumB,train +MB-0328,CLAUDIN_SUBTYPE,claudin-low,0.00035626948,LumB,LumB,train +MB-5534,CLAUDIN_SUBTYPE,Basal,0.017993208,claudin-low,claudin-low,train +MB-5534,CLAUDIN_SUBTYPE,Her2,0.0006160128,claudin-low,claudin-low,train 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+MB-5206,CLAUDIN_SUBTYPE,Basal,0.00023490845,LumA,LumA,train +MB-5206,CLAUDIN_SUBTYPE,Her2,0.00017687031,LumA,LumA,train +MB-5206,CLAUDIN_SUBTYPE,LumA,0.99003917,LumA,LumA,train +MB-5206,CLAUDIN_SUBTYPE,LumB,0.0007938427,LumA,LumA,train +MB-5206,CLAUDIN_SUBTYPE,NC,0.00096769666,LumA,LumA,train +MB-5206,CLAUDIN_SUBTYPE,Normal,0.0075366455,LumA,LumA,train +MB-5206,CLAUDIN_SUBTYPE,claudin-low,0.00025094123,LumA,LumA,train +MB-4593,CLAUDIN_SUBTYPE,Basal,0.0002562981,LumA,LumA,train +MB-4593,CLAUDIN_SUBTYPE,Her2,0.00019336307,LumA,LumA,train +MB-4593,CLAUDIN_SUBTYPE,LumA,0.9925932,LumA,LumA,train +MB-4593,CLAUDIN_SUBTYPE,LumB,0.0017249119,LumA,LumA,train +MB-4593,CLAUDIN_SUBTYPE,NC,0.00073385803,LumA,LumA,train +MB-4593,CLAUDIN_SUBTYPE,Normal,0.0042835674,LumA,LumA,train +MB-4593,CLAUDIN_SUBTYPE,claudin-low,0.00021473222,LumA,LumA,train +MB-4978,CLAUDIN_SUBTYPE,Basal,0.023083955,Normal,Normal,train +MB-4978,CLAUDIN_SUBTYPE,Her2,0.031568985,Normal,Normal,train +MB-4978,CLAUDIN_SUBTYPE,LumA,0.015417075,Normal,Normal,train +MB-4978,CLAUDIN_SUBTYPE,LumB,0.00081056764,Normal,Normal,train +MB-4978,CLAUDIN_SUBTYPE,NC,0.004812277,Normal,Normal,train +MB-4978,CLAUDIN_SUBTYPE,Normal,0.92357886,Normal,Normal,train +MB-4978,CLAUDIN_SUBTYPE,claudin-low,0.00072831206,Normal,Normal,train +MB-7087,CLAUDIN_SUBTYPE,Basal,0.98772484,Basal,Basal,train +MB-7087,CLAUDIN_SUBTYPE,Her2,0.0015129962,Basal,Basal,train +MB-7087,CLAUDIN_SUBTYPE,LumA,0.0002660714,Basal,Basal,train +MB-7087,CLAUDIN_SUBTYPE,LumB,0.0016357407,Basal,Basal,train +MB-7087,CLAUDIN_SUBTYPE,NC,0.00039693306,Basal,Basal,train +MB-7087,CLAUDIN_SUBTYPE,Normal,0.004267516,Basal,Basal,train +MB-7087,CLAUDIN_SUBTYPE,claudin-low,0.004195901,Basal,Basal,train +MB-7007,CLAUDIN_SUBTYPE,Basal,0.98601586,Basal,Basal,train +MB-7007,CLAUDIN_SUBTYPE,Her2,0.0008951136,Basal,Basal,train +MB-7007,CLAUDIN_SUBTYPE,LumA,0.00044912793,Basal,Basal,train +MB-7007,CLAUDIN_SUBTYPE,LumB,0.0026458045,Basal,Basal,train 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+MB-4999,CLAUDIN_SUBTYPE,LumB,0.00056548807,LumA,LumA,train +MB-4999,CLAUDIN_SUBTYPE,NC,0.00038311197,LumA,LumA,train +MB-4999,CLAUDIN_SUBTYPE,Normal,0.0038178035,LumA,LumA,train +MB-4999,CLAUDIN_SUBTYPE,claudin-low,5.447422e-05,LumA,LumA,train +MB-2844,CLAUDIN_SUBTYPE,Basal,0.0025792634,LumB,LumB,train +MB-2844,CLAUDIN_SUBTYPE,Her2,0.00047714147,LumB,LumB,train +MB-2844,CLAUDIN_SUBTYPE,LumA,0.0026033083,LumB,LumB,train +MB-2844,CLAUDIN_SUBTYPE,LumB,0.9929889,LumB,LumB,train +MB-2844,CLAUDIN_SUBTYPE,NC,0.0008083924,LumB,LumB,train +MB-2844,CLAUDIN_SUBTYPE,Normal,0.00029404287,LumB,LumB,train +MB-2844,CLAUDIN_SUBTYPE,claudin-low,0.000249012,LumB,LumB,train +MB-7299,CLAUDIN_SUBTYPE,Basal,0.0054185907,LumB,LumB,train +MB-7299,CLAUDIN_SUBTYPE,Her2,0.00058973266,LumB,LumB,train +MB-7299,CLAUDIN_SUBTYPE,LumA,0.0071252016,LumB,LumB,train +MB-7299,CLAUDIN_SUBTYPE,LumB,0.984148,LumB,LumB,train +MB-7299,CLAUDIN_SUBTYPE,NC,0.0015077846,LumB,LumB,train 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+MB-2642,CLAUDIN_SUBTYPE,NC,0.0004901406,LumB,LumB,train +MB-2642,CLAUDIN_SUBTYPE,Normal,0.00015886143,LumB,LumB,train +MB-2642,CLAUDIN_SUBTYPE,claudin-low,0.000120862314,LumB,LumB,train +MB-0150,CLAUDIN_SUBTYPE,Basal,0.9857496,Basal,Basal,train +MB-0150,CLAUDIN_SUBTYPE,Her2,0.0006470082,Basal,Basal,train +MB-0150,CLAUDIN_SUBTYPE,LumA,0.00032946677,Basal,Basal,train +MB-0150,CLAUDIN_SUBTYPE,LumB,0.0012127956,Basal,Basal,train +MB-0150,CLAUDIN_SUBTYPE,NC,0.00033788188,Basal,Basal,train +MB-0150,CLAUDIN_SUBTYPE,Normal,0.001616794,Basal,Basal,train +MB-0150,CLAUDIN_SUBTYPE,claudin-low,0.010106327,Basal,Basal,train +MB-3429,CLAUDIN_SUBTYPE,Basal,0.013013761,Normal,Normal,train +MB-3429,CLAUDIN_SUBTYPE,Her2,0.017863162,Normal,Normal,train +MB-3429,CLAUDIN_SUBTYPE,LumA,0.0103078075,Normal,Normal,train +MB-3429,CLAUDIN_SUBTYPE,LumB,0.000296698,Normal,Normal,train +MB-3429,CLAUDIN_SUBTYPE,NC,0.0026051956,Normal,Normal,train +MB-3429,CLAUDIN_SUBTYPE,Normal,0.95563304,Normal,Normal,train 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+MB-0524,CLAUDIN_SUBTYPE,Normal,0.9450988,Normal,Normal,train +MB-0524,CLAUDIN_SUBTYPE,claudin-low,0.00044668323,Normal,Normal,train +MB-7149,CLAUDIN_SUBTYPE,Basal,0.0018839329,LumB,LumB,train +MB-7149,CLAUDIN_SUBTYPE,Her2,7.0591814e-05,LumB,LumB,train +MB-7149,CLAUDIN_SUBTYPE,LumA,0.0010669868,LumB,LumB,train +MB-7149,CLAUDIN_SUBTYPE,LumB,0.9965473,LumB,LumB,train +MB-7149,CLAUDIN_SUBTYPE,NC,0.00028291094,LumB,LumB,train +MB-7149,CLAUDIN_SUBTYPE,Normal,8.757647e-05,LumB,LumB,train +MB-7149,CLAUDIN_SUBTYPE,claudin-low,6.0797218e-05,LumB,LumB,train +MB-0381,CLAUDIN_SUBTYPE,Basal,0.0144469375,Her2,Her2,train +MB-0381,CLAUDIN_SUBTYPE,Her2,0.96116096,Her2,Her2,train +MB-0381,CLAUDIN_SUBTYPE,LumA,0.00072717504,Her2,Her2,train +MB-0381,CLAUDIN_SUBTYPE,LumB,0.0062840236,Her2,Her2,train +MB-0381,CLAUDIN_SUBTYPE,NC,0.0013612095,Her2,Her2,train +MB-0381,CLAUDIN_SUBTYPE,Normal,0.013472134,Her2,Her2,train +MB-0381,CLAUDIN_SUBTYPE,claudin-low,0.0025476974,Her2,Her2,train 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+MB-5243,CLAUDIN_SUBTYPE,Her2,0.015899153,LumB,LumA,test +MB-5243,CLAUDIN_SUBTYPE,LumA,0.47718257,LumB,LumA,test +MB-5243,CLAUDIN_SUBTYPE,LumB,0.38075033,LumB,LumA,test +MB-5243,CLAUDIN_SUBTYPE,NC,0.027327167,LumB,LumA,test +MB-5243,CLAUDIN_SUBTYPE,Normal,0.03441906,LumB,LumA,test +MB-5243,CLAUDIN_SUBTYPE,claudin-low,0.023827486,LumB,LumA,test +MB-2984,CLAUDIN_SUBTYPE,Basal,0.004155519,LumB,LumB,test +MB-2984,CLAUDIN_SUBTYPE,Her2,0.0015310476,LumB,LumB,test +MB-2984,CLAUDIN_SUBTYPE,LumA,0.005869551,LumB,LumB,test +MB-2984,CLAUDIN_SUBTYPE,LumB,0.9860745,LumB,LumB,test +MB-2984,CLAUDIN_SUBTYPE,NC,0.0012708233,LumB,LumB,test +MB-2984,CLAUDIN_SUBTYPE,Normal,0.0005769722,LumB,LumB,test +MB-2984,CLAUDIN_SUBTYPE,claudin-low,0.0005215232,LumB,LumB,test +MB-4017,CLAUDIN_SUBTYPE,Basal,0.005148993,LumB,LumB,test +MB-4017,CLAUDIN_SUBTYPE,Her2,0.0010974812,LumB,LumB,test +MB-4017,CLAUDIN_SUBTYPE,LumA,0.003569688,LumB,LumB,test +MB-4017,CLAUDIN_SUBTYPE,LumB,0.9877529,LumB,LumB,test +MB-4017,CLAUDIN_SUBTYPE,NC,0.0013701178,LumB,LumB,test +MB-4017,CLAUDIN_SUBTYPE,Normal,0.00054689246,LumB,LumB,test +MB-4017,CLAUDIN_SUBTYPE,claudin-low,0.0005138966,LumB,LumB,test +MB-5447,CLAUDIN_SUBTYPE,Basal,0.019656463,LumB,LumB,test +MB-5447,CLAUDIN_SUBTYPE,Her2,0.008101183,LumB,LumB,test +MB-5447,CLAUDIN_SUBTYPE,LumA,0.061312884,LumB,LumB,test +MB-5447,CLAUDIN_SUBTYPE,LumB,0.88341874,LumB,LumB,test +MB-5447,CLAUDIN_SUBTYPE,NC,0.011158793,LumB,LumB,test +MB-5447,CLAUDIN_SUBTYPE,Normal,0.007136572,LumB,LumB,test +MB-5447,CLAUDIN_SUBTYPE,claudin-low,0.009215302,LumB,LumB,test +MB-5616,CLAUDIN_SUBTYPE,Basal,0.17296688,claudin-low,claudin-low,test +MB-5616,CLAUDIN_SUBTYPE,Her2,0.004025186,claudin-low,claudin-low,test +MB-5616,CLAUDIN_SUBTYPE,LumA,0.009818127,claudin-low,claudin-low,test +MB-5616,CLAUDIN_SUBTYPE,LumB,0.00068920694,claudin-low,claudin-low,test +MB-5616,CLAUDIN_SUBTYPE,NC,0.0026505745,claudin-low,claudin-low,test +MB-5616,CLAUDIN_SUBTYPE,Normal,0.002081566,claudin-low,claudin-low,test +MB-5616,CLAUDIN_SUBTYPE,claudin-low,0.8077685,claudin-low,claudin-low,test +MB-3021,CLAUDIN_SUBTYPE,Basal,0.0047936346,LumA,LumA,test +MB-3021,CLAUDIN_SUBTYPE,Her2,0.0008082361,LumA,LumA,test +MB-3021,CLAUDIN_SUBTYPE,LumA,0.91946197,LumA,LumA,test +MB-3021,CLAUDIN_SUBTYPE,LumB,0.05293621,LumA,LumA,test +MB-3021,CLAUDIN_SUBTYPE,NC,0.0045436905,LumA,LumA,test +MB-3021,CLAUDIN_SUBTYPE,Normal,0.016557915,LumA,LumA,test +MB-3021,CLAUDIN_SUBTYPE,claudin-low,0.00089837116,LumA,LumA,test +MB-0872,CLAUDIN_SUBTYPE,Basal,0.008130632,Normal,Normal,test +MB-0872,CLAUDIN_SUBTYPE,Her2,0.008342696,Normal,Normal,test +MB-0872,CLAUDIN_SUBTYPE,LumA,0.41768274,Normal,Normal,test +MB-0872,CLAUDIN_SUBTYPE,LumB,0.0020778866,Normal,Normal,test +MB-0872,CLAUDIN_SUBTYPE,NC,0.010398379,Normal,Normal,test +MB-0872,CLAUDIN_SUBTYPE,Normal,0.5520613,Normal,Normal,test +MB-0872,CLAUDIN_SUBTYPE,claudin-low,0.0013063421,Normal,Normal,test +MB-3386,CLAUDIN_SUBTYPE,Basal,0.012321706,Her2,Her2,test +MB-3386,CLAUDIN_SUBTYPE,Her2,0.9705054,Her2,Her2,test +MB-3386,CLAUDIN_SUBTYPE,LumA,0.00022240526,Her2,Her2,test +MB-3386,CLAUDIN_SUBTYPE,LumB,0.0020912127,Her2,Her2,test +MB-3386,CLAUDIN_SUBTYPE,NC,0.00057374797,Her2,Her2,test +MB-3386,CLAUDIN_SUBTYPE,Normal,0.013328741,Her2,Her2,test +MB-3386,CLAUDIN_SUBTYPE,claudin-low,0.0009569158,Her2,Her2,test +MB-7080,CLAUDIN_SUBTYPE,Basal,0.00022694626,LumA,LumA,test +MB-7080,CLAUDIN_SUBTYPE,Her2,0.00020653722,LumA,LumA,test +MB-7080,CLAUDIN_SUBTYPE,LumA,0.9918407,LumA,LumA,test +MB-7080,CLAUDIN_SUBTYPE,LumB,0.0013462551,LumA,LumA,test +MB-7080,CLAUDIN_SUBTYPE,NC,0.000791443,LumA,LumA,test +MB-7080,CLAUDIN_SUBTYPE,Normal,0.0054007657,LumA,LumA,test +MB-7080,CLAUDIN_SUBTYPE,claudin-low,0.00018724683,LumA,LumA,test +MB-5405,CLAUDIN_SUBTYPE,Basal,0.068026006,claudin-low,claudin-low,test +MB-5405,CLAUDIN_SUBTYPE,Her2,0.027408984,claudin-low,claudin-low,test +MB-5405,CLAUDIN_SUBTYPE,LumA,0.032356545,claudin-low,claudin-low,test +MB-5405,CLAUDIN_SUBTYPE,LumB,0.011396877,claudin-low,claudin-low,test +MB-5405,CLAUDIN_SUBTYPE,NC,0.011295101,claudin-low,claudin-low,test +MB-5405,CLAUDIN_SUBTYPE,Normal,0.003973542,claudin-low,claudin-low,test +MB-5405,CLAUDIN_SUBTYPE,claudin-low,0.84554297,claudin-low,claudin-low,test +MB-4357,CLAUDIN_SUBTYPE,Basal,0.06376728,LumA,Her2,test +MB-4357,CLAUDIN_SUBTYPE,Her2,0.72772115,LumA,Her2,test +MB-4357,CLAUDIN_SUBTYPE,LumA,0.036867093,LumA,Her2,test +MB-4357,CLAUDIN_SUBTYPE,LumB,0.014464638,LumA,Her2,test +MB-4357,CLAUDIN_SUBTYPE,NC,0.012233847,LumA,Her2,test +MB-4357,CLAUDIN_SUBTYPE,Normal,0.12958597,LumA,Her2,test +MB-4357,CLAUDIN_SUBTYPE,claudin-low,0.015360091,LumA,Her2,test +MB-6286,CLAUDIN_SUBTYPE,Basal,0.00011293625,LumA,LumA,test +MB-6286,CLAUDIN_SUBTYPE,Her2,9.342016e-05,LumA,LumA,test +MB-6286,CLAUDIN_SUBTYPE,LumA,0.99478453,LumA,LumA,test +MB-6286,CLAUDIN_SUBTYPE,LumB,0.0008433022,LumA,LumA,test +MB-6286,CLAUDIN_SUBTYPE,NC,0.00045895917,LumA,LumA,test +MB-6286,CLAUDIN_SUBTYPE,Normal,0.0036210825,LumA,LumA,test +MB-6286,CLAUDIN_SUBTYPE,claudin-low,8.591475e-05,LumA,LumA,test +MB-5134,CLAUDIN_SUBTYPE,Basal,3.4737288e-05,LumA,LumA,test +MB-5134,CLAUDIN_SUBTYPE,Her2,2.6566526e-05,LumA,LumA,test +MB-5134,CLAUDIN_SUBTYPE,LumA,0.99763346,LumA,LumA,test +MB-5134,CLAUDIN_SUBTYPE,LumB,0.00010027489,LumA,LumA,test +MB-5134,CLAUDIN_SUBTYPE,NC,0.00019697966,LumA,LumA,test +MB-5134,CLAUDIN_SUBTYPE,Normal,0.0019576324,LumA,LumA,test +MB-5134,CLAUDIN_SUBTYPE,claudin-low,5.0379225e-05,LumA,LumA,test +MB-4942,CLAUDIN_SUBTYPE,Basal,0.0806648,claudin-low,claudin-low,test +MB-4942,CLAUDIN_SUBTYPE,Her2,0.0026069887,claudin-low,claudin-low,test +MB-4942,CLAUDIN_SUBTYPE,LumA,0.015564011,claudin-low,claudin-low,test +MB-4942,CLAUDIN_SUBTYPE,LumB,0.0008644035,claudin-low,claudin-low,test +MB-4942,CLAUDIN_SUBTYPE,NC,0.0029436671,claudin-low,claudin-low,test +MB-4942,CLAUDIN_SUBTYPE,Normal,0.00112632,claudin-low,claudin-low,test +MB-4942,CLAUDIN_SUBTYPE,claudin-low,0.8962298,claudin-low,claudin-low,test +MB-6238,CLAUDIN_SUBTYPE,Basal,0.004182132,LumA,LumA,test +MB-6238,CLAUDIN_SUBTYPE,Her2,0.0032596437,LumA,LumA,test +MB-6238,CLAUDIN_SUBTYPE,LumA,0.94185513,LumA,LumA,test +MB-6238,CLAUDIN_SUBTYPE,LumB,0.010503856,LumA,LumA,test +MB-6238,CLAUDIN_SUBTYPE,NC,0.007515457,LumA,LumA,test +MB-6238,CLAUDIN_SUBTYPE,Normal,0.027835622,LumA,LumA,test +MB-6238,CLAUDIN_SUBTYPE,claudin-low,0.004848287,LumA,LumA,test +MB-0127,CLAUDIN_SUBTYPE,Basal,0.14812747,Normal,Her2,test +MB-0127,CLAUDIN_SUBTYPE,Her2,0.3176424,Normal,Her2,test +MB-0127,CLAUDIN_SUBTYPE,LumA,0.0921754,Normal,Her2,test +MB-0127,CLAUDIN_SUBTYPE,LumB,0.09252077,Normal,Her2,test +MB-0127,CLAUDIN_SUBTYPE,NC,0.05230724,Normal,Her2,test +MB-0127,CLAUDIN_SUBTYPE,Normal,0.09914056,Normal,Her2,test +MB-0127,CLAUDIN_SUBTYPE,claudin-low,0.19808611,Normal,Her2,test +MB-7277,CLAUDIN_SUBTYPE,Basal,0.00010833181,LumA,LumA,test +MB-7277,CLAUDIN_SUBTYPE,Her2,0.00010763515,LumA,LumA,test +MB-7277,CLAUDIN_SUBTYPE,LumA,0.99612254,LumA,LumA,test +MB-7277,CLAUDIN_SUBTYPE,LumB,0.0013386146,LumA,LumA,test +MB-7277,CLAUDIN_SUBTYPE,NC,0.00032877544,LumA,LumA,test +MB-7277,CLAUDIN_SUBTYPE,Normal,0.0019145999,LumA,LumA,test +MB-7277,CLAUDIN_SUBTYPE,claudin-low,7.94472e-05,LumA,LumA,test +MB-0060,CLAUDIN_SUBTYPE,Basal,0.42745838,LumB,LumB,test +MB-0060,CLAUDIN_SUBTYPE,Her2,0.07695145,LumB,LumB,test +MB-0060,CLAUDIN_SUBTYPE,LumA,0.0029748783,LumB,LumB,test +MB-0060,CLAUDIN_SUBTYPE,LumB,0.46517357,LumB,LumB,test +MB-0060,CLAUDIN_SUBTYPE,NC,0.0059550703,LumB,LumB,test +MB-0060,CLAUDIN_SUBTYPE,Normal,0.008437709,LumB,LumB,test +MB-0060,CLAUDIN_SUBTYPE,claudin-low,0.013048967,LumB,LumB,test +MB-4721,CLAUDIN_SUBTYPE,Basal,0.0001352974,LumA,LumA,test +MB-4721,CLAUDIN_SUBTYPE,Her2,0.00010935756,LumA,LumA,test +MB-4721,CLAUDIN_SUBTYPE,LumA,0.99075526,LumA,LumA,test +MB-4721,CLAUDIN_SUBTYPE,LumB,0.0008439287,LumA,LumA,test +MB-4721,CLAUDIN_SUBTYPE,NC,0.0006964188,LumA,LumA,test +MB-4721,CLAUDIN_SUBTYPE,Normal,0.0073751165,LumA,LumA,test +MB-4721,CLAUDIN_SUBTYPE,claudin-low,8.476722e-05,LumA,LumA,test +MB-0882,CLAUDIN_SUBTYPE,Basal,0.004198095,LumB,LumB,test +MB-0882,CLAUDIN_SUBTYPE,Her2,0.0006174503,LumB,LumB,test +MB-0882,CLAUDIN_SUBTYPE,LumA,0.0026727426,LumB,LumB,test +MB-0882,CLAUDIN_SUBTYPE,LumB,0.9908228,LumB,LumB,test +MB-0882,CLAUDIN_SUBTYPE,NC,0.0009888266,LumB,LumB,test +MB-0882,CLAUDIN_SUBTYPE,Normal,0.00037018515,LumB,LumB,test +MB-0882,CLAUDIN_SUBTYPE,claudin-low,0.000329837,LumB,LumB,test +MB-3271,CLAUDIN_SUBTYPE,Basal,0.7585569,claudin-low,Basal,test +MB-3271,CLAUDIN_SUBTYPE,Her2,0.001788683,claudin-low,Basal,test +MB-3271,CLAUDIN_SUBTYPE,LumA,0.0033320892,claudin-low,Basal,test +MB-3271,CLAUDIN_SUBTYPE,LumB,0.0012189874,claudin-low,Basal,test +MB-3271,CLAUDIN_SUBTYPE,NC,0.0014190648,claudin-low,Basal,test +MB-3271,CLAUDIN_SUBTYPE,Normal,0.0020395012,claudin-low,Basal,test +MB-3271,CLAUDIN_SUBTYPE,claudin-low,0.23164482,claudin-low,Basal,test +MB-4746,CLAUDIN_SUBTYPE,Basal,0.023426726,Normal,LumA,test +MB-4746,CLAUDIN_SUBTYPE,Her2,0.015977094,Normal,LumA,test +MB-4746,CLAUDIN_SUBTYPE,LumA,0.7239382,Normal,LumA,test +MB-4746,CLAUDIN_SUBTYPE,LumB,0.14363255,Normal,LumA,test +MB-4746,CLAUDIN_SUBTYPE,NC,0.025430718,Normal,LumA,test +MB-4746,CLAUDIN_SUBTYPE,Normal,0.047693152,Normal,LumA,test +MB-4746,CLAUDIN_SUBTYPE,claudin-low,0.019901505,Normal,LumA,test +MB-6069,CLAUDIN_SUBTYPE,Basal,0.011962601,LumA,LumA,test +MB-6069,CLAUDIN_SUBTYPE,Her2,0.019899664,LumA,LumA,test +MB-6069,CLAUDIN_SUBTYPE,LumA,0.83359724,LumA,LumA,test +MB-6069,CLAUDIN_SUBTYPE,LumB,0.045562144,LumA,LumA,test +MB-6069,CLAUDIN_SUBTYPE,NC,0.018178709,LumA,LumA,test +MB-6069,CLAUDIN_SUBTYPE,Normal,0.05969956,LumA,LumA,test +MB-6069,CLAUDIN_SUBTYPE,claudin-low,0.011100207,LumA,LumA,test +MB-6044,CLAUDIN_SUBTYPE,Basal,0.091202796,Her2,LumA,test +MB-6044,CLAUDIN_SUBTYPE,Her2,0.01731999,Her2,LumA,test +MB-6044,CLAUDIN_SUBTYPE,LumA,0.45770028,Her2,LumA,test +MB-6044,CLAUDIN_SUBTYPE,LumB,0.13290253,Her2,LumA,test +MB-6044,CLAUDIN_SUBTYPE,NC,0.03785806,Her2,LumA,test +MB-6044,CLAUDIN_SUBTYPE,Normal,0.25358894,Her2,LumA,test +MB-6044,CLAUDIN_SUBTYPE,claudin-low,0.009427433,Her2,LumA,test +MB-0601,CLAUDIN_SUBTYPE,Basal,0.09948703,LumB,LumB,test +MB-0601,CLAUDIN_SUBTYPE,Her2,0.24979374,LumB,LumB,test +MB-0601,CLAUDIN_SUBTYPE,LumA,0.016356353,LumB,LumB,test +MB-0601,CLAUDIN_SUBTYPE,LumB,0.54843056,LumB,LumB,test +MB-0601,CLAUDIN_SUBTYPE,NC,0.02044955,LumB,LumB,test +MB-0601,CLAUDIN_SUBTYPE,Normal,0.017284252,LumB,LumB,test +MB-0601,CLAUDIN_SUBTYPE,claudin-low,0.048198543,LumB,LumB,test +MB-4887,CLAUDIN_SUBTYPE,Basal,0.045928933,Normal,Normal,test +MB-4887,CLAUDIN_SUBTYPE,Her2,0.049525633,Normal,Normal,test +MB-4887,CLAUDIN_SUBTYPE,LumA,0.15061107,Normal,Normal,test +MB-4887,CLAUDIN_SUBTYPE,LumB,0.013998083,Normal,Normal,test +MB-4887,CLAUDIN_SUBTYPE,NC,0.03430641,Normal,Normal,test +MB-4887,CLAUDIN_SUBTYPE,Normal,0.696072,Normal,Normal,test +MB-4887,CLAUDIN_SUBTYPE,claudin-low,0.009557832,Normal,Normal,test +MB-7111,CLAUDIN_SUBTYPE,Basal,0.68688107,Basal,Basal,test +MB-7111,CLAUDIN_SUBTYPE,Her2,0.047529243,Basal,Basal,test +MB-7111,CLAUDIN_SUBTYPE,LumA,0.008517364,Basal,Basal,test +MB-7111,CLAUDIN_SUBTYPE,LumB,0.022029182,Basal,Basal,test +MB-7111,CLAUDIN_SUBTYPE,NC,0.009254042,Basal,Basal,test +MB-7111,CLAUDIN_SUBTYPE,Normal,0.2173946,Basal,Basal,test +MB-7111,CLAUDIN_SUBTYPE,claudin-low,0.008394432,Basal,Basal,test +MB-7174,CLAUDIN_SUBTYPE,Basal,0.037639856,LumB,LumB,test +MB-7174,CLAUDIN_SUBTYPE,Her2,0.053278543,LumB,LumB,test +MB-7174,CLAUDIN_SUBTYPE,LumA,0.017415937,LumB,LumB,test +MB-7174,CLAUDIN_SUBTYPE,LumB,0.8563336,LumB,LumB,test +MB-7174,CLAUDIN_SUBTYPE,NC,0.013450412,LumB,LumB,test +MB-7174,CLAUDIN_SUBTYPE,Normal,0.012735451,LumB,LumB,test +MB-7174,CLAUDIN_SUBTYPE,claudin-low,0.009146114,LumB,LumB,test +MB-0317,CLAUDIN_SUBTYPE,Basal,0.0013807476,LumA,LumA,test +MB-0317,CLAUDIN_SUBTYPE,Her2,0.0005111223,LumA,LumA,test +MB-0317,CLAUDIN_SUBTYPE,LumA,0.97434676,LumA,LumA,test +MB-0317,CLAUDIN_SUBTYPE,LumB,0.006682322,LumA,LumA,test +MB-0317,CLAUDIN_SUBTYPE,NC,0.0023018245,LumA,LumA,test +MB-0317,CLAUDIN_SUBTYPE,Normal,0.014251732,LumA,LumA,test +MB-0317,CLAUDIN_SUBTYPE,claudin-low,0.00052552787,LumA,LumA,test +MB-4712,CLAUDIN_SUBTYPE,Basal,0.04694011,Normal,Her2,test +MB-4712,CLAUDIN_SUBTYPE,Her2,0.8317232,Normal,Her2,test +MB-4712,CLAUDIN_SUBTYPE,LumA,0.00066406565,Normal,Her2,test +MB-4712,CLAUDIN_SUBTYPE,LumB,0.0022492844,Normal,Her2,test +MB-4712,CLAUDIN_SUBTYPE,NC,0.0016010996,Normal,Her2,test +MB-4712,CLAUDIN_SUBTYPE,Normal,0.11550032,Normal,Her2,test +MB-4712,CLAUDIN_SUBTYPE,claudin-low,0.0013219714,Normal,Her2,test +MB-7263,CLAUDIN_SUBTYPE,Basal,0.008590267,LumB,LumB,test +MB-7263,CLAUDIN_SUBTYPE,Her2,0.004546427,LumB,LumB,test +MB-7263,CLAUDIN_SUBTYPE,LumA,0.011541079,LumB,LumB,test +MB-7263,CLAUDIN_SUBTYPE,LumB,0.9694856,LumB,LumB,test +MB-7263,CLAUDIN_SUBTYPE,NC,0.0028452768,LumB,LumB,test +MB-7263,CLAUDIN_SUBTYPE,Normal,0.0015389689,LumB,LumB,test +MB-7263,CLAUDIN_SUBTYPE,claudin-low,0.0014524327,LumB,LumB,test +MB-5582,CLAUDIN_SUBTYPE,Basal,0.00032956575,LumA,LumA,test +MB-5582,CLAUDIN_SUBTYPE,Her2,0.00025045132,LumA,LumA,test +MB-5582,CLAUDIN_SUBTYPE,LumA,0.9905443,LumA,LumA,test +MB-5582,CLAUDIN_SUBTYPE,LumB,0.0007470003,LumA,LumA,test +MB-5582,CLAUDIN_SUBTYPE,NC,0.0010946637,LumA,LumA,test +MB-5582,CLAUDIN_SUBTYPE,Normal,0.0065286946,LumA,LumA,test +MB-5582,CLAUDIN_SUBTYPE,claudin-low,0.00050536374,LumA,LumA,test +MB-5420,CLAUDIN_SUBTYPE,Basal,0.14000916,Basal,Normal,test +MB-5420,CLAUDIN_SUBTYPE,Her2,0.17762958,Basal,Normal,test +MB-5420,CLAUDIN_SUBTYPE,LumA,0.031242821,Basal,Normal,test +MB-5420,CLAUDIN_SUBTYPE,LumB,0.0054707946,Basal,Normal,test +MB-5420,CLAUDIN_SUBTYPE,NC,0.015333159,Basal,Normal,test +MB-5420,CLAUDIN_SUBTYPE,Normal,0.61726785,Basal,Normal,test +MB-5420,CLAUDIN_SUBTYPE,claudin-low,0.013046603,Basal,Normal,test +MB-2718,CLAUDIN_SUBTYPE,Basal,0.9568239,Basal,Basal,test +MB-2718,CLAUDIN_SUBTYPE,Her2,0.0004053648,Basal,Basal,test +MB-2718,CLAUDIN_SUBTYPE,LumA,0.00075790676,Basal,Basal,test +MB-2718,CLAUDIN_SUBTYPE,LumB,0.0012056639,Basal,Basal,test +MB-2718,CLAUDIN_SUBTYPE,NC,0.00046162336,Basal,Basal,test +MB-2718,CLAUDIN_SUBTYPE,Normal,0.0008418761,Basal,Basal,test +MB-2718,CLAUDIN_SUBTYPE,claudin-low,0.03950364,Basal,Basal,test +MB-5268,CLAUDIN_SUBTYPE,Basal,0.00022492505,LumA,LumA,test +MB-5268,CLAUDIN_SUBTYPE,Her2,0.00020404311,LumA,LumA,test +MB-5268,CLAUDIN_SUBTYPE,LumA,0.9796448,LumA,LumA,test +MB-5268,CLAUDIN_SUBTYPE,LumB,0.0005350691,LumA,LumA,test +MB-5268,CLAUDIN_SUBTYPE,NC,0.0009272936,LumA,LumA,test +MB-5268,CLAUDIN_SUBTYPE,Normal,0.018363189,LumA,LumA,test +MB-5268,CLAUDIN_SUBTYPE,claudin-low,0.00010081196,LumA,LumA,test +MB-5514,CLAUDIN_SUBTYPE,Basal,0.011733811,LumA,LumA,test +MB-5514,CLAUDIN_SUBTYPE,Her2,0.0056705093,LumA,LumA,test +MB-5514,CLAUDIN_SUBTYPE,LumA,0.6239441,LumA,LumA,test +MB-5514,CLAUDIN_SUBTYPE,LumB,0.32324916,LumA,LumA,test +MB-5514,CLAUDIN_SUBTYPE,NC,0.011889628,LumA,LumA,test +MB-5514,CLAUDIN_SUBTYPE,Normal,0.017782448,LumA,LumA,test +MB-5514,CLAUDIN_SUBTYPE,claudin-low,0.005730407,LumA,LumA,test +MB-7053,CLAUDIN_SUBTYPE,Basal,0.054197155,LumA,LumA,test +MB-7053,CLAUDIN_SUBTYPE,Her2,0.0949781,LumA,LumA,test +MB-7053,CLAUDIN_SUBTYPE,LumA,0.46591944,LumA,LumA,test +MB-7053,CLAUDIN_SUBTYPE,LumB,0.20881669,LumA,LumA,test +MB-7053,CLAUDIN_SUBTYPE,NC,0.045415875,LumA,LumA,test +MB-7053,CLAUDIN_SUBTYPE,Normal,0.07420422,LumA,LumA,test +MB-7053,CLAUDIN_SUBTYPE,claudin-low,0.056468546,LumA,LumA,test +MB-5348,CLAUDIN_SUBTYPE,Basal,0.31805244,claudin-low,claudin-low,test +MB-5348,CLAUDIN_SUBTYPE,Her2,0.03307286,claudin-low,claudin-low,test +MB-5348,CLAUDIN_SUBTYPE,LumA,0.026233759,claudin-low,claudin-low,test +MB-5348,CLAUDIN_SUBTYPE,LumB,0.0029525491,claudin-low,claudin-low,test +MB-5348,CLAUDIN_SUBTYPE,NC,0.010220849,claudin-low,claudin-low,test +MB-5348,CLAUDIN_SUBTYPE,Normal,0.022855597,claudin-low,claudin-low,test +MB-5348,CLAUDIN_SUBTYPE,claudin-low,0.586612,claudin-low,claudin-low,test +MB-0901,CLAUDIN_SUBTYPE,Basal,0.91394204,Basal,Basal,test +MB-0901,CLAUDIN_SUBTYPE,Her2,0.012898583,Basal,Basal,test +MB-0901,CLAUDIN_SUBTYPE,LumA,0.0043018963,Basal,Basal,test +MB-0901,CLAUDIN_SUBTYPE,LumB,0.012890012,Basal,Basal,test +MB-0901,CLAUDIN_SUBTYPE,NC,0.004542573,Basal,Basal,test +MB-0901,CLAUDIN_SUBTYPE,Normal,0.027188944,Basal,Basal,test +MB-0901,CLAUDIN_SUBTYPE,claudin-low,0.024235928,Basal,Basal,test +MB-5381,CLAUDIN_SUBTYPE,Basal,0.14966057,Her2,Her2,test +MB-5381,CLAUDIN_SUBTYPE,Her2,0.30854216,Her2,Her2,test +MB-5381,CLAUDIN_SUBTYPE,LumA,0.1352157,Her2,Her2,test +MB-5381,CLAUDIN_SUBTYPE,LumB,0.044988386,Her2,Her2,test +MB-5381,CLAUDIN_SUBTYPE,NC,0.047616947,Her2,Her2,test +MB-5381,CLAUDIN_SUBTYPE,Normal,0.11051114,Her2,Her2,test +MB-5381,CLAUDIN_SUBTYPE,claudin-low,0.20346513,Her2,Her2,test +MB-3153,CLAUDIN_SUBTYPE,Basal,0.54439086,Basal,Basal,test +MB-3153,CLAUDIN_SUBTYPE,Her2,0.04645258,Basal,Basal,test +MB-3153,CLAUDIN_SUBTYPE,LumA,0.10245758,Basal,Basal,test +MB-3153,CLAUDIN_SUBTYPE,LumB,0.033101987,Basal,Basal,test +MB-3153,CLAUDIN_SUBTYPE,NC,0.030700775,Basal,Basal,test +MB-3153,CLAUDIN_SUBTYPE,Normal,0.16180402,Basal,Basal,test +MB-3153,CLAUDIN_SUBTYPE,claudin-low,0.081092186,Basal,Basal,test +MB-5366,CLAUDIN_SUBTYPE,Basal,0.03821787,Her2,Her2,test +MB-5366,CLAUDIN_SUBTYPE,Her2,0.5648941,Her2,Her2,test +MB-5366,CLAUDIN_SUBTYPE,LumA,0.08640161,Her2,Her2,test +MB-5366,CLAUDIN_SUBTYPE,LumB,0.17000087,Her2,Her2,test +MB-5366,CLAUDIN_SUBTYPE,NC,0.022833824,Her2,Her2,test +MB-5366,CLAUDIN_SUBTYPE,Normal,0.018065074,Her2,Her2,test +MB-5366,CLAUDIN_SUBTYPE,claudin-low,0.099586666,Her2,Her2,test +MB-7107,CLAUDIN_SUBTYPE,Basal,0.011886511,LumA,LumB,test +MB-7107,CLAUDIN_SUBTYPE,Her2,0.0070273047,LumA,LumB,test +MB-7107,CLAUDIN_SUBTYPE,LumA,0.13815092,LumA,LumB,test +MB-7107,CLAUDIN_SUBTYPE,LumB,0.8276684,LumA,LumB,test +MB-7107,CLAUDIN_SUBTYPE,NC,0.006403086,LumA,LumB,test +MB-7107,CLAUDIN_SUBTYPE,Normal,0.006036586,LumA,LumB,test +MB-7107,CLAUDIN_SUBTYPE,claudin-low,0.002827183,LumA,LumB,test +MB-4697,CLAUDIN_SUBTYPE,Basal,0.02601451,NC,LumA,test +MB-4697,CLAUDIN_SUBTYPE,Her2,0.12119043,NC,LumA,test +MB-4697,CLAUDIN_SUBTYPE,LumA,0.63912225,NC,LumA,test +MB-4697,CLAUDIN_SUBTYPE,LumB,0.025344143,NC,LumA,test +MB-4697,CLAUDIN_SUBTYPE,NC,0.019179175,NC,LumA,test +MB-4697,CLAUDIN_SUBTYPE,Normal,0.15589285,NC,LumA,test +MB-4697,CLAUDIN_SUBTYPE,claudin-low,0.013256662,NC,LumA,test +MB-5070,CLAUDIN_SUBTYPE,Basal,0.55893034,Basal,Basal,test +MB-5070,CLAUDIN_SUBTYPE,Her2,0.0045466917,Basal,Basal,test +MB-5070,CLAUDIN_SUBTYPE,LumA,0.024959952,Basal,Basal,test +MB-5070,CLAUDIN_SUBTYPE,LumB,0.004937899,Basal,Basal,test +MB-5070,CLAUDIN_SUBTYPE,NC,0.0061387857,Basal,Basal,test +MB-5070,CLAUDIN_SUBTYPE,Normal,0.00648548,Basal,Basal,test +MB-5070,CLAUDIN_SUBTYPE,claudin-low,0.39400077,Basal,Basal,test +MB-0598,CLAUDIN_SUBTYPE,Basal,0.025924109,LumB,LumB,test +MB-0598,CLAUDIN_SUBTYPE,Her2,0.12566581,LumB,LumB,test +MB-0598,CLAUDIN_SUBTYPE,LumA,0.014405619,LumB,LumB,test +MB-0598,CLAUDIN_SUBTYPE,LumB,0.81282157,LumB,LumB,test +MB-0598,CLAUDIN_SUBTYPE,NC,0.0066927955,LumB,LumB,test +MB-0598,CLAUDIN_SUBTYPE,Normal,0.00932529,LumB,LumB,test +MB-0598,CLAUDIN_SUBTYPE,claudin-low,0.0051648836,LumB,LumB,test +MB-4374,CLAUDIN_SUBTYPE,Basal,5.950361e-05,LumA,LumA,test +MB-4374,CLAUDIN_SUBTYPE,Her2,4.637006e-05,LumA,LumA,test +MB-4374,CLAUDIN_SUBTYPE,LumA,0.99746215,LumA,LumA,test +MB-4374,CLAUDIN_SUBTYPE,LumB,0.0006256336,LumA,LumA,test +MB-4374,CLAUDIN_SUBTYPE,NC,0.00021799731,LumA,LumA,test +MB-4374,CLAUDIN_SUBTYPE,Normal,0.0015406966,LumA,LumA,test +MB-4374,CLAUDIN_SUBTYPE,claudin-low,4.7625e-05,LumA,LumA,test +MB-0264,CLAUDIN_SUBTYPE,Basal,0.064288855,Her2,LumA,test +MB-0264,CLAUDIN_SUBTYPE,Her2,0.055220354,Her2,LumA,test +MB-0264,CLAUDIN_SUBTYPE,LumA,0.32572377,Her2,LumA,test +MB-0264,CLAUDIN_SUBTYPE,LumB,0.19630031,Her2,LumA,test +MB-0264,CLAUDIN_SUBTYPE,NC,0.044060472,Her2,LumA,test +MB-0264,CLAUDIN_SUBTYPE,Normal,0.3010724,Her2,LumA,test +MB-0264,CLAUDIN_SUBTYPE,claudin-low,0.013333805,Her2,LumA,test +MB-4688,CLAUDIN_SUBTYPE,Basal,0.020050965,LumB,LumB,test +MB-4688,CLAUDIN_SUBTYPE,Her2,0.26258272,LumB,LumB,test +MB-4688,CLAUDIN_SUBTYPE,LumA,0.003064361,LumB,LumB,test +MB-4688,CLAUDIN_SUBTYPE,LumB,0.7042296,LumB,LumB,test +MB-4688,CLAUDIN_SUBTYPE,NC,0.0032299715,LumB,LumB,test +MB-4688,CLAUDIN_SUBTYPE,Normal,0.0035742212,LumB,LumB,test +MB-4688,CLAUDIN_SUBTYPE,claudin-low,0.0032681746,LumB,LumB,test +MB-7003,CLAUDIN_SUBTYPE,Basal,0.0070154336,Normal,LumA,test +MB-7003,CLAUDIN_SUBTYPE,Her2,0.0070004533,Normal,LumA,test +MB-7003,CLAUDIN_SUBTYPE,LumA,0.70013684,Normal,LumA,test +MB-7003,CLAUDIN_SUBTYPE,LumB,0.0037167834,Normal,LumA,test +MB-7003,CLAUDIN_SUBTYPE,NC,0.012570911,Normal,LumA,test +MB-7003,CLAUDIN_SUBTYPE,Normal,0.2672172,Normal,LumA,test +MB-7003,CLAUDIN_SUBTYPE,claudin-low,0.0023424944,Normal,LumA,test +MB-2964,CLAUDIN_SUBTYPE,Basal,0.22110376,Her2,Normal,test +MB-2964,CLAUDIN_SUBTYPE,Her2,0.07186889,Her2,Normal,test +MB-2964,CLAUDIN_SUBTYPE,LumA,0.16190808,Her2,Normal,test +MB-2964,CLAUDIN_SUBTYPE,LumB,0.16794717,Her2,Normal,test +MB-2964,CLAUDIN_SUBTYPE,NC,0.041152216,Her2,Normal,test +MB-2964,CLAUDIN_SUBTYPE,Normal,0.31995127,Her2,Normal,test +MB-2964,CLAUDIN_SUBTYPE,claudin-low,0.016068567,Her2,Normal,test +MB-6237,CLAUDIN_SUBTYPE,Basal,0.79525214,Basal,Basal,test +MB-6237,CLAUDIN_SUBTYPE,Her2,0.004470664,Basal,Basal,test +MB-6237,CLAUDIN_SUBTYPE,LumA,0.004495337,Basal,Basal,test +MB-6237,CLAUDIN_SUBTYPE,LumB,0.0023870433,Basal,Basal,test +MB-6237,CLAUDIN_SUBTYPE,NC,0.0024417634,Basal,Basal,test +MB-6237,CLAUDIN_SUBTYPE,Normal,0.0048755365,Basal,Basal,test +MB-6237,CLAUDIN_SUBTYPE,claudin-low,0.1860776,Basal,Basal,test +MB-4977,CLAUDIN_SUBTYPE,Basal,0.008476745,LumA,LumB,test +MB-4977,CLAUDIN_SUBTYPE,Her2,0.004987781,LumA,LumB,test +MB-4977,CLAUDIN_SUBTYPE,LumA,0.43477765,LumA,LumB,test +MB-4977,CLAUDIN_SUBTYPE,LumB,0.531178,LumA,LumB,test +MB-4977,CLAUDIN_SUBTYPE,NC,0.0074250456,LumA,LumB,test +MB-4977,CLAUDIN_SUBTYPE,Normal,0.01083057,LumA,LumB,test +MB-4977,CLAUDIN_SUBTYPE,claudin-low,0.002324187,LumA,LumB,test +MB-4329,CLAUDIN_SUBTYPE,Basal,0.0005693444,LumA,LumA,test +MB-4329,CLAUDIN_SUBTYPE,Her2,0.0003965184,LumA,LumA,test +MB-4329,CLAUDIN_SUBTYPE,LumA,0.9860961,LumA,LumA,test +MB-4329,CLAUDIN_SUBTYPE,LumB,0.0016150519,LumA,LumA,test +MB-4329,CLAUDIN_SUBTYPE,NC,0.0015471219,LumA,LumA,test +MB-4329,CLAUDIN_SUBTYPE,Normal,0.009183378,LumA,LumA,test +MB-4329,CLAUDIN_SUBTYPE,claudin-low,0.000592569,LumA,LumA,test +MB-4001,CLAUDIN_SUBTYPE,Basal,0.040497895,LumA,LumA,test +MB-4001,CLAUDIN_SUBTYPE,Her2,0.043647517,LumA,LumA,test +MB-4001,CLAUDIN_SUBTYPE,LumA,0.63410205,LumA,LumA,test +MB-4001,CLAUDIN_SUBTYPE,LumB,0.07853336,LumA,LumA,test +MB-4001,CLAUDIN_SUBTYPE,NC,0.023902692,LumA,LumA,test +MB-4001,CLAUDIN_SUBTYPE,Normal,0.17050855,LumA,LumA,test +MB-4001,CLAUDIN_SUBTYPE,claudin-low,0.008807909,LumA,LumA,test +MB-6163,CLAUDIN_SUBTYPE,Basal,0.01724588,LumA,LumA,test +MB-6163,CLAUDIN_SUBTYPE,Her2,0.0030911458,LumA,LumA,test +MB-6163,CLAUDIN_SUBTYPE,LumA,0.538675,LumA,LumA,test +MB-6163,CLAUDIN_SUBTYPE,LumB,0.4005972,LumA,LumA,test +MB-6163,CLAUDIN_SUBTYPE,NC,0.011565048,LumA,LumA,test +MB-6163,CLAUDIN_SUBTYPE,Normal,0.026400665,LumA,LumA,test +MB-6163,CLAUDIN_SUBTYPE,claudin-low,0.002425035,LumA,LumA,test +MB-7151,CLAUDIN_SUBTYPE,Basal,0.99036413,Basal,Basal,test +MB-7151,CLAUDIN_SUBTYPE,Her2,0.00059524504,Basal,Basal,test +MB-7151,CLAUDIN_SUBTYPE,LumA,0.00025821727,Basal,Basal,test +MB-7151,CLAUDIN_SUBTYPE,LumB,0.0029223557,Basal,Basal,test +MB-7151,CLAUDIN_SUBTYPE,NC,0.0003628901,Basal,Basal,test +MB-7151,CLAUDIN_SUBTYPE,Normal,0.002072799,Basal,Basal,test +MB-7151,CLAUDIN_SUBTYPE,claudin-low,0.0034243062,Basal,Basal,test +MB-3341,CLAUDIN_SUBTYPE,Basal,0.00052954024,LumA,LumA,test +MB-3341,CLAUDIN_SUBTYPE,Her2,0.00045399842,LumA,LumA,test +MB-3341,CLAUDIN_SUBTYPE,LumA,0.9772389,LumA,LumA,test +MB-3341,CLAUDIN_SUBTYPE,LumB,0.015800055,LumA,LumA,test +MB-3341,CLAUDIN_SUBTYPE,NC,0.0012836047,LumA,LumA,test +MB-3341,CLAUDIN_SUBTYPE,Normal,0.0043141632,LumA,LumA,test +MB-3341,CLAUDIN_SUBTYPE,claudin-low,0.00037980807,LumA,LumA,test +MB-5378,CLAUDIN_SUBTYPE,Basal,0.99011266,Basal,Basal,test +MB-5378,CLAUDIN_SUBTYPE,Her2,0.0015760915,Basal,Basal,test +MB-5378,CLAUDIN_SUBTYPE,LumA,0.00013602771,Basal,Basal,test +MB-5378,CLAUDIN_SUBTYPE,LumB,0.0011702108,Basal,Basal,test +MB-5378,CLAUDIN_SUBTYPE,NC,0.00026391319,Basal,Basal,test +MB-5378,CLAUDIN_SUBTYPE,Normal,0.0045570573,Basal,Basal,test +MB-5378,CLAUDIN_SUBTYPE,claudin-low,0.0021841677,Basal,Basal,test +MB-0458,CLAUDIN_SUBTYPE,Basal,0.023540689,Normal,Normal,test +MB-0458,CLAUDIN_SUBTYPE,Her2,0.030063543,Normal,Normal,test +MB-0458,CLAUDIN_SUBTYPE,LumA,0.023595085,Normal,Normal,test +MB-0458,CLAUDIN_SUBTYPE,LumB,0.0011185193,Normal,Normal,test +MB-0458,CLAUDIN_SUBTYPE,NC,0.0063781627,Normal,Normal,test +MB-0458,CLAUDIN_SUBTYPE,Normal,0.91429996,Normal,Normal,test +MB-0458,CLAUDIN_SUBTYPE,claudin-low,0.0010040667,Normal,Normal,test +MB-0197,CLAUDIN_SUBTYPE,Basal,0.011809357,LumB,LumB,test +MB-0197,CLAUDIN_SUBTYPE,Her2,0.0015060275,LumB,LumB,test +MB-0197,CLAUDIN_SUBTYPE,LumA,0.006200228,LumB,LumB,test +MB-0197,CLAUDIN_SUBTYPE,LumB,0.9744417,LumB,LumB,test +MB-0197,CLAUDIN_SUBTYPE,NC,0.0029581494,LumB,LumB,test +MB-0197,CLAUDIN_SUBTYPE,Normal,0.0010105978,LumB,LumB,test +MB-0197,CLAUDIN_SUBTYPE,claudin-low,0.0020738535,LumB,LumB,test +MB-3002,CLAUDIN_SUBTYPE,Basal,0.004542802,LumA,LumA,test +MB-3002,CLAUDIN_SUBTYPE,Her2,0.0017584204,LumA,LumA,test +MB-3002,CLAUDIN_SUBTYPE,LumA,0.9416784,LumA,LumA,test +MB-3002,CLAUDIN_SUBTYPE,LumB,0.024939753,LumA,LumA,test +MB-3002,CLAUDIN_SUBTYPE,NC,0.0055692336,LumA,LumA,test +MB-3002,CLAUDIN_SUBTYPE,Normal,0.019383462,LumA,LumA,test +MB-3002,CLAUDIN_SUBTYPE,claudin-low,0.0021278327,LumA,LumA,test +MB-0411,CLAUDIN_SUBTYPE,Basal,0.033319343,LumA,LumA,test +MB-0411,CLAUDIN_SUBTYPE,Her2,0.020574514,LumA,LumA,test +MB-0411,CLAUDIN_SUBTYPE,LumA,0.53795135,LumA,LumA,test +MB-0411,CLAUDIN_SUBTYPE,LumB,0.013417016,LumA,LumA,test +MB-0411,CLAUDIN_SUBTYPE,NC,0.02987797,LumA,LumA,test +MB-0411,CLAUDIN_SUBTYPE,Normal,0.35260585,LumA,LumA,test +MB-0411,CLAUDIN_SUBTYPE,claudin-low,0.012254007,LumA,LumA,test +MB-0230,CLAUDIN_SUBTYPE,Basal,0.0413835,Her2,Her2,test +MB-0230,CLAUDIN_SUBTYPE,Her2,0.8278978,Her2,Her2,test +MB-0230,CLAUDIN_SUBTYPE,LumA,0.022923226,Her2,Her2,test +MB-0230,CLAUDIN_SUBTYPE,LumB,0.021944974,Her2,Her2,test +MB-0230,CLAUDIN_SUBTYPE,NC,0.010425611,Her2,Her2,test +MB-0230,CLAUDIN_SUBTYPE,Normal,0.058778338,Her2,Her2,test +MB-0230,CLAUDIN_SUBTYPE,claudin-low,0.01664649,Her2,Her2,test +MB-0188,CLAUDIN_SUBTYPE,Basal,0.04173352,Her2,LumB,test +MB-0188,CLAUDIN_SUBTYPE,Her2,0.13367997,Her2,LumB,test +MB-0188,CLAUDIN_SUBTYPE,LumA,0.27478936,Her2,LumB,test +MB-0188,CLAUDIN_SUBTYPE,LumB,0.45727363,Her2,LumB,test +MB-0188,CLAUDIN_SUBTYPE,NC,0.025468761,Her2,LumB,test +MB-0188,CLAUDIN_SUBTYPE,Normal,0.048896022,Her2,LumB,test +MB-0188,CLAUDIN_SUBTYPE,claudin-low,0.018158704,Her2,LumB,test +MB-4911,CLAUDIN_SUBTYPE,Basal,0.99012136,Basal,Basal,test +MB-4911,CLAUDIN_SUBTYPE,Her2,0.0005396234,Basal,Basal,test +MB-4911,CLAUDIN_SUBTYPE,LumA,0.00026915054,Basal,Basal,test +MB-4911,CLAUDIN_SUBTYPE,LumB,0.0015418107,Basal,Basal,test +MB-4911,CLAUDIN_SUBTYPE,NC,0.0003053525,Basal,Basal,test +MB-4911,CLAUDIN_SUBTYPE,Normal,0.0017124958,Basal,Basal,test +MB-4911,CLAUDIN_SUBTYPE,claudin-low,0.005510237,Basal,Basal,test +MB-0428,CLAUDIN_SUBTYPE,Basal,0.089249864,LumA,LumA,test +MB-0428,CLAUDIN_SUBTYPE,Her2,0.20728701,LumA,LumA,test +MB-0428,CLAUDIN_SUBTYPE,LumA,0.25158626,LumA,LumA,test +MB-0428,CLAUDIN_SUBTYPE,LumB,0.20639218,LumA,LumA,test +MB-0428,CLAUDIN_SUBTYPE,NC,0.05120578,LumA,LumA,test +MB-0428,CLAUDIN_SUBTYPE,Normal,0.08582219,LumA,LumA,test +MB-0428,CLAUDIN_SUBTYPE,claudin-low,0.108456664,LumA,LumA,test +MB-5068,CLAUDIN_SUBTYPE,Basal,0.0002629537,LumA,LumA,test +MB-5068,CLAUDIN_SUBTYPE,Her2,0.00020617519,LumA,LumA,test +MB-5068,CLAUDIN_SUBTYPE,LumA,0.9906632,LumA,LumA,test +MB-5068,CLAUDIN_SUBTYPE,LumB,0.0020486603,LumA,LumA,test +MB-5068,CLAUDIN_SUBTYPE,NC,0.00087967026,LumA,LumA,test +MB-5068,CLAUDIN_SUBTYPE,Normal,0.0057417396,LumA,LumA,test +MB-5068,CLAUDIN_SUBTYPE,claudin-low,0.00019771479,LumA,LumA,test +MB-5518,CLAUDIN_SUBTYPE,Basal,0.017793423,LumB,LumB,test +MB-5518,CLAUDIN_SUBTYPE,Her2,0.013118724,LumB,LumB,test +MB-5518,CLAUDIN_SUBTYPE,LumA,0.008469443,LumB,LumB,test +MB-5518,CLAUDIN_SUBTYPE,LumB,0.9512653,LumB,LumB,test +MB-5518,CLAUDIN_SUBTYPE,NC,0.0042027645,LumB,LumB,test +MB-5518,CLAUDIN_SUBTYPE,Normal,0.0025801745,LumB,LumB,test +MB-5518,CLAUDIN_SUBTYPE,claudin-low,0.002570223,LumB,LumB,test +MB-5185,CLAUDIN_SUBTYPE,Basal,0.008536392,LumA,LumA,test +MB-5185,CLAUDIN_SUBTYPE,Her2,0.021774039,LumA,LumA,test +MB-5185,CLAUDIN_SUBTYPE,LumA,0.8727301,LumA,LumA,test +MB-5185,CLAUDIN_SUBTYPE,LumB,0.035564654,LumA,LumA,test +MB-5185,CLAUDIN_SUBTYPE,NC,0.011424317,LumA,LumA,test +MB-5185,CLAUDIN_SUBTYPE,Normal,0.044040825,LumA,LumA,test +MB-5185,CLAUDIN_SUBTYPE,claudin-low,0.0059297523,LumA,LumA,test +MB-4836,CLAUDIN_SUBTYPE,Basal,0.25713205,Her2,Her2,test +MB-4836,CLAUDIN_SUBTYPE,Her2,0.5029091,Her2,Her2,test +MB-4836,CLAUDIN_SUBTYPE,LumA,0.0045750714,Her2,Her2,test +MB-4836,CLAUDIN_SUBTYPE,LumB,0.1035517,Her2,Her2,test +MB-4836,CLAUDIN_SUBTYPE,NC,0.011277,Her2,Her2,test +MB-4836,CLAUDIN_SUBTYPE,Normal,0.11213675,Her2,Her2,test +MB-4836,CLAUDIN_SUBTYPE,claudin-low,0.008418248,Her2,Her2,test +MB-6125,CLAUDIN_SUBTYPE,Basal,0.042460058,Normal,LumA,test +MB-6125,CLAUDIN_SUBTYPE,Her2,0.013968797,Normal,LumA,test +MB-6125,CLAUDIN_SUBTYPE,LumA,0.6854334,Normal,LumA,test +MB-6125,CLAUDIN_SUBTYPE,LumB,0.009226941,Normal,LumA,test +MB-6125,CLAUDIN_SUBTYPE,NC,0.033245955,Normal,LumA,test +MB-6125,CLAUDIN_SUBTYPE,Normal,0.07698593,Normal,LumA,test +MB-6125,CLAUDIN_SUBTYPE,claudin-low,0.13867891,Normal,LumA,test +MB-2932,CLAUDIN_SUBTYPE,Basal,0.010055175,LumB,LumB,test +MB-2932,CLAUDIN_SUBTYPE,Her2,0.0011023908,LumB,LumB,test +MB-2932,CLAUDIN_SUBTYPE,LumA,0.00921021,LumB,LumB,test +MB-2932,CLAUDIN_SUBTYPE,LumB,0.9746833,LumB,LumB,test +MB-2932,CLAUDIN_SUBTYPE,NC,0.0026313285,LumB,LumB,test +MB-2932,CLAUDIN_SUBTYPE,Normal,0.0013921638,LumB,LumB,test +MB-2932,CLAUDIN_SUBTYPE,claudin-low,0.0009252997,LumB,LumB,test +MB-0095,CLAUDIN_SUBTYPE,Basal,0.0011303613,LumB,LumB,test +MB-0095,CLAUDIN_SUBTYPE,Her2,9.25287e-05,LumB,LumB,test +MB-0095,CLAUDIN_SUBTYPE,LumA,0.0007837039,LumB,LumB,test +MB-0095,CLAUDIN_SUBTYPE,LumB,0.9976737,LumB,LumB,test +MB-0095,CLAUDIN_SUBTYPE,NC,0.00021169994,LumB,LumB,test +MB-0095,CLAUDIN_SUBTYPE,Normal,5.843949e-05,LumB,LumB,test +MB-0095,CLAUDIN_SUBTYPE,claudin-low,4.960045e-05,LumB,LumB,test +MB-2564,CLAUDIN_SUBTYPE,Basal,0.00018593732,LumA,LumA,test +MB-2564,CLAUDIN_SUBTYPE,Her2,0.00015529865,LumA,LumA,test +MB-2564,CLAUDIN_SUBTYPE,LumA,0.9929253,LumA,LumA,test +MB-2564,CLAUDIN_SUBTYPE,LumB,0.00065572886,LumA,LumA,test +MB-2564,CLAUDIN_SUBTYPE,NC,0.00071759196,LumA,LumA,test +MB-2564,CLAUDIN_SUBTYPE,Normal,0.005143678,LumA,LumA,test +MB-2564,CLAUDIN_SUBTYPE,claudin-low,0.00021649951,LumA,LumA,test +MB-7155,CLAUDIN_SUBTYPE,Basal,0.90355,Basal,Basal,test +MB-7155,CLAUDIN_SUBTYPE,Her2,0.005915135,Basal,Basal,test +MB-7155,CLAUDIN_SUBTYPE,LumA,0.0046726726,Basal,Basal,test +MB-7155,CLAUDIN_SUBTYPE,LumB,0.007604214,Basal,Basal,test +MB-7155,CLAUDIN_SUBTYPE,NC,0.0031512384,Basal,Basal,test +MB-7155,CLAUDIN_SUBTYPE,Normal,0.0076686363,Basal,Basal,test +MB-7155,CLAUDIN_SUBTYPE,claudin-low,0.067438155,Basal,Basal,test +MB-4603,CLAUDIN_SUBTYPE,Basal,0.0017825573,Normal,LumA,test +MB-4603,CLAUDIN_SUBTYPE,Her2,0.0014209285,Normal,LumA,test +MB-4603,CLAUDIN_SUBTYPE,LumA,0.9554897,Normal,LumA,test +MB-4603,CLAUDIN_SUBTYPE,LumB,0.0022861199,Normal,LumA,test +MB-4603,CLAUDIN_SUBTYPE,NC,0.0033237038,Normal,LumA,test +MB-4603,CLAUDIN_SUBTYPE,Normal,0.03476004,Normal,LumA,test +MB-4603,CLAUDIN_SUBTYPE,claudin-low,0.0009368243,Normal,LumA,test +MB-4173,CLAUDIN_SUBTYPE,Basal,6.163649e-05,LumA,LumA,test +MB-4173,CLAUDIN_SUBTYPE,Her2,4.9998987e-05,LumA,LumA,test +MB-4173,CLAUDIN_SUBTYPE,LumA,0.997384,LumA,LumA,test +MB-4173,CLAUDIN_SUBTYPE,LumB,0.00023000411,LumA,LumA,test +MB-4173,CLAUDIN_SUBTYPE,NC,0.00026021327,LumA,LumA,test +MB-4173,CLAUDIN_SUBTYPE,Normal,0.0019295207,LumA,LumA,test +MB-4173,CLAUDIN_SUBTYPE,claudin-low,8.4651394e-05,LumA,LumA,test +MB-0578,CLAUDIN_SUBTYPE,Basal,0.013469911,Normal,Normal,test +MB-0578,CLAUDIN_SUBTYPE,Her2,0.017588947,Normal,Normal,test +MB-0578,CLAUDIN_SUBTYPE,LumA,0.014263198,Normal,Normal,test +MB-0578,CLAUDIN_SUBTYPE,LumB,0.00038764143,Normal,Normal,test +MB-0578,CLAUDIN_SUBTYPE,NC,0.0032670712,Normal,Normal,test +MB-0578,CLAUDIN_SUBTYPE,Normal,0.9506578,Normal,Normal,test +MB-0578,CLAUDIN_SUBTYPE,claudin-low,0.00036543675,Normal,Normal,test +MB-3272,CLAUDIN_SUBTYPE,Basal,0.033196483,LumB,LumB,test +MB-3272,CLAUDIN_SUBTYPE,Her2,0.015818756,LumB,LumB,test +MB-3272,CLAUDIN_SUBTYPE,LumA,0.40473,LumB,LumB,test +MB-3272,CLAUDIN_SUBTYPE,LumB,0.4920376,LumB,LumB,test +MB-3272,CLAUDIN_SUBTYPE,NC,0.018592643,LumB,LumB,test +MB-3272,CLAUDIN_SUBTYPE,Normal,0.026696589,LumB,LumB,test +MB-3272,CLAUDIN_SUBTYPE,claudin-low,0.008927902,LumB,LumB,test +MB-4695,CLAUDIN_SUBTYPE,Basal,0.0014625929,Normal,LumA,test +MB-4695,CLAUDIN_SUBTYPE,Her2,0.0011435975,Normal,LumA,test +MB-4695,CLAUDIN_SUBTYPE,LumA,0.9612335,Normal,LumA,test +MB-4695,CLAUDIN_SUBTYPE,LumB,0.0036459784,Normal,LumA,test +MB-4695,CLAUDIN_SUBTYPE,NC,0.0043218313,Normal,LumA,test +MB-4695,CLAUDIN_SUBTYPE,Normal,0.026778478,Normal,LumA,test +MB-4695,CLAUDIN_SUBTYPE,claudin-low,0.0014140033,Normal,LumA,test +MB-0455,CLAUDIN_SUBTYPE,Basal,0.12362967,LumB,claudin-low,test +MB-0455,CLAUDIN_SUBTYPE,Her2,0.028494794,LumB,claudin-low,test +MB-0455,CLAUDIN_SUBTYPE,LumA,0.09530895,LumB,claudin-low,test +MB-0455,CLAUDIN_SUBTYPE,LumB,0.31189463,LumB,claudin-low,test +MB-0455,CLAUDIN_SUBTYPE,NC,0.022450596,LumB,claudin-low,test +MB-0455,CLAUDIN_SUBTYPE,Normal,0.0062943264,LumB,claudin-low,test +MB-0455,CLAUDIN_SUBTYPE,claudin-low,0.41192707,LumB,claudin-low,test +MB-2863,CLAUDIN_SUBTYPE,Basal,0.00010688343,LumA,LumA,test +MB-2863,CLAUDIN_SUBTYPE,Her2,8.670522e-05,LumA,LumA,test +MB-2863,CLAUDIN_SUBTYPE,LumA,0.995008,LumA,LumA,test +MB-2863,CLAUDIN_SUBTYPE,LumB,0.0008054251,LumA,LumA,test +MB-2863,CLAUDIN_SUBTYPE,NC,0.00043851385,LumA,LumA,test +MB-2863,CLAUDIN_SUBTYPE,Normal,0.003471609,LumA,LumA,test +MB-2863,CLAUDIN_SUBTYPE,claudin-low,8.292317e-05,LumA,LumA,test +MB-0346,CLAUDIN_SUBTYPE,Basal,0.010869512,Her2,Her2,test +MB-0346,CLAUDIN_SUBTYPE,Her2,0.97435826,Her2,Her2,test +MB-0346,CLAUDIN_SUBTYPE,LumA,0.0004575393,Her2,Her2,test +MB-0346,CLAUDIN_SUBTYPE,LumB,0.0051625036,Her2,Her2,test +MB-0346,CLAUDIN_SUBTYPE,NC,0.00080566213,Her2,Her2,test +MB-0346,CLAUDIN_SUBTYPE,Normal,0.0057067084,Her2,Her2,test +MB-0346,CLAUDIN_SUBTYPE,claudin-low,0.0026397756,Her2,Her2,test +MB-4709,CLAUDIN_SUBTYPE,Basal,0.00011124542,LumA,LumA,test +MB-4709,CLAUDIN_SUBTYPE,Her2,8.736801e-05,LumA,LumA,test +MB-4709,CLAUDIN_SUBTYPE,LumA,0.99634594,LumA,LumA,test +MB-4709,CLAUDIN_SUBTYPE,LumB,0.00042645462,LumA,LumA,test +MB-4709,CLAUDIN_SUBTYPE,NC,0.00039114757,LumA,LumA,test +MB-4709,CLAUDIN_SUBTYPE,Normal,0.002489674,LumA,LumA,test +MB-4709,CLAUDIN_SUBTYPE,claudin-low,0.0001483529,LumA,LumA,test +MB-5057,CLAUDIN_SUBTYPE,Basal,0.82365197,Basal,Basal,test +MB-5057,CLAUDIN_SUBTYPE,Her2,0.007376968,Basal,Basal,test +MB-5057,CLAUDIN_SUBTYPE,LumA,0.007895235,Basal,Basal,test +MB-5057,CLAUDIN_SUBTYPE,LumB,0.0060785245,Basal,Basal,test +MB-5057,CLAUDIN_SUBTYPE,NC,0.004552448,Basal,Basal,test +MB-5057,CLAUDIN_SUBTYPE,Normal,0.010215684,Basal,Basal,test +MB-5057,CLAUDIN_SUBTYPE,claudin-low,0.14022915,Basal,Basal,test +MB-4724,CLAUDIN_SUBTYPE,Basal,0.02104304,Her2,Her2,test +MB-4724,CLAUDIN_SUBTYPE,Her2,0.95852804,Her2,Her2,test +MB-4724,CLAUDIN_SUBTYPE,LumA,0.0008265699,Her2,Her2,test +MB-4724,CLAUDIN_SUBTYPE,LumB,0.0034909286,Her2,Her2,test +MB-4724,CLAUDIN_SUBTYPE,NC,0.0011144008,Her2,Her2,test +MB-4724,CLAUDIN_SUBTYPE,Normal,0.007023054,Her2,Her2,test +MB-4724,CLAUDIN_SUBTYPE,claudin-low,0.007973953,Her2,Her2,test +MB-6217,CLAUDIN_SUBTYPE,Basal,0.01368638,LumB,LumB,test +MB-6217,CLAUDIN_SUBTYPE,Her2,0.0058450657,LumB,LumB,test +MB-6217,CLAUDIN_SUBTYPE,LumA,0.37031564,LumB,LumB,test +MB-6217,CLAUDIN_SUBTYPE,LumB,0.5858359,LumB,LumB,test +MB-6217,CLAUDIN_SUBTYPE,NC,0.009114739,LumB,LumB,test +MB-6217,CLAUDIN_SUBTYPE,Normal,0.011897688,LumB,LumB,test +MB-6217,CLAUDIN_SUBTYPE,claudin-low,0.0033046752,LumB,LumB,test +MB-7160,CLAUDIN_SUBTYPE,Basal,0.63306177,Her2,Basal,test +MB-7160,CLAUDIN_SUBTYPE,Her2,0.06629914,Her2,Basal,test +MB-7160,CLAUDIN_SUBTYPE,LumA,0.02409286,Her2,Basal,test +MB-7160,CLAUDIN_SUBTYPE,LumB,0.08623299,Her2,Basal,test +MB-7160,CLAUDIN_SUBTYPE,NC,0.024035005,Her2,Basal,test +MB-7160,CLAUDIN_SUBTYPE,Normal,0.13661739,Her2,Basal,test +MB-7160,CLAUDIN_SUBTYPE,claudin-low,0.029660828,Her2,Basal,test +MB-4548,CLAUDIN_SUBTYPE,Basal,0.7617707,Her2,Basal,test +MB-4548,CLAUDIN_SUBTYPE,Her2,0.19727321,Her2,Basal,test +MB-4548,CLAUDIN_SUBTYPE,LumA,0.00079085067,Her2,Basal,test +MB-4548,CLAUDIN_SUBTYPE,LumB,0.0038938916,Her2,Basal,test +MB-4548,CLAUDIN_SUBTYPE,NC,0.0013319331,Her2,Basal,test +MB-4548,CLAUDIN_SUBTYPE,Normal,0.0216287,Her2,Basal,test +MB-4548,CLAUDIN_SUBTYPE,claudin-low,0.013310716,Her2,Basal,test +MB-5222,CLAUDIN_SUBTYPE,Basal,0.040132806,claudin-low,claudin-low,test +MB-5222,CLAUDIN_SUBTYPE,Her2,0.0018620446,claudin-low,claudin-low,test +MB-5222,CLAUDIN_SUBTYPE,LumA,0.00929445,claudin-low,claudin-low,test +MB-5222,CLAUDIN_SUBTYPE,LumB,0.00034078187,claudin-low,claudin-low,test +MB-5222,CLAUDIN_SUBTYPE,NC,0.0017237159,claudin-low,claudin-low,test +MB-5222,CLAUDIN_SUBTYPE,Normal,0.00055188267,claudin-low,claudin-low,test +MB-5222,CLAUDIN_SUBTYPE,claudin-low,0.94609433,claudin-low,claudin-low,test +MB-5422,CLAUDIN_SUBTYPE,Basal,0.00061716465,LumA,LumA,test +MB-5422,CLAUDIN_SUBTYPE,Her2,0.0005173711,LumA,LumA,test +MB-5422,CLAUDIN_SUBTYPE,LumA,0.97413105,LumA,LumA,test +MB-5422,CLAUDIN_SUBTYPE,LumB,0.0031063487,LumA,LumA,test +MB-5422,CLAUDIN_SUBTYPE,NC,0.0017344021,LumA,LumA,test +MB-5422,CLAUDIN_SUBTYPE,Normal,0.019634193,LumA,LumA,test +MB-5422,CLAUDIN_SUBTYPE,claudin-low,0.0002594521,LumA,LumA,test +MB-0384,CLAUDIN_SUBTYPE,Basal,0.008731177,LumB,LumA,test +MB-0384,CLAUDIN_SUBTYPE,Her2,0.002251768,LumB,LumA,test +MB-0384,CLAUDIN_SUBTYPE,LumA,0.76048726,LumB,LumA,test +MB-0384,CLAUDIN_SUBTYPE,LumB,0.19441803,LumB,LumA,test +MB-0384,CLAUDIN_SUBTYPE,NC,0.009067324,LumB,LumA,test +MB-0384,CLAUDIN_SUBTYPE,Normal,0.023075713,LumB,LumA,test +MB-0384,CLAUDIN_SUBTYPE,claudin-low,0.001968699,LumB,LumA,test +MB-5335,CLAUDIN_SUBTYPE,Basal,0.98229927,Basal,Basal,test +MB-5335,CLAUDIN_SUBTYPE,Her2,0.0011095493,Basal,Basal,test +MB-5335,CLAUDIN_SUBTYPE,LumA,0.0006156649,Basal,Basal,test +MB-5335,CLAUDIN_SUBTYPE,LumB,0.0027453098,Basal,Basal,test +MB-5335,CLAUDIN_SUBTYPE,NC,0.0006370859,Basal,Basal,test +MB-5335,CLAUDIN_SUBTYPE,Normal,0.0031816312,Basal,Basal,test +MB-5335,CLAUDIN_SUBTYPE,claudin-low,0.009411483,Basal,Basal,test +MB-0157,CLAUDIN_SUBTYPE,Basal,0.021822063,claudin-low,claudin-low,test +MB-0157,CLAUDIN_SUBTYPE,Her2,0.00043872203,claudin-low,claudin-low,test +MB-0157,CLAUDIN_SUBTYPE,LumA,0.0036812846,claudin-low,claudin-low,test +MB-0157,CLAUDIN_SUBTYPE,LumB,6.666282e-05,claudin-low,claudin-low,test +MB-0157,CLAUDIN_SUBTYPE,NC,0.0005445782,claudin-low,claudin-low,test +MB-0157,CLAUDIN_SUBTYPE,Normal,0.00012612915,claudin-low,claudin-low,test +MB-0157,CLAUDIN_SUBTYPE,claudin-low,0.97332054,claudin-low,claudin-low,test +MB-5324,CLAUDIN_SUBTYPE,Basal,0.00030340505,LumA,LumA,test +MB-5324,CLAUDIN_SUBTYPE,Her2,0.00022950709,LumA,LumA,test +MB-5324,CLAUDIN_SUBTYPE,LumA,0.9865398,LumA,LumA,test +MB-5324,CLAUDIN_SUBTYPE,LumB,0.0006072712,LumA,LumA,test +MB-5324,CLAUDIN_SUBTYPE,NC,0.0013107867,LumA,LumA,test +MB-5324,CLAUDIN_SUBTYPE,Normal,0.010619464,LumA,LumA,test +MB-5324,CLAUDIN_SUBTYPE,claudin-low,0.00038972695,LumA,LumA,test +MB-5150,CLAUDIN_SUBTYPE,Basal,0.0014000323,Normal,LumA,test +MB-5150,CLAUDIN_SUBTYPE,Her2,0.001091039,Normal,LumA,test +MB-5150,CLAUDIN_SUBTYPE,LumA,0.9620282,Normal,LumA,test +MB-5150,CLAUDIN_SUBTYPE,LumB,0.007164492,Normal,LumA,test +MB-5150,CLAUDIN_SUBTYPE,NC,0.0039808257,Normal,LumA,test +MB-5150,CLAUDIN_SUBTYPE,Normal,0.023355525,Normal,LumA,test +MB-5150,CLAUDIN_SUBTYPE,claudin-low,0.0009800057,Normal,LumA,test +MB-7073,CLAUDIN_SUBTYPE,Basal,0.8283376,Basal,Basal,test +MB-7073,CLAUDIN_SUBTYPE,Her2,0.09673134,Basal,Basal,test +MB-7073,CLAUDIN_SUBTYPE,LumA,0.0007000669,Basal,Basal,test +MB-7073,CLAUDIN_SUBTYPE,LumB,0.049291786,Basal,Basal,test +MB-7073,CLAUDIN_SUBTYPE,NC,0.00207384,Basal,Basal,test +MB-7073,CLAUDIN_SUBTYPE,Normal,0.0180834,Basal,Basal,test +MB-7073,CLAUDIN_SUBTYPE,claudin-low,0.004781913,Basal,Basal,test +MB-0136,CLAUDIN_SUBTYPE,Basal,0.006129607,LumA,LumA,test +MB-0136,CLAUDIN_SUBTYPE,Her2,0.0015425504,LumA,LumA,test +MB-0136,CLAUDIN_SUBTYPE,LumA,0.95681274,LumA,LumA,test +MB-0136,CLAUDIN_SUBTYPE,LumB,0.008142737,LumA,LumA,test +MB-0136,CLAUDIN_SUBTYPE,NC,0.005105211,LumA,LumA,test +MB-0136,CLAUDIN_SUBTYPE,Normal,0.013016649,LumA,LumA,test +MB-0136,CLAUDIN_SUBTYPE,claudin-low,0.009250428,LumA,LumA,test +MB-0163,CLAUDIN_SUBTYPE,Basal,0.99020535,Basal,Basal,test +MB-0163,CLAUDIN_SUBTYPE,Her2,0.0004236053,Basal,Basal,test +MB-0163,CLAUDIN_SUBTYPE,LumA,0.00026932,Basal,Basal,test +MB-0163,CLAUDIN_SUBTYPE,LumB,0.0038867297,Basal,Basal,test +MB-0163,CLAUDIN_SUBTYPE,NC,0.00036756534,Basal,Basal,test +MB-0163,CLAUDIN_SUBTYPE,Normal,0.0016007841,Basal,Basal,test +MB-0163,CLAUDIN_SUBTYPE,claudin-low,0.0032464438,Basal,Basal,test +MB-4834,CLAUDIN_SUBTYPE,Basal,0.0062780203,LumB,LumB,test +MB-4834,CLAUDIN_SUBTYPE,Her2,0.00053316524,LumB,LumB,test +MB-4834,CLAUDIN_SUBTYPE,LumA,0.00043632486,LumB,LumB,test +MB-4834,CLAUDIN_SUBTYPE,LumB,0.9918864,LumB,LumB,test +MB-4834,CLAUDIN_SUBTYPE,NC,0.0004963943,LumB,LumB,test +MB-4834,CLAUDIN_SUBTYPE,Normal,0.0002417398,LumB,LumB,test +MB-4834,CLAUDIN_SUBTYPE,claudin-low,0.00012807715,LumB,LumB,test +MB-5465,CLAUDIN_SUBTYPE,Basal,0.8397852,Basal,Basal,test +MB-5465,CLAUDIN_SUBTYPE,Her2,0.018824356,Basal,Basal,test +MB-5465,CLAUDIN_SUBTYPE,LumA,0.0036013753,Basal,Basal,test +MB-5465,CLAUDIN_SUBTYPE,LumB,0.0022628468,Basal,Basal,test +MB-5465,CLAUDIN_SUBTYPE,NC,0.0026725656,Basal,Basal,test +MB-5465,CLAUDIN_SUBTYPE,Normal,0.01259789,Basal,Basal,test +MB-5465,CLAUDIN_SUBTYPE,claudin-low,0.120255776,Basal,Basal,test +MB-5330,CLAUDIN_SUBTYPE,Basal,0.0018246461,LumA,LumA,test +MB-5330,CLAUDIN_SUBTYPE,Her2,0.00025108704,LumA,LumA,test +MB-5330,CLAUDIN_SUBTYPE,LumA,0.977811,LumA,LumA,test +MB-5330,CLAUDIN_SUBTYPE,LumB,0.01160246,LumA,LumA,test +MB-5330,CLAUDIN_SUBTYPE,NC,0.0015217592,LumA,LumA,test +MB-5330,CLAUDIN_SUBTYPE,Normal,0.006602427,LumA,LumA,test +MB-5330,CLAUDIN_SUBTYPE,claudin-low,0.00038666642,LumA,LumA,test +MB-0489,CLAUDIN_SUBTYPE,Basal,0.0018973575,claudin-low,claudin-low,test +MB-0489,CLAUDIN_SUBTYPE,Her2,5.446271e-06,claudin-low,claudin-low,test +MB-0489,CLAUDIN_SUBTYPE,LumA,0.00011413054,claudin-low,claudin-low,test +MB-0489,CLAUDIN_SUBTYPE,LumB,2.2721616e-07,claudin-low,claudin-low,test +MB-0489,CLAUDIN_SUBTYPE,NC,8.45834e-06,claudin-low,claudin-low,test +MB-0489,CLAUDIN_SUBTYPE,Normal,5.7799116e-07,claudin-low,claudin-low,test +MB-0489,CLAUDIN_SUBTYPE,claudin-low,0.99797386,claudin-low,claudin-low,test +MB-0107,CLAUDIN_SUBTYPE,Basal,0.019695183,LumB,LumB,test +MB-0107,CLAUDIN_SUBTYPE,Her2,0.08439352,LumB,LumB,test +MB-0107,CLAUDIN_SUBTYPE,LumA,0.0005521762,LumB,LumB,test +MB-0107,CLAUDIN_SUBTYPE,LumB,0.89045584,LumB,LumB,test +MB-0107,CLAUDIN_SUBTYPE,NC,0.0019311904,LumB,LumB,test +MB-0107,CLAUDIN_SUBTYPE,Normal,0.0016727037,LumB,LumB,test +MB-0107,CLAUDIN_SUBTYPE,claudin-low,0.0012992495,LumB,LumB,test +MB-5593,CLAUDIN_SUBTYPE,Basal,0.019911716,Her2,Her2,test +MB-5593,CLAUDIN_SUBTYPE,Her2,0.9512099,Her2,Her2,test +MB-5593,CLAUDIN_SUBTYPE,LumA,0.00034126398,Her2,Her2,test +MB-5593,CLAUDIN_SUBTYPE,LumB,0.0022427281,Her2,Her2,test +MB-5593,CLAUDIN_SUBTYPE,NC,0.00085395324,Her2,Her2,test +MB-5593,CLAUDIN_SUBTYPE,Normal,0.02415187,Her2,Her2,test +MB-5593,CLAUDIN_SUBTYPE,claudin-low,0.0012885649,Her2,Her2,test +MB-6245,CLAUDIN_SUBTYPE,Basal,0.97986525,Basal,Basal,test +MB-6245,CLAUDIN_SUBTYPE,Her2,0.0007341914,Basal,Basal,test +MB-6245,CLAUDIN_SUBTYPE,LumA,0.0008404831,Basal,Basal,test +MB-6245,CLAUDIN_SUBTYPE,LumB,0.0058874083,Basal,Basal,test +MB-6245,CLAUDIN_SUBTYPE,NC,0.0008209092,Basal,Basal,test +MB-6245,CLAUDIN_SUBTYPE,Normal,0.002403318,Basal,Basal,test +MB-6245,CLAUDIN_SUBTYPE,claudin-low,0.009448445,Basal,Basal,test +MB-5329,CLAUDIN_SUBTYPE,Basal,0.062605105,LumA,Normal,test +MB-5329,CLAUDIN_SUBTYPE,Her2,0.06933001,LumA,Normal,test +MB-5329,CLAUDIN_SUBTYPE,LumA,0.2806559,LumA,Normal,test +MB-5329,CLAUDIN_SUBTYPE,LumB,0.02278587,LumA,Normal,test +MB-5329,CLAUDIN_SUBTYPE,NC,0.037140056,LumA,Normal,test +MB-5329,CLAUDIN_SUBTYPE,Normal,0.5138657,LumA,Normal,test +MB-5329,CLAUDIN_SUBTYPE,claudin-low,0.013617365,LumA,Normal,test +MB-6346,CLAUDIN_SUBTYPE,Basal,0.0035589235,LumB,LumA,test +MB-6346,CLAUDIN_SUBTYPE,Her2,0.0021520269,LumB,LumA,test +MB-6346,CLAUDIN_SUBTYPE,LumA,0.93079394,LumB,LumA,test +MB-6346,CLAUDIN_SUBTYPE,LumB,0.04233247,LumB,LumA,test +MB-6346,CLAUDIN_SUBTYPE,NC,0.0050123762,LumB,LumA,test +MB-6346,CLAUDIN_SUBTYPE,Normal,0.014239625,LumB,LumA,test +MB-6346,CLAUDIN_SUBTYPE,claudin-low,0.001910591,LumB,LumA,test +MB-0200,CLAUDIN_SUBTYPE,Basal,0.99442106,Basal,Basal,test +MB-0200,CLAUDIN_SUBTYPE,Her2,0.00043531143,Basal,Basal,test +MB-0200,CLAUDIN_SUBTYPE,LumA,8.93446e-05,Basal,Basal,test +MB-0200,CLAUDIN_SUBTYPE,LumB,0.00042547105,Basal,Basal,test +MB-0200,CLAUDIN_SUBTYPE,NC,0.00011991666,Basal,Basal,test +MB-0200,CLAUDIN_SUBTYPE,Normal,0.0013281619,Basal,Basal,test +MB-0200,CLAUDIN_SUBTYPE,claudin-low,0.0031806196,Basal,Basal,test +MB-0354,CLAUDIN_SUBTYPE,Basal,0.005794085,claudin-low,claudin-low,test +MB-0354,CLAUDIN_SUBTYPE,Her2,4.847253e-05,claudin-low,claudin-low,test +MB-0354,CLAUDIN_SUBTYPE,LumA,0.00061461807,claudin-low,claudin-low,test +MB-0354,CLAUDIN_SUBTYPE,LumB,3.6719073e-06,claudin-low,claudin-low,test +MB-0354,CLAUDIN_SUBTYPE,NC,6.5531436e-05,claudin-low,claudin-low,test +MB-0354,CLAUDIN_SUBTYPE,Normal,7.868e-06,claudin-low,claudin-low,test +MB-0354,CLAUDIN_SUBTYPE,claudin-low,0.9934657,claudin-low,claudin-low,test +MB-5474,CLAUDIN_SUBTYPE,Basal,0.59014565,claudin-low,Basal,test +MB-5474,CLAUDIN_SUBTYPE,Her2,0.026026504,claudin-low,Basal,test +MB-5474,CLAUDIN_SUBTYPE,LumA,0.026886113,claudin-low,Basal,test +MB-5474,CLAUDIN_SUBTYPE,LumB,0.010157257,claudin-low,Basal,test +MB-5474,CLAUDIN_SUBTYPE,NC,0.01306659,claudin-low,Basal,test +MB-5474,CLAUDIN_SUBTYPE,Normal,0.028489625,claudin-low,Basal,test +MB-5474,CLAUDIN_SUBTYPE,claudin-low,0.30522814,claudin-low,Basal,test +MB-3328,CLAUDIN_SUBTYPE,Basal,0.0009819119,LumA,LumA,test +MB-3328,CLAUDIN_SUBTYPE,Her2,0.00042817526,LumA,LumA,test +MB-3328,CLAUDIN_SUBTYPE,LumA,0.97830164,LumA,LumA,test +MB-3328,CLAUDIN_SUBTYPE,LumB,0.012868978,LumA,LumA,test +MB-3328,CLAUDIN_SUBTYPE,NC,0.0015469969,LumA,LumA,test +MB-3328,CLAUDIN_SUBTYPE,Normal,0.005298146,LumA,LumA,test +MB-3328,CLAUDIN_SUBTYPE,claudin-low,0.00057407515,LumA,LumA,test +MB-6018,CLAUDIN_SUBTYPE,Basal,0.0031151162,LumA,LumA,test +MB-6018,CLAUDIN_SUBTYPE,Her2,0.0026866607,LumA,LumA,test +MB-6018,CLAUDIN_SUBTYPE,LumA,0.9622179,LumA,LumA,test +MB-6018,CLAUDIN_SUBTYPE,LumB,0.0062252376,LumA,LumA,test +MB-6018,CLAUDIN_SUBTYPE,NC,0.00490985,LumA,LumA,test +MB-6018,CLAUDIN_SUBTYPE,Normal,0.01530417,LumA,LumA,test +MB-6018,CLAUDIN_SUBTYPE,claudin-low,0.005540924,LumA,LumA,test +MB-0599,CLAUDIN_SUBTYPE,Basal,0.03173055,LumA,Normal,test +MB-0599,CLAUDIN_SUBTYPE,Her2,0.02945164,LumA,Normal,test +MB-0599,CLAUDIN_SUBTYPE,LumA,0.35670266,LumA,Normal,test +MB-0599,CLAUDIN_SUBTYPE,LumB,0.006152484,LumA,Normal,test +MB-0599,CLAUDIN_SUBTYPE,NC,0.029533572,LumA,Normal,test +MB-0599,CLAUDIN_SUBTYPE,Normal,0.5337738,LumA,Normal,test +MB-0599,CLAUDIN_SUBTYPE,claudin-low,0.01265531,LumA,Normal,test +MB-4591,CLAUDIN_SUBTYPE,Basal,0.006855861,LumB,LumB,test +MB-4591,CLAUDIN_SUBTYPE,Her2,0.0013459875,LumB,LumB,test +MB-4591,CLAUDIN_SUBTYPE,LumA,0.005637093,LumB,LumB,test +MB-4591,CLAUDIN_SUBTYPE,LumB,0.9829184,LumB,LumB,test +MB-4591,CLAUDIN_SUBTYPE,NC,0.0017569592,LumB,LumB,test +MB-4591,CLAUDIN_SUBTYPE,Normal,0.0008024882,LumB,LumB,test +MB-4591,CLAUDIN_SUBTYPE,claudin-low,0.0006831725,LumB,LumB,test +MB-0378,CLAUDIN_SUBTYPE,Basal,0.05696687,Her2,Her2,test +MB-0378,CLAUDIN_SUBTYPE,Her2,0.89783406,Her2,Her2,test +MB-0378,CLAUDIN_SUBTYPE,LumA,0.0012419116,Her2,Her2,test +MB-0378,CLAUDIN_SUBTYPE,LumB,0.005475914,Her2,Her2,test +MB-0378,CLAUDIN_SUBTYPE,NC,0.0021235158,Her2,Her2,test +MB-0378,CLAUDIN_SUBTYPE,Normal,0.030060448,Her2,Her2,test +MB-0378,CLAUDIN_SUBTYPE,claudin-low,0.006297382,Her2,Her2,test +MB-3548,CLAUDIN_SUBTYPE,Basal,0.00068786135,LumA,LumA,test +MB-3548,CLAUDIN_SUBTYPE,Her2,0.0012818055,LumA,LumA,test +MB-3548,CLAUDIN_SUBTYPE,LumA,0.9824154,LumA,LumA,test +MB-3548,CLAUDIN_SUBTYPE,LumB,0.0037028068,LumA,LumA,test +MB-3548,CLAUDIN_SUBTYPE,NC,0.0017755938,LumA,LumA,test +MB-3548,CLAUDIN_SUBTYPE,Normal,0.009512234,LumA,LumA,test +MB-3548,CLAUDIN_SUBTYPE,claudin-low,0.00062434917,LumA,LumA,test +MB-0226,CLAUDIN_SUBTYPE,Basal,0.0013146834,LumA,LumA,test +MB-0226,CLAUDIN_SUBTYPE,Her2,0.001929155,LumA,LumA,test +MB-0226,CLAUDIN_SUBTYPE,LumA,0.95042825,LumA,LumA,test +MB-0226,CLAUDIN_SUBTYPE,LumB,0.0029996198,LumA,LumA,test +MB-0226,CLAUDIN_SUBTYPE,NC,0.0034058886,LumA,LumA,test +MB-0226,CLAUDIN_SUBTYPE,Normal,0.039215956,LumA,LumA,test +MB-0226,CLAUDIN_SUBTYPE,claudin-low,0.00070648117,LumA,LumA,test +MB-7193,CLAUDIN_SUBTYPE,Basal,0.0012215632,LumB,LumB,test +MB-7193,CLAUDIN_SUBTYPE,Her2,0.0001728941,LumB,LumB,test +MB-7193,CLAUDIN_SUBTYPE,LumA,0.0008516535,LumB,LumB,test +MB-7193,CLAUDIN_SUBTYPE,LumB,0.9973285,LumB,LumB,test +MB-7193,CLAUDIN_SUBTYPE,NC,0.00027582748,LumB,LumB,test +MB-7193,CLAUDIN_SUBTYPE,Normal,7.5855234e-05,LumB,LumB,test +MB-7193,CLAUDIN_SUBTYPE,claudin-low,7.368609e-05,LumB,LumB,test +MB-5622,CLAUDIN_SUBTYPE,Basal,0.0045035863,LumB,LumB,test +MB-5622,CLAUDIN_SUBTYPE,Her2,0.00034412174,LumB,LumB,test +MB-5622,CLAUDIN_SUBTYPE,LumA,0.002357914,LumB,LumB,test +MB-5622,CLAUDIN_SUBTYPE,LumB,0.99136704,LumB,LumB,test +MB-5622,CLAUDIN_SUBTYPE,NC,0.0008346909,LumB,LumB,test +MB-5622,CLAUDIN_SUBTYPE,Normal,0.00036980398,LumB,LumB,test +MB-5622,CLAUDIN_SUBTYPE,claudin-low,0.00022271194,LumB,LumB,test +MB-0171,CLAUDIN_SUBTYPE,Basal,0.014331588,Normal,Normal,test +MB-0171,CLAUDIN_SUBTYPE,Her2,0.01503805,Normal,Normal,test +MB-0171,CLAUDIN_SUBTYPE,LumA,0.22129503,Normal,Normal,test +MB-0171,CLAUDIN_SUBTYPE,LumB,0.0023330725,Normal,Normal,test +MB-0171,CLAUDIN_SUBTYPE,NC,0.01466963,Normal,Normal,test +MB-0171,CLAUDIN_SUBTYPE,Normal,0.73005444,Normal,Normal,test +MB-0171,CLAUDIN_SUBTYPE,claudin-low,0.0022782055,Normal,Normal,test +MB-7286,CLAUDIN_SUBTYPE,Basal,0.0062232437,LumB,LumB,test +MB-7286,CLAUDIN_SUBTYPE,Her2,0.0020256003,LumB,LumB,test +MB-7286,CLAUDIN_SUBTYPE,LumA,0.003231481,LumB,LumB,test +MB-7286,CLAUDIN_SUBTYPE,LumB,0.9860157,LumB,LumB,test +MB-7286,CLAUDIN_SUBTYPE,NC,0.001309898,LumB,LumB,test +MB-7286,CLAUDIN_SUBTYPE,Normal,0.0006824868,LumB,LumB,test +MB-7286,CLAUDIN_SUBTYPE,claudin-low,0.00051164866,LumB,LumB,test +MB-4974,CLAUDIN_SUBTYPE,Basal,0.12730515,Basal,claudin-low,test +MB-4974,CLAUDIN_SUBTYPE,Her2,0.010846745,Basal,claudin-low,test +MB-4974,CLAUDIN_SUBTYPE,LumA,0.035765685,Basal,claudin-low,test +MB-4974,CLAUDIN_SUBTYPE,LumB,0.0032986917,Basal,claudin-low,test +MB-4974,CLAUDIN_SUBTYPE,NC,0.009316575,Basal,claudin-low,test +MB-4974,CLAUDIN_SUBTYPE,Normal,0.006187646,Basal,claudin-low,test +MB-4974,CLAUDIN_SUBTYPE,claudin-low,0.8072795,Basal,claudin-low,test +MB-0452,CLAUDIN_SUBTYPE,Basal,0.0023872657,LumB,LumB,test +MB-0452,CLAUDIN_SUBTYPE,Her2,0.00023604075,LumB,LumB,test +MB-0452,CLAUDIN_SUBTYPE,LumA,0.001304779,LumB,LumB,test +MB-0452,CLAUDIN_SUBTYPE,LumB,0.99533325,LumB,LumB,test +MB-0452,CLAUDIN_SUBTYPE,NC,0.00046335763,LumB,LumB,test +MB-0452,CLAUDIN_SUBTYPE,Normal,0.00014548887,LumB,LumB,test +MB-0452,CLAUDIN_SUBTYPE,claudin-low,0.00012985157,LumB,LumB,test +MB-2846,CLAUDIN_SUBTYPE,Basal,0.110638395,Basal,Normal,test +MB-2846,CLAUDIN_SUBTYPE,Her2,0.28339845,Basal,Normal,test +MB-2846,CLAUDIN_SUBTYPE,LumA,0.021716429,Basal,Normal,test +MB-2846,CLAUDIN_SUBTYPE,LumB,0.008299545,Basal,Normal,test +MB-2846,CLAUDIN_SUBTYPE,NC,0.014856493,Basal,Normal,test +MB-2846,CLAUDIN_SUBTYPE,Normal,0.5522956,Basal,Normal,test +MB-2846,CLAUDIN_SUBTYPE,claudin-low,0.008795154,Basal,Normal,test +MB-5195,CLAUDIN_SUBTYPE,Basal,0.029660814,LumA,LumB,test +MB-5195,CLAUDIN_SUBTYPE,Her2,0.1255134,LumA,LumB,test +MB-5195,CLAUDIN_SUBTYPE,LumA,0.03739614,LumA,LumB,test +MB-5195,CLAUDIN_SUBTYPE,LumB,0.7677423,LumA,LumB,test +MB-5195,CLAUDIN_SUBTYPE,NC,0.014032701,LumA,LumB,test +MB-5195,CLAUDIN_SUBTYPE,Normal,0.011845237,LumA,LumB,test +MB-5195,CLAUDIN_SUBTYPE,claudin-low,0.01380942,LumA,LumB,test +MB-0302,CLAUDIN_SUBTYPE,Basal,0.10346622,LumA,LumA,test +MB-0302,CLAUDIN_SUBTYPE,Her2,0.029196136,LumA,LumA,test +MB-0302,CLAUDIN_SUBTYPE,LumA,0.4232991,LumA,LumA,test +MB-0302,CLAUDIN_SUBTYPE,LumB,0.020209284,LumA,LumA,test +MB-0302,CLAUDIN_SUBTYPE,NC,0.045238934,LumA,LumA,test +MB-0302,CLAUDIN_SUBTYPE,Normal,0.080011025,LumA,LumA,test +MB-0302,CLAUDIN_SUBTYPE,claudin-low,0.29857925,LumA,LumA,test +MB-2712,CLAUDIN_SUBTYPE,Basal,0.0008071044,LumA,LumA,test +MB-2712,CLAUDIN_SUBTYPE,Her2,0.0006295172,LumA,LumA,test +MB-2712,CLAUDIN_SUBTYPE,LumA,0.98680824,LumA,LumA,test +MB-2712,CLAUDIN_SUBTYPE,LumB,0.002795903,LumA,LumA,test +MB-2712,CLAUDIN_SUBTYPE,NC,0.0016702322,LumA,LumA,test +MB-2712,CLAUDIN_SUBTYPE,Normal,0.006054648,LumA,LumA,test +MB-2712,CLAUDIN_SUBTYPE,claudin-low,0.001234531,LumA,LumA,test +MB-4896,CLAUDIN_SUBTYPE,Basal,0.31161806,Basal,Her2,test +MB-4896,CLAUDIN_SUBTYPE,Her2,0.43723983,Basal,Her2,test +MB-4896,CLAUDIN_SUBTYPE,LumA,0.010825897,Basal,Her2,test +MB-4896,CLAUDIN_SUBTYPE,LumB,0.0286701,Basal,Her2,test +MB-4896,CLAUDIN_SUBTYPE,NC,0.013717769,Basal,Her2,test +MB-4896,CLAUDIN_SUBTYPE,Normal,0.17777227,Basal,Her2,test +MB-4896,CLAUDIN_SUBTYPE,claudin-low,0.02015613,Basal,Her2,test +MB-7084,CLAUDIN_SUBTYPE,Basal,0.9638875,Basal,Basal,test +MB-7084,CLAUDIN_SUBTYPE,Her2,0.010101002,Basal,Basal,test +MB-7084,CLAUDIN_SUBTYPE,LumA,0.00025319093,Basal,Basal,test +MB-7084,CLAUDIN_SUBTYPE,LumB,0.0021677336,Basal,Basal,test +MB-7084,CLAUDIN_SUBTYPE,NC,0.0006389675,Basal,Basal,test +MB-7084,CLAUDIN_SUBTYPE,Normal,0.020604003,Basal,Basal,test +MB-7084,CLAUDIN_SUBTYPE,claudin-low,0.002347646,Basal,Basal,test +MB-2772,CLAUDIN_SUBTYPE,Basal,0.08007874,LumB,LumB,test +MB-2772,CLAUDIN_SUBTYPE,Her2,0.011490737,LumB,LumB,test +MB-2772,CLAUDIN_SUBTYPE,LumA,0.030813143,LumB,LumB,test +MB-2772,CLAUDIN_SUBTYPE,LumB,0.8219049,LumB,LumB,test +MB-2772,CLAUDIN_SUBTYPE,NC,0.0177151,LumB,LumB,test +MB-2772,CLAUDIN_SUBTYPE,Normal,0.007908472,LumB,LumB,test +MB-2772,CLAUDIN_SUBTYPE,claudin-low,0.030088907,LumB,LumB,test +MB-5221,CLAUDIN_SUBTYPE,Basal,0.0001289943,LumA,LumA,test +MB-5221,CLAUDIN_SUBTYPE,Her2,0.00011228466,LumA,LumA,test +MB-5221,CLAUDIN_SUBTYPE,LumA,0.9937459,LumA,LumA,test +MB-5221,CLAUDIN_SUBTYPE,LumB,0.00067790877,LumA,LumA,test +MB-5221,CLAUDIN_SUBTYPE,NC,0.00055455347,LumA,LumA,test +MB-5221,CLAUDIN_SUBTYPE,Normal,0.0046759807,LumA,LumA,test +MB-5221,CLAUDIN_SUBTYPE,claudin-low,0.00010429723,LumA,LumA,test +MB-5572,CLAUDIN_SUBTYPE,Basal,0.012371493,claudin-low,claudin-low,test +MB-5572,CLAUDIN_SUBTYPE,Her2,0.00030154982,claudin-low,claudin-low,test +MB-5572,CLAUDIN_SUBTYPE,LumA,0.001977929,claudin-low,claudin-low,test +MB-5572,CLAUDIN_SUBTYPE,LumB,2.4615501e-05,claudin-low,claudin-low,test +MB-5572,CLAUDIN_SUBTYPE,NC,0.00024770346,claudin-low,claudin-low,test +MB-5572,CLAUDIN_SUBTYPE,Normal,4.4324002e-05,claudin-low,claudin-low,test +MB-5572,CLAUDIN_SUBTYPE,claudin-low,0.98503244,claudin-low,claudin-low,test +MB-5045,CLAUDIN_SUBTYPE,Basal,0.14420292,LumA,Normal,test +MB-5045,CLAUDIN_SUBTYPE,Her2,0.19401816,LumA,Normal,test +MB-5045,CLAUDIN_SUBTYPE,LumA,0.12840854,LumA,Normal,test +MB-5045,CLAUDIN_SUBTYPE,LumB,0.050270002,LumA,Normal,test +MB-5045,CLAUDIN_SUBTYPE,NC,0.038111843,LumA,Normal,test +MB-5045,CLAUDIN_SUBTYPE,Normal,0.42516655,LumA,Normal,test +MB-5045,CLAUDIN_SUBTYPE,claudin-low,0.019822055,LumA,Normal,test +MB-5093,CLAUDIN_SUBTYPE,Basal,0.008165335,Her2,LumB,test +MB-5093,CLAUDIN_SUBTYPE,Her2,0.0021940663,Her2,LumB,test +MB-5093,CLAUDIN_SUBTYPE,LumA,0.015042088,Her2,LumB,test +MB-5093,CLAUDIN_SUBTYPE,LumB,0.96898377,Her2,LumB,test +MB-5093,CLAUDIN_SUBTYPE,NC,0.0028081436,Her2,LumB,test +MB-5093,CLAUDIN_SUBTYPE,Normal,0.001648241,Her2,LumB,test +MB-5093,CLAUDIN_SUBTYPE,claudin-low,0.0011583052,Her2,LumB,test +MB-5044,CLAUDIN_SUBTYPE,Basal,0.018178718,LumB,LumB,test +MB-5044,CLAUDIN_SUBTYPE,Her2,0.0021943243,LumB,LumB,test +MB-5044,CLAUDIN_SUBTYPE,LumA,0.0034657521,LumB,LumB,test +MB-5044,CLAUDIN_SUBTYPE,LumB,0.9706497,LumB,LumB,test +MB-5044,CLAUDIN_SUBTYPE,NC,0.0027495916,LumB,LumB,test +MB-5044,CLAUDIN_SUBTYPE,Normal,0.0018174367,LumB,LumB,test +MB-5044,CLAUDIN_SUBTYPE,claudin-low,0.00094437704,LumB,LumB,test +MB-3028,CLAUDIN_SUBTYPE,Basal,0.08454357,LumB,LumB,test +MB-3028,CLAUDIN_SUBTYPE,Her2,0.31060788,LumB,LumB,test +MB-3028,CLAUDIN_SUBTYPE,LumA,0.08979801,LumB,LumB,test +MB-3028,CLAUDIN_SUBTYPE,LumB,0.36766714,LumB,LumB,test +MB-3028,CLAUDIN_SUBTYPE,NC,0.036492378,LumB,LumB,test +MB-3028,CLAUDIN_SUBTYPE,Normal,0.06750283,LumB,LumB,test +MB-3028,CLAUDIN_SUBTYPE,claudin-low,0.043388158,LumB,LumB,test +MB-0658,CLAUDIN_SUBTYPE,Basal,0.230179,claudin-low,claudin-low,test +MB-0658,CLAUDIN_SUBTYPE,Her2,0.004315916,claudin-low,claudin-low,test +MB-0658,CLAUDIN_SUBTYPE,LumA,0.024485221,claudin-low,claudin-low,test +MB-0658,CLAUDIN_SUBTYPE,LumB,0.0041930703,claudin-low,claudin-low,test +MB-0658,CLAUDIN_SUBTYPE,NC,0.006640446,claudin-low,claudin-low,test +MB-0658,CLAUDIN_SUBTYPE,Normal,0.003231114,claudin-low,claudin-low,test +MB-0658,CLAUDIN_SUBTYPE,claudin-low,0.7269553,claudin-low,claudin-low,test +MB-7005,CLAUDIN_SUBTYPE,Basal,0.008641446,LumB,LumB,test +MB-7005,CLAUDIN_SUBTYPE,Her2,0.007197737,LumB,LumB,test +MB-7005,CLAUDIN_SUBTYPE,LumA,0.41212815,LumB,LumB,test +MB-7005,CLAUDIN_SUBTYPE,LumB,0.54820335,LumB,LumB,test +MB-7005,CLAUDIN_SUBTYPE,NC,0.008690691,LumB,LumB,test +MB-7005,CLAUDIN_SUBTYPE,Normal,0.012102828,LumB,LumB,test +MB-7005,CLAUDIN_SUBTYPE,claudin-low,0.0030358897,LumB,LumB,test +MB-5228,CLAUDIN_SUBTYPE,Basal,0.054715365,LumB,LumB,test +MB-5228,CLAUDIN_SUBTYPE,Her2,0.02648703,LumB,LumB,test +MB-5228,CLAUDIN_SUBTYPE,LumA,0.20750119,LumB,LumB,test +MB-5228,CLAUDIN_SUBTYPE,LumB,0.67596215,LumB,LumB,test +MB-5228,CLAUDIN_SUBTYPE,NC,0.011354954,LumB,LumB,test +MB-5228,CLAUDIN_SUBTYPE,Normal,0.009894002,LumB,LumB,test +MB-5228,CLAUDIN_SUBTYPE,claudin-low,0.014085332,LumB,LumB,test +MB-0314,CLAUDIN_SUBTYPE,Basal,0.048630077,Her2,Her2,test +MB-0314,CLAUDIN_SUBTYPE,Her2,0.85279554,Her2,Her2,test +MB-0314,CLAUDIN_SUBTYPE,LumA,0.009348301,Her2,Her2,test +MB-0314,CLAUDIN_SUBTYPE,LumB,0.021795448,Her2,Her2,test +MB-0314,CLAUDIN_SUBTYPE,NC,0.008145786,Her2,Her2,test +MB-0314,CLAUDIN_SUBTYPE,Normal,0.025682362,Her2,Her2,test +MB-0314,CLAUDIN_SUBTYPE,claudin-low,0.03360249,Her2,Her2,test +MB-7293,CLAUDIN_SUBTYPE,Basal,0.000700282,LumA,LumA,test +MB-7293,CLAUDIN_SUBTYPE,Her2,0.0005786058,LumA,LumA,test +MB-7293,CLAUDIN_SUBTYPE,LumA,0.9827321,LumA,LumA,test +MB-7293,CLAUDIN_SUBTYPE,LumB,0.0029389493,LumA,LumA,test +MB-7293,CLAUDIN_SUBTYPE,NC,0.0019503491,LumA,LumA,test +MB-7293,CLAUDIN_SUBTYPE,Normal,0.010379566,LumA,LumA,test +MB-7293,CLAUDIN_SUBTYPE,claudin-low,0.00072008657,LumA,LumA,test +MB-5602,CLAUDIN_SUBTYPE,Basal,0.5253072,Basal,Basal,test +MB-5602,CLAUDIN_SUBTYPE,Her2,0.10884465,Basal,Basal,test +MB-5602,CLAUDIN_SUBTYPE,LumA,0.011321066,Basal,Basal,test +MB-5602,CLAUDIN_SUBTYPE,LumB,0.006323863,Basal,Basal,test +MB-5602,CLAUDIN_SUBTYPE,NC,0.0069872392,Basal,Basal,test +MB-5602,CLAUDIN_SUBTYPE,Normal,0.016678615,Basal,Basal,test +MB-5602,CLAUDIN_SUBTYPE,claudin-low,0.32453734,Basal,Basal,test +MB-5406,CLAUDIN_SUBTYPE,Basal,0.02733475,LumB,LumB,test +MB-5406,CLAUDIN_SUBTYPE,Her2,0.010730498,LumB,LumB,test +MB-5406,CLAUDIN_SUBTYPE,LumA,0.015097026,LumB,LumB,test +MB-5406,CLAUDIN_SUBTYPE,LumB,0.93343306,LumB,LumB,test +MB-5406,CLAUDIN_SUBTYPE,NC,0.0057496256,LumB,LumB,test +MB-5406,CLAUDIN_SUBTYPE,Normal,0.003354072,LumB,LumB,test +MB-5406,CLAUDIN_SUBTYPE,claudin-low,0.0043009287,LumB,LumB,test +MB-0884,CLAUDIN_SUBTYPE,Basal,0.0040842826,LumB,LumB,test +MB-0884,CLAUDIN_SUBTYPE,Her2,1.01684645e-05,LumB,LumB,test +MB-0884,CLAUDIN_SUBTYPE,LumA,0.00017605079,LumB,LumB,test +MB-0884,CLAUDIN_SUBTYPE,LumB,0.9955973,LumB,LumB,test +MB-0884,CLAUDIN_SUBTYPE,NC,8.761029e-05,LumB,LumB,test +MB-0884,CLAUDIN_SUBTYPE,Normal,1.4501355e-05,LumB,LumB,test +MB-0884,CLAUDIN_SUBTYPE,claudin-low,3.0114461e-05,LumB,LumB,test +MB-7112,CLAUDIN_SUBTYPE,Basal,0.038913336,LumB,LumA,test +MB-7112,CLAUDIN_SUBTYPE,Her2,0.011491224,LumB,LumA,test +MB-7112,CLAUDIN_SUBTYPE,LumA,0.5622121,LumB,LumA,test +MB-7112,CLAUDIN_SUBTYPE,LumB,0.31165478,LumB,LumA,test +MB-7112,CLAUDIN_SUBTYPE,NC,0.020050026,LumB,LumA,test +MB-7112,CLAUDIN_SUBTYPE,Normal,0.018981256,LumB,LumA,test +MB-7112,CLAUDIN_SUBTYPE,claudin-low,0.0366973,LumB,LumA,test +MB-2939,CLAUDIN_SUBTYPE,Basal,0.0050817286,LumB,LumB,test +MB-2939,CLAUDIN_SUBTYPE,Her2,0.009520266,LumB,LumB,test +MB-2939,CLAUDIN_SUBTYPE,LumA,0.0101869255,LumB,LumB,test +MB-2939,CLAUDIN_SUBTYPE,LumB,0.9694585,LumB,LumB,test +MB-2939,CLAUDIN_SUBTYPE,NC,0.0027447564,LumB,LumB,test +MB-2939,CLAUDIN_SUBTYPE,Normal,0.0013527008,LumB,LumB,test +MB-2939,CLAUDIN_SUBTYPE,claudin-low,0.0016550828,LumB,LumB,test +MB-0541,CLAUDIN_SUBTYPE,Basal,0.018826589,LumA,LumB,test +MB-0541,CLAUDIN_SUBTYPE,Her2,0.008765432,LumA,LumB,test +MB-0541,CLAUDIN_SUBTYPE,LumA,0.38146126,LumA,LumB,test +MB-0541,CLAUDIN_SUBTYPE,LumB,0.54758435,LumA,LumB,test +MB-0541,CLAUDIN_SUBTYPE,NC,0.01568812,LumA,LumB,test +MB-0541,CLAUDIN_SUBTYPE,Normal,0.016853202,LumA,LumB,test +MB-0541,CLAUDIN_SUBTYPE,claudin-low,0.010820989,LumA,LumB,test +MB-7186,CLAUDIN_SUBTYPE,Basal,0.005265429,LumB,LumB,test +MB-7186,CLAUDIN_SUBTYPE,Her2,0.00028712302,LumB,LumB,test +MB-7186,CLAUDIN_SUBTYPE,LumA,0.002471965,LumB,LumB,test +MB-7186,CLAUDIN_SUBTYPE,LumB,0.9905765,LumB,LumB,test +MB-7186,CLAUDIN_SUBTYPE,NC,0.0008387393,LumB,LumB,test +MB-7186,CLAUDIN_SUBTYPE,Normal,0.00032219797,LumB,LumB,test +MB-7186,CLAUDIN_SUBTYPE,claudin-low,0.00023791309,LumB,LumB,test +MB-5230,CLAUDIN_SUBTYPE,Basal,0.00295254,LumA,LumA,test +MB-5230,CLAUDIN_SUBTYPE,Her2,0.0019219932,LumA,LumA,test +MB-5230,CLAUDIN_SUBTYPE,LumA,0.95250654,LumA,LumA,test +MB-5230,CLAUDIN_SUBTYPE,LumB,0.0068567945,LumA,LumA,test +MB-5230,CLAUDIN_SUBTYPE,NC,0.0060444092,LumA,LumA,test +MB-5230,CLAUDIN_SUBTYPE,Normal,0.026354332,LumA,LumA,test +MB-5230,CLAUDIN_SUBTYPE,claudin-low,0.0033635292,LumA,LumA,test +MB-5059,CLAUDIN_SUBTYPE,Basal,3.445285e-05,LumA,LumA,test +MB-5059,CLAUDIN_SUBTYPE,Her2,2.7561044e-05,LumA,LumA,test +MB-5059,CLAUDIN_SUBTYPE,LumA,0.9976178,LumA,LumA,test +MB-5059,CLAUDIN_SUBTYPE,LumB,0.00020445613,LumA,LumA,test +MB-5059,CLAUDIN_SUBTYPE,NC,0.00018747442,LumA,LumA,test +MB-5059,CLAUDIN_SUBTYPE,Normal,0.001896174,LumA,LumA,test +MB-5059,CLAUDIN_SUBTYPE,claudin-low,3.220526e-05,LumA,LumA,test +MB-0656,CLAUDIN_SUBTYPE,Basal,0.59791833,claudin-low,Basal,test +MB-0656,CLAUDIN_SUBTYPE,Her2,0.021894483,claudin-low,Basal,test +MB-0656,CLAUDIN_SUBTYPE,LumA,0.009623723,claudin-low,Basal,test +MB-0656,CLAUDIN_SUBTYPE,LumB,0.00095515774,claudin-low,Basal,test +MB-0656,CLAUDIN_SUBTYPE,NC,0.0041578948,claudin-low,Basal,test +MB-0656,CLAUDIN_SUBTYPE,Normal,0.02205138,claudin-low,Basal,test +MB-0656,CLAUDIN_SUBTYPE,claudin-low,0.34339896,claudin-low,Basal,test +MB-6059,CLAUDIN_SUBTYPE,Basal,0.10510234,Normal,LumB,test +MB-6059,CLAUDIN_SUBTYPE,Her2,0.023143405,Normal,LumB,test +MB-6059,CLAUDIN_SUBTYPE,LumA,0.09925069,Normal,LumB,test +MB-6059,CLAUDIN_SUBTYPE,LumB,0.64914685,Normal,LumB,test +MB-6059,CLAUDIN_SUBTYPE,NC,0.029758465,Normal,LumB,test +MB-6059,CLAUDIN_SUBTYPE,Normal,0.084322006,Normal,LumB,test +MB-6059,CLAUDIN_SUBTYPE,claudin-low,0.009276208,Normal,LumB,test +MB-3062,CLAUDIN_SUBTYPE,Basal,0.010768656,claudin-low,claudin-low,test +MB-3062,CLAUDIN_SUBTYPE,Her2,9.253797e-05,claudin-low,claudin-low,test +MB-3062,CLAUDIN_SUBTYPE,LumA,0.0011569741,claudin-low,claudin-low,test +MB-3062,CLAUDIN_SUBTYPE,LumB,9.502358e-06,claudin-low,claudin-low,test +MB-3062,CLAUDIN_SUBTYPE,NC,0.00012969463,claudin-low,claudin-low,test +MB-3062,CLAUDIN_SUBTYPE,Normal,2.0737487e-05,claudin-low,claudin-low,test +MB-3062,CLAUDIN_SUBTYPE,claudin-low,0.9878219,claudin-low,claudin-low,test +MB-0393,CLAUDIN_SUBTYPE,Basal,0.116923705,claudin-low,LumA,test +MB-0393,CLAUDIN_SUBTYPE,Her2,0.06599456,claudin-low,LumA,test +MB-0393,CLAUDIN_SUBTYPE,LumA,0.33939835,claudin-low,LumA,test +MB-0393,CLAUDIN_SUBTYPE,LumB,0.06432091,claudin-low,LumA,test +MB-0393,CLAUDIN_SUBTYPE,NC,0.071096055,claudin-low,LumA,test +MB-0393,CLAUDIN_SUBTYPE,Normal,0.2363686,claudin-low,LumA,test +MB-0393,CLAUDIN_SUBTYPE,claudin-low,0.105897844,claudin-low,LumA,test +MB-3379,CLAUDIN_SUBTYPE,Basal,0.0040908083,LumA,LumA,test +MB-3379,CLAUDIN_SUBTYPE,Her2,0.0060990807,LumA,LumA,test +MB-3379,CLAUDIN_SUBTYPE,LumA,0.9084948,LumA,LumA,test +MB-3379,CLAUDIN_SUBTYPE,LumB,0.030871313,LumA,LumA,test +MB-3379,CLAUDIN_SUBTYPE,NC,0.009075231,LumA,LumA,test +MB-3379,CLAUDIN_SUBTYPE,Normal,0.03853429,LumA,LumA,test +MB-3379,CLAUDIN_SUBTYPE,claudin-low,0.0028345874,LumA,LumA,test +MB-4601,CLAUDIN_SUBTYPE,Basal,0.28315553,Basal,Her2,test +MB-4601,CLAUDIN_SUBTYPE,Her2,0.5329331,Basal,Her2,test +MB-4601,CLAUDIN_SUBTYPE,LumA,0.00902736,Basal,Her2,test +MB-4601,CLAUDIN_SUBTYPE,LumB,0.020525876,Basal,Her2,test +MB-4601,CLAUDIN_SUBTYPE,NC,0.011310963,Basal,Her2,test +MB-4601,CLAUDIN_SUBTYPE,Normal,0.113307506,Basal,Her2,test +MB-4601,CLAUDIN_SUBTYPE,claudin-low,0.029739585,Basal,Her2,test +MB-5310,CLAUDIN_SUBTYPE,Basal,0.018802995,LumA,LumA,test +MB-5310,CLAUDIN_SUBTYPE,Her2,0.006530711,LumA,LumA,test +MB-5310,CLAUDIN_SUBTYPE,LumA,0.8804244,LumA,LumA,test +MB-5310,CLAUDIN_SUBTYPE,LumB,0.015939787,LumA,LumA,test +MB-5310,CLAUDIN_SUBTYPE,NC,0.01266396,LumA,LumA,test +MB-5310,CLAUDIN_SUBTYPE,Normal,0.051735997,LumA,LumA,test +MB-5310,CLAUDIN_SUBTYPE,claudin-low,0.013902213,LumA,LumA,test +MB-0412,CLAUDIN_SUBTYPE,Basal,0.0015564469,LumB,LumB,test +MB-0412,CLAUDIN_SUBTYPE,Her2,7.11326e-05,LumB,LumB,test +MB-0412,CLAUDIN_SUBTYPE,LumA,6.1277344e-05,LumB,LumB,test +MB-0412,CLAUDIN_SUBTYPE,LumB,0.99819297,LumB,LumB,test +MB-0412,CLAUDIN_SUBTYPE,NC,8.1893966e-05,LumB,LumB,test +MB-0412,CLAUDIN_SUBTYPE,Normal,1.9199128e-05,LumB,LumB,test +MB-0412,CLAUDIN_SUBTYPE,claudin-low,1.710042e-05,LumB,LumB,test +MB-5527,CLAUDIN_SUBTYPE,Basal,0.027947528,claudin-low,claudin-low,test +MB-5527,CLAUDIN_SUBTYPE,Her2,0.0013176474,claudin-low,claudin-low,test +MB-5527,CLAUDIN_SUBTYPE,LumA,0.0048621907,claudin-low,claudin-low,test +MB-5527,CLAUDIN_SUBTYPE,LumB,0.000136839,claudin-low,claudin-low,test +MB-5527,CLAUDIN_SUBTYPE,NC,0.0008003644,claudin-low,claudin-low,test +MB-5527,CLAUDIN_SUBTYPE,Normal,0.00021154602,claudin-low,claudin-low,test +MB-5527,CLAUDIN_SUBTYPE,claudin-low,0.9647239,claudin-low,claudin-low,test +MB-3007,CLAUDIN_SUBTYPE,Basal,0.011360846,LumB,LumB,test +MB-3007,CLAUDIN_SUBTYPE,Her2,0.0019883497,LumB,LumB,test +MB-3007,CLAUDIN_SUBTYPE,LumA,0.15359674,LumB,LumB,test +MB-3007,CLAUDIN_SUBTYPE,LumB,0.81907034,LumB,LumB,test +MB-3007,CLAUDIN_SUBTYPE,NC,0.0059142504,LumB,LumB,test +MB-3007,CLAUDIN_SUBTYPE,Normal,0.0064829956,LumB,LumB,test +MB-3007,CLAUDIN_SUBTYPE,claudin-low,0.0015864568,LumB,LumB,test +MB-2951,CLAUDIN_SUBTYPE,Basal,0.005496098,LumA,LumA,test +MB-2951,CLAUDIN_SUBTYPE,Her2,0.0048072212,LumA,LumA,test +MB-2951,CLAUDIN_SUBTYPE,LumA,0.82693297,LumA,LumA,test +MB-2951,CLAUDIN_SUBTYPE,LumB,0.007421095,LumA,LumA,test +MB-2951,CLAUDIN_SUBTYPE,NC,0.009682699,LumA,LumA,test +MB-2951,CLAUDIN_SUBTYPE,Normal,0.14374293,LumA,LumA,test +MB-2951,CLAUDIN_SUBTYPE,claudin-low,0.001917009,LumA,LumA,test +MB-7027,CLAUDIN_SUBTYPE,Basal,0.18513304,Her2,claudin-low,test +MB-7027,CLAUDIN_SUBTYPE,Her2,0.1501839,Her2,claudin-low,test +MB-7027,CLAUDIN_SUBTYPE,LumA,0.038322393,Her2,claudin-low,test +MB-7027,CLAUDIN_SUBTYPE,LumB,0.01817255,Her2,claudin-low,test +MB-7027,CLAUDIN_SUBTYPE,NC,0.017443357,Her2,claudin-low,test +MB-7027,CLAUDIN_SUBTYPE,Normal,0.01818784,Her2,claudin-low,test +MB-7027,CLAUDIN_SUBTYPE,claudin-low,0.5725569,Her2,claudin-low,test +MB-0500,CLAUDIN_SUBTYPE,Basal,0.99305624,Basal,Basal,test +MB-0500,CLAUDIN_SUBTYPE,Her2,0.00044188555,Basal,Basal,test +MB-0500,CLAUDIN_SUBTYPE,LumA,0.00016003738,Basal,Basal,test +MB-0500,CLAUDIN_SUBTYPE,LumB,0.0012280799,Basal,Basal,test +MB-0500,CLAUDIN_SUBTYPE,NC,0.0002120907,Basal,Basal,test +MB-0500,CLAUDIN_SUBTYPE,Normal,0.0014788347,Basal,Basal,test +MB-0500,CLAUDIN_SUBTYPE,claudin-low,0.003422724,Basal,Basal,test +MB-3064,CLAUDIN_SUBTYPE,Basal,0.09197106,LumA,Normal,test +MB-3064,CLAUDIN_SUBTYPE,Her2,0.0819575,LumA,Normal,test +MB-3064,CLAUDIN_SUBTYPE,LumA,0.2097115,LumA,Normal,test +MB-3064,CLAUDIN_SUBTYPE,LumB,0.025300588,LumA,Normal,test +MB-3064,CLAUDIN_SUBTYPE,NC,0.057162773,LumA,Normal,test +MB-3064,CLAUDIN_SUBTYPE,Normal,0.4911267,LumA,Normal,test +MB-3064,CLAUDIN_SUBTYPE,claudin-low,0.042769782,LumA,Normal,test +MB-2792,CLAUDIN_SUBTYPE,Basal,0.035945714,Her2,LumA,test +MB-2792,CLAUDIN_SUBTYPE,Her2,0.0743812,Her2,LumA,test +MB-2792,CLAUDIN_SUBTYPE,LumA,0.5167135,Her2,LumA,test +MB-2792,CLAUDIN_SUBTYPE,LumB,0.21791446,Her2,LumA,test +MB-2792,CLAUDIN_SUBTYPE,NC,0.039588887,Her2,LumA,test +MB-2792,CLAUDIN_SUBTYPE,Normal,0.049744673,Her2,LumA,test +MB-2792,CLAUDIN_SUBTYPE,claudin-low,0.065711625,Her2,LumA,test +MB-4375,CLAUDIN_SUBTYPE,Basal,0.005555877,Normal,Normal,test +MB-4375,CLAUDIN_SUBTYPE,Her2,0.008072405,Normal,Normal,test +MB-4375,CLAUDIN_SUBTYPE,LumA,0.43135908,Normal,Normal,test +MB-4375,CLAUDIN_SUBTYPE,LumB,0.0006171336,Normal,Normal,test +MB-4375,CLAUDIN_SUBTYPE,NC,0.0063248384,Normal,Normal,test +MB-4375,CLAUDIN_SUBTYPE,Normal,0.5473488,Normal,Normal,test +MB-4375,CLAUDIN_SUBTYPE,claudin-low,0.0007218237,Normal,Normal,test +MB-4908,CLAUDIN_SUBTYPE,Basal,0.003958556,LumB,LumB,test +MB-4908,CLAUDIN_SUBTYPE,Her2,0.0039398037,LumB,LumB,test +MB-4908,CLAUDIN_SUBTYPE,LumA,0.0053106635,LumB,LumB,test +MB-4908,CLAUDIN_SUBTYPE,LumB,0.98394036,LumB,LumB,test +MB-4908,CLAUDIN_SUBTYPE,NC,0.0014650807,LumB,LumB,test +MB-4908,CLAUDIN_SUBTYPE,Normal,0.00062478875,LumB,LumB,test +MB-4908,CLAUDIN_SUBTYPE,claudin-low,0.00076068804,LumB,LumB,test +MB-5628,CLAUDIN_SUBTYPE,Basal,0.012981304,LumB,LumB,test +MB-5628,CLAUDIN_SUBTYPE,Her2,0.0028434508,LumB,LumB,test +MB-5628,CLAUDIN_SUBTYPE,LumA,0.03325409,LumB,LumB,test +MB-5628,CLAUDIN_SUBTYPE,LumB,0.94304246,LumB,LumB,test +MB-5628,CLAUDIN_SUBTYPE,NC,0.0037866984,LumB,LumB,test +MB-5628,CLAUDIN_SUBTYPE,Normal,0.002556737,LumB,LumB,test +MB-5628,CLAUDIN_SUBTYPE,claudin-low,0.0015352007,LumB,LumB,test +MB-3381,CLAUDIN_SUBTYPE,Basal,0.0020334984,LumA,LumA,test +MB-3381,CLAUDIN_SUBTYPE,Her2,0.00066026,LumA,LumA,test +MB-3381,CLAUDIN_SUBTYPE,LumA,0.97903836,LumA,LumA,test +MB-3381,CLAUDIN_SUBTYPE,LumB,0.0017459794,LumA,LumA,test +MB-3381,CLAUDIN_SUBTYPE,NC,0.0026210693,LumA,LumA,test +MB-3381,CLAUDIN_SUBTYPE,Normal,0.009385565,LumA,LumA,test +MB-3381,CLAUDIN_SUBTYPE,claudin-low,0.00451523,LumA,LumA,test +MB-7011,CLAUDIN_SUBTYPE,Basal,0.0033411589,LumB,LumB,test +MB-7011,CLAUDIN_SUBTYPE,Her2,0.0011834987,LumB,LumB,test +MB-7011,CLAUDIN_SUBTYPE,LumA,9.7521144e-05,LumB,LumB,test +MB-7011,CLAUDIN_SUBTYPE,LumB,0.9949411,LumB,LumB,test +MB-7011,CLAUDIN_SUBTYPE,NC,0.0002659362,LumB,LumB,test +MB-7011,CLAUDIN_SUBTYPE,Normal,7.072481e-05,LumB,LumB,test +MB-7011,CLAUDIN_SUBTYPE,claudin-low,0.00010008585,LumB,LumB,test +MB-4640,CLAUDIN_SUBTYPE,Basal,0.045325782,Her2,Her2,test +MB-4640,CLAUDIN_SUBTYPE,Her2,0.793973,Her2,Her2,test +MB-4640,CLAUDIN_SUBTYPE,LumA,0.013347938,Her2,Her2,test +MB-4640,CLAUDIN_SUBTYPE,LumB,0.06833189,Her2,Her2,test +MB-4640,CLAUDIN_SUBTYPE,NC,0.012738866,Her2,Her2,test +MB-4640,CLAUDIN_SUBTYPE,Normal,0.023476625,Her2,Her2,test +MB-4640,CLAUDIN_SUBTYPE,claudin-low,0.04280572,Her2,Her2,test +MB-0666,CLAUDIN_SUBTYPE,Basal,0.021183776,LumA,LumB,test +MB-0666,CLAUDIN_SUBTYPE,Her2,0.019537766,LumA,LumB,test +MB-0666,CLAUDIN_SUBTYPE,LumA,0.33781692,LumA,LumB,test +MB-0666,CLAUDIN_SUBTYPE,LumB,0.5680305,LumA,LumB,test +MB-0666,CLAUDIN_SUBTYPE,NC,0.019041568,LumA,LumB,test +MB-0666,CLAUDIN_SUBTYPE,Normal,0.023204282,LumA,LumB,test +MB-0666,CLAUDIN_SUBTYPE,claudin-low,0.011185225,LumA,LumB,test +MB-4059,CLAUDIN_SUBTYPE,Basal,0.003601682,Normal,LumA,test +MB-4059,CLAUDIN_SUBTYPE,Her2,0.0029606416,Normal,LumA,test +MB-4059,CLAUDIN_SUBTYPE,LumA,0.8900589,Normal,LumA,test +MB-4059,CLAUDIN_SUBTYPE,LumB,0.002183746,Normal,LumA,test +MB-4059,CLAUDIN_SUBTYPE,NC,0.0069050374,Normal,LumA,test +MB-4059,CLAUDIN_SUBTYPE,Normal,0.09197775,Normal,LumA,test +MB-4059,CLAUDIN_SUBTYPE,claudin-low,0.002312408,Normal,LumA,test +MB-7150,CLAUDIN_SUBTYPE,Basal,0.0064166198,LumB,LumB,test +MB-7150,CLAUDIN_SUBTYPE,Her2,0.0025905133,LumB,LumB,test +MB-7150,CLAUDIN_SUBTYPE,LumA,0.005174778,LumB,LumB,test +MB-7150,CLAUDIN_SUBTYPE,LumB,0.9823282,LumB,LumB,test +MB-7150,CLAUDIN_SUBTYPE,NC,0.001839606,LumB,LumB,test +MB-7150,CLAUDIN_SUBTYPE,Normal,0.0008020947,LumB,LumB,test +MB-7150,CLAUDIN_SUBTYPE,claudin-low,0.0008481796,LumB,LumB,test +MB-7262,CLAUDIN_SUBTYPE,Basal,0.013179999,Her2,Her2,test +MB-7262,CLAUDIN_SUBTYPE,Her2,0.9484334,Her2,Her2,test +MB-7262,CLAUDIN_SUBTYPE,LumA,0.00031268035,Her2,Her2,test +MB-7262,CLAUDIN_SUBTYPE,LumB,0.03143319,Her2,Her2,test +MB-7262,CLAUDIN_SUBTYPE,NC,0.00090116024,Her2,Her2,test +MB-7262,CLAUDIN_SUBTYPE,Normal,0.004326943,Her2,Her2,test +MB-7262,CLAUDIN_SUBTYPE,claudin-low,0.0014125666,Her2,Her2,test +MB-0133,CLAUDIN_SUBTYPE,Basal,0.00045371466,LumA,LumA,test +MB-0133,CLAUDIN_SUBTYPE,Her2,0.0005848446,LumA,LumA,test +MB-0133,CLAUDIN_SUBTYPE,LumA,0.97884643,LumA,LumA,test +MB-0133,CLAUDIN_SUBTYPE,LumB,0.0014364616,LumA,LumA,test +MB-0133,CLAUDIN_SUBTYPE,NC,0.0013645435,LumA,LumA,test +MB-0133,CLAUDIN_SUBTYPE,Normal,0.017095944,LumA,LumA,test +MB-0133,CLAUDIN_SUBTYPE,claudin-low,0.00021816751,LumA,LumA,test +MB-4343,CLAUDIN_SUBTYPE,Basal,0.47470322,Her2,Basal,test +MB-4343,CLAUDIN_SUBTYPE,Her2,0.17440778,Her2,Basal,test +MB-4343,CLAUDIN_SUBTYPE,LumA,0.06775188,Her2,Basal,test +MB-4343,CLAUDIN_SUBTYPE,LumB,0.02564412,Her2,Basal,test +MB-4343,CLAUDIN_SUBTYPE,NC,0.022474827,Her2,Basal,test +MB-4343,CLAUDIN_SUBTYPE,Normal,0.08448548,Her2,Basal,test +MB-4343,CLAUDIN_SUBTYPE,claudin-low,0.15053263,Her2,Basal,test +MB-4015,CLAUDIN_SUBTYPE,Basal,0.010890819,Her2,Her2,test +MB-4015,CLAUDIN_SUBTYPE,Her2,0.9744804,Her2,Her2,test +MB-4015,CLAUDIN_SUBTYPE,LumA,0.0005409653,Her2,Her2,test +MB-4015,CLAUDIN_SUBTYPE,LumB,0.0034801434,Her2,Her2,test +MB-4015,CLAUDIN_SUBTYPE,NC,0.0008652594,Her2,Her2,test +MB-4015,CLAUDIN_SUBTYPE,Normal,0.0069617536,Her2,Her2,test +MB-4015,CLAUDIN_SUBTYPE,claudin-low,0.002780637,Her2,Her2,test +MB-2708,CLAUDIN_SUBTYPE,Basal,0.0040587,LumB,LumA,test +MB-2708,CLAUDIN_SUBTYPE,Her2,0.0021809204,LumB,LumA,test +MB-2708,CLAUDIN_SUBTYPE,LumA,0.7978747,LumB,LumA,test +MB-2708,CLAUDIN_SUBTYPE,LumB,0.18160287,LumB,LumA,test +MB-2708,CLAUDIN_SUBTYPE,NC,0.00471715,LumB,LumA,test +MB-2708,CLAUDIN_SUBTYPE,Normal,0.007210988,LumB,LumA,test +MB-2708,CLAUDIN_SUBTYPE,claudin-low,0.0023546047,LumB,LumA,test +MB-3462,CLAUDIN_SUBTYPE,Basal,0.0016569006,LumA,LumA,test +MB-3462,CLAUDIN_SUBTYPE,Her2,0.0014245388,LumA,LumA,test +MB-3462,CLAUDIN_SUBTYPE,LumA,0.93998325,LumA,LumA,test +MB-3462,CLAUDIN_SUBTYPE,LumB,0.0028402456,LumA,LumA,test +MB-3462,CLAUDIN_SUBTYPE,NC,0.0041087233,LumA,LumA,test +MB-3462,CLAUDIN_SUBTYPE,Normal,0.049085792,LumA,LumA,test +MB-3462,CLAUDIN_SUBTYPE,claudin-low,0.00090061233,LumA,LumA,test +MB-5383,CLAUDIN_SUBTYPE,Basal,0.026178962,LumA,LumB,test +MB-5383,CLAUDIN_SUBTYPE,Her2,0.013180049,LumA,LumB,test +MB-5383,CLAUDIN_SUBTYPE,LumA,0.07154327,LumA,LumB,test +MB-5383,CLAUDIN_SUBTYPE,LumB,0.8574958,LumA,LumB,test +MB-5383,CLAUDIN_SUBTYPE,NC,0.012685523,LumA,LumB,test +MB-5383,CLAUDIN_SUBTYPE,Normal,0.012509056,LumA,LumB,test +MB-5383,CLAUDIN_SUBTYPE,claudin-low,0.0064073335,LumA,LumB,test +MB-7294,CLAUDIN_SUBTYPE,Basal,0.013935004,LumB,LumB,test +MB-7294,CLAUDIN_SUBTYPE,Her2,0.0025501708,LumB,LumB,test +MB-7294,CLAUDIN_SUBTYPE,LumA,0.1432904,LumB,LumB,test +MB-7294,CLAUDIN_SUBTYPE,LumB,0.82445294,LumB,LumB,test +MB-7294,CLAUDIN_SUBTYPE,NC,0.006747572,LumB,LumB,test +MB-7294,CLAUDIN_SUBTYPE,Normal,0.0070230197,LumB,LumB,test +MB-7294,CLAUDIN_SUBTYPE,claudin-low,0.0020008762,LumB,LumB,test +MB-2833,CLAUDIN_SUBTYPE,Basal,0.016667495,claudin-low,claudin-low,test +MB-2833,CLAUDIN_SUBTYPE,Her2,0.0007512599,claudin-low,claudin-low,test +MB-2833,CLAUDIN_SUBTYPE,LumA,0.0031730556,claudin-low,claudin-low,test +MB-2833,CLAUDIN_SUBTYPE,LumB,6.964962e-05,claudin-low,claudin-low,test +MB-2833,CLAUDIN_SUBTYPE,NC,0.00051642297,claudin-low,claudin-low,test +MB-2833,CLAUDIN_SUBTYPE,Normal,0.00010766187,claudin-low,claudin-low,test +MB-2833,CLAUDIN_SUBTYPE,claudin-low,0.9787145,claudin-low,claudin-low,test +MB-0419,CLAUDIN_SUBTYPE,Basal,0.0048514134,LumA,LumA,test +MB-0419,CLAUDIN_SUBTYPE,Her2,0.0031569623,LumA,LumA,test +MB-0419,CLAUDIN_SUBTYPE,LumA,0.7339591,LumA,LumA,test +MB-0419,CLAUDIN_SUBTYPE,LumB,0.24074769,LumA,LumA,test +MB-0419,CLAUDIN_SUBTYPE,NC,0.0056522866,LumA,LumA,test +MB-0419,CLAUDIN_SUBTYPE,Normal,0.009660609,LumA,LumA,test +MB-0419,CLAUDIN_SUBTYPE,claudin-low,0.0019718553,LumA,LumA,test +MB-6050,CLAUDIN_SUBTYPE,Basal,0.0017174709,LumA,LumA,test +MB-6050,CLAUDIN_SUBTYPE,Her2,0.0008713278,LumA,LumA,test +MB-6050,CLAUDIN_SUBTYPE,LumA,0.9612962,LumA,LumA,test +MB-6050,CLAUDIN_SUBTYPE,LumB,0.009326928,LumA,LumA,test +MB-6050,CLAUDIN_SUBTYPE,NC,0.002598183,LumA,LumA,test +MB-6050,CLAUDIN_SUBTYPE,Normal,0.023775762,LumA,LumA,test +MB-6050,CLAUDIN_SUBTYPE,claudin-low,0.00041405656,LumA,LumA,test +MB-7092,CLAUDIN_SUBTYPE,Basal,0.09593538,Her2,LumB,test +MB-7092,CLAUDIN_SUBTYPE,Her2,0.12242819,Her2,LumB,test +MB-7092,CLAUDIN_SUBTYPE,LumA,0.11289457,Her2,LumB,test +MB-7092,CLAUDIN_SUBTYPE,LumB,0.44667622,Her2,LumB,test +MB-7092,CLAUDIN_SUBTYPE,NC,0.039782666,Her2,LumB,test +MB-7092,CLAUDIN_SUBTYPE,Normal,0.16539073,Her2,LumB,test +MB-7092,CLAUDIN_SUBTYPE,claudin-low,0.0168923,Her2,LumB,test +MB-0114,CLAUDIN_SUBTYPE,Basal,0.0022584063,LumA,LumA,test +MB-0114,CLAUDIN_SUBTYPE,Her2,0.002160519,LumA,LumA,test +MB-0114,CLAUDIN_SUBTYPE,LumA,0.9623465,LumA,LumA,test +MB-0114,CLAUDIN_SUBTYPE,LumB,0.010733846,LumA,LumA,test +MB-0114,CLAUDIN_SUBTYPE,NC,0.004094921,LumA,LumA,test +MB-0114,CLAUDIN_SUBTYPE,Normal,0.016599985,LumA,LumA,test +MB-0114,CLAUDIN_SUBTYPE,claudin-low,0.0018058723,LumA,LumA,test +MB-7079,CLAUDIN_SUBTYPE,Basal,0.0065553426,claudin-low,claudin-low,test +MB-7079,CLAUDIN_SUBTYPE,Her2,0.00013380895,claudin-low,claudin-low,test +MB-7079,CLAUDIN_SUBTYPE,LumA,0.0007512974,claudin-low,claudin-low,test +MB-7079,CLAUDIN_SUBTYPE,LumB,6.7275632e-06,claudin-low,claudin-low,test +MB-7079,CLAUDIN_SUBTYPE,NC,9.0018526e-05,claudin-low,claudin-low,test +MB-7079,CLAUDIN_SUBTYPE,Normal,1.1655847e-05,claudin-low,claudin-low,test +MB-7079,CLAUDIN_SUBTYPE,claudin-low,0.99245113,claudin-low,claudin-low,test +MB-0425,CLAUDIN_SUBTYPE,Basal,0.0048174113,LumA,LumA,test +MB-0425,CLAUDIN_SUBTYPE,Her2,0.0024959578,LumA,LumA,test +MB-0425,CLAUDIN_SUBTYPE,LumA,0.86893785,LumA,LumA,test +MB-0425,CLAUDIN_SUBTYPE,LumB,0.09028413,LumA,LumA,test +MB-0425,CLAUDIN_SUBTYPE,NC,0.007825845,LumA,LumA,test +MB-0425,CLAUDIN_SUBTYPE,Normal,0.023765737,LumA,LumA,test +MB-0425,CLAUDIN_SUBTYPE,claudin-low,0.001873053,LumA,LumA,test +MB-0285,CLAUDIN_SUBTYPE,Basal,0.015996402,claudin-low,claudin-low,test +MB-0285,CLAUDIN_SUBTYPE,Her2,0.00037597463,claudin-low,claudin-low,test +MB-0285,CLAUDIN_SUBTYPE,LumA,0.002935055,claudin-low,claudin-low,test +MB-0285,CLAUDIN_SUBTYPE,LumB,4.9373895e-05,claudin-low,claudin-low,test +MB-0285,CLAUDIN_SUBTYPE,NC,0.00044300893,claudin-low,claudin-low,test +MB-0285,CLAUDIN_SUBTYPE,Normal,8.946197e-05,claudin-low,claudin-low,test +MB-0285,CLAUDIN_SUBTYPE,claudin-low,0.9801107,claudin-low,claudin-low,test +MB-7164,CLAUDIN_SUBTYPE,Basal,0.0008814891,LumA,LumA,test +MB-7164,CLAUDIN_SUBTYPE,Her2,0.0007854757,LumA,LumA,test +MB-7164,CLAUDIN_SUBTYPE,LumA,0.96292347,LumA,LumA,test +MB-7164,CLAUDIN_SUBTYPE,LumB,0.0026790085,LumA,LumA,test +MB-7164,CLAUDIN_SUBTYPE,NC,0.0027690595,LumA,LumA,test +MB-7164,CLAUDIN_SUBTYPE,Normal,0.029501902,LumA,LumA,test +MB-7164,CLAUDIN_SUBTYPE,claudin-low,0.00045956974,LumA,LumA,test +MB-2786,CLAUDIN_SUBTYPE,Basal,0.02980681,LumA,LumB,test +MB-2786,CLAUDIN_SUBTYPE,Her2,0.022112958,LumA,LumB,test +MB-2786,CLAUDIN_SUBTYPE,LumA,0.3055593,LumA,LumB,test +MB-2786,CLAUDIN_SUBTYPE,LumB,0.585493,LumA,LumB,test +MB-2786,CLAUDIN_SUBTYPE,NC,0.019474203,LumA,LumB,test +MB-2786,CLAUDIN_SUBTYPE,Normal,0.028324448,LumA,LumB,test +MB-2786,CLAUDIN_SUBTYPE,claudin-low,0.009229281,LumA,LumB,test +MB-4322,CLAUDIN_SUBTYPE,Basal,0.0022297003,LumA,LumA,test +MB-4322,CLAUDIN_SUBTYPE,Her2,0.0030350136,LumA,LumA,test +MB-4322,CLAUDIN_SUBTYPE,LumA,0.9531283,LumA,LumA,test +MB-4322,CLAUDIN_SUBTYPE,LumB,0.0106164375,LumA,LumA,test +MB-4322,CLAUDIN_SUBTYPE,NC,0.0048646657,LumA,LumA,test +MB-4322,CLAUDIN_SUBTYPE,Normal,0.024548743,LumA,LumA,test +MB-4322,CLAUDIN_SUBTYPE,claudin-low,0.0015771028,LumA,LumA,test +MB-4929,CLAUDIN_SUBTYPE,Basal,0.036082525,Her2,LumA,test +MB-4929,CLAUDIN_SUBTYPE,Her2,0.35908023,Her2,LumA,test +MB-4929,CLAUDIN_SUBTYPE,LumA,0.37693068,Her2,LumA,test +MB-4929,CLAUDIN_SUBTYPE,LumB,0.09665409,Her2,LumA,test +MB-4929,CLAUDIN_SUBTYPE,NC,0.028376725,Her2,LumA,test +MB-4929,CLAUDIN_SUBTYPE,Normal,0.05045343,Her2,LumA,test +MB-4929,CLAUDIN_SUBTYPE,claudin-low,0.05242229,Her2,LumA,test +MB-3049,CLAUDIN_SUBTYPE,Basal,0.009222006,LumA,LumA,test +MB-3049,CLAUDIN_SUBTYPE,Her2,0.0037532349,LumA,LumA,test +MB-3049,CLAUDIN_SUBTYPE,LumA,0.916257,LumA,LumA,test +MB-3049,CLAUDIN_SUBTYPE,LumB,0.0061381236,LumA,LumA,test +MB-3049,CLAUDIN_SUBTYPE,NC,0.011044999,LumA,LumA,test +MB-3049,CLAUDIN_SUBTYPE,Normal,0.03306588,LumA,LumA,test +MB-3049,CLAUDIN_SUBTYPE,claudin-low,0.020518873,LumA,LumA,test +MB-4797,CLAUDIN_SUBTYPE,Basal,0.006543896,LumA,LumA,test +MB-4797,CLAUDIN_SUBTYPE,Her2,0.002287037,LumA,LumA,test +MB-4797,CLAUDIN_SUBTYPE,LumA,0.8497937,LumA,LumA,test +MB-4797,CLAUDIN_SUBTYPE,LumB,0.10440446,LumA,LumA,test +MB-4797,CLAUDIN_SUBTYPE,NC,0.008651719,LumA,LumA,test +MB-4797,CLAUDIN_SUBTYPE,Normal,0.02639117,LumA,LumA,test +MB-4797,CLAUDIN_SUBTYPE,claudin-low,0.0019281027,LumA,LumA,test +MB-0324,CLAUDIN_SUBTYPE,Basal,0.01106631,LumA,LumB,test +MB-0324,CLAUDIN_SUBTYPE,Her2,0.0056499275,LumA,LumB,test +MB-0324,CLAUDIN_SUBTYPE,LumA,0.10007352,LumA,LumB,test +MB-0324,CLAUDIN_SUBTYPE,LumB,0.86878407,LumA,LumB,test +MB-0324,CLAUDIN_SUBTYPE,NC,0.0062801857,LumA,LumB,test +MB-0324,CLAUDIN_SUBTYPE,Normal,0.005333651,LumA,LumB,test +MB-0324,CLAUDIN_SUBTYPE,claudin-low,0.0028124144,LumA,LumB,test +MB-4701,CLAUDIN_SUBTYPE,Basal,1.7004955e-05,LumA,LumA,test +MB-4701,CLAUDIN_SUBTYPE,Her2,1.22426045e-05,LumA,LumA,test +MB-4701,CLAUDIN_SUBTYPE,LumA,0.999009,LumA,LumA,test +MB-4701,CLAUDIN_SUBTYPE,LumB,0.00011581094,LumA,LumA,test +MB-4701,CLAUDIN_SUBTYPE,NC,8.0239406e-05,LumA,LumA,test +MB-4701,CLAUDIN_SUBTYPE,Normal,0.0007484768,LumA,LumA,test +MB-4701,CLAUDIN_SUBTYPE,claudin-low,1.7140028e-05,LumA,LumA,test +MB-0244,CLAUDIN_SUBTYPE,Basal,0.016717277,Normal,LumA,test +MB-0244,CLAUDIN_SUBTYPE,Her2,0.008711012,Normal,LumA,test +MB-0244,CLAUDIN_SUBTYPE,LumA,0.80767983,Normal,LumA,test +MB-0244,CLAUDIN_SUBTYPE,LumB,0.0024268886,Normal,LumA,test +MB-0244,CLAUDIN_SUBTYPE,NC,0.017965944,Normal,LumA,test +MB-0244,CLAUDIN_SUBTYPE,Normal,0.11448215,Normal,LumA,test +MB-0244,CLAUDIN_SUBTYPE,claudin-low,0.032016896,Normal,LumA,test +MB-4681,CLAUDIN_SUBTYPE,Basal,0.00028730012,LumA,LumA,test +MB-4681,CLAUDIN_SUBTYPE,Her2,0.0003329631,LumA,LumA,test +MB-4681,CLAUDIN_SUBTYPE,LumA,0.9890497,LumA,LumA,test +MB-4681,CLAUDIN_SUBTYPE,LumB,0.000996601,LumA,LumA,test +MB-4681,CLAUDIN_SUBTYPE,NC,0.0010733826,LumA,LumA,test +MB-4681,CLAUDIN_SUBTYPE,Normal,0.007978269,LumA,LumA,test +MB-4681,CLAUDIN_SUBTYPE,claudin-low,0.00028170884,LumA,LumA,test +MB-7201,CLAUDIN_SUBTYPE,Basal,0.13286604,claudin-low,claudin-low,test +MB-7201,CLAUDIN_SUBTYPE,Her2,0.2255149,claudin-low,claudin-low,test +MB-7201,CLAUDIN_SUBTYPE,LumA,0.01259813,claudin-low,claudin-low,test +MB-7201,CLAUDIN_SUBTYPE,LumB,0.002975394,claudin-low,claudin-low,test +MB-7201,CLAUDIN_SUBTYPE,NC,0.00544952,claudin-low,claudin-low,test +MB-7201,CLAUDIN_SUBTYPE,Normal,0.0066124215,claudin-low,claudin-low,test +MB-7201,CLAUDIN_SUBTYPE,claudin-low,0.6139836,claudin-low,claudin-low,test +MB-2556,CLAUDIN_SUBTYPE,Basal,0.019965198,claudin-low,claudin-low,test +MB-2556,CLAUDIN_SUBTYPE,Her2,0.0005793484,claudin-low,claudin-low,test +MB-2556,CLAUDIN_SUBTYPE,LumA,0.009504317,claudin-low,claudin-low,test +MB-2556,CLAUDIN_SUBTYPE,LumB,7.7138386e-05,claudin-low,claudin-low,test +MB-2556,CLAUDIN_SUBTYPE,NC,0.0007904524,claudin-low,claudin-low,test +MB-2556,CLAUDIN_SUBTYPE,Normal,0.00022169598,claudin-low,claudin-low,test +MB-2556,CLAUDIN_SUBTYPE,claudin-low,0.9688618,claudin-low,claudin-low,test +MB-5451,CLAUDIN_SUBTYPE,Basal,0.00019718484,LumA,LumA,test +MB-5451,CLAUDIN_SUBTYPE,Her2,0.00016448187,LumA,LumA,test +MB-5451,CLAUDIN_SUBTYPE,LumA,0.9903661,LumA,LumA,test +MB-5451,CLAUDIN_SUBTYPE,LumB,0.000910582,LumA,LumA,test +MB-5451,CLAUDIN_SUBTYPE,NC,0.00085349364,LumA,LumA,test +MB-5451,CLAUDIN_SUBTYPE,Normal,0.0073515014,LumA,LumA,test +MB-5451,CLAUDIN_SUBTYPE,claudin-low,0.00015663628,LumA,LumA,test +MB-6071,CLAUDIN_SUBTYPE,Basal,0.0063935183,LumA,LumA,test +MB-6071,CLAUDIN_SUBTYPE,Her2,0.0044436455,LumA,LumA,test +MB-6071,CLAUDIN_SUBTYPE,LumA,0.91219616,LumA,LumA,test +MB-6071,CLAUDIN_SUBTYPE,LumB,0.041640952,LumA,LumA,test +MB-6071,CLAUDIN_SUBTYPE,NC,0.008643396,LumA,LumA,test +MB-6071,CLAUDIN_SUBTYPE,Normal,0.01919162,LumA,LumA,test +MB-6071,CLAUDIN_SUBTYPE,claudin-low,0.0074907434,LumA,LumA,test +MB-7121,CLAUDIN_SUBTYPE,Basal,0.28942513,claudin-low,claudin-low,test +MB-7121,CLAUDIN_SUBTYPE,Her2,0.0119283255,claudin-low,claudin-low,test +MB-7121,CLAUDIN_SUBTYPE,LumA,0.012078179,claudin-low,claudin-low,test +MB-7121,CLAUDIN_SUBTYPE,LumB,0.0010380081,claudin-low,claudin-low,test +MB-7121,CLAUDIN_SUBTYPE,NC,0.004173852,claudin-low,claudin-low,test +MB-7121,CLAUDIN_SUBTYPE,Normal,0.006880722,claudin-low,claudin-low,test +MB-7121,CLAUDIN_SUBTYPE,claudin-low,0.6744758,claudin-low,claudin-low,test +MB-4691,CLAUDIN_SUBTYPE,Basal,0.0004175498,LumA,LumA,test +MB-4691,CLAUDIN_SUBTYPE,Her2,0.00031894146,LumA,LumA,test +MB-4691,CLAUDIN_SUBTYPE,LumA,0.99012774,LumA,LumA,test +MB-4691,CLAUDIN_SUBTYPE,LumB,0.001796842,LumA,LumA,test +MB-4691,CLAUDIN_SUBTYPE,NC,0.001056201,LumA,LumA,test +MB-4691,CLAUDIN_SUBTYPE,Normal,0.005916056,LumA,LumA,test +MB-4691,CLAUDIN_SUBTYPE,claudin-low,0.00036674208,LumA,LumA,test +MB-0234,CLAUDIN_SUBTYPE,Basal,0.013009974,LumB,LumB,test +MB-0234,CLAUDIN_SUBTYPE,Her2,0.0025477514,LumB,LumB,test +MB-0234,CLAUDIN_SUBTYPE,LumA,0.4572835,LumB,LumB,test +MB-0234,CLAUDIN_SUBTYPE,LumB,0.49925724,LumB,LumB,test +MB-0234,CLAUDIN_SUBTYPE,NC,0.009447233,LumB,LumB,test +MB-0234,CLAUDIN_SUBTYPE,Normal,0.016230559,LumB,LumB,test +MB-0234,CLAUDIN_SUBTYPE,claudin-low,0.0022236882,LumB,LumB,test +MB-6017,CLAUDIN_SUBTYPE,Basal,0.00013364745,LumA,LumA,test +MB-6017,CLAUDIN_SUBTYPE,Her2,0.000116440715,LumA,LumA,test +MB-6017,CLAUDIN_SUBTYPE,LumA,0.9919682,LumA,LumA,test +MB-6017,CLAUDIN_SUBTYPE,LumB,0.0005847468,LumA,LumA,test +MB-6017,CLAUDIN_SUBTYPE,NC,0.0006034885,LumA,LumA,test +MB-6017,CLAUDIN_SUBTYPE,Normal,0.006500447,LumA,LumA,test +MB-6017,CLAUDIN_SUBTYPE,claudin-low,9.311393e-05,LumA,LumA,test +MB-4008,CLAUDIN_SUBTYPE,Basal,0.00715301,LumB,LumB,test +MB-4008,CLAUDIN_SUBTYPE,Her2,0.0012020504,LumB,LumB,test +MB-4008,CLAUDIN_SUBTYPE,LumA,0.016381906,LumB,LumB,test +MB-4008,CLAUDIN_SUBTYPE,LumB,0.9701892,LumB,LumB,test +MB-4008,CLAUDIN_SUBTYPE,NC,0.0026120257,LumB,LumB,test +MB-4008,CLAUDIN_SUBTYPE,Normal,0.0015602786,LumB,LumB,test +MB-4008,CLAUDIN_SUBTYPE,claudin-low,0.00090146903,LumB,LumB,test +MB-0542,CLAUDIN_SUBTYPE,Basal,0.18582183,Normal,LumA,test +MB-0542,CLAUDIN_SUBTYPE,Her2,0.042816397,Normal,LumA,test +MB-0542,CLAUDIN_SUBTYPE,LumA,0.3383907,Normal,LumA,test +MB-0542,CLAUDIN_SUBTYPE,LumB,0.053271253,Normal,LumA,test +MB-0542,CLAUDIN_SUBTYPE,NC,0.058939602,Normal,LumA,test +MB-0542,CLAUDIN_SUBTYPE,Normal,0.21818122,Normal,LumA,test +MB-0542,CLAUDIN_SUBTYPE,claudin-low,0.102579,Normal,LumA,test +MB-5563,CLAUDIN_SUBTYPE,Basal,2.8127823e-05,LumA,LumA,test +MB-5563,CLAUDIN_SUBTYPE,Her2,2.4740613e-05,LumA,LumA,test +MB-5563,CLAUDIN_SUBTYPE,LumA,0.9978269,LumA,LumA,test +MB-5563,CLAUDIN_SUBTYPE,LumB,0.00015803134,LumA,LumA,test +MB-5563,CLAUDIN_SUBTYPE,NC,0.00016231148,LumA,LumA,test +MB-5563,CLAUDIN_SUBTYPE,Normal,0.0017752199,LumA,LumA,test +MB-5563,CLAUDIN_SUBTYPE,claudin-low,2.4653655e-05,LumA,LumA,test +MB-4945,CLAUDIN_SUBTYPE,Basal,0.92402095,Basal,Basal,test +MB-4945,CLAUDIN_SUBTYPE,Her2,0.01144419,Basal,Basal,test +MB-4945,CLAUDIN_SUBTYPE,LumA,0.003552352,Basal,Basal,test +MB-4945,CLAUDIN_SUBTYPE,LumB,0.0062211314,Basal,Basal,test +MB-4945,CLAUDIN_SUBTYPE,NC,0.0032963855,Basal,Basal,test +MB-4945,CLAUDIN_SUBTYPE,Normal,0.030182417,Basal,Basal,test +MB-4945,CLAUDIN_SUBTYPE,claudin-low,0.021282477,Basal,Basal,test +MB-0081,CLAUDIN_SUBTYPE,Basal,0.26086026,claudin-low,claudin-low,test +MB-0081,CLAUDIN_SUBTYPE,Her2,0.16597845,claudin-low,claudin-low,test +MB-0081,CLAUDIN_SUBTYPE,LumA,0.060808122,claudin-low,claudin-low,test +MB-0081,CLAUDIN_SUBTYPE,LumB,0.026617011,claudin-low,claudin-low,test +MB-0081,CLAUDIN_SUBTYPE,NC,0.03393925,claudin-low,claudin-low,test +MB-0081,CLAUDIN_SUBTYPE,Normal,0.06793986,claudin-low,claudin-low,test +MB-0081,CLAUDIN_SUBTYPE,claudin-low,0.38385698,claudin-low,claudin-low,test +MB-0106,CLAUDIN_SUBTYPE,Basal,0.0007867359,LumA,LumA,test +MB-0106,CLAUDIN_SUBTYPE,Her2,0.0007449476,LumA,LumA,test +MB-0106,CLAUDIN_SUBTYPE,LumA,0.8885387,LumA,LumA,test +MB-0106,CLAUDIN_SUBTYPE,LumB,0.00058893545,LumA,LumA,test +MB-0106,CLAUDIN_SUBTYPE,NC,0.002413269,LumA,LumA,test +MB-0106,CLAUDIN_SUBTYPE,Normal,0.10672483,LumA,LumA,test +MB-0106,CLAUDIN_SUBTYPE,claudin-low,0.00020267171,LumA,LumA,test +MB-5049,CLAUDIN_SUBTYPE,Basal,0.008915669,LumB,LumA,test +MB-5049,CLAUDIN_SUBTYPE,Her2,0.0030393503,LumB,LumA,test +MB-5049,CLAUDIN_SUBTYPE,LumA,0.66901016,LumB,LumA,test +MB-5049,CLAUDIN_SUBTYPE,LumB,0.29405984,LumB,LumA,test +MB-5049,CLAUDIN_SUBTYPE,NC,0.007853609,LumB,LumA,test +MB-5049,CLAUDIN_SUBTYPE,Normal,0.014904582,LumB,LumA,test +MB-5049,CLAUDIN_SUBTYPE,claudin-low,0.002216795,LumB,LumA,test +MB-0442,CLAUDIN_SUBTYPE,Basal,0.018254837,claudin-low,claudin-low,test +MB-0442,CLAUDIN_SUBTYPE,Her2,0.0007486542,claudin-low,claudin-low,test +MB-0442,CLAUDIN_SUBTYPE,LumA,0.035000745,claudin-low,claudin-low,test +MB-0442,CLAUDIN_SUBTYPE,LumB,8.8414694e-05,claudin-low,claudin-low,test +MB-0442,CLAUDIN_SUBTYPE,NC,0.0013256494,claudin-low,claudin-low,test +MB-0442,CLAUDIN_SUBTYPE,Normal,0.0005201884,claudin-low,claudin-low,test +MB-0442,CLAUDIN_SUBTYPE,claudin-low,0.9440615,claudin-low,claudin-low,test +MB-0534,CLAUDIN_SUBTYPE,Basal,0.035875645,claudin-low,Normal,test +MB-0534,CLAUDIN_SUBTYPE,Her2,0.02943975,claudin-low,Normal,test +MB-0534,CLAUDIN_SUBTYPE,LumA,0.03144266,claudin-low,Normal,test +MB-0534,CLAUDIN_SUBTYPE,LumB,0.0007051336,claudin-low,Normal,test +MB-0534,CLAUDIN_SUBTYPE,NC,0.006620483,claudin-low,Normal,test +MB-0534,CLAUDIN_SUBTYPE,Normal,0.8934994,claudin-low,Normal,test +MB-0534,CLAUDIN_SUBTYPE,claudin-low,0.002416972,claudin-low,Normal,test +MB-2721,CLAUDIN_SUBTYPE,Basal,0.0027118893,LumA,LumA,test +MB-2721,CLAUDIN_SUBTYPE,Her2,0.0016617366,LumA,LumA,test +MB-2721,CLAUDIN_SUBTYPE,LumA,0.923096,LumA,LumA,test +MB-2721,CLAUDIN_SUBTYPE,LumB,0.050816685,LumA,LumA,test +MB-2721,CLAUDIN_SUBTYPE,NC,0.004834802,LumA,LumA,test +MB-2721,CLAUDIN_SUBTYPE,Normal,0.015699524,LumA,LumA,test +MB-2721,CLAUDIN_SUBTYPE,claudin-low,0.0011794304,LumA,LumA,test +MB-7088,CLAUDIN_SUBTYPE,Basal,0.11950952,Her2,LumB,test +MB-7088,CLAUDIN_SUBTYPE,Her2,0.21710758,Her2,LumB,test +MB-7088,CLAUDIN_SUBTYPE,LumA,0.0099061,Her2,LumB,test +MB-7088,CLAUDIN_SUBTYPE,LumB,0.6021679,Her2,LumB,test +MB-7088,CLAUDIN_SUBTYPE,NC,0.013182743,Her2,LumB,test +MB-7088,CLAUDIN_SUBTYPE,Normal,0.0279525,Her2,LumB,test +MB-7088,CLAUDIN_SUBTYPE,claudin-low,0.010173694,Her2,LumB,test +MB-6019,CLAUDIN_SUBTYPE,Basal,0.17273197,Normal,Her2,test +MB-6019,CLAUDIN_SUBTYPE,Her2,0.40139306,Normal,Her2,test +MB-6019,CLAUDIN_SUBTYPE,LumA,0.037800174,Normal,Her2,test +MB-6019,CLAUDIN_SUBTYPE,LumB,0.03446432,Normal,Her2,test +MB-6019,CLAUDIN_SUBTYPE,NC,0.025530364,Normal,Her2,test +MB-6019,CLAUDIN_SUBTYPE,Normal,0.3075011,Normal,Her2,test +MB-6019,CLAUDIN_SUBTYPE,claudin-low,0.020579034,Normal,Her2,test +MB-0377,CLAUDIN_SUBTYPE,Basal,0.097247094,LumA,Normal,test +MB-0377,CLAUDIN_SUBTYPE,Her2,0.042718947,LumA,Normal,test +MB-0377,CLAUDIN_SUBTYPE,LumA,0.2859904,LumA,Normal,test +MB-0377,CLAUDIN_SUBTYPE,LumB,0.006370738,LumA,Normal,test +MB-0377,CLAUDIN_SUBTYPE,NC,0.038256545,LumA,Normal,test +MB-0377,CLAUDIN_SUBTYPE,Normal,0.4636091,LumA,Normal,test +MB-0377,CLAUDIN_SUBTYPE,claudin-low,0.0658072,LumA,Normal,test +MB-7145,CLAUDIN_SUBTYPE,Basal,0.9859118,Basal,Basal,test +MB-7145,CLAUDIN_SUBTYPE,Her2,0.0027224608,Basal,Basal,test +MB-7145,CLAUDIN_SUBTYPE,LumA,0.00022845657,Basal,Basal,test +MB-7145,CLAUDIN_SUBTYPE,LumB,0.0016707595,Basal,Basal,test +MB-7145,CLAUDIN_SUBTYPE,NC,0.0003959038,Basal,Basal,test +MB-7145,CLAUDIN_SUBTYPE,Normal,0.005564319,Basal,Basal,test +MB-7145,CLAUDIN_SUBTYPE,claudin-low,0.0035061976,Basal,Basal,test +MB-4362,CLAUDIN_SUBTYPE,Basal,4.8199137e-05,Normal,LumA,test +MB-4362,CLAUDIN_SUBTYPE,Her2,3.986516e-05,Normal,LumA,test +MB-4362,CLAUDIN_SUBTYPE,LumA,0.99679786,Normal,LumA,test +MB-4362,CLAUDIN_SUBTYPE,LumB,0.00024256826,Normal,LumA,test +MB-4362,CLAUDIN_SUBTYPE,NC,0.0002561863,Normal,LumA,test +MB-4362,CLAUDIN_SUBTYPE,Normal,0.0025707337,Normal,LumA,test +MB-4362,CLAUDIN_SUBTYPE,claudin-low,4.4711243e-05,Normal,LumA,test +MB-3001,CLAUDIN_SUBTYPE,Basal,0.8703276,claudin-low,Basal,test +MB-3001,CLAUDIN_SUBTYPE,Her2,0.009200398,claudin-low,Basal,test +MB-3001,CLAUDIN_SUBTYPE,LumA,0.009171234,claudin-low,Basal,test +MB-3001,CLAUDIN_SUBTYPE,LumB,0.016850747,claudin-low,Basal,test +MB-3001,CLAUDIN_SUBTYPE,NC,0.0066489256,claudin-low,Basal,test +MB-3001,CLAUDIN_SUBTYPE,Normal,0.016416637,claudin-low,Basal,test +MB-3001,CLAUDIN_SUBTYPE,claudin-low,0.071384534,claudin-low,Basal,test +MB-5364,CLAUDIN_SUBTYPE,Basal,0.017264724,Normal,LumA,test +MB-5364,CLAUDIN_SUBTYPE,Her2,0.015385536,Normal,LumA,test +MB-5364,CLAUDIN_SUBTYPE,LumA,0.66187626,Normal,LumA,test +MB-5364,CLAUDIN_SUBTYPE,LumB,0.012003464,Normal,LumA,test +MB-5364,CLAUDIN_SUBTYPE,NC,0.021222766,Normal,LumA,test +MB-5364,CLAUDIN_SUBTYPE,Normal,0.26555765,Normal,LumA,test +MB-5364,CLAUDIN_SUBTYPE,claudin-low,0.0066895243,Normal,LumA,test +MB-4292,CLAUDIN_SUBTYPE,Basal,0.002748507,LumA,LumA,test +MB-4292,CLAUDIN_SUBTYPE,Her2,0.0019597695,LumA,LumA,test +MB-4292,CLAUDIN_SUBTYPE,LumA,0.95322317,LumA,LumA,test +MB-4292,CLAUDIN_SUBTYPE,LumB,0.018502505,LumA,LumA,test +MB-4292,CLAUDIN_SUBTYPE,NC,0.0044927043,LumA,LumA,test +MB-4292,CLAUDIN_SUBTYPE,Normal,0.017691793,LumA,LumA,test +MB-4292,CLAUDIN_SUBTYPE,claudin-low,0.0013815486,LumA,LumA,test +MB-0294,CLAUDIN_SUBTYPE,Basal,0.080543205,Normal,claudin-low,test +MB-0294,CLAUDIN_SUBTYPE,Her2,0.022058526,Normal,claudin-low,test +MB-0294,CLAUDIN_SUBTYPE,LumA,0.27412522,Normal,claudin-low,test +MB-0294,CLAUDIN_SUBTYPE,LumB,0.0043000043,Normal,claudin-low,test +MB-0294,CLAUDIN_SUBTYPE,NC,0.01616209,Normal,claudin-low,test +MB-0294,CLAUDIN_SUBTYPE,Normal,0.0152093265,Normal,claudin-low,test +MB-0294,CLAUDIN_SUBTYPE,claudin-low,0.58760166,Normal,claudin-low,test +MB-4395,CLAUDIN_SUBTYPE,Basal,0.048069697,Her2,LumB,test +MB-4395,CLAUDIN_SUBTYPE,Her2,0.008818352,Her2,LumB,test +MB-4395,CLAUDIN_SUBTYPE,LumA,0.010039249,Her2,LumB,test +MB-4395,CLAUDIN_SUBTYPE,LumB,0.92406553,Her2,LumB,test +MB-4395,CLAUDIN_SUBTYPE,NC,0.0035328905,Her2,LumB,test +MB-4395,CLAUDIN_SUBTYPE,Normal,0.003705546,Her2,LumB,test +MB-4395,CLAUDIN_SUBTYPE,claudin-low,0.0017687024,Her2,LumB,test +MB-3707,CLAUDIN_SUBTYPE,Basal,0.028681524,claudin-low,claudin-low,test +MB-3707,CLAUDIN_SUBTYPE,Her2,0.0029488194,claudin-low,claudin-low,test +MB-3707,CLAUDIN_SUBTYPE,LumA,0.04709891,claudin-low,claudin-low,test +MB-3707,CLAUDIN_SUBTYPE,LumB,0.0003828117,claudin-low,claudin-low,test +MB-3707,CLAUDIN_SUBTYPE,NC,0.003181193,claudin-low,claudin-low,test +MB-3707,CLAUDIN_SUBTYPE,Normal,0.001433073,claudin-low,claudin-low,test +MB-3707,CLAUDIN_SUBTYPE,claudin-low,0.91627365,claudin-low,claudin-low,test +MB-0606,CLAUDIN_SUBTYPE,Basal,0.007836574,LumB,LumB,test +MB-0606,CLAUDIN_SUBTYPE,Her2,0.0010747805,LumB,LumB,test +MB-0606,CLAUDIN_SUBTYPE,LumA,0.095562406,LumB,LumB,test +MB-0606,CLAUDIN_SUBTYPE,LumB,0.88798916,LumB,LumB,test +MB-0606,CLAUDIN_SUBTYPE,NC,0.0034377137,LumB,LumB,test +MB-0606,CLAUDIN_SUBTYPE,Normal,0.0032419227,LumB,LumB,test +MB-0606,CLAUDIN_SUBTYPE,claudin-low,0.0008573985,LumB,LumB,test +MB-5360,CLAUDIN_SUBTYPE,Basal,0.0031488223,LumA,LumA,test +MB-5360,CLAUDIN_SUBTYPE,Her2,0.0025404184,LumA,LumA,test +MB-5360,CLAUDIN_SUBTYPE,LumA,0.9505819,LumA,LumA,test +MB-5360,CLAUDIN_SUBTYPE,LumB,0.027213415,LumA,LumA,test +MB-5360,CLAUDIN_SUBTYPE,NC,0.0037624235,LumA,LumA,test +MB-5360,CLAUDIN_SUBTYPE,Normal,0.010715112,LumA,LumA,test +MB-5360,CLAUDIN_SUBTYPE,claudin-low,0.002037864,LumA,LumA,test +MB-3300,CLAUDIN_SUBTYPE,Basal,0.026190653,LumB,LumB,test +MB-3300,CLAUDIN_SUBTYPE,Her2,0.004534307,LumB,LumB,test +MB-3300,CLAUDIN_SUBTYPE,LumA,0.050886184,LumB,LumB,test +MB-3300,CLAUDIN_SUBTYPE,LumB,0.89641804,LumB,LumB,test +MB-3300,CLAUDIN_SUBTYPE,NC,0.008257844,LumB,LumB,test +MB-3300,CLAUDIN_SUBTYPE,Normal,0.0043604593,LumB,LumB,test +MB-3300,CLAUDIN_SUBTYPE,claudin-low,0.009352643,LumB,LumB,test +MB-3748,CLAUDIN_SUBTYPE,Basal,0.0010757027,LumA,LumA,test +MB-3748,CLAUDIN_SUBTYPE,Her2,0.0008261617,LumA,LumA,test +MB-3748,CLAUDIN_SUBTYPE,LumA,0.97685087,LumA,LumA,test +MB-3748,CLAUDIN_SUBTYPE,LumB,0.0032946446,LumA,LumA,test +MB-3748,CLAUDIN_SUBTYPE,NC,0.0027865095,LumA,LumA,test +MB-3748,CLAUDIN_SUBTYPE,Normal,0.013961524,LumA,LumA,test +MB-3748,CLAUDIN_SUBTYPE,claudin-low,0.0012046822,LumA,LumA,test +MB-4665,CLAUDIN_SUBTYPE,Basal,0.0040027923,LumA,LumA,test +MB-4665,CLAUDIN_SUBTYPE,Her2,0.0013002802,LumA,LumA,test +MB-4665,CLAUDIN_SUBTYPE,LumA,0.9497041,LumA,LumA,test +MB-4665,CLAUDIN_SUBTYPE,LumB,0.025166146,LumA,LumA,test +MB-4665,CLAUDIN_SUBTYPE,NC,0.004234078,LumA,LumA,test +MB-4665,CLAUDIN_SUBTYPE,Normal,0.0140283955,LumA,LumA,test +MB-4665,CLAUDIN_SUBTYPE,claudin-low,0.0015642861,LumA,LumA,test +MB-3702,CLAUDIN_SUBTYPE,Basal,0.41824463,claudin-low,Basal,test +MB-3702,CLAUDIN_SUBTYPE,Her2,0.061829798,claudin-low,Basal,test +MB-3702,CLAUDIN_SUBTYPE,LumA,0.052840386,claudin-low,Basal,test +MB-3702,CLAUDIN_SUBTYPE,LumB,0.003650244,claudin-low,Basal,test +MB-3702,CLAUDIN_SUBTYPE,NC,0.017210482,claudin-low,Basal,test +MB-3702,CLAUDIN_SUBTYPE,Normal,0.10756965,claudin-low,Basal,test +MB-3702,CLAUDIN_SUBTYPE,claudin-low,0.3386548,claudin-low,Basal,test +MB-4770,CLAUDIN_SUBTYPE,Basal,0.3075867,Her2,Her2,test +MB-4770,CLAUDIN_SUBTYPE,Her2,0.5351838,Her2,Her2,test +MB-4770,CLAUDIN_SUBTYPE,LumA,0.007842485,Her2,Her2,test +MB-4770,CLAUDIN_SUBTYPE,LumB,0.009996546,Her2,Her2,test +MB-4770,CLAUDIN_SUBTYPE,NC,0.0084160585,Her2,Her2,test +MB-4770,CLAUDIN_SUBTYPE,Normal,0.07097413,Her2,Her2,test +MB-4770,CLAUDIN_SUBTYPE,claudin-low,0.06000036,Her2,Her2,test +MB-5175,CLAUDIN_SUBTYPE,Basal,0.086505786,claudin-low,claudin-low,test +MB-5175,CLAUDIN_SUBTYPE,Her2,0.0057535875,claudin-low,claudin-low,test +MB-5175,CLAUDIN_SUBTYPE,LumA,0.18537974,claudin-low,claudin-low,test +MB-5175,CLAUDIN_SUBTYPE,LumB,0.0015258914,claudin-low,claudin-low,test +MB-5175,CLAUDIN_SUBTYPE,NC,0.012702196,claudin-low,claudin-low,test +MB-5175,CLAUDIN_SUBTYPE,Normal,0.016518,claudin-low,claudin-low,test +MB-5175,CLAUDIN_SUBTYPE,claudin-low,0.69161475,claudin-low,claudin-low,test +MB-6231,CLAUDIN_SUBTYPE,Basal,0.015856754,Normal,LumA,test +MB-6231,CLAUDIN_SUBTYPE,Her2,0.00852486,Normal,LumA,test +MB-6231,CLAUDIN_SUBTYPE,LumA,0.76511014,Normal,LumA,test +MB-6231,CLAUDIN_SUBTYPE,LumB,0.023133427,Normal,LumA,test +MB-6231,CLAUDIN_SUBTYPE,NC,0.016729105,Normal,LumA,test +MB-6231,CLAUDIN_SUBTYPE,Normal,0.16683394,Normal,LumA,test +MB-6231,CLAUDIN_SUBTYPE,claudin-low,0.0038118155,Normal,LumA,test +MB-2735,CLAUDIN_SUBTYPE,Basal,0.027673326,LumB,LumB,test +MB-2735,CLAUDIN_SUBTYPE,Her2,0.028147627,LumB,LumB,test +MB-2735,CLAUDIN_SUBTYPE,LumA,0.024419026,LumB,LumB,test +MB-2735,CLAUDIN_SUBTYPE,LumB,0.89668804,LumB,LumB,test +MB-2735,CLAUDIN_SUBTYPE,NC,0.009383203,LumB,LumB,test +MB-2735,CLAUDIN_SUBTYPE,Normal,0.0069796243,LumB,LumB,test +MB-2735,CLAUDIN_SUBTYPE,claudin-low,0.0067092185,LumB,LumB,test +MB-4894,CLAUDIN_SUBTYPE,Basal,0.008146837,LumA,LumB,test +MB-4894,CLAUDIN_SUBTYPE,Her2,5.0267496e-05,LumA,LumB,test +MB-4894,CLAUDIN_SUBTYPE,LumA,0.0008432778,LumA,LumB,test +MB-4894,CLAUDIN_SUBTYPE,LumB,0.9904221,LumA,LumB,test +MB-4894,CLAUDIN_SUBTYPE,NC,0.00033386314,LumA,LumB,test +MB-4894,CLAUDIN_SUBTYPE,Normal,8.965775e-05,LumA,LumB,test +MB-4894,CLAUDIN_SUBTYPE,claudin-low,0.00011399013,LumA,LumB,test +MB-3292,CLAUDIN_SUBTYPE,Basal,0.12310144,claudin-low,claudin-low,test +MB-3292,CLAUDIN_SUBTYPE,Her2,0.004987264,claudin-low,claudin-low,test +MB-3292,CLAUDIN_SUBTYPE,LumA,0.017173538,claudin-low,claudin-low,test +MB-3292,CLAUDIN_SUBTYPE,LumB,0.00054751534,claudin-low,claudin-low,test +MB-3292,CLAUDIN_SUBTYPE,NC,0.003436721,claudin-low,claudin-low,test +MB-3292,CLAUDIN_SUBTYPE,Normal,0.0034642518,claudin-low,claudin-low,test +MB-3292,CLAUDIN_SUBTYPE,claudin-low,0.8472893,claudin-low,claudin-low,test +MB-4872,CLAUDIN_SUBTYPE,Basal,0.03850913,LumA,LumA,test +MB-4872,CLAUDIN_SUBTYPE,Her2,0.016782073,LumA,LumA,test +MB-4872,CLAUDIN_SUBTYPE,LumA,0.60313284,LumA,LumA,test +MB-4872,CLAUDIN_SUBTYPE,LumB,0.1189394,LumA,LumA,test +MB-4872,CLAUDIN_SUBTYPE,NC,0.028856628,LumA,LumA,test +MB-4872,CLAUDIN_SUBTYPE,Normal,0.18653317,LumA,LumA,test +MB-4872,CLAUDIN_SUBTYPE,claudin-low,0.0072467034,LumA,LumA,test +MB-4266,CLAUDIN_SUBTYPE,Basal,0.20300272,LumA,LumB,test +MB-4266,CLAUDIN_SUBTYPE,Her2,0.24488714,LumA,LumB,test +MB-4266,CLAUDIN_SUBTYPE,LumA,0.089972176,LumA,LumB,test +MB-4266,CLAUDIN_SUBTYPE,LumB,0.29489613,LumA,LumB,test +MB-4266,CLAUDIN_SUBTYPE,NC,0.03749178,LumA,LumB,test +MB-4266,CLAUDIN_SUBTYPE,Normal,0.08040899,LumA,LumB,test +MB-4266,CLAUDIN_SUBTYPE,claudin-low,0.049341135,LumA,LumB,test +MB-0536,CLAUDIN_SUBTYPE,Basal,0.07104641,LumB,LumB,test +MB-0536,CLAUDIN_SUBTYPE,Her2,0.015672542,LumB,LumB,test +MB-0536,CLAUDIN_SUBTYPE,LumA,0.03267727,LumB,LumB,test +MB-0536,CLAUDIN_SUBTYPE,LumB,0.8203492,LumB,LumB,test +MB-0536,CLAUDIN_SUBTYPE,NC,0.017044472,LumB,LumB,test +MB-0536,CLAUDIN_SUBTYPE,Normal,0.007040359,LumB,LumB,test +MB-0536,CLAUDIN_SUBTYPE,claudin-low,0.03616978,LumB,LumB,test +MB-7057,CLAUDIN_SUBTYPE,Basal,0.033891283,Normal,Normal,test +MB-7057,CLAUDIN_SUBTYPE,Her2,0.08408664,Normal,Normal,test +MB-7057,CLAUDIN_SUBTYPE,LumA,0.035663918,Normal,Normal,test +MB-7057,CLAUDIN_SUBTYPE,LumB,0.002441542,Normal,Normal,test +MB-7057,CLAUDIN_SUBTYPE,NC,0.009771162,Normal,Normal,test +MB-7057,CLAUDIN_SUBTYPE,Normal,0.8318555,Normal,Normal,test +MB-7057,CLAUDIN_SUBTYPE,claudin-low,0.0022899685,Normal,Normal,test +MB-6055,CLAUDIN_SUBTYPE,Basal,0.10617896,claudin-low,claudin-low,test +MB-6055,CLAUDIN_SUBTYPE,Her2,0.001496232,claudin-low,claudin-low,test +MB-6055,CLAUDIN_SUBTYPE,LumA,0.013315984,claudin-low,claudin-low,test +MB-6055,CLAUDIN_SUBTYPE,LumB,0.00075303536,claudin-low,claudin-low,test +MB-6055,CLAUDIN_SUBTYPE,NC,0.0024673694,claudin-low,claudin-low,test +MB-6055,CLAUDIN_SUBTYPE,Normal,0.00094941724,claudin-low,claudin-low,test +MB-6055,CLAUDIN_SUBTYPE,claudin-low,0.874839,claudin-low,claudin-low,test +MB-5116,CLAUDIN_SUBTYPE,Basal,0.0019858023,LumB,LumB,test +MB-5116,CLAUDIN_SUBTYPE,Her2,0.0001653645,LumB,LumB,test +MB-5116,CLAUDIN_SUBTYPE,LumA,0.00054296374,LumB,LumB,test +MB-5116,CLAUDIN_SUBTYPE,LumB,0.9969386,LumB,LumB,test +MB-5116,CLAUDIN_SUBTYPE,NC,0.00023703123,LumB,LumB,test +MB-5116,CLAUDIN_SUBTYPE,Normal,6.612016e-05,LumB,LumB,test +MB-5116,CLAUDIN_SUBTYPE,claudin-low,6.428596e-05,LumB,LumB,test +MB-5264,CLAUDIN_SUBTYPE,Basal,9.177315e-05,LumA,LumA,test +MB-5264,CLAUDIN_SUBTYPE,Her2,7.016429e-05,LumA,LumA,test +MB-5264,CLAUDIN_SUBTYPE,LumA,0.99385107,LumA,LumA,test +MB-5264,CLAUDIN_SUBTYPE,LumB,0.000990209,LumA,LumA,test +MB-5264,CLAUDIN_SUBTYPE,NC,0.00045073955,LumA,LumA,test +MB-5264,CLAUDIN_SUBTYPE,Normal,0.004494469,LumA,LumA,test +MB-5264,CLAUDIN_SUBTYPE,claudin-low,5.1539806e-05,LumA,LumA,test +MB-6232,CLAUDIN_SUBTYPE,Basal,0.0003516687,LumA,LumA,test +MB-6232,CLAUDIN_SUBTYPE,Her2,0.00028731397,LumA,LumA,test +MB-6232,CLAUDIN_SUBTYPE,LumA,0.985743,LumA,LumA,test +MB-6232,CLAUDIN_SUBTYPE,LumB,0.0012544888,LumA,LumA,test +MB-6232,CLAUDIN_SUBTYPE,NC,0.0013779921,LumA,LumA,test +MB-6232,CLAUDIN_SUBTYPE,Normal,0.010672159,LumA,LumA,test +MB-6232,CLAUDIN_SUBTYPE,claudin-low,0.00031323318,LumA,LumA,test +MB-0586,CLAUDIN_SUBTYPE,Basal,0.00016750579,LumA,LumA,test +MB-0586,CLAUDIN_SUBTYPE,Her2,0.00012837946,LumA,LumA,test +MB-0586,CLAUDIN_SUBTYPE,LumA,0.9938294,LumA,LumA,test +MB-0586,CLAUDIN_SUBTYPE,LumB,0.00070089364,LumA,LumA,test +MB-0586,CLAUDIN_SUBTYPE,NC,0.00063036376,LumA,LumA,test +MB-0586,CLAUDIN_SUBTYPE,Normal,0.004353527,LumA,LumA,test +MB-0586,CLAUDIN_SUBTYPE,claudin-low,0.00018993042,LumA,LumA,test +MB-3079,CLAUDIN_SUBTYPE,Basal,0.0012705416,LumA,LumA,test +MB-3079,CLAUDIN_SUBTYPE,Her2,0.0019069187,LumA,LumA,test +MB-3079,CLAUDIN_SUBTYPE,LumA,0.97098833,LumA,LumA,test +MB-3079,CLAUDIN_SUBTYPE,LumB,0.005789256,LumA,LumA,test +MB-3079,CLAUDIN_SUBTYPE,NC,0.0031056574,LumA,LumA,test +MB-3079,CLAUDIN_SUBTYPE,Normal,0.015837869,LumA,LumA,test +MB-3079,CLAUDIN_SUBTYPE,claudin-low,0.0011013215,LumA,LumA,test +MB-7046,CLAUDIN_SUBTYPE,Basal,0.020394996,Her2,LumB,test +MB-7046,CLAUDIN_SUBTYPE,Her2,0.14808494,Her2,LumB,test +MB-7046,CLAUDIN_SUBTYPE,LumA,0.09730367,Her2,LumB,test +MB-7046,CLAUDIN_SUBTYPE,LumB,0.6918551,Her2,LumB,test +MB-7046,CLAUDIN_SUBTYPE,NC,0.0134256845,Her2,LumB,test +MB-7046,CLAUDIN_SUBTYPE,Normal,0.009914473,Her2,LumB,test +MB-7046,CLAUDIN_SUBTYPE,claudin-low,0.019021135,Her2,LumB,test +MB-0609,CLAUDIN_SUBTYPE,Basal,0.0038115378,LumA,LumA,test +MB-0609,CLAUDIN_SUBTYPE,Her2,0.0060629644,LumA,LumA,test +MB-0609,CLAUDIN_SUBTYPE,LumA,0.922815,LumA,LumA,test +MB-0609,CLAUDIN_SUBTYPE,LumB,0.040993918,LumA,LumA,test +MB-0609,CLAUDIN_SUBTYPE,NC,0.006055424,LumA,LumA,test +MB-0609,CLAUDIN_SUBTYPE,Normal,0.017466042,LumA,LumA,test +MB-0609,CLAUDIN_SUBTYPE,claudin-low,0.002795165,LumA,LumA,test +MB-5642,CLAUDIN_SUBTYPE,Basal,0.000386987,LumA,LumA,test +MB-5642,CLAUDIN_SUBTYPE,Her2,0.0004581459,LumA,LumA,test +MB-5642,CLAUDIN_SUBTYPE,LumA,0.9896773,LumA,LumA,test +MB-5642,CLAUDIN_SUBTYPE,LumB,0.0018305077,LumA,LumA,test +MB-5642,CLAUDIN_SUBTYPE,NC,0.0011075115,LumA,LumA,test +MB-5642,CLAUDIN_SUBTYPE,Normal,0.006136999,LumA,LumA,test +MB-5642,CLAUDIN_SUBTYPE,claudin-low,0.00040250205,LumA,LumA,test +MB-2536,CLAUDIN_SUBTYPE,Basal,0.000158365,LumA,LumA,test +MB-2536,CLAUDIN_SUBTYPE,Her2,8.2762395e-05,LumA,LumA,test +MB-2536,CLAUDIN_SUBTYPE,LumA,0.99655306,LumA,LumA,test +MB-2536,CLAUDIN_SUBTYPE,LumB,0.00026362055,LumA,LumA,test +MB-2536,CLAUDIN_SUBTYPE,NC,0.00042462535,LumA,LumA,test +MB-2536,CLAUDIN_SUBTYPE,Normal,0.002106054,LumA,LumA,test +MB-2536,CLAUDIN_SUBTYPE,claudin-low,0.00041149568,LumA,LumA,test +MB-4849,CLAUDIN_SUBTYPE,Basal,0.014060427,LumA,LumA,test +MB-4849,CLAUDIN_SUBTYPE,Her2,0.0023404222,LumA,LumA,test +MB-4849,CLAUDIN_SUBTYPE,LumA,0.5464444,LumA,LumA,test +MB-4849,CLAUDIN_SUBTYPE,LumB,0.4161527,LumA,LumA,test +MB-4849,CLAUDIN_SUBTYPE,NC,0.007270987,LumA,LumA,test +MB-4849,CLAUDIN_SUBTYPE,Normal,0.011411558,LumA,LumA,test +MB-4849,CLAUDIN_SUBTYPE,claudin-low,0.0023194426,LumA,LumA,test +MB-5481,CLAUDIN_SUBTYPE,Basal,0.04727273,LumB,LumB,test +MB-5481,CLAUDIN_SUBTYPE,Her2,0.078455746,LumB,LumB,test +MB-5481,CLAUDIN_SUBTYPE,LumA,0.18691343,LumB,LumB,test +MB-5481,CLAUDIN_SUBTYPE,LumB,0.58688575,LumB,LumB,test +MB-5481,CLAUDIN_SUBTYPE,NC,0.028282693,LumB,LumB,test +MB-5481,CLAUDIN_SUBTYPE,Normal,0.05606999,LumB,LumB,test +MB-5481,CLAUDIN_SUBTYPE,claudin-low,0.01611968,LumB,LumB,test +MB-2904,CLAUDIN_SUBTYPE,Basal,0.820908,claudin-low,Basal,test +MB-2904,CLAUDIN_SUBTYPE,Her2,0.009951586,claudin-low,Basal,test +MB-2904,CLAUDIN_SUBTYPE,LumA,0.00938493,claudin-low,Basal,test +MB-2904,CLAUDIN_SUBTYPE,LumB,0.0073889997,claudin-low,Basal,test +MB-2904,CLAUDIN_SUBTYPE,NC,0.0055719325,claudin-low,Basal,test +MB-2904,CLAUDIN_SUBTYPE,Normal,0.014180461,claudin-low,Basal,test +MB-2904,CLAUDIN_SUBTYPE,claudin-low,0.13261399,claudin-low,Basal,test +MB-5345,CLAUDIN_SUBTYPE,Basal,0.0003942885,Normal,LumA,test +MB-5345,CLAUDIN_SUBTYPE,Her2,0.00023656567,Normal,LumA,test +MB-5345,CLAUDIN_SUBTYPE,LumA,0.98909587,Normal,LumA,test +MB-5345,CLAUDIN_SUBTYPE,LumB,0.00066572434,Normal,LumA,test +MB-5345,CLAUDIN_SUBTYPE,NC,0.0011896465,Normal,LumA,test +MB-5345,CLAUDIN_SUBTYPE,Normal,0.007863635,Normal,LumA,test +MB-5345,CLAUDIN_SUBTYPE,claudin-low,0.0005544429,Normal,LumA,test +MB-5256,CLAUDIN_SUBTYPE,Basal,0.0052847103,LumA,LumA,test +MB-5256,CLAUDIN_SUBTYPE,Her2,0.0030043318,LumA,LumA,test +MB-5256,CLAUDIN_SUBTYPE,LumA,0.8620137,LumA,LumA,test +MB-5256,CLAUDIN_SUBTYPE,LumB,0.09799618,LumA,LumA,test +MB-5256,CLAUDIN_SUBTYPE,NC,0.0077908053,LumA,LumA,test +MB-5256,CLAUDIN_SUBTYPE,Normal,0.021882134,LumA,LumA,test +MB-5256,CLAUDIN_SUBTYPE,claudin-low,0.0020280594,LumA,LumA,test +MB-3329,CLAUDIN_SUBTYPE,Basal,0.46680883,Her2,Basal,test +MB-3329,CLAUDIN_SUBTYPE,Her2,0.1317724,Her2,Basal,test +MB-3329,CLAUDIN_SUBTYPE,LumA,0.015809255,Her2,Basal,test +MB-3329,CLAUDIN_SUBTYPE,LumB,0.05080374,Her2,Basal,test +MB-3329,CLAUDIN_SUBTYPE,NC,0.019283922,Her2,Basal,test +MB-3329,CLAUDIN_SUBTYPE,Normal,0.30385002,Her2,Basal,test +MB-3329,CLAUDIN_SUBTYPE,claudin-low,0.01167187,Her2,Basal,test +MB-2725,CLAUDIN_SUBTYPE,Basal,0.0114249615,LumA,Normal,test +MB-2725,CLAUDIN_SUBTYPE,Her2,0.012254139,LumA,Normal,test +MB-2725,CLAUDIN_SUBTYPE,LumA,0.3566892,LumA,Normal,test +MB-2725,CLAUDIN_SUBTYPE,LumB,0.0024819542,LumA,Normal,test +MB-2725,CLAUDIN_SUBTYPE,NC,0.013698303,LumA,Normal,test +MB-2725,CLAUDIN_SUBTYPE,Normal,0.6013761,LumA,Normal,test +MB-2725,CLAUDIN_SUBTYPE,claudin-low,0.0020752698,LumA,Normal,test +MB-6192,CLAUDIN_SUBTYPE,Basal,0.020725993,LumB,LumB,test +MB-6192,CLAUDIN_SUBTYPE,Her2,0.0012642726,LumB,LumB,test +MB-6192,CLAUDIN_SUBTYPE,LumA,0.03174131,LumB,LumB,test +MB-6192,CLAUDIN_SUBTYPE,LumB,0.93846875,LumB,LumB,test +MB-6192,CLAUDIN_SUBTYPE,NC,0.0036902647,LumB,LumB,test +MB-6192,CLAUDIN_SUBTYPE,Normal,0.0023842063,LumB,LumB,test +MB-6192,CLAUDIN_SUBTYPE,claudin-low,0.0017252095,LumB,LumB,test +MB-6007,CLAUDIN_SUBTYPE,Basal,0.15368254,Her2,LumB,test +MB-6007,CLAUDIN_SUBTYPE,Her2,0.036665946,Her2,LumB,test +MB-6007,CLAUDIN_SUBTYPE,LumA,0.073763534,Her2,LumB,test +MB-6007,CLAUDIN_SUBTYPE,LumB,0.60618144,Her2,LumB,test +MB-6007,CLAUDIN_SUBTYPE,NC,0.02797106,Her2,LumB,test +MB-6007,CLAUDIN_SUBTYPE,Normal,0.091433145,Her2,LumB,test +MB-6007,CLAUDIN_SUBTYPE,claudin-low,0.010302293,Her2,LumB,test +MB-5440,CLAUDIN_SUBTYPE,Basal,0.018648334,claudin-low,claudin-low,test +MB-5440,CLAUDIN_SUBTYPE,Her2,0.0001302548,claudin-low,claudin-low,test +MB-5440,CLAUDIN_SUBTYPE,LumA,0.0017404946,claudin-low,claudin-low,test +MB-5440,CLAUDIN_SUBTYPE,LumB,1.8812469e-05,claudin-low,claudin-low,test +MB-5440,CLAUDIN_SUBTYPE,NC,0.00020037545,claudin-low,claudin-low,test +MB-5440,CLAUDIN_SUBTYPE,Normal,3.868957e-05,claudin-low,claudin-low,test +MB-5440,CLAUDIN_SUBTYPE,claudin-low,0.979223,claudin-low,claudin-low,test +MB-2617,CLAUDIN_SUBTYPE,Basal,0.0055856854,LumB,LumA,test +MB-2617,CLAUDIN_SUBTYPE,Her2,0.0017773147,LumB,LumA,test +MB-2617,CLAUDIN_SUBTYPE,LumA,0.6011409,LumB,LumA,test +MB-2617,CLAUDIN_SUBTYPE,LumB,0.37400123,LumB,LumA,test +MB-2617,CLAUDIN_SUBTYPE,NC,0.005768856,LumB,LumA,test +MB-2617,CLAUDIN_SUBTYPE,Normal,0.010480555,LumB,LumA,test +MB-2617,CLAUDIN_SUBTYPE,claudin-low,0.0012453878,LumB,LumA,test +MB-0517,CLAUDIN_SUBTYPE,Basal,0.0005509023,LumA,LumA,test +MB-0517,CLAUDIN_SUBTYPE,Her2,0.00045434615,LumA,LumA,test +MB-0517,CLAUDIN_SUBTYPE,LumA,0.9861783,LumA,LumA,test +MB-0517,CLAUDIN_SUBTYPE,LumB,0.002652709,LumA,LumA,test +MB-0517,CLAUDIN_SUBTYPE,NC,0.0015271364,LumA,LumA,test +MB-0517,CLAUDIN_SUBTYPE,Normal,0.008113339,LumA,LumA,test +MB-0517,CLAUDIN_SUBTYPE,claudin-low,0.00052343245,LumA,LumA,test +MB-6257,CLAUDIN_SUBTYPE,Basal,0.00825107,LumB,LumB,test +MB-6257,CLAUDIN_SUBTYPE,Her2,0.00042712747,LumB,LumB,test +MB-6257,CLAUDIN_SUBTYPE,LumA,0.0032855328,LumB,LumB,test +MB-6257,CLAUDIN_SUBTYPE,LumB,0.98575115,LumB,LumB,test +MB-6257,CLAUDIN_SUBTYPE,NC,0.0013314235,LumB,LumB,test +MB-6257,CLAUDIN_SUBTYPE,Normal,0.00055160705,LumB,LumB,test +MB-6257,CLAUDIN_SUBTYPE,claudin-low,0.00040217565,LumB,LumB,test +MB-5463,CLAUDIN_SUBTYPE,Basal,0.10012772,LumB,Her2,test +MB-5463,CLAUDIN_SUBTYPE,Her2,0.5882122,LumB,Her2,test +MB-5463,CLAUDIN_SUBTYPE,LumA,0.04216189,LumB,Her2,test +MB-5463,CLAUDIN_SUBTYPE,LumB,0.14849487,LumB,Her2,test +MB-5463,CLAUDIN_SUBTYPE,NC,0.01954044,LumB,Her2,test +MB-5463,CLAUDIN_SUBTYPE,Normal,0.079304315,LumB,Her2,test +MB-5463,CLAUDIN_SUBTYPE,claudin-low,0.022158533,LumB,Her2,test +MB-4704,CLAUDIN_SUBTYPE,Basal,0.0030723102,LumA,LumA,test +MB-4704,CLAUDIN_SUBTYPE,Her2,0.0026524793,LumA,LumA,test +MB-4704,CLAUDIN_SUBTYPE,LumA,0.8585891,LumA,LumA,test +MB-4704,CLAUDIN_SUBTYPE,LumB,0.0041292943,LumA,LumA,test +MB-4704,CLAUDIN_SUBTYPE,NC,0.007165401,LumA,LumA,test +MB-4704,CLAUDIN_SUBTYPE,Normal,0.12327678,LumA,LumA,test +MB-4704,CLAUDIN_SUBTYPE,claudin-low,0.0011145911,LumA,LumA,test +MB-5019,CLAUDIN_SUBTYPE,Basal,0.1187088,Normal,Her2,test +MB-5019,CLAUDIN_SUBTYPE,Her2,0.75915796,Normal,Her2,test +MB-5019,CLAUDIN_SUBTYPE,LumA,0.00063102634,Normal,Her2,test +MB-5019,CLAUDIN_SUBTYPE,LumB,0.0025139758,Normal,Her2,test +MB-5019,CLAUDIN_SUBTYPE,NC,0.0016164869,Normal,Her2,test +MB-5019,CLAUDIN_SUBTYPE,Normal,0.11557573,Normal,Her2,test +MB-5019,CLAUDIN_SUBTYPE,claudin-low,0.0017961453,Normal,Her2,test +MB-2705,CLAUDIN_SUBTYPE,Basal,0.0049891807,LumB,LumB,test +MB-2705,CLAUDIN_SUBTYPE,Her2,0.0009949313,LumB,LumB,test +MB-2705,CLAUDIN_SUBTYPE,LumA,0.020613268,LumB,LumB,test +MB-2705,CLAUDIN_SUBTYPE,LumB,0.9693272,LumB,LumB,test +MB-2705,CLAUDIN_SUBTYPE,NC,0.0021145619,LumB,LumB,test +MB-2705,CLAUDIN_SUBTYPE,Normal,0.001284121,LumB,LumB,test +MB-2705,CLAUDIN_SUBTYPE,claudin-low,0.0006766574,LumB,LumB,test +MB-7207,CLAUDIN_SUBTYPE,Basal,0.022932222,Her2,Her2,test +MB-7207,CLAUDIN_SUBTYPE,Her2,0.9476807,Her2,Her2,test +MB-7207,CLAUDIN_SUBTYPE,LumA,0.0014489809,Her2,Her2,test +MB-7207,CLAUDIN_SUBTYPE,LumB,0.0048357323,Her2,Her2,test +MB-7207,CLAUDIN_SUBTYPE,NC,0.0018889166,Her2,Her2,test +MB-7207,CLAUDIN_SUBTYPE,Normal,0.010912587,Her2,Her2,test +MB-7207,CLAUDIN_SUBTYPE,claudin-low,0.010300868,Her2,Her2,test +MB-0223,CLAUDIN_SUBTYPE,Basal,0.0013372044,LumA,LumA,test +MB-0223,CLAUDIN_SUBTYPE,Her2,0.0011561452,LumA,LumA,test +MB-0223,CLAUDIN_SUBTYPE,LumA,0.95658284,LumA,LumA,test +MB-0223,CLAUDIN_SUBTYPE,LumB,0.0051606083,LumA,LumA,test +MB-0223,CLAUDIN_SUBTYPE,NC,0.00338522,LumA,LumA,test +MB-0223,CLAUDIN_SUBTYPE,Normal,0.03174772,LumA,LumA,test +MB-0223,CLAUDIN_SUBTYPE,claudin-low,0.00063020707,LumA,LumA,test +MB-6224,CLAUDIN_SUBTYPE,Basal,0.19748071,Her2,claudin-low,test +MB-6224,CLAUDIN_SUBTYPE,Her2,0.30547282,Her2,claudin-low,test +MB-6224,CLAUDIN_SUBTYPE,LumA,0.037900396,Her2,claudin-low,test +MB-6224,CLAUDIN_SUBTYPE,LumB,0.020334618,Her2,claudin-low,test +MB-6224,CLAUDIN_SUBTYPE,NC,0.020819342,Her2,claudin-low,test +MB-6224,CLAUDIN_SUBTYPE,Normal,0.034233626,Her2,claudin-low,test +MB-6224,CLAUDIN_SUBTYPE,claudin-low,0.3837585,Her2,claudin-low,test +MB-3058,CLAUDIN_SUBTYPE,Basal,0.43238187,Basal,Basal,test +MB-3058,CLAUDIN_SUBTYPE,Her2,0.051558863,Basal,Basal,test +MB-3058,CLAUDIN_SUBTYPE,LumA,0.063174866,Basal,Basal,test +MB-3058,CLAUDIN_SUBTYPE,LumB,0.005632813,Basal,Basal,test +MB-3058,CLAUDIN_SUBTYPE,NC,0.01986279,Basal,Basal,test +MB-3058,CLAUDIN_SUBTYPE,Normal,0.096289,Basal,Basal,test +MB-3058,CLAUDIN_SUBTYPE,claudin-low,0.33109975,Basal,Basal,test +MB-0427,CLAUDIN_SUBTYPE,Basal,0.13718928,LumA,claudin-low,test +MB-0427,CLAUDIN_SUBTYPE,Her2,0.06995862,LumA,claudin-low,test +MB-0427,CLAUDIN_SUBTYPE,LumA,0.2619364,LumA,claudin-low,test +MB-0427,CLAUDIN_SUBTYPE,LumB,0.13041283,LumA,claudin-low,test +MB-0427,CLAUDIN_SUBTYPE,NC,0.05982177,LumA,claudin-low,test +MB-0427,CLAUDIN_SUBTYPE,Normal,0.06052351,LumA,claudin-low,test +MB-0427,CLAUDIN_SUBTYPE,claudin-low,0.28015766,LumA,claudin-low,test +MB-5176,CLAUDIN_SUBTYPE,Basal,0.16037229,claudin-low,claudin-low,test +MB-5176,CLAUDIN_SUBTYPE,Her2,0.0661255,claudin-low,claudin-low,test +MB-5176,CLAUDIN_SUBTYPE,LumA,0.0612973,claudin-low,claudin-low,test +MB-5176,CLAUDIN_SUBTYPE,LumB,0.056646936,claudin-low,claudin-low,test +MB-5176,CLAUDIN_SUBTYPE,NC,0.026954293,claudin-low,claudin-low,test +MB-5176,CLAUDIN_SUBTYPE,Normal,0.013832181,claudin-low,claudin-low,test +MB-5176,CLAUDIN_SUBTYPE,claudin-low,0.6147715,claudin-low,claudin-low,test +MB-5491,CLAUDIN_SUBTYPE,Basal,0.02443612,LumB,LumB,test +MB-5491,CLAUDIN_SUBTYPE,Her2,0.0011186892,LumB,LumB,test +MB-5491,CLAUDIN_SUBTYPE,LumA,0.36086515,LumB,LumB,test +MB-5491,CLAUDIN_SUBTYPE,LumB,0.59970105,LumB,LumB,test +MB-5491,CLAUDIN_SUBTYPE,NC,0.005322091,LumB,LumB,test +MB-5491,CLAUDIN_SUBTYPE,Normal,0.006492182,LumB,LumB,test +MB-5491,CLAUDIN_SUBTYPE,claudin-low,0.002064708,LumB,LumB,test +MB-7225,CLAUDIN_SUBTYPE,Basal,0.99748164,Basal,Basal,test +MB-7225,CLAUDIN_SUBTYPE,Her2,0.00013718236,Basal,Basal,test +MB-7225,CLAUDIN_SUBTYPE,LumA,3.6161822e-05,Basal,Basal,test +MB-7225,CLAUDIN_SUBTYPE,LumB,0.00083541445,Basal,Basal,test +MB-7225,CLAUDIN_SUBTYPE,NC,6.9276684e-05,Basal,Basal,test +MB-7225,CLAUDIN_SUBTYPE,Normal,0.000599963,Basal,Basal,test +MB-7225,CLAUDIN_SUBTYPE,claudin-low,0.0008402285,Basal,Basal,test +MB-5533,CLAUDIN_SUBTYPE,Basal,0.0533677,Normal,Normal,test +MB-5533,CLAUDIN_SUBTYPE,Her2,0.08368385,Normal,Normal,test +MB-5533,CLAUDIN_SUBTYPE,LumA,0.10845259,Normal,Normal,test +MB-5533,CLAUDIN_SUBTYPE,LumB,0.008664376,Normal,Normal,test +MB-5533,CLAUDIN_SUBTYPE,NC,0.02630107,Normal,Normal,test +MB-5533,CLAUDIN_SUBTYPE,Normal,0.7097745,Normal,Normal,test +MB-5533,CLAUDIN_SUBTYPE,claudin-low,0.009755975,Normal,Normal,test +MB-0010,CLAUDIN_SUBTYPE,Basal,0.00858182,LumB,LumB,test +MB-0010,CLAUDIN_SUBTYPE,Her2,0.008301599,LumB,LumB,test +MB-0010,CLAUDIN_SUBTYPE,LumA,0.0018815905,LumB,LumB,test +MB-0010,CLAUDIN_SUBTYPE,LumB,0.97768015,LumB,LumB,test +MB-0010,CLAUDIN_SUBTYPE,NC,0.0016992692,LumB,LumB,test +MB-0010,CLAUDIN_SUBTYPE,Normal,0.0010644977,LumB,LumB,test +MB-0010,CLAUDIN_SUBTYPE,claudin-low,0.0007910328,LumB,LumB,test +MB-0366,CLAUDIN_SUBTYPE,Basal,0.0043867035,LumA,LumA,test +MB-0366,CLAUDIN_SUBTYPE,Her2,0.0010917375,LumA,LumA,test +MB-0366,CLAUDIN_SUBTYPE,LumA,0.90755254,LumA,LumA,test +MB-0366,CLAUDIN_SUBTYPE,LumB,0.074085616,LumA,LumA,test +MB-0366,CLAUDIN_SUBTYPE,NC,0.0034596603,LumA,LumA,test +MB-0366,CLAUDIN_SUBTYPE,Normal,0.00819048,LumA,LumA,test +MB-0366,CLAUDIN_SUBTYPE,claudin-low,0.0012331429,LumA,LumA,test +MB-4000,CLAUDIN_SUBTYPE,Basal,0.0070070336,LumA,LumA,test +MB-4000,CLAUDIN_SUBTYPE,Her2,0.0028344907,LumA,LumA,test +MB-4000,CLAUDIN_SUBTYPE,LumA,0.9384553,LumA,LumA,test +MB-4000,CLAUDIN_SUBTYPE,LumB,0.022958927,LumA,LumA,test +MB-4000,CLAUDIN_SUBTYPE,NC,0.006362848,LumA,LumA,test +MB-4000,CLAUDIN_SUBTYPE,Normal,0.012617606,LumA,LumA,test +MB-4000,CLAUDIN_SUBTYPE,claudin-low,0.009763771,LumA,LumA,test +MB-0131,CLAUDIN_SUBTYPE,Basal,0.010145989,LumA,LumA,test +MB-0131,CLAUDIN_SUBTYPE,Her2,0.006223523,LumA,LumA,test +MB-0131,CLAUDIN_SUBTYPE,LumA,0.8622126,LumA,LumA,test +MB-0131,CLAUDIN_SUBTYPE,LumB,0.033921234,LumA,LumA,test +MB-0131,CLAUDIN_SUBTYPE,NC,0.015955936,LumA,LumA,test +MB-0131,CLAUDIN_SUBTYPE,Normal,0.06565811,LumA,LumA,test +MB-0131,CLAUDIN_SUBTYPE,claudin-low,0.005882538,LumA,LumA,test +MB-6107,CLAUDIN_SUBTYPE,Basal,0.11152945,Normal,Normal,test +MB-6107,CLAUDIN_SUBTYPE,Her2,0.13318455,Normal,Normal,test +MB-6107,CLAUDIN_SUBTYPE,LumA,0.11334351,Normal,Normal,test +MB-6107,CLAUDIN_SUBTYPE,LumB,0.025388772,Normal,Normal,test +MB-6107,CLAUDIN_SUBTYPE,NC,0.037881877,Normal,Normal,test +MB-6107,CLAUDIN_SUBTYPE,Normal,0.56060225,Normal,Normal,test +MB-6107,CLAUDIN_SUBTYPE,claudin-low,0.01806957,Normal,Normal,test +MB-5613,CLAUDIN_SUBTYPE,Basal,0.040446434,LumB,LumB,test +MB-5613,CLAUDIN_SUBTYPE,Her2,0.0076712677,LumB,LumB,test +MB-5613,CLAUDIN_SUBTYPE,LumA,0.016288834,LumB,LumB,test +MB-5613,CLAUDIN_SUBTYPE,LumB,0.9180186,LumB,LumB,test +MB-5613,CLAUDIN_SUBTYPE,NC,0.007423211,LumB,LumB,test +MB-5613,CLAUDIN_SUBTYPE,Normal,0.0039939303,LumB,LumB,test +MB-5613,CLAUDIN_SUBTYPE,claudin-low,0.0061577917,LumB,LumB,test +MB-0467,CLAUDIN_SUBTYPE,Basal,0.086296946,Her2,Her2,test +MB-0467,CLAUDIN_SUBTYPE,Her2,0.8481237,Her2,Her2,test +MB-0467,CLAUDIN_SUBTYPE,LumA,0.002243284,Her2,Her2,test +MB-0467,CLAUDIN_SUBTYPE,LumB,0.003938186,Her2,Her2,test +MB-0467,CLAUDIN_SUBTYPE,NC,0.0029772238,Her2,Her2,test +MB-0467,CLAUDIN_SUBTYPE,Normal,0.044144284,Her2,Her2,test +MB-0467,CLAUDIN_SUBTYPE,claudin-low,0.012276272,Her2,Her2,test +MB-3525,CLAUDIN_SUBTYPE,Basal,0.005030327,LumB,LumB,test +MB-3525,CLAUDIN_SUBTYPE,Her2,0.0069327177,LumB,LumB,test +MB-3525,CLAUDIN_SUBTYPE,LumA,0.010782997,LumB,LumB,test +MB-3525,CLAUDIN_SUBTYPE,LumB,0.9716523,LumB,LumB,test +MB-3525,CLAUDIN_SUBTYPE,NC,0.0027265868,LumB,LumB,test +MB-3525,CLAUDIN_SUBTYPE,Normal,0.0013726434,LumB,LumB,test +MB-3525,CLAUDIN_SUBTYPE,claudin-low,0.0015023713,LumB,LumB,test +MB-5532,CLAUDIN_SUBTYPE,Basal,0.011970935,LumA,LumB,test +MB-5532,CLAUDIN_SUBTYPE,Her2,0.0045113247,LumA,LumB,test +MB-5532,CLAUDIN_SUBTYPE,LumA,0.43562013,LumA,LumB,test +MB-5532,CLAUDIN_SUBTYPE,LumB,0.5231806,LumA,LumB,test +MB-5532,CLAUDIN_SUBTYPE,NC,0.008853719,LumA,LumB,test +MB-5532,CLAUDIN_SUBTYPE,Normal,0.012916474,LumA,LumB,test +MB-5532,CLAUDIN_SUBTYPE,claudin-low,0.0029468338,LumA,LumB,test +MB-5201,CLAUDIN_SUBTYPE,Basal,1.3542817e-05,LumA,LumA,test +MB-5201,CLAUDIN_SUBTYPE,Her2,1.0732956e-05,LumA,LumA,test +MB-5201,CLAUDIN_SUBTYPE,LumA,0.9990331,LumA,LumA,test +MB-5201,CLAUDIN_SUBTYPE,LumB,7.204375e-05,LumA,LumA,test +MB-5201,CLAUDIN_SUBTYPE,NC,7.788947e-05,LumA,LumA,test +MB-5201,CLAUDIN_SUBTYPE,Normal,0.00077552046,LumA,LumA,test +MB-5201,CLAUDIN_SUBTYPE,claudin-low,1.7102657e-05,LumA,LumA,test +MB-5041,CLAUDIN_SUBTYPE,Basal,0.059350874,claudin-low,claudin-low,test +MB-5041,CLAUDIN_SUBTYPE,Her2,0.067049,claudin-low,claudin-low,test +MB-5041,CLAUDIN_SUBTYPE,LumA,0.03320396,claudin-low,claudin-low,test +MB-5041,CLAUDIN_SUBTYPE,LumB,0.0038862198,claudin-low,claudin-low,test +MB-5041,CLAUDIN_SUBTYPE,NC,0.0065182718,claudin-low,claudin-low,test +MB-5041,CLAUDIN_SUBTYPE,Normal,0.0028859877,claudin-low,claudin-low,test +MB-5041,CLAUDIN_SUBTYPE,claudin-low,0.8271057,claudin-low,claudin-low,test +MB-7251,CLAUDIN_SUBTYPE,Basal,0.04400487,Her2,Her2,test +MB-7251,CLAUDIN_SUBTYPE,Her2,0.92788106,Her2,Her2,test +MB-7251,CLAUDIN_SUBTYPE,LumA,0.0005623687,Her2,Her2,test +MB-7251,CLAUDIN_SUBTYPE,LumB,0.0016131906,Her2,Her2,test +MB-7251,CLAUDIN_SUBTYPE,NC,0.00097431894,Her2,Her2,test +MB-7251,CLAUDIN_SUBTYPE,Normal,0.021103706,Her2,Her2,test +MB-7251,CLAUDIN_SUBTYPE,claudin-low,0.0038605742,Her2,Her2,test +MB-5632,CLAUDIN_SUBTYPE,Basal,0.02690288,LumB,LumB,test +MB-5632,CLAUDIN_SUBTYPE,Her2,0.030400781,LumB,LumB,test +MB-5632,CLAUDIN_SUBTYPE,LumA,0.013240004,LumB,LumB,test +MB-5632,CLAUDIN_SUBTYPE,LumB,0.9115808,LumB,LumB,test +MB-5632,CLAUDIN_SUBTYPE,NC,0.0069117853,LumB,LumB,test +MB-5632,CLAUDIN_SUBTYPE,Normal,0.006797652,LumB,LumB,test +MB-5632,CLAUDIN_SUBTYPE,claudin-low,0.004166055,LumB,LumB,test +MB-7008,CLAUDIN_SUBTYPE,Basal,0.14291425,claudin-low,claudin-low,test +MB-7008,CLAUDIN_SUBTYPE,Her2,0.12977289,claudin-low,claudin-low,test +MB-7008,CLAUDIN_SUBTYPE,LumA,0.07321149,claudin-low,claudin-low,test +MB-7008,CLAUDIN_SUBTYPE,LumB,0.022568073,claudin-low,claudin-low,test +MB-7008,CLAUDIN_SUBTYPE,NC,0.02953903,claudin-low,claudin-low,test +MB-7008,CLAUDIN_SUBTYPE,Normal,0.034220066,claudin-low,claudin-low,test +MB-7008,CLAUDIN_SUBTYPE,claudin-low,0.5677742,claudin-low,claudin-low,test +MB-5174,CLAUDIN_SUBTYPE,Basal,0.47107643,Her2,Basal,test +MB-5174,CLAUDIN_SUBTYPE,Her2,0.17926496,Her2,Basal,test +MB-5174,CLAUDIN_SUBTYPE,LumA,0.03852033,Her2,Basal,test +MB-5174,CLAUDIN_SUBTYPE,LumB,0.17285067,Her2,Basal,test +MB-5174,CLAUDIN_SUBTYPE,NC,0.022109628,Her2,Basal,test +MB-5174,CLAUDIN_SUBTYPE,Normal,0.07938229,Her2,Basal,test +MB-5174,CLAUDIN_SUBTYPE,claudin-low,0.036795635,Her2,Basal,test +MB-5305,CLAUDIN_SUBTYPE,Basal,0.00010249849,LumA,LumA,test +MB-5305,CLAUDIN_SUBTYPE,Her2,8.941118e-05,LumA,LumA,test +MB-5305,CLAUDIN_SUBTYPE,LumA,0.99568045,LumA,LumA,test +MB-5305,CLAUDIN_SUBTYPE,LumB,0.0012168208,LumA,LumA,test +MB-5305,CLAUDIN_SUBTYPE,NC,0.00036107007,LumA,LumA,test +MB-5305,CLAUDIN_SUBTYPE,Normal,0.0024821202,LumA,LumA,test +MB-5305,CLAUDIN_SUBTYPE,claudin-low,6.749161e-05,LumA,LumA,test +MB-5407,CLAUDIN_SUBTYPE,Basal,0.0011000666,LumA,LumA,test +MB-5407,CLAUDIN_SUBTYPE,Her2,0.0011284665,LumA,LumA,test +MB-5407,CLAUDIN_SUBTYPE,LumA,0.878507,LumA,LumA,test +MB-5407,CLAUDIN_SUBTYPE,LumB,0.0007977193,LumA,LumA,test +MB-5407,CLAUDIN_SUBTYPE,NC,0.0026134953,LumA,LumA,test +MB-5407,CLAUDIN_SUBTYPE,Normal,0.115609355,LumA,LumA,test +MB-5407,CLAUDIN_SUBTYPE,claudin-low,0.00024378802,LumA,LumA,test +MB-0256,CLAUDIN_SUBTYPE,Basal,0.0016889563,LumA,LumA,test +MB-0256,CLAUDIN_SUBTYPE,Her2,0.0012458963,LumA,LumA,test +MB-0256,CLAUDIN_SUBTYPE,LumA,0.9603704,LumA,LumA,test +MB-0256,CLAUDIN_SUBTYPE,LumB,0.0056280266,LumA,LumA,test +MB-0256,CLAUDIN_SUBTYPE,NC,0.0046125194,LumA,LumA,test +MB-0256,CLAUDIN_SUBTYPE,Normal,0.024847658,LumA,LumA,test +MB-0256,CLAUDIN_SUBTYPE,claudin-low,0.0016067195,LumA,LumA,test +MB-5166,CLAUDIN_SUBTYPE,Basal,0.036223304,LumB,LumB,test +MB-5166,CLAUDIN_SUBTYPE,Her2,0.033879034,LumB,LumB,test +MB-5166,CLAUDIN_SUBTYPE,LumA,0.022316916,LumB,LumB,test +MB-5166,CLAUDIN_SUBTYPE,LumB,0.8839152,LumB,LumB,test +MB-5166,CLAUDIN_SUBTYPE,NC,0.008065719,LumB,LumB,test +MB-5166,CLAUDIN_SUBTYPE,Normal,0.011143799,LumB,LumB,test +MB-5166,CLAUDIN_SUBTYPE,claudin-low,0.004456025,LumB,LumB,test +MB-5377,CLAUDIN_SUBTYPE,Basal,0.017830601,LumB,LumB,test +MB-5377,CLAUDIN_SUBTYPE,Her2,0.0037543192,LumB,LumB,test +MB-5377,CLAUDIN_SUBTYPE,LumA,0.16030575,LumB,LumB,test +MB-5377,CLAUDIN_SUBTYPE,LumB,0.79299885,LumB,LumB,test +MB-5377,CLAUDIN_SUBTYPE,NC,0.010154969,LumB,LumB,test +MB-5377,CLAUDIN_SUBTYPE,Normal,0.011852117,LumB,LumB,test +MB-5377,CLAUDIN_SUBTYPE,claudin-low,0.0031033584,LumB,LumB,test +MB-0464,CLAUDIN_SUBTYPE,Basal,0.7071817,Basal,Basal,test +MB-0464,CLAUDIN_SUBTYPE,Her2,0.08423533,Basal,Basal,test +MB-0464,CLAUDIN_SUBTYPE,LumA,0.010658599,Basal,Basal,test +MB-0464,CLAUDIN_SUBTYPE,LumB,0.09104047,Basal,Basal,test +MB-0464,CLAUDIN_SUBTYPE,NC,0.014371751,Basal,Basal,test +MB-0464,CLAUDIN_SUBTYPE,Normal,0.064728774,Basal,Basal,test +MB-0464,CLAUDIN_SUBTYPE,claudin-low,0.027783388,Basal,Basal,test +MB-4949,CLAUDIN_SUBTYPE,Basal,0.047740042,LumB,LumB,test +MB-4949,CLAUDIN_SUBTYPE,Her2,0.046571936,LumB,LumB,test +MB-4949,CLAUDIN_SUBTYPE,LumA,0.13707429,LumB,LumB,test +MB-4949,CLAUDIN_SUBTYPE,LumB,0.67613703,LumB,LumB,test +MB-4949,CLAUDIN_SUBTYPE,NC,0.027928436,LumB,LumB,test +MB-4949,CLAUDIN_SUBTYPE,Normal,0.019753853,LumB,LumB,test +MB-4949,CLAUDIN_SUBTYPE,claudin-low,0.044794403,LumB,LumB,test +MB-5162,CLAUDIN_SUBTYPE,Basal,0.0034282694,claudin-low,claudin-low,test +MB-5162,CLAUDIN_SUBTYPE,Her2,2.9107554e-05,claudin-low,claudin-low,test 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+MB-0257,CLAUDIN_SUBTYPE,claudin-low,0.004903291,LumA,LumA,test +MB-4878,CLAUDIN_SUBTYPE,Basal,0.019948626,LumA,LumA,test +MB-4878,CLAUDIN_SUBTYPE,Her2,0.026228216,LumA,LumA,test +MB-4878,CLAUDIN_SUBTYPE,LumA,0.62314767,LumA,LumA,test +MB-4878,CLAUDIN_SUBTYPE,LumB,0.015841708,LumA,LumA,test +MB-4878,CLAUDIN_SUBTYPE,NC,0.021411145,LumA,LumA,test +MB-4878,CLAUDIN_SUBTYPE,Normal,0.28726542,LumA,LumA,test +MB-4878,CLAUDIN_SUBTYPE,claudin-low,0.0061572623,LumA,LumA,test +MB-7298,CLAUDIN_SUBTYPE,Basal,0.0045288745,LumB,LumB,test +MB-7298,CLAUDIN_SUBTYPE,Her2,0.0006617211,LumB,LumB,test +MB-7298,CLAUDIN_SUBTYPE,LumA,0.016409365,LumB,LumB,test +MB-7298,CLAUDIN_SUBTYPE,LumB,0.97551763,LumB,LumB,test +MB-7298,CLAUDIN_SUBTYPE,NC,0.001534101,LumB,LumB,test +MB-7298,CLAUDIN_SUBTYPE,Normal,0.00088432914,LumB,LumB,test +MB-7298,CLAUDIN_SUBTYPE,claudin-low,0.00046394696,LumB,LumB,test +MB-3254,CLAUDIN_SUBTYPE,Basal,0.00022470046,LumA,LumA,test +MB-3254,CLAUDIN_SUBTYPE,Her2,0.00016900666,LumA,LumA,test +MB-3254,CLAUDIN_SUBTYPE,LumA,0.988957,LumA,LumA,test +MB-3254,CLAUDIN_SUBTYPE,LumB,0.0009095796,LumA,LumA,test +MB-3254,CLAUDIN_SUBTYPE,NC,0.000992811,LumA,LumA,test +MB-3254,CLAUDIN_SUBTYPE,Normal,0.008545985,LumA,LumA,test +MB-3254,CLAUDIN_SUBTYPE,claudin-low,0.00020101585,LumA,LumA,test +MB-7109,CLAUDIN_SUBTYPE,Basal,0.00033619878,LumB,LumB,test +MB-7109,CLAUDIN_SUBTYPE,Her2,1.4544278e-05,LumB,LumB,test +MB-7109,CLAUDIN_SUBTYPE,LumA,4.237156e-05,LumB,LumB,test +MB-7109,CLAUDIN_SUBTYPE,LumB,0.9995695,LumB,LumB,test +MB-7109,CLAUDIN_SUBTYPE,NC,2.8508326e-05,LumB,LumB,test +MB-7109,CLAUDIN_SUBTYPE,Normal,3.7190641e-06,LumB,LumB,test +MB-7109,CLAUDIN_SUBTYPE,claudin-low,5.27827e-06,LumB,LumB,test +MB-2517,CLAUDIN_SUBTYPE,Basal,0.046940178,Her2,LumA,test +MB-2517,CLAUDIN_SUBTYPE,Her2,0.24499682,Her2,LumA,test +MB-2517,CLAUDIN_SUBTYPE,LumA,0.347526,Her2,LumA,test +MB-2517,CLAUDIN_SUBTYPE,LumB,0.19244932,Her2,LumA,test +MB-2517,CLAUDIN_SUBTYPE,NC,0.04124129,Her2,LumA,test +MB-2517,CLAUDIN_SUBTYPE,Normal,0.07804989,Her2,LumA,test +MB-2517,CLAUDIN_SUBTYPE,claudin-low,0.048796453,Her2,LumA,test +MB-0125,CLAUDIN_SUBTYPE,Basal,0.0001302165,LumB,LumA,test +MB-0125,CLAUDIN_SUBTYPE,Her2,7.813851e-05,LumB,LumA,test +MB-0125,CLAUDIN_SUBTYPE,LumA,0.9969547,LumB,LumA,test +MB-0125,CLAUDIN_SUBTYPE,LumB,0.000356139,LumB,LumA,test +MB-0125,CLAUDIN_SUBTYPE,NC,0.00034599777,LumB,LumA,test +MB-0125,CLAUDIN_SUBTYPE,Normal,0.0019296771,LumB,LumA,test +MB-0125,CLAUDIN_SUBTYPE,claudin-low,0.00020517645,LumB,LumA,test +MB-6319,CLAUDIN_SUBTYPE,Basal,0.0036058899,Normal,LumA,test +MB-6319,CLAUDIN_SUBTYPE,Her2,0.0032133383,Normal,LumA,test +MB-6319,CLAUDIN_SUBTYPE,LumA,0.90045905,Normal,LumA,test +MB-6319,CLAUDIN_SUBTYPE,LumB,0.007562116,Normal,LumA,test +MB-6319,CLAUDIN_SUBTYPE,NC,0.008644736,Normal,LumA,test +MB-6319,CLAUDIN_SUBTYPE,Normal,0.07455699,Normal,LumA,test +MB-6319,CLAUDIN_SUBTYPE,claudin-low,0.001957904,Normal,LumA,test +MB-4952,CLAUDIN_SUBTYPE,Basal,0.11574637,Her2,claudin-low,test +MB-4952,CLAUDIN_SUBTYPE,Her2,0.040334105,Her2,claudin-low,test +MB-4952,CLAUDIN_SUBTYPE,LumA,0.03434895,Her2,claudin-low,test +MB-4952,CLAUDIN_SUBTYPE,LumB,0.0046201646,Her2,claudin-low,test +MB-4952,CLAUDIN_SUBTYPE,NC,0.009911048,Her2,claudin-low,test +MB-4952,CLAUDIN_SUBTYPE,Normal,0.0069000884,Her2,claudin-low,test +MB-4952,CLAUDIN_SUBTYPE,claudin-low,0.7881393,Her2,claudin-low,test +MB-4602,CLAUDIN_SUBTYPE,Basal,0.0030722558,LumB,LumB,test +MB-4602,CLAUDIN_SUBTYPE,Her2,6.9811176e-05,LumB,LumB,test +MB-4602,CLAUDIN_SUBTYPE,LumA,0.00091308117,LumB,LumB,test +MB-4602,CLAUDIN_SUBTYPE,LumB,0.99545467,LumB,LumB,test +MB-4602,CLAUDIN_SUBTYPE,NC,0.00032160062,LumB,LumB,test +MB-4602,CLAUDIN_SUBTYPE,Normal,9.822259e-05,LumB,LumB,test +MB-4602,CLAUDIN_SUBTYPE,claudin-low,7.0369584e-05,LumB,LumB,test +MB-5382,CLAUDIN_SUBTYPE,Basal,0.0065480038,LumA,LumA,test +MB-5382,CLAUDIN_SUBTYPE,Her2,0.008923108,LumA,LumA,test +MB-5382,CLAUDIN_SUBTYPE,LumA,0.8954671,LumA,LumA,test +MB-5382,CLAUDIN_SUBTYPE,LumB,0.020320376,LumA,LumA,test +MB-5382,CLAUDIN_SUBTYPE,NC,0.012307536,LumA,LumA,test +MB-5382,CLAUDIN_SUBTYPE,Normal,0.05084869,LumA,LumA,test +MB-5382,CLAUDIN_SUBTYPE,claudin-low,0.0055852453,LumA,LumA,test +MB-3222,CLAUDIN_SUBTYPE,Basal,0.042421207,LumA,LumA,test +MB-3222,CLAUDIN_SUBTYPE,Her2,0.022832511,LumA,LumA,test +MB-3222,CLAUDIN_SUBTYPE,LumA,0.40861142,LumA,LumA,test +MB-3222,CLAUDIN_SUBTYPE,LumB,0.3943242,LumA,LumA,test +MB-3222,CLAUDIN_SUBTYPE,NC,0.041033227,LumA,LumA,test +MB-3222,CLAUDIN_SUBTYPE,Normal,0.070027925,LumA,LumA,test +MB-3222,CLAUDIN_SUBTYPE,claudin-low,0.020749426,LumA,LumA,test +MB-4351,CLAUDIN_SUBTYPE,Basal,0.39117947,Her2,Her2,test +MB-4351,CLAUDIN_SUBTYPE,Her2,0.53924966,Her2,Her2,test +MB-4351,CLAUDIN_SUBTYPE,LumA,0.0010119907,Her2,Her2,test +MB-4351,CLAUDIN_SUBTYPE,LumB,0.008567148,Her2,Her2,test +MB-4351,CLAUDIN_SUBTYPE,NC,0.002336265,Her2,Her2,test +MB-4351,CLAUDIN_SUBTYPE,Normal,0.051329356,Her2,Her2,test +MB-4351,CLAUDIN_SUBTYPE,claudin-low,0.006326082,Her2,Her2,test +MB-2801,CLAUDIN_SUBTYPE,Basal,0.0105636865,LumA,LumB,test +MB-2801,CLAUDIN_SUBTYPE,Her2,0.001414694,LumA,LumB,test +MB-2801,CLAUDIN_SUBTYPE,LumA,0.107799575,LumA,LumB,test +MB-2801,CLAUDIN_SUBTYPE,LumB,0.8685968,LumA,LumB,test +MB-2801,CLAUDIN_SUBTYPE,NC,0.005031302,LumA,LumB,test +MB-2801,CLAUDIN_SUBTYPE,Normal,0.0053568427,LumA,LumB,test +MB-2801,CLAUDIN_SUBTYPE,claudin-low,0.0012370794,LumA,LumB,test +MB-6336,CLAUDIN_SUBTYPE,Basal,0.9780357,Basal,Basal,test +MB-6336,CLAUDIN_SUBTYPE,Her2,0.0027875355,Basal,Basal,test +MB-6336,CLAUDIN_SUBTYPE,LumA,0.00062807027,Basal,Basal,test +MB-6336,CLAUDIN_SUBTYPE,LumB,0.0035593126,Basal,Basal,test +MB-6336,CLAUDIN_SUBTYPE,NC,0.0008633278,Basal,Basal,test +MB-6336,CLAUDIN_SUBTYPE,Normal,0.007401606,Basal,Basal,test +MB-6336,CLAUDIN_SUBTYPE,claudin-low,0.0067243446,Basal,Basal,test +MB-0238,CLAUDIN_SUBTYPE,Basal,0.4415894,claudin-low,claudin-low,test +MB-0238,CLAUDIN_SUBTYPE,Her2,0.0056006503,claudin-low,claudin-low,test +MB-0238,CLAUDIN_SUBTYPE,LumA,0.023654182,claudin-low,claudin-low,test +MB-0238,CLAUDIN_SUBTYPE,LumB,0.004661244,claudin-low,claudin-low,test +MB-0238,CLAUDIN_SUBTYPE,NC,0.006281509,claudin-low,claudin-low,test +MB-0238,CLAUDIN_SUBTYPE,Normal,0.005293704,claudin-low,claudin-low,test +MB-0238,CLAUDIN_SUBTYPE,claudin-low,0.5129193,claudin-low,claudin-low,test +MB-6051,CLAUDIN_SUBTYPE,Basal,7.83062e-05,LumA,LumA,test +MB-6051,CLAUDIN_SUBTYPE,Her2,4.798627e-05,LumA,LumA,test +MB-6051,CLAUDIN_SUBTYPE,LumA,0.99721503,LumA,LumA,test +MB-6051,CLAUDIN_SUBTYPE,LumB,0.0003813685,LumA,LumA,test +MB-6051,CLAUDIN_SUBTYPE,NC,0.00028162994,LumA,LumA,test +MB-6051,CLAUDIN_SUBTYPE,Normal,0.0018918527,LumA,LumA,test +MB-6051,CLAUDIN_SUBTYPE,claudin-low,0.00010395812,LumA,LumA,test +MB-0035,CLAUDIN_SUBTYPE,Basal,0.04660786,Her2,Her2,test +MB-0035,CLAUDIN_SUBTYPE,Her2,0.65994567,Her2,Her2,test +MB-0035,CLAUDIN_SUBTYPE,LumA,0.10018125,Her2,Her2,test +MB-0035,CLAUDIN_SUBTYPE,LumB,0.0510064,Her2,Her2,test +MB-0035,CLAUDIN_SUBTYPE,NC,0.01951806,Her2,Her2,test +MB-0035,CLAUDIN_SUBTYPE,Normal,0.028087057,Her2,Her2,test +MB-0035,CLAUDIN_SUBTYPE,claudin-low,0.09465375,Her2,Her2,test +MB-0258,CLAUDIN_SUBTYPE,Basal,0.01340173,LumA,LumB,test +MB-0258,CLAUDIN_SUBTYPE,Her2,0.003736662,LumA,LumB,test +MB-0258,CLAUDIN_SUBTYPE,LumA,0.22608465,LumA,LumB,test +MB-0258,CLAUDIN_SUBTYPE,LumB,0.73518604,LumA,LumB,test +MB-0258,CLAUDIN_SUBTYPE,NC,0.008630021,LumA,LumB,test +MB-0258,CLAUDIN_SUBTYPE,Normal,0.009602534,LumA,LumB,test +MB-0258,CLAUDIN_SUBTYPE,claudin-low,0.003358323,LumA,LumB,test +MB-7196,CLAUDIN_SUBTYPE,Basal,0.014710226,Her2,LumB,test +MB-7196,CLAUDIN_SUBTYPE,Her2,0.029851833,Her2,LumB,test +MB-7196,CLAUDIN_SUBTYPE,LumA,0.0073686526,Her2,LumB,test +MB-7196,CLAUDIN_SUBTYPE,LumB,0.9373308,Her2,LumB,test +MB-7196,CLAUDIN_SUBTYPE,NC,0.0043802806,Her2,LumB,test +MB-7196,CLAUDIN_SUBTYPE,Normal,0.0037208993,Her2,LumB,test +MB-7196,CLAUDIN_SUBTYPE,claudin-low,0.0026373279,Her2,LumB,test +MB-7010,CLAUDIN_SUBTYPE,Basal,0.0014947575,LumA,LumA,test +MB-7010,CLAUDIN_SUBTYPE,Her2,0.0010225666,LumA,LumA,test +MB-7010,CLAUDIN_SUBTYPE,LumA,0.97982657,LumA,LumA,test +MB-7010,CLAUDIN_SUBTYPE,LumB,0.0028756203,LumA,LumA,test +MB-7010,CLAUDIN_SUBTYPE,NC,0.0026658229,LumA,LumA,test +MB-7010,CLAUDIN_SUBTYPE,Normal,0.009690935,LumA,LumA,test +MB-7010,CLAUDIN_SUBTYPE,claudin-low,0.002423731,LumA,LumA,test +MB-0507,CLAUDIN_SUBTYPE,Basal,0.014943987,LumA,LumA,test +MB-0507,CLAUDIN_SUBTYPE,Her2,0.0040165386,LumA,LumA,test +MB-0507,CLAUDIN_SUBTYPE,LumA,0.8572474,LumA,LumA,test +MB-0507,CLAUDIN_SUBTYPE,LumB,0.07209509,LumA,LumA,test +MB-0507,CLAUDIN_SUBTYPE,NC,0.012701135,LumA,LumA,test +MB-0507,CLAUDIN_SUBTYPE,Normal,0.031073244,LumA,LumA,test +MB-0507,CLAUDIN_SUBTYPE,claudin-low,0.007922543,LumA,LumA,test +MB-3033,CLAUDIN_SUBTYPE,Basal,7.264832e-05,LumA,LumA,test +MB-3033,CLAUDIN_SUBTYPE,Her2,5.9212518e-05,LumA,LumA,test +MB-3033,CLAUDIN_SUBTYPE,LumA,0.9957065,LumA,LumA,test +MB-3033,CLAUDIN_SUBTYPE,LumB,0.0005262075,LumA,LumA,test +MB-3033,CLAUDIN_SUBTYPE,NC,0.0003474316,LumA,LumA,test +MB-3033,CLAUDIN_SUBTYPE,Normal,0.003233643,LumA,LumA,test +MB-3033,CLAUDIN_SUBTYPE,claudin-low,5.4313197e-05,LumA,LumA,test +MB-6225,CLAUDIN_SUBTYPE,Basal,0.0036495982,LumA,LumA,test +MB-6225,CLAUDIN_SUBTYPE,Her2,0.0028682956,LumA,LumA,test +MB-6225,CLAUDIN_SUBTYPE,LumA,0.92908776,LumA,LumA,test +MB-6225,CLAUDIN_SUBTYPE,LumB,0.010023851,LumA,LumA,test +MB-6225,CLAUDIN_SUBTYPE,NC,0.008721789,LumA,LumA,test +MB-6225,CLAUDIN_SUBTYPE,Normal,0.042303283,LumA,LumA,test +MB-6225,CLAUDIN_SUBTYPE,claudin-low,0.0033453663,LumA,LumA,test +MB-2917,CLAUDIN_SUBTYPE,Basal,0.9463504,Basal,Basal,test +MB-2917,CLAUDIN_SUBTYPE,Her2,0.0028290534,Basal,Basal,test +MB-2917,CLAUDIN_SUBTYPE,LumA,0.00330777,Basal,Basal,test +MB-2917,CLAUDIN_SUBTYPE,LumB,0.013542856,Basal,Basal,test +MB-2917,CLAUDIN_SUBTYPE,NC,0.0027901977,Basal,Basal,test +MB-2917,CLAUDIN_SUBTYPE,Normal,0.007519347,Basal,Basal,test +MB-2917,CLAUDIN_SUBTYPE,claudin-low,0.02366035,Basal,Basal,test +MB-4250,CLAUDIN_SUBTYPE,Basal,0.0023491702,LumA,LumA,test +MB-4250,CLAUDIN_SUBTYPE,Her2,0.0007037493,LumA,LumA,test +MB-4250,CLAUDIN_SUBTYPE,LumA,0.96705854,LumA,LumA,test +MB-4250,CLAUDIN_SUBTYPE,LumB,0.01197163,LumA,LumA,test +MB-4250,CLAUDIN_SUBTYPE,NC,0.0030324513,LumA,LumA,test +MB-4250,CLAUDIN_SUBTYPE,Normal,0.014117124,LumA,LumA,test +MB-4250,CLAUDIN_SUBTYPE,claudin-low,0.0007673572,LumA,LumA,test +MB-0897,CLAUDIN_SUBTYPE,Basal,0.0013110188,Normal,LumA,test +MB-0897,CLAUDIN_SUBTYPE,Her2,0.0011118067,Normal,LumA,test +MB-0897,CLAUDIN_SUBTYPE,LumA,0.94872904,Normal,LumA,test +MB-0897,CLAUDIN_SUBTYPE,LumB,0.0036052847,Normal,LumA,test +MB-0897,CLAUDIN_SUBTYPE,NC,0.004126412,Normal,LumA,test +MB-0897,CLAUDIN_SUBTYPE,Normal,0.04037566,Normal,LumA,test +MB-0897,CLAUDIN_SUBTYPE,claudin-low,0.00074086594,Normal,LumA,test +MB-5039,CLAUDIN_SUBTYPE,Basal,0.0922615,LumB,LumB,test +MB-5039,CLAUDIN_SUBTYPE,Her2,0.38389358,LumB,LumB,test +MB-5039,CLAUDIN_SUBTYPE,LumA,0.0108020725,LumB,LumB,test +MB-5039,CLAUDIN_SUBTYPE,LumB,0.46645644,LumB,LumB,test +MB-5039,CLAUDIN_SUBTYPE,NC,0.010844907,LumB,LumB,test +MB-5039,CLAUDIN_SUBTYPE,Normal,0.025401061,LumB,LumB,test +MB-5039,CLAUDIN_SUBTYPE,claudin-low,0.010340486,LumB,LumB,test +MB-7017,CLAUDIN_SUBTYPE,Basal,0.40332106,claudin-low,claudin-low,test +MB-7017,CLAUDIN_SUBTYPE,Her2,0.017064724,claudin-low,claudin-low,test +MB-7017,CLAUDIN_SUBTYPE,LumA,0.072031975,claudin-low,claudin-low,test +MB-7017,CLAUDIN_SUBTYPE,LumB,0.0052946857,claudin-low,claudin-low,test +MB-7017,CLAUDIN_SUBTYPE,NC,0.016066015,claudin-low,claudin-low,test +MB-7017,CLAUDIN_SUBTYPE,Normal,0.03934111,claudin-low,claudin-low,test +MB-7017,CLAUDIN_SUBTYPE,claudin-low,0.44688043,claudin-low,claudin-low,test +MB-5014,CLAUDIN_SUBTYPE,Basal,0.025201658,LumB,LumB,test +MB-5014,CLAUDIN_SUBTYPE,Her2,0.0037534859,LumB,LumB,test +MB-5014,CLAUDIN_SUBTYPE,LumA,0.024768991,LumB,LumB,test +MB-5014,CLAUDIN_SUBTYPE,LumB,0.9313439,LumB,LumB,test +MB-5014,CLAUDIN_SUBTYPE,NC,0.0062741013,LumB,LumB,test +MB-5014,CLAUDIN_SUBTYPE,Normal,0.006453664,LumB,LumB,test +MB-5014,CLAUDIN_SUBTYPE,claudin-low,0.0022041334,LumB,LumB,test +MB-4318,CLAUDIN_SUBTYPE,Basal,0.0012839211,LumB,LumB,test +MB-4318,CLAUDIN_SUBTYPE,Her2,8.11275e-05,LumB,LumB,test +MB-4318,CLAUDIN_SUBTYPE,LumA,0.0003528728,LumB,LumB,test +MB-4318,CLAUDIN_SUBTYPE,LumB,0.9980482,LumB,LumB,test +MB-4318,CLAUDIN_SUBTYPE,NC,0.00015920102,LumB,LumB,test +MB-4318,CLAUDIN_SUBTYPE,Normal,3.6170768e-05,LumB,LumB,test +MB-4318,CLAUDIN_SUBTYPE,claudin-low,3.8538776e-05,LumB,LumB,test +MB-2744,CLAUDIN_SUBTYPE,Basal,0.013939582,Normal,Normal,test +MB-2744,CLAUDIN_SUBTYPE,Her2,0.015774278,Normal,Normal,test +MB-2744,CLAUDIN_SUBTYPE,LumA,0.034546684,Normal,Normal,test +MB-2744,CLAUDIN_SUBTYPE,LumB,0.00075295026,Normal,Normal,test +MB-2744,CLAUDIN_SUBTYPE,NC,0.0058484124,Normal,Normal,test +MB-2744,CLAUDIN_SUBTYPE,Normal,0.9284294,Normal,Normal,test +MB-2744,CLAUDIN_SUBTYPE,claudin-low,0.00070866855,Normal,Normal,test +MB-7131,CLAUDIN_SUBTYPE,Basal,0.018158045,LumB,LumB,test +MB-7131,CLAUDIN_SUBTYPE,Her2,0.0040388377,LumB,LumB,test +MB-7131,CLAUDIN_SUBTYPE,LumA,0.048327167,LumB,LumB,test +MB-7131,CLAUDIN_SUBTYPE,LumB,0.9163342,LumB,LumB,test +MB-7131,CLAUDIN_SUBTYPE,NC,0.0059060436,LumB,LumB,test +MB-7131,CLAUDIN_SUBTYPE,Normal,0.0042536026,LumB,LumB,test +MB-7131,CLAUDIN_SUBTYPE,claudin-low,0.002982112,LumB,LumB,test +MB-7163,CLAUDIN_SUBTYPE,Basal,0.00030775947,LumA,LumA,test +MB-7163,CLAUDIN_SUBTYPE,Her2,0.00023453443,LumA,LumA,test +MB-7163,CLAUDIN_SUBTYPE,LumA,0.9849229,LumA,LumA,test +MB-7163,CLAUDIN_SUBTYPE,LumB,0.0014429955,LumA,LumA,test +MB-7163,CLAUDIN_SUBTYPE,NC,0.0013268874,LumA,LumA,test +MB-7163,CLAUDIN_SUBTYPE,Normal,0.01153345,LumA,LumA,test +MB-7163,CLAUDIN_SUBTYPE,claudin-low,0.0002314625,LumA,LumA,test +MB-7095,CLAUDIN_SUBTYPE,Basal,0.0032390642,LumA,LumA,test +MB-7095,CLAUDIN_SUBTYPE,Her2,0.0016781399,LumA,LumA,test +MB-7095,CLAUDIN_SUBTYPE,LumA,0.95694125,LumA,LumA,test +MB-7095,CLAUDIN_SUBTYPE,LumB,0.01621852,LumA,LumA,test +MB-7095,CLAUDIN_SUBTYPE,NC,0.0045821145,LumA,LumA,test +MB-7095,CLAUDIN_SUBTYPE,Normal,0.014794563,LumA,LumA,test +MB-7095,CLAUDIN_SUBTYPE,claudin-low,0.0025463211,LumA,LumA,test +MB-5110,CLAUDIN_SUBTYPE,Basal,0.044399105,Normal,Normal,test +MB-5110,CLAUDIN_SUBTYPE,Her2,0.110396214,Normal,Normal,test +MB-5110,CLAUDIN_SUBTYPE,LumA,0.19375534,Normal,Normal,test +MB-5110,CLAUDIN_SUBTYPE,LumB,0.0067795557,Normal,Normal,test +MB-5110,CLAUDIN_SUBTYPE,NC,0.023167932,Normal,Normal,test +MB-5110,CLAUDIN_SUBTYPE,Normal,0.6113185,Normal,Normal,test +MB-5110,CLAUDIN_SUBTYPE,claudin-low,0.010183372,Normal,Normal,test +MB-5191,CLAUDIN_SUBTYPE,Basal,0.010420343,LumA,LumA,test +MB-5191,CLAUDIN_SUBTYPE,Her2,0.011732795,LumA,LumA,test +MB-5191,CLAUDIN_SUBTYPE,LumA,0.7058615,LumA,LumA,test +MB-5191,CLAUDIN_SUBTYPE,LumB,0.0066495375,LumA,LumA,test +MB-5191,CLAUDIN_SUBTYPE,NC,0.0135594625,LumA,LumA,test +MB-5191,CLAUDIN_SUBTYPE,Normal,0.2488326,LumA,LumA,test +MB-5191,CLAUDIN_SUBTYPE,claudin-low,0.0029436091,LumA,LumA,test +MB-5052,CLAUDIN_SUBTYPE,Basal,0.017237134,claudin-low,claudin-low,test +MB-5052,CLAUDIN_SUBTYPE,Her2,0.00067498983,claudin-low,claudin-low,test +MB-5052,CLAUDIN_SUBTYPE,LumA,0.0031752023,claudin-low,claudin-low,test +MB-5052,CLAUDIN_SUBTYPE,LumB,7.484714e-05,claudin-low,claudin-low,test +MB-5052,CLAUDIN_SUBTYPE,NC,0.00051500765,claudin-low,claudin-low,test +MB-5052,CLAUDIN_SUBTYPE,Normal,0.00010504326,claudin-low,claudin-low,test +MB-5052,CLAUDIN_SUBTYPE,claudin-low,0.9782178,claudin-low,claudin-low,test +MB-5078,CLAUDIN_SUBTYPE,Basal,0.24473657,LumB,Her2,test +MB-5078,CLAUDIN_SUBTYPE,Her2,0.5051008,LumB,Her2,test +MB-5078,CLAUDIN_SUBTYPE,LumA,0.014035251,LumB,Her2,test +MB-5078,CLAUDIN_SUBTYPE,LumB,0.0702858,LumB,Her2,test +MB-5078,CLAUDIN_SUBTYPE,NC,0.017791374,LumB,Her2,test +MB-5078,CLAUDIN_SUBTYPE,Normal,0.12457725,LumB,Her2,test +MB-5078,CLAUDIN_SUBTYPE,claudin-low,0.023473049,LumB,Her2,test +MB-7078,CLAUDIN_SUBTYPE,Basal,0.01774906,claudin-low,claudin-low,test +MB-7078,CLAUDIN_SUBTYPE,Her2,0.0010599276,claudin-low,claudin-low,test +MB-7078,CLAUDIN_SUBTYPE,LumA,0.0016910788,claudin-low,claudin-low,test +MB-7078,CLAUDIN_SUBTYPE,LumB,3.468118e-05,claudin-low,claudin-low,test +MB-7078,CLAUDIN_SUBTYPE,NC,0.00024689283,claudin-low,claudin-low,test +MB-7078,CLAUDIN_SUBTYPE,Normal,5.491362e-05,claudin-low,claudin-low,test +MB-7078,CLAUDIN_SUBTYPE,claudin-low,0.97916347,claudin-low,claudin-low,test +MB-7279,CLAUDIN_SUBTYPE,Basal,0.10951925,Her2,Her2,test +MB-7279,CLAUDIN_SUBTYPE,Her2,0.7361225,Her2,Her2,test +MB-7279,CLAUDIN_SUBTYPE,LumA,0.003050818,Her2,Her2,test +MB-7279,CLAUDIN_SUBTYPE,LumB,0.095851846,Her2,Her2,test +MB-7279,CLAUDIN_SUBTYPE,NC,0.006879992,Her2,Her2,test +MB-7279,CLAUDIN_SUBTYPE,Normal,0.041317035,Her2,Her2,test +MB-7279,CLAUDIN_SUBTYPE,claudin-low,0.007258661,Her2,Her2,test +MB-5172,CLAUDIN_SUBTYPE,Basal,0.017404724,Her2,Her2,test +MB-5172,CLAUDIN_SUBTYPE,Her2,0.93626463,Her2,Her2,test +MB-5172,CLAUDIN_SUBTYPE,LumA,0.0017596051,Her2,Her2,test +MB-5172,CLAUDIN_SUBTYPE,LumB,0.025243178,Her2,Her2,test +MB-5172,CLAUDIN_SUBTYPE,NC,0.0027755275,Her2,Her2,test +MB-5172,CLAUDIN_SUBTYPE,Normal,0.011186486,Her2,Her2,test +MB-5172,CLAUDIN_SUBTYPE,claudin-low,0.0053658914,Her2,Her2,test +MB-5138,CLAUDIN_SUBTYPE,Basal,0.96672106,Basal,Basal,test +MB-5138,CLAUDIN_SUBTYPE,Her2,0.00211543,Basal,Basal,test +MB-5138,CLAUDIN_SUBTYPE,LumA,0.001618966,Basal,Basal,test +MB-5138,CLAUDIN_SUBTYPE,LumB,0.0102585135,Basal,Basal,test +MB-5138,CLAUDIN_SUBTYPE,NC,0.0016664847,Basal,Basal,test +MB-5138,CLAUDIN_SUBTYPE,Normal,0.0061687264,Basal,Basal,test +MB-5138,CLAUDIN_SUBTYPE,claudin-low,0.011450917,Basal,Basal,test +MB-0512,CLAUDIN_SUBTYPE,Basal,0.023697501,LumA,LumB,test +MB-0512,CLAUDIN_SUBTYPE,Her2,0.0063531334,LumA,LumB,test +MB-0512,CLAUDIN_SUBTYPE,LumA,0.35753232,LumA,LumB,test +MB-0512,CLAUDIN_SUBTYPE,LumB,0.5736426,LumA,LumB,test +MB-0512,CLAUDIN_SUBTYPE,NC,0.01409163,LumA,LumB,test +MB-0512,CLAUDIN_SUBTYPE,Normal,0.016634844,LumA,LumB,test +MB-0512,CLAUDIN_SUBTYPE,claudin-low,0.008047989,LumA,LumB,test +MB-7173,CLAUDIN_SUBTYPE,Basal,0.01869835,LumA,LumB,test +MB-7173,CLAUDIN_SUBTYPE,Her2,0.006758309,LumA,LumB,test +MB-7173,CLAUDIN_SUBTYPE,LumA,0.28442663,LumA,LumB,test +MB-7173,CLAUDIN_SUBTYPE,LumB,0.658036,LumA,LumB,test +MB-7173,CLAUDIN_SUBTYPE,NC,0.011925883,LumA,LumB,test +MB-7173,CLAUDIN_SUBTYPE,Normal,0.016036578,LumA,LumB,test +MB-7173,CLAUDIN_SUBTYPE,claudin-low,0.004118198,LumA,LumB,test +MB-0288,CLAUDIN_SUBTYPE,Basal,0.0023877192,Normal,LumA,test +MB-0288,CLAUDIN_SUBTYPE,Her2,0.0014660286,Normal,LumA,test +MB-0288,CLAUDIN_SUBTYPE,LumA,0.94829893,Normal,LumA,test +MB-0288,CLAUDIN_SUBTYPE,LumB,0.017367525,Normal,LumA,test +MB-0288,CLAUDIN_SUBTYPE,NC,0.0046949503,Normal,LumA,test +MB-0288,CLAUDIN_SUBTYPE,Normal,0.02476029,Normal,LumA,test +MB-0288,CLAUDIN_SUBTYPE,claudin-low,0.0010246839,Normal,LumA,test +MB-5651,CLAUDIN_SUBTYPE,Basal,0.1600857,claudin-low,claudin-low,test +MB-5651,CLAUDIN_SUBTYPE,Her2,0.002128136,claudin-low,claudin-low,test +MB-5651,CLAUDIN_SUBTYPE,LumA,0.02194875,claudin-low,claudin-low,test +MB-5651,CLAUDIN_SUBTYPE,LumB,0.0018125367,claudin-low,claudin-low,test +MB-5651,CLAUDIN_SUBTYPE,NC,0.0037911488,claudin-low,claudin-low,test +MB-5651,CLAUDIN_SUBTYPE,Normal,0.0014305927,claudin-low,claudin-low,test +MB-5651,CLAUDIN_SUBTYPE,claudin-low,0.80880314,claudin-low,claudin-low,test +MB-4706,CLAUDIN_SUBTYPE,Basal,0.0035911708,LumA,LumA,test +MB-4706,CLAUDIN_SUBTYPE,Her2,0.0011486132,LumA,LumA,test +MB-4706,CLAUDIN_SUBTYPE,LumA,0.9681369,LumA,LumA,test +MB-4706,CLAUDIN_SUBTYPE,LumB,0.0024275337,LumA,LumA,test +MB-4706,CLAUDIN_SUBTYPE,NC,0.0035141793,LumA,LumA,test +MB-4706,CLAUDIN_SUBTYPE,Normal,0.008218716,LumA,LumA,test +MB-4706,CLAUDIN_SUBTYPE,claudin-low,0.01296284,LumA,LumA,test +MB-0229,CLAUDIN_SUBTYPE,Basal,0.0027642664,LumA,LumA,test +MB-0229,CLAUDIN_SUBTYPE,Her2,0.0025236614,LumA,LumA,test +MB-0229,CLAUDIN_SUBTYPE,LumA,0.942827,LumA,LumA,test +MB-0229,CLAUDIN_SUBTYPE,LumB,0.021635422,LumA,LumA,test +MB-0229,CLAUDIN_SUBTYPE,NC,0.0058930004,LumA,LumA,test +MB-0229,CLAUDIN_SUBTYPE,Normal,0.02232362,LumA,LumA,test +MB-0229,CLAUDIN_SUBTYPE,claudin-low,0.0020330064,LumA,LumA,test +MB-5173,CLAUDIN_SUBTYPE,Basal,0.843011,Basal,Basal,test +MB-5173,CLAUDIN_SUBTYPE,Her2,0.0052611968,Basal,Basal,test +MB-5173,CLAUDIN_SUBTYPE,LumA,0.004134291,Basal,Basal,test +MB-5173,CLAUDIN_SUBTYPE,LumB,0.0021304502,Basal,Basal,test +MB-5173,CLAUDIN_SUBTYPE,NC,0.0023225532,Basal,Basal,test +MB-5173,CLAUDIN_SUBTYPE,Normal,0.00675861,Basal,Basal,test +MB-5173,CLAUDIN_SUBTYPE,claudin-low,0.13638191,Basal,Basal,test +MB-6273,CLAUDIN_SUBTYPE,Basal,0.0009950558,LumA,LumA,test +MB-6273,CLAUDIN_SUBTYPE,Her2,0.0009799494,LumA,LumA,test +MB-6273,CLAUDIN_SUBTYPE,LumA,0.93644994,LumA,LumA,test +MB-6273,CLAUDIN_SUBTYPE,LumB,0.0014936096,LumA,LumA,test +MB-6273,CLAUDIN_SUBTYPE,NC,0.0025053897,LumA,LumA,test +MB-6273,CLAUDIN_SUBTYPE,Normal,0.057265796,LumA,LumA,test +MB-6273,CLAUDIN_SUBTYPE,claudin-low,0.00031018013,LumA,LumA,test +MB-2927,CLAUDIN_SUBTYPE,Basal,0.046562012,LumA,LumA,test +MB-2927,CLAUDIN_SUBTYPE,Her2,0.0032901752,LumA,LumA,test +MB-2927,CLAUDIN_SUBTYPE,LumA,0.6954671,LumA,LumA,test +MB-2927,CLAUDIN_SUBTYPE,LumB,0.1894075,LumA,LumA,test +MB-2927,CLAUDIN_SUBTYPE,NC,0.016318189,LumA,LumA,test +MB-2927,CLAUDIN_SUBTYPE,Normal,0.042053856,LumA,LumA,test +MB-2927,CLAUDIN_SUBTYPE,claudin-low,0.0069011543,LumA,LumA,test +MB-0227,CLAUDIN_SUBTYPE,Basal,0.0040115644,LumA,LumA,test +MB-0227,CLAUDIN_SUBTYPE,Her2,0.0016656937,LumA,LumA,test +MB-0227,CLAUDIN_SUBTYPE,LumA,0.9292107,LumA,LumA,test +MB-0227,CLAUDIN_SUBTYPE,LumB,0.020547125,LumA,LumA,test +MB-0227,CLAUDIN_SUBTYPE,NC,0.0065998696,LumA,LumA,test +MB-0227,CLAUDIN_SUBTYPE,Normal,0.036567695,LumA,LumA,test +MB-0227,CLAUDIN_SUBTYPE,claudin-low,0.0013973863,LumA,LumA,test +MB-6168,CLAUDIN_SUBTYPE,Basal,0.002689905,LumA,LumA,test +MB-6168,CLAUDIN_SUBTYPE,Her2,0.0016274673,LumA,LumA,test +MB-6168,CLAUDIN_SUBTYPE,LumA,0.9593509,LumA,LumA,test +MB-6168,CLAUDIN_SUBTYPE,LumB,0.0038674246,LumA,LumA,test +MB-6168,CLAUDIN_SUBTYPE,NC,0.0054613915,LumA,LumA,test +MB-6168,CLAUDIN_SUBTYPE,Normal,0.022599677,LumA,LumA,test +MB-6168,CLAUDIN_SUBTYPE,claudin-low,0.0044031995,LumA,LumA,test +MB-4843,CLAUDIN_SUBTYPE,Basal,0.0002493313,LumA,LumA,test +MB-4843,CLAUDIN_SUBTYPE,Her2,0.00020575435,LumA,LumA,test +MB-4843,CLAUDIN_SUBTYPE,LumA,0.99021494,LumA,LumA,test +MB-4843,CLAUDIN_SUBTYPE,LumB,0.000960113,LumA,LumA,test +MB-4843,CLAUDIN_SUBTYPE,NC,0.00096211996,LumA,LumA,test +MB-4843,CLAUDIN_SUBTYPE,Normal,0.007170022,LumA,LumA,test +MB-4843,CLAUDIN_SUBTYPE,claudin-low,0.00023764305,LumA,LumA,test +MB-7171,CLAUDIN_SUBTYPE,Basal,0.057506997,LumB,LumB,test +MB-7171,CLAUDIN_SUBTYPE,Her2,0.026993234,LumB,LumB,test +MB-7171,CLAUDIN_SUBTYPE,LumA,0.14533858,LumB,LumB,test +MB-7171,CLAUDIN_SUBTYPE,LumB,0.698943,LumB,LumB,test +MB-7171,CLAUDIN_SUBTYPE,NC,0.022895383,LumB,LumB,test +MB-7171,CLAUDIN_SUBTYPE,Normal,0.037279457,LumB,LumB,test +MB-7171,CLAUDIN_SUBTYPE,claudin-low,0.01104336,LumB,LumB,test +MB-4722,CLAUDIN_SUBTYPE,Basal,0.0013486504,LumA,LumA,test +MB-4722,CLAUDIN_SUBTYPE,Her2,0.00082986936,LumA,LumA,test +MB-4722,CLAUDIN_SUBTYPE,LumA,0.9703522,LumA,LumA,test +MB-4722,CLAUDIN_SUBTYPE,LumB,0.010965341,LumA,LumA,test +MB-4722,CLAUDIN_SUBTYPE,NC,0.0027530408,LumA,LumA,test +MB-4722,CLAUDIN_SUBTYPE,Normal,0.013086699,LumA,LumA,test +MB-4722,CLAUDIN_SUBTYPE,claudin-low,0.0006642989,LumA,LumA,test +MB-4825,CLAUDIN_SUBTYPE,Basal,0.010020296,LumA,LumA,test +MB-4825,CLAUDIN_SUBTYPE,Her2,0.014577018,LumA,LumA,test +MB-4825,CLAUDIN_SUBTYPE,LumA,0.7748071,LumA,LumA,test +MB-4825,CLAUDIN_SUBTYPE,LumB,0.12119704,LumA,LumA,test +MB-4825,CLAUDIN_SUBTYPE,NC,0.019617897,LumA,LumA,test +MB-4825,CLAUDIN_SUBTYPE,Normal,0.052143298,LumA,LumA,test +MB-4825,CLAUDIN_SUBTYPE,claudin-low,0.007637305,LumA,LumA,test +MB-7270,CLAUDIN_SUBTYPE,Basal,0.4941126,Basal,Basal,test +MB-7270,CLAUDIN_SUBTYPE,Her2,0.46343333,Basal,Basal,test +MB-7270,CLAUDIN_SUBTYPE,LumA,0.00010576815,Basal,Basal,test +MB-7270,CLAUDIN_SUBTYPE,LumB,0.030268583,Basal,Basal,test +MB-7270,CLAUDIN_SUBTYPE,NC,0.00058804115,Basal,Basal,test +MB-7270,CLAUDIN_SUBTYPE,Normal,0.010139465,Basal,Basal,test +MB-7270,CLAUDIN_SUBTYPE,claudin-low,0.0013523471,Basal,Basal,test +MB-0503,CLAUDIN_SUBTYPE,Basal,0.0030855036,LumA,LumA,test +MB-0503,CLAUDIN_SUBTYPE,Her2,0.002020763,LumA,LumA,test +MB-0503,CLAUDIN_SUBTYPE,LumA,0.94532907,LumA,LumA,test +MB-0503,CLAUDIN_SUBTYPE,LumB,0.0073841014,LumA,LumA,test +MB-0503,CLAUDIN_SUBTYPE,NC,0.006135566,LumA,LumA,test +MB-0503,CLAUDIN_SUBTYPE,Normal,0.03352952,LumA,LumA,test +MB-0503,CLAUDIN_SUBTYPE,claudin-low,0.0025155037,LumA,LumA,test +MB-3123,CLAUDIN_SUBTYPE,Basal,0.9821264,Basal,Basal,test +MB-3123,CLAUDIN_SUBTYPE,Her2,0.0019536368,Basal,Basal,test +MB-3123,CLAUDIN_SUBTYPE,LumA,0.0004023898,Basal,Basal,test +MB-3123,CLAUDIN_SUBTYPE,LumB,0.0010834255,Basal,Basal,test +MB-3123,CLAUDIN_SUBTYPE,NC,0.00046778435,Basal,Basal,test +MB-3123,CLAUDIN_SUBTYPE,Normal,0.0045061954,Basal,Basal,test +MB-3123,CLAUDIN_SUBTYPE,claudin-low,0.009460044,Basal,Basal,test +MB-4323,CLAUDIN_SUBTYPE,Basal,0.0014945951,LumA,LumA,test +MB-4323,CLAUDIN_SUBTYPE,Her2,0.002491133,LumA,LumA,test +MB-4323,CLAUDIN_SUBTYPE,LumA,0.9779848,LumA,LumA,test +MB-4323,CLAUDIN_SUBTYPE,LumB,0.006838652,LumA,LumA,test +MB-4323,CLAUDIN_SUBTYPE,NC,0.002284689,LumA,LumA,test +MB-4323,CLAUDIN_SUBTYPE,Normal,0.006784686,LumA,LumA,test +MB-4323,CLAUDIN_SUBTYPE,claudin-low,0.002121536,LumA,LumA,test +MB-3371,CLAUDIN_SUBTYPE,Basal,0.00894019,LumB,LumB,test +MB-3371,CLAUDIN_SUBTYPE,Her2,0.0068824715,LumB,LumB,test +MB-3371,CLAUDIN_SUBTYPE,LumA,0.092367746,LumB,LumB,test +MB-3371,CLAUDIN_SUBTYPE,LumB,0.88011366,LumB,LumB,test +MB-3371,CLAUDIN_SUBTYPE,NC,0.0051434976,LumB,LumB,test +MB-3371,CLAUDIN_SUBTYPE,Normal,0.004246169,LumB,LumB,test +MB-3371,CLAUDIN_SUBTYPE,claudin-low,0.0023062571,LumB,LumB,test +MB-6122,CLAUDIN_SUBTYPE,Basal,0.48250183,Basal,Basal,test +MB-6122,CLAUDIN_SUBTYPE,Her2,0.026105376,Basal,Basal,test +MB-6122,CLAUDIN_SUBTYPE,LumA,0.024484828,Basal,Basal,test +MB-6122,CLAUDIN_SUBTYPE,LumB,0.005265373,Basal,Basal,test +MB-6122,CLAUDIN_SUBTYPE,NC,0.010705925,Basal,Basal,test +MB-6122,CLAUDIN_SUBTYPE,Normal,0.023399375,Basal,Basal,test +MB-6122,CLAUDIN_SUBTYPE,claudin-low,0.42753732,Basal,Basal,test +MB-4702,CLAUDIN_SUBTYPE,Basal,0.028206088,LumB,LumB,test +MB-4702,CLAUDIN_SUBTYPE,Her2,0.0001712073,LumB,LumB,test +MB-4702,CLAUDIN_SUBTYPE,LumA,0.0004408314,LumB,LumB,test +MB-4702,CLAUDIN_SUBTYPE,LumB,0.9703325,LumB,LumB,test +MB-4702,CLAUDIN_SUBTYPE,NC,0.0004429989,LumB,LumB,test +MB-4702,CLAUDIN_SUBTYPE,Normal,0.000285439,LumB,LumB,test +MB-4702,CLAUDIN_SUBTYPE,claudin-low,0.00012083885,LumB,LumB,test +MB-5596,CLAUDIN_SUBTYPE,Basal,3.3043274e-05,LumA,LumA,test +MB-5596,CLAUDIN_SUBTYPE,Her2,2.7676808e-05,LumA,LumA,test +MB-5596,CLAUDIN_SUBTYPE,LumA,0.99593157,LumA,LumA,test +MB-5596,CLAUDIN_SUBTYPE,LumB,0.00012081484,LumA,LumA,test +MB-5596,CLAUDIN_SUBTYPE,NC,0.0002183972,LumA,LumA,test +MB-5596,CLAUDIN_SUBTYPE,Normal,0.0036440692,LumA,LumA,test +MB-5596,CLAUDIN_SUBTYPE,claudin-low,2.4293075e-05,LumA,LumA,test +MB-0471,CLAUDIN_SUBTYPE,Basal,0.011027864,LumA,LumB,test +MB-0471,CLAUDIN_SUBTYPE,Her2,0.018887326,LumA,LumB,test +MB-0471,CLAUDIN_SUBTYPE,LumA,0.0595816,LumA,LumB,test +MB-0471,CLAUDIN_SUBTYPE,LumB,0.89380926,LumA,LumB,test +MB-0471,CLAUDIN_SUBTYPE,NC,0.006550939,LumA,LumB,test +MB-0471,CLAUDIN_SUBTYPE,Normal,0.0039617484,LumA,LumB,test +MB-0471,CLAUDIN_SUBTYPE,claudin-low,0.006181321,LumA,LumB,test +MB-5384,CLAUDIN_SUBTYPE,Basal,0.120825455,LumA,LumB,test +MB-5384,CLAUDIN_SUBTYPE,Her2,0.13836564,LumA,LumB,test +MB-5384,CLAUDIN_SUBTYPE,LumA,0.030039953,LumA,LumB,test +MB-5384,CLAUDIN_SUBTYPE,LumB,0.61667645,LumA,LumB,test +MB-5384,CLAUDIN_SUBTYPE,NC,0.02188759,LumA,LumB,test +MB-5384,CLAUDIN_SUBTYPE,Normal,0.058822203,LumA,LumB,test +MB-5384,CLAUDIN_SUBTYPE,claudin-low,0.013382754,LumA,LumB,test +MB-4779,CLAUDIN_SUBTYPE,Basal,6.0203776e-05,LumA,LumA,test +MB-4779,CLAUDIN_SUBTYPE,Her2,4.24379e-05,LumA,LumA,test +MB-4779,CLAUDIN_SUBTYPE,LumA,0.99622476,LumA,LumA,test +MB-4779,CLAUDIN_SUBTYPE,LumB,0.0002118298,LumA,LumA,test +MB-4779,CLAUDIN_SUBTYPE,NC,0.0003207959,LumA,LumA,test +MB-4779,CLAUDIN_SUBTYPE,Normal,0.0030641153,LumA,LumA,test +MB-4779,CLAUDIN_SUBTYPE,claudin-low,7.588554e-05,LumA,LumA,test +MB-5396,CLAUDIN_SUBTYPE,Basal,0.0028882464,LumB,LumB,test +MB-5396,CLAUDIN_SUBTYPE,Her2,0.000297021,LumB,LumB,test +MB-5396,CLAUDIN_SUBTYPE,LumA,0.012122595,LumB,LumB,test +MB-5396,CLAUDIN_SUBTYPE,LumB,0.98310995,LumB,LumB,test +MB-5396,CLAUDIN_SUBTYPE,NC,0.00087821606,LumB,LumB,test +MB-5396,CLAUDIN_SUBTYPE,Normal,0.00047854017,LumB,LumB,test +MB-5396,CLAUDIN_SUBTYPE,claudin-low,0.0002253449,LumB,LumB,test +MB-5638,CLAUDIN_SUBTYPE,Basal,0.057065018,LumA,LumA,test +MB-5638,CLAUDIN_SUBTYPE,Her2,0.006962372,LumA,LumA,test +MB-5638,CLAUDIN_SUBTYPE,LumA,0.5261452,LumA,LumA,test +MB-5638,CLAUDIN_SUBTYPE,LumB,0.35459816,LumA,LumA,test +MB-5638,CLAUDIN_SUBTYPE,NC,0.01666393,LumA,LumA,test +MB-5638,CLAUDIN_SUBTYPE,Normal,0.019745486,LumA,LumA,test +MB-5638,CLAUDIN_SUBTYPE,claudin-low,0.018819774,LumA,LumA,test +MB-0573,CLAUDIN_SUBTYPE,Basal,0.08095056,claudin-low,claudin-low,test +MB-0573,CLAUDIN_SUBTYPE,Her2,0.026777864,claudin-low,claudin-low,test +MB-0573,CLAUDIN_SUBTYPE,LumA,0.061370127,claudin-low,claudin-low,test +MB-0573,CLAUDIN_SUBTYPE,LumB,0.0053074453,claudin-low,claudin-low,test +MB-0573,CLAUDIN_SUBTYPE,NC,0.013409102,claudin-low,claudin-low,test +MB-0573,CLAUDIN_SUBTYPE,Normal,0.007857346,claudin-low,claudin-low,test +MB-0573,CLAUDIN_SUBTYPE,claudin-low,0.80432755,claudin-low,claudin-low,test +MB-4679,CLAUDIN_SUBTYPE,Basal,0.98210365,Basal,Basal,test +MB-4679,CLAUDIN_SUBTYPE,Her2,0.0006832666,Basal,Basal,test +MB-4679,CLAUDIN_SUBTYPE,LumA,0.00066558336,Basal,Basal,test +MB-4679,CLAUDIN_SUBTYPE,LumB,0.003039096,Basal,Basal,test +MB-4679,CLAUDIN_SUBTYPE,NC,0.0006039078,Basal,Basal,test +MB-4679,CLAUDIN_SUBTYPE,Normal,0.0020943922,Basal,Basal,test +MB-4679,CLAUDIN_SUBTYPE,claudin-low,0.010810168,Basal,Basal,test +MB-5645,CLAUDIN_SUBTYPE,Basal,0.015252581,LumA,LumA,test +MB-5645,CLAUDIN_SUBTYPE,Her2,0.005437457,LumA,LumA,test +MB-5645,CLAUDIN_SUBTYPE,LumA,0.7025358,LumA,LumA,test +MB-5645,CLAUDIN_SUBTYPE,LumB,0.24427547,LumA,LumA,test +MB-5645,CLAUDIN_SUBTYPE,NC,0.010356465,LumA,LumA,test +MB-5645,CLAUDIN_SUBTYPE,Normal,0.013240908,LumA,LumA,test +MB-5645,CLAUDIN_SUBTYPE,claudin-low,0.008901234,LumA,LumA,test +MB-0389,CLAUDIN_SUBTYPE,Basal,0.012667824,LumB,LumB,test +MB-0389,CLAUDIN_SUBTYPE,Her2,0.0077983444,LumB,LumB,test +MB-0389,CLAUDIN_SUBTYPE,LumA,0.16492866,LumB,LumB,test +MB-0389,CLAUDIN_SUBTYPE,LumB,0.78598756,LumB,LumB,test +MB-0389,CLAUDIN_SUBTYPE,NC,0.011555692,LumB,LumB,test +MB-0389,CLAUDIN_SUBTYPE,Normal,0.012638524,LumB,LumB,test +MB-0389,CLAUDIN_SUBTYPE,claudin-low,0.0044234637,LumB,LumB,test +MB-0484,CLAUDIN_SUBTYPE,Basal,0.05460147,Her2,LumB,test +MB-0484,CLAUDIN_SUBTYPE,Her2,0.178826,Her2,LumB,test +MB-0484,CLAUDIN_SUBTYPE,LumA,0.0651101,Her2,LumB,test +MB-0484,CLAUDIN_SUBTYPE,LumB,0.6097517,Her2,LumB,test +MB-0484,CLAUDIN_SUBTYPE,NC,0.028694307,Her2,LumB,test +MB-0484,CLAUDIN_SUBTYPE,Normal,0.029898899,Her2,LumB,test +MB-0484,CLAUDIN_SUBTYPE,claudin-low,0.03311738,Her2,LumB,test +MB-4992,CLAUDIN_SUBTYPE,Basal,0.013725633,LumA,LumA,test +MB-4992,CLAUDIN_SUBTYPE,Her2,0.023836475,LumA,LumA,test +MB-4992,CLAUDIN_SUBTYPE,LumA,0.6269136,LumA,LumA,test +MB-4992,CLAUDIN_SUBTYPE,LumB,0.00790964,LumA,LumA,test +MB-4992,CLAUDIN_SUBTYPE,NC,0.015937628,LumA,LumA,test +MB-4992,CLAUDIN_SUBTYPE,Normal,0.30776274,LumA,LumA,test +MB-4992,CLAUDIN_SUBTYPE,claudin-low,0.003914339,LumA,LumA,test +MB-0224,CLAUDIN_SUBTYPE,Basal,0.0020582175,LumA,LumA,test +MB-0224,CLAUDIN_SUBTYPE,Her2,0.0011007835,LumA,LumA,test +MB-0224,CLAUDIN_SUBTYPE,LumA,0.9484927,LumA,LumA,test +MB-0224,CLAUDIN_SUBTYPE,LumB,0.011243571,LumA,LumA,test +MB-0224,CLAUDIN_SUBTYPE,NC,0.0051305867,LumA,LumA,test +MB-0224,CLAUDIN_SUBTYPE,Normal,0.030965006,LumA,LumA,test +MB-0224,CLAUDIN_SUBTYPE,claudin-low,0.0010090226,LumA,LumA,test +MB-7235,CLAUDIN_SUBTYPE,Basal,0.0020686353,LumA,LumA,test +MB-7235,CLAUDIN_SUBTYPE,Her2,0.0014450907,LumA,LumA,test +MB-7235,CLAUDIN_SUBTYPE,LumA,0.9449625,LumA,LumA,test +MB-7235,CLAUDIN_SUBTYPE,LumB,0.0072197164,LumA,LumA,test +MB-7235,CLAUDIN_SUBTYPE,NC,0.004341549,LumA,LumA,test +MB-7235,CLAUDIN_SUBTYPE,Normal,0.039146822,LumA,LumA,test +MB-7235,CLAUDIN_SUBTYPE,claudin-low,0.00081556465,LumA,LumA,test +MB-3355,CLAUDIN_SUBTYPE,Basal,0.29062548,Her2,Her2,test +MB-3355,CLAUDIN_SUBTYPE,Her2,0.33545223,Her2,Her2,test +MB-3355,CLAUDIN_SUBTYPE,LumA,0.023453575,Her2,Her2,test +MB-3355,CLAUDIN_SUBTYPE,LumB,0.025373712,Her2,Her2,test +MB-3355,CLAUDIN_SUBTYPE,NC,0.020860702,Her2,Her2,test +MB-3355,CLAUDIN_SUBTYPE,Normal,0.27616632,Her2,Her2,test +MB-3355,CLAUDIN_SUBTYPE,claudin-low,0.02806806,Her2,Her2,test +MB-7217,CLAUDIN_SUBTYPE,Basal,0.057230562,LumA,LumA,test +MB-7217,CLAUDIN_SUBTYPE,Her2,0.019055383,LumA,LumA,test +MB-7217,CLAUDIN_SUBTYPE,LumA,0.6031853,LumA,LumA,test +MB-7217,CLAUDIN_SUBTYPE,LumB,0.013952217,LumA,LumA,test +MB-7217,CLAUDIN_SUBTYPE,NC,0.03455719,LumA,LumA,test +MB-7217,CLAUDIN_SUBTYPE,Normal,0.055566996,LumA,LumA,test +MB-7217,CLAUDIN_SUBTYPE,claudin-low,0.21645242,LumA,LumA,test +MB-2754,CLAUDIN_SUBTYPE,Basal,0.13703783,Normal,Normal,test +MB-2754,CLAUDIN_SUBTYPE,Her2,0.3746773,Normal,Normal,test +MB-2754,CLAUDIN_SUBTYPE,LumA,0.0337689,Normal,Normal,test +MB-2754,CLAUDIN_SUBTYPE,LumB,0.0121790925,Normal,Normal,test +MB-2754,CLAUDIN_SUBTYPE,NC,0.02043624,Normal,Normal,test +MB-2754,CLAUDIN_SUBTYPE,Normal,0.39898866,Normal,Normal,test +MB-2754,CLAUDIN_SUBTYPE,claudin-low,0.022912063,Normal,Normal,test +MB-5478,CLAUDIN_SUBTYPE,Basal,0.0038339214,LumA,LumA,test +MB-5478,CLAUDIN_SUBTYPE,Her2,0.0020369552,LumA,LumA,test +MB-5478,CLAUDIN_SUBTYPE,LumA,0.95990103,LumA,LumA,test +MB-5478,CLAUDIN_SUBTYPE,LumB,0.008388593,LumA,LumA,test +MB-5478,CLAUDIN_SUBTYPE,NC,0.005127524,LumA,LumA,test +MB-5478,CLAUDIN_SUBTYPE,Normal,0.013894472,LumA,LumA,test +MB-5478,CLAUDIN_SUBTYPE,claudin-low,0.0068174493,LumA,LumA,test +MB-3363,CLAUDIN_SUBTYPE,Basal,0.9548865,Basal,Basal,test +MB-3363,CLAUDIN_SUBTYPE,Her2,0.0014532984,Basal,Basal,test +MB-3363,CLAUDIN_SUBTYPE,LumA,0.00031503756,Basal,Basal,test +MB-3363,CLAUDIN_SUBTYPE,LumB,0.03756875,Basal,Basal,test +MB-3363,CLAUDIN_SUBTYPE,NC,0.00079227326,Basal,Basal,test +MB-3363,CLAUDIN_SUBTYPE,Normal,0.0031477523,Basal,Basal,test +MB-3363,CLAUDIN_SUBTYPE,claudin-low,0.0018362998,Basal,Basal,test +MB-7250,CLAUDIN_SUBTYPE,Basal,0.008389959,Her2,Her2,test +MB-7250,CLAUDIN_SUBTYPE,Her2,0.98213756,Her2,Her2,test +MB-7250,CLAUDIN_SUBTYPE,LumA,0.00011490752,Her2,Her2,test +MB-7250,CLAUDIN_SUBTYPE,LumB,0.0010611825,Her2,Her2,test +MB-7250,CLAUDIN_SUBTYPE,NC,0.0002975422,Her2,Her2,test +MB-7250,CLAUDIN_SUBTYPE,Normal,0.0073320502,Her2,Her2,test +MB-7250,CLAUDIN_SUBTYPE,claudin-low,0.0006668307,Her2,Her2,test +MB-3466,CLAUDIN_SUBTYPE,Basal,0.0054750456,Her2,LumB,test +MB-3466,CLAUDIN_SUBTYPE,Her2,0.003964098,Her2,LumB,test +MB-3466,CLAUDIN_SUBTYPE,LumA,0.0035540352,Her2,LumB,test +MB-3466,CLAUDIN_SUBTYPE,LumB,0.98412436,Her2,LumB,test +MB-3466,CLAUDIN_SUBTYPE,NC,0.001498746,Her2,LumB,test +MB-3466,CLAUDIN_SUBTYPE,Normal,0.0005833299,Her2,LumB,test +MB-3466,CLAUDIN_SUBTYPE,claudin-low,0.0008004121,Her2,LumB,test +MB-5063,CLAUDIN_SUBTYPE,Basal,0.24830134,Her2,Her2,test +MB-5063,CLAUDIN_SUBTYPE,Her2,0.602954,Her2,Her2,test +MB-5063,CLAUDIN_SUBTYPE,LumA,0.0059241354,Her2,Her2,test +MB-5063,CLAUDIN_SUBTYPE,LumB,0.053600147,Her2,Her2,test +MB-5063,CLAUDIN_SUBTYPE,NC,0.009340591,Her2,Her2,test +MB-5063,CLAUDIN_SUBTYPE,Normal,0.059576664,Her2,Her2,test +MB-5063,CLAUDIN_SUBTYPE,claudin-low,0.020303164,Her2,Her2,test +MB-6190,CLAUDIN_SUBTYPE,Basal,0.010308503,LumA,LumA,test +MB-6190,CLAUDIN_SUBTYPE,Her2,0.016824046,LumA,LumA,test +MB-6190,CLAUDIN_SUBTYPE,LumA,0.8415277,LumA,LumA,test +MB-6190,CLAUDIN_SUBTYPE,LumB,0.06703427,LumA,LumA,test +MB-6190,CLAUDIN_SUBTYPE,NC,0.015910096,LumA,LumA,test +MB-6190,CLAUDIN_SUBTYPE,Normal,0.035777118,LumA,LumA,test +MB-6190,CLAUDIN_SUBTYPE,claudin-low,0.012618329,LumA,LumA,test +MB-5155,CLAUDIN_SUBTYPE,Basal,0.000935166,Normal,LumA,test +MB-5155,CLAUDIN_SUBTYPE,Her2,0.00056379044,Normal,LumA,test +MB-5155,CLAUDIN_SUBTYPE,LumA,0.97078305,Normal,LumA,test +MB-5155,CLAUDIN_SUBTYPE,LumB,0.001067765,Normal,LumA,test +MB-5155,CLAUDIN_SUBTYPE,NC,0.0026438304,Normal,LumA,test +MB-5155,CLAUDIN_SUBTYPE,Normal,0.023128627,Normal,LumA,test +MB-5155,CLAUDIN_SUBTYPE,claudin-low,0.0008776246,Normal,LumA,test +MB-4341,CLAUDIN_SUBTYPE,Basal,0.06784694,Her2,Her2,test +MB-4341,CLAUDIN_SUBTYPE,Her2,0.89519835,Her2,Her2,test +MB-4341,CLAUDIN_SUBTYPE,LumA,0.00054695713,Her2,Her2,test +MB-4341,CLAUDIN_SUBTYPE,LumB,0.0045495206,Her2,Her2,test +MB-4341,CLAUDIN_SUBTYPE,NC,0.0012871752,Her2,Her2,test +MB-4341,CLAUDIN_SUBTYPE,Normal,0.02763436,Her2,Her2,test +MB-4341,CLAUDIN_SUBTYPE,claudin-low,0.002936796,Her2,Her2,test +MB-0311,CLAUDIN_SUBTYPE,Basal,0.019236883,LumB,LumB,test +MB-0311,CLAUDIN_SUBTYPE,Her2,0.0040399022,LumB,LumB,test +MB-0311,CLAUDIN_SUBTYPE,LumA,0.04047827,LumB,LumB,test +MB-0311,CLAUDIN_SUBTYPE,LumB,0.92328763,LumB,LumB,test +MB-0311,CLAUDIN_SUBTYPE,NC,0.0058489763,LumB,LumB,test +MB-0311,CLAUDIN_SUBTYPE,Normal,0.004129544,LumB,LumB,test +MB-0311,CLAUDIN_SUBTYPE,claudin-low,0.0029788786,LumB,LumB,test +MB-0417,CLAUDIN_SUBTYPE,Basal,0.00608791,Her2,LumA,test +MB-0417,CLAUDIN_SUBTYPE,Her2,0.0042832145,Her2,LumA,test +MB-0417,CLAUDIN_SUBTYPE,LumA,0.9278516,Her2,LumA,test +MB-0417,CLAUDIN_SUBTYPE,LumB,0.031648647,Her2,LumA,test +MB-0417,CLAUDIN_SUBTYPE,NC,0.0067407205,Her2,LumA,test +MB-0417,CLAUDIN_SUBTYPE,Normal,0.019503815,Her2,LumA,test +MB-0417,CLAUDIN_SUBTYPE,claudin-low,0.0038841509,Her2,LumA,test +MB-0495,CLAUDIN_SUBTYPE,Basal,0.0354971,claudin-low,claudin-low,test +MB-0495,CLAUDIN_SUBTYPE,Her2,0.0012552363,claudin-low,claudin-low,test +MB-0495,CLAUDIN_SUBTYPE,LumA,0.008080568,claudin-low,claudin-low,test +MB-0495,CLAUDIN_SUBTYPE,LumB,0.00025088916,claudin-low,claudin-low,test +MB-0495,CLAUDIN_SUBTYPE,NC,0.0014400693,claudin-low,claudin-low,test +MB-0495,CLAUDIN_SUBTYPE,Normal,0.00043221258,claudin-low,claudin-low,test +MB-0495,CLAUDIN_SUBTYPE,claudin-low,0.95304394,claudin-low,claudin-low,test +MB-4350,CLAUDIN_SUBTYPE,Basal,0.66395986,Her2,Basal,test +MB-4350,CLAUDIN_SUBTYPE,Her2,0.20628975,Her2,Basal,test +MB-4350,CLAUDIN_SUBTYPE,LumA,0.0053502456,Her2,Basal,test +MB-4350,CLAUDIN_SUBTYPE,LumB,0.009757432,Her2,Basal,test +MB-4350,CLAUDIN_SUBTYPE,NC,0.006232595,Her2,Basal,test +MB-4350,CLAUDIN_SUBTYPE,Normal,0.06943414,Her2,Basal,test +MB-4350,CLAUDIN_SUBTYPE,claudin-low,0.038976017,Her2,Basal,test +MB-3487,CLAUDIN_SUBTYPE,Basal,0.0041024117,LumB,LumB,test +MB-3487,CLAUDIN_SUBTYPE,Her2,0.00025619115,LumB,LumB,test +MB-3487,CLAUDIN_SUBTYPE,LumA,0.0018171456,LumB,LumB,test +MB-3487,CLAUDIN_SUBTYPE,LumB,0.99271,LumB,LumB,test +MB-3487,CLAUDIN_SUBTYPE,NC,0.0006646329,LumB,LumB,test +MB-3487,CLAUDIN_SUBTYPE,Normal,0.0002819818,LumB,LumB,test +MB-3487,CLAUDIN_SUBTYPE,claudin-low,0.00016772882,LumB,LumB,test +MB-4212,CLAUDIN_SUBTYPE,Basal,9.000377e-06,LumA,LumA,test +MB-4212,CLAUDIN_SUBTYPE,Her2,7.7027125e-06,LumA,LumA,test +MB-4212,CLAUDIN_SUBTYPE,LumA,0.9989773,LumA,LumA,test +MB-4212,CLAUDIN_SUBTYPE,LumB,9.389267e-05,LumA,LumA,test +MB-4212,CLAUDIN_SUBTYPE,NC,6.309513e-05,LumA,LumA,test +MB-4212,CLAUDIN_SUBTYPE,Normal,0.0008427291,LumA,LumA,test +MB-4212,CLAUDIN_SUBTYPE,claudin-low,6.2841987e-06,LumA,LumA,test +MB-6344,CLAUDIN_SUBTYPE,Basal,0.00653923,LumB,LumB,test +MB-6344,CLAUDIN_SUBTYPE,Her2,0.0009357594,LumB,LumB,test +MB-6344,CLAUDIN_SUBTYPE,LumA,0.0009519841,LumB,LumB,test +MB-6344,CLAUDIN_SUBTYPE,LumB,0.9900122,LumB,LumB,test 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+MB-4838,CLAUDIN_SUBTYPE,NC,0.00031453182,LumB,LumB,test +MB-4838,CLAUDIN_SUBTYPE,Normal,0.00010995176,LumB,LumB,test +MB-4838,CLAUDIN_SUBTYPE,claudin-low,9.459353e-05,LumB,LumB,test +MB-0235,CLAUDIN_SUBTYPE,Basal,0.00012883723,LumA,LumA,test +MB-0235,CLAUDIN_SUBTYPE,Her2,0.00010585912,LumA,LumA,test +MB-0235,CLAUDIN_SUBTYPE,LumA,0.99198896,LumA,LumA,test +MB-0235,CLAUDIN_SUBTYPE,LumB,0.00083313504,LumA,LumA,test +MB-0235,CLAUDIN_SUBTYPE,NC,0.0006193761,LumA,LumA,test +MB-0235,CLAUDIN_SUBTYPE,Normal,0.0062438394,LumA,LumA,test +MB-0235,CLAUDIN_SUBTYPE,claudin-low,7.997748e-05,LumA,LumA,test +MB-0349,CLAUDIN_SUBTYPE,Basal,0.004910741,LumB,LumA,test +MB-0349,CLAUDIN_SUBTYPE,Her2,0.0016563726,LumB,LumA,test +MB-0349,CLAUDIN_SUBTYPE,LumA,0.6851496,LumB,LumA,test +MB-0349,CLAUDIN_SUBTYPE,LumB,0.2934193,LumB,LumA,test +MB-0349,CLAUDIN_SUBTYPE,NC,0.004813591,LumB,LumA,test +MB-0349,CLAUDIN_SUBTYPE,Normal,0.008936683,LumB,LumA,test +MB-0349,CLAUDIN_SUBTYPE,claudin-low,0.0011137478,LumB,LumA,test +MB-3013,CLAUDIN_SUBTYPE,Basal,0.008502817,claudin-low,LumA,test +MB-3013,CLAUDIN_SUBTYPE,Her2,0.0048782327,claudin-low,LumA,test +MB-3013,CLAUDIN_SUBTYPE,LumA,0.9049381,claudin-low,LumA,test +MB-3013,CLAUDIN_SUBTYPE,LumB,0.007390758,claudin-low,LumA,test +MB-3013,CLAUDIN_SUBTYPE,NC,0.013371146,claudin-low,LumA,test +MB-3013,CLAUDIN_SUBTYPE,Normal,0.044690877,claudin-low,LumA,test +MB-3013,CLAUDIN_SUBTYPE,claudin-low,0.016228087,claudin-low,LumA,test +MB-0559,CLAUDIN_SUBTYPE,Basal,0.014843292,LumA,LumB,test +MB-0559,CLAUDIN_SUBTYPE,Her2,0.003006201,LumA,LumB,test +MB-0559,CLAUDIN_SUBTYPE,LumA,0.06243749,LumA,LumB,test +MB-0559,CLAUDIN_SUBTYPE,LumB,0.9075007,LumA,LumB,test +MB-0559,CLAUDIN_SUBTYPE,NC,0.005586882,LumA,LumB,test +MB-0559,CLAUDIN_SUBTYPE,Normal,0.0044616275,LumA,LumB,test +MB-0559,CLAUDIN_SUBTYPE,claudin-low,0.0021637743,LumA,LumB,test +MB-5227,CLAUDIN_SUBTYPE,Basal,0.012661014,LumA,LumA,test +MB-5227,CLAUDIN_SUBTYPE,Her2,0.026591014,LumA,LumA,test +MB-5227,CLAUDIN_SUBTYPE,LumA,0.8009665,LumA,LumA,test +MB-5227,CLAUDIN_SUBTYPE,LumB,0.08344296,LumA,LumA,test +MB-5227,CLAUDIN_SUBTYPE,NC,0.018963087,LumA,LumA,test +MB-5227,CLAUDIN_SUBTYPE,Normal,0.042780362,LumA,LumA,test +MB-5227,CLAUDIN_SUBTYPE,claudin-low,0.014595067,LumA,LumA,test +MB-5084,CLAUDIN_SUBTYPE,Basal,4.069903e-05,LumA,LumA,test +MB-5084,CLAUDIN_SUBTYPE,Her2,3.313348e-05,LumA,LumA,test +MB-5084,CLAUDIN_SUBTYPE,LumA,0.9955923,LumA,LumA,test +MB-5084,CLAUDIN_SUBTYPE,LumB,0.00030075837,LumA,LumA,test +MB-5084,CLAUDIN_SUBTYPE,NC,0.00027305918,LumA,LumA,test +MB-5084,CLAUDIN_SUBTYPE,Normal,0.003735649,LumA,LumA,test +MB-5084,CLAUDIN_SUBTYPE,claudin-low,2.4386358e-05,LumA,LumA,test +MB-4234,CLAUDIN_SUBTYPE,Basal,0.0006037344,LumA,LumA,test +MB-4234,CLAUDIN_SUBTYPE,Her2,0.00051431457,LumA,LumA,test +MB-4234,CLAUDIN_SUBTYPE,LumA,0.9780937,LumA,LumA,test +MB-4234,CLAUDIN_SUBTYPE,LumB,0.0032974398,LumA,LumA,test +MB-4234,CLAUDIN_SUBTYPE,NC,0.002083711,LumA,LumA,test +MB-4234,CLAUDIN_SUBTYPE,Normal,0.015019456,LumA,LumA,test +MB-4234,CLAUDIN_SUBTYPE,claudin-low,0.0003877144,LumA,LumA,test +MB-4641,CLAUDIN_SUBTYPE,Basal,5.447803e-05,LumA,LumA,test +MB-4641,CLAUDIN_SUBTYPE,Her2,4.1685074e-05,LumA,LumA,test +MB-4641,CLAUDIN_SUBTYPE,LumA,0.99596244,LumA,LumA,test +MB-4641,CLAUDIN_SUBTYPE,LumB,0.00022054747,LumA,LumA,test +MB-4641,CLAUDIN_SUBTYPE,NC,0.0003122513,LumA,LumA,test +MB-4641,CLAUDIN_SUBTYPE,Normal,0.003353514,LumA,LumA,test +MB-4641,CLAUDIN_SUBTYPE,claudin-low,5.5094555e-05,LumA,LumA,test +MB-0286,CLAUDIN_SUBTYPE,Basal,0.045152564,claudin-low,claudin-low,test +MB-0286,CLAUDIN_SUBTYPE,Her2,0.0034112423,claudin-low,claudin-low,test +MB-0286,CLAUDIN_SUBTYPE,LumA,0.032736983,claudin-low,claudin-low,test +MB-0286,CLAUDIN_SUBTYPE,LumB,0.0008377833,claudin-low,claudin-low,test +MB-0286,CLAUDIN_SUBTYPE,NC,0.004954695,claudin-low,claudin-low,test +MB-0286,CLAUDIN_SUBTYPE,Normal,0.0023719622,claudin-low,claudin-low,test +MB-0286,CLAUDIN_SUBTYPE,claudin-low,0.91053474,claudin-low,claudin-low,test +MB-3014,CLAUDIN_SUBTYPE,Basal,0.9668346,Basal,Basal,test +MB-3014,CLAUDIN_SUBTYPE,Her2,0.0030217469,Basal,Basal,test +MB-3014,CLAUDIN_SUBTYPE,LumA,0.0013958198,Basal,Basal,test +MB-3014,CLAUDIN_SUBTYPE,LumB,0.006682645,Basal,Basal,test +MB-3014,CLAUDIN_SUBTYPE,NC,0.0015458055,Basal,Basal,test +MB-3014,CLAUDIN_SUBTYPE,Normal,0.0077170297,Basal,Basal,test +MB-3014,CLAUDIN_SUBTYPE,claudin-low,0.0128022125,Basal,Basal,test +MB-2796,CLAUDIN_SUBTYPE,Basal,0.0099408,claudin-low,LumA,test +MB-2796,CLAUDIN_SUBTYPE,Her2,0.012738842,claudin-low,LumA,test +MB-2796,CLAUDIN_SUBTYPE,LumA,0.8638587,claudin-low,LumA,test +MB-2796,CLAUDIN_SUBTYPE,LumB,0.038795978,claudin-low,LumA,test +MB-2796,CLAUDIN_SUBTYPE,NC,0.01633317,claudin-low,LumA,test +MB-2796,CLAUDIN_SUBTYPE,Normal,0.04770924,claudin-low,LumA,test +MB-2796,CLAUDIN_SUBTYPE,claudin-low,0.010623205,claudin-low,LumA,test +MB-7058,CLAUDIN_SUBTYPE,Basal,0.004823737,Normal,LumA,test +MB-7058,CLAUDIN_SUBTYPE,Her2,0.0049863625,Normal,LumA,test +MB-7058,CLAUDIN_SUBTYPE,LumA,0.807321,Normal,LumA,test +MB-7058,CLAUDIN_SUBTYPE,LumB,0.0042488733,Normal,LumA,test +MB-7058,CLAUDIN_SUBTYPE,NC,0.008254303,Normal,LumA,test +MB-7058,CLAUDIN_SUBTYPE,Normal,0.16895607,Normal,LumA,test +MB-7058,CLAUDIN_SUBTYPE,claudin-low,0.0014095572,Normal,LumA,test +MB-5287,CLAUDIN_SUBTYPE,Basal,0.00011211436,LumA,LumA,test +MB-5287,CLAUDIN_SUBTYPE,Her2,9.4074334e-05,LumA,LumA,test +MB-5287,CLAUDIN_SUBTYPE,LumA,0.9937255,LumA,LumA,test +MB-5287,CLAUDIN_SUBTYPE,LumB,0.0008258469,LumA,LumA,test +MB-5287,CLAUDIN_SUBTYPE,NC,0.000510222,LumA,LumA,test +MB-5287,CLAUDIN_SUBTYPE,Normal,0.004657664,LumA,LumA,test +MB-5287,CLAUDIN_SUBTYPE,claudin-low,7.462731e-05,LumA,LumA,test +MB-7281,CLAUDIN_SUBTYPE,Basal,0.13046472,Her2,Her2,test +MB-7281,CLAUDIN_SUBTYPE,Her2,0.69531393,Her2,Her2,test +MB-7281,CLAUDIN_SUBTYPE,LumA,0.013255671,Her2,Her2,test +MB-7281,CLAUDIN_SUBTYPE,LumB,0.024778293,Her2,Her2,test +MB-7281,CLAUDIN_SUBTYPE,NC,0.013294455,Her2,Her2,test +MB-7281,CLAUDIN_SUBTYPE,Normal,0.05936815,Her2,Her2,test +MB-7281,CLAUDIN_SUBTYPE,claudin-low,0.06352487,Her2,Her2,test +MB-4011,CLAUDIN_SUBTYPE,Basal,0.013587133,LumA,LumA,test +MB-4011,CLAUDIN_SUBTYPE,Her2,0.025001219,LumA,LumA,test +MB-4011,CLAUDIN_SUBTYPE,LumA,0.8087616,LumA,LumA,test +MB-4011,CLAUDIN_SUBTYPE,LumB,0.08504042,LumA,LumA,test +MB-4011,CLAUDIN_SUBTYPE,NC,0.014051675,LumA,LumA,test +MB-4011,CLAUDIN_SUBTYPE,Normal,0.046814404,LumA,LumA,test +MB-4011,CLAUDIN_SUBTYPE,claudin-low,0.0067434954,LumA,LumA,test +MB-3102,CLAUDIN_SUBTYPE,Basal,0.006243442,LumA,LumB,test +MB-3102,CLAUDIN_SUBTYPE,Her2,0.0024468775,LumA,LumB,test +MB-3102,CLAUDIN_SUBTYPE,LumA,0.05410744,LumA,LumB,test +MB-3102,CLAUDIN_SUBTYPE,LumB,0.9292802,LumA,LumB,test +MB-3102,CLAUDIN_SUBTYPE,NC,0.0037186984,LumA,LumB,test +MB-3102,CLAUDIN_SUBTYPE,Normal,0.0029182052,LumA,LumB,test +MB-3102,CLAUDIN_SUBTYPE,claudin-low,0.001285043,LumA,LumB,test +MB-6194,CLAUDIN_SUBTYPE,Basal,0.23802574,Normal,Normal,test +MB-6194,CLAUDIN_SUBTYPE,Her2,0.18965796,Normal,Normal,test +MB-6194,CLAUDIN_SUBTYPE,LumA,0.06475697,Normal,Normal,test +MB-6194,CLAUDIN_SUBTYPE,LumB,0.019776484,Normal,Normal,test +MB-6194,CLAUDIN_SUBTYPE,NC,0.034550738,Normal,Normal,test +MB-6194,CLAUDIN_SUBTYPE,Normal,0.39449188,Normal,Normal,test +MB-6194,CLAUDIN_SUBTYPE,claudin-low,0.058740236,Normal,Normal,test +MB-3026,CLAUDIN_SUBTYPE,Basal,0.008249727,LumA,LumA,test +MB-3026,CLAUDIN_SUBTYPE,Her2,0.0059386985,LumA,LumA,test +MB-3026,CLAUDIN_SUBTYPE,LumA,0.8489762,LumA,LumA,test +MB-3026,CLAUDIN_SUBTYPE,LumB,0.057868633,LumA,LumA,test +MB-3026,CLAUDIN_SUBTYPE,NC,0.016451295,LumA,LumA,test +MB-3026,CLAUDIN_SUBTYPE,Normal,0.05685805,LumA,LumA,test +MB-3026,CLAUDIN_SUBTYPE,claudin-low,0.00565741,LumA,LumA,test +MB-7052,CLAUDIN_SUBTYPE,Basal,0.58712304,claudin-low,Basal,test +MB-7052,CLAUDIN_SUBTYPE,Her2,0.07264461,claudin-low,Basal,test +MB-7052,CLAUDIN_SUBTYPE,LumA,0.008565084,claudin-low,Basal,test +MB-7052,CLAUDIN_SUBTYPE,LumB,0.0026574226,claudin-low,Basal,test +MB-7052,CLAUDIN_SUBTYPE,NC,0.005033583,claudin-low,Basal,test +MB-7052,CLAUDIN_SUBTYPE,Normal,0.019163303,claudin-low,Basal,test +MB-7052,CLAUDIN_SUBTYPE,claudin-low,0.3048129,claudin-low,Basal,test +MB-5291,CLAUDIN_SUBTYPE,Basal,0.005792461,LumB,LumB,test +MB-5291,CLAUDIN_SUBTYPE,Her2,0.0007016247,LumB,LumB,test +MB-5291,CLAUDIN_SUBTYPE,LumA,0.0062884274,LumB,LumB,test +MB-5291,CLAUDIN_SUBTYPE,LumB,0.98432446,LumB,LumB,test +MB-5291,CLAUDIN_SUBTYPE,NC,0.0016098918,LumB,LumB,test +MB-5291,CLAUDIN_SUBTYPE,Normal,0.00076227856,LumB,LumB,test +MB-5291,CLAUDIN_SUBTYPE,claudin-low,0.0005208675,LumB,LumB,test +MB-4767,CLAUDIN_SUBTYPE,Basal,0.11165398,LumB,LumB,test +MB-4767,CLAUDIN_SUBTYPE,Her2,0.07286488,LumB,LumB,test +MB-4767,CLAUDIN_SUBTYPE,LumA,0.15985003,LumB,LumB,test +MB-4767,CLAUDIN_SUBTYPE,LumB,0.49294478,LumB,LumB,test +MB-4767,CLAUDIN_SUBTYPE,NC,0.04016477,LumB,LumB,test +MB-4767,CLAUDIN_SUBTYPE,Normal,0.03678647,LumB,LumB,test +MB-4767,CLAUDIN_SUBTYPE,claudin-low,0.08573509,LumB,LumB,test +MB-7043,CLAUDIN_SUBTYPE,Basal,0.115664475,claudin-low,claudin-low,test +MB-7043,CLAUDIN_SUBTYPE,Her2,0.016165059,claudin-low,claudin-low,test +MB-7043,CLAUDIN_SUBTYPE,LumA,0.15923825,claudin-low,claudin-low,test +MB-7043,CLAUDIN_SUBTYPE,LumB,0.0074056233,claudin-low,claudin-low,test +MB-7043,CLAUDIN_SUBTYPE,NC,0.021221412,claudin-low,claudin-low,test +MB-7043,CLAUDIN_SUBTYPE,Normal,0.01840529,claudin-low,claudin-low,test +MB-7043,CLAUDIN_SUBTYPE,claudin-low,0.66189986,claudin-low,claudin-low,test +MB-0472,CLAUDIN_SUBTYPE,Basal,0.0007786848,LumB,LumA,test +MB-0472,CLAUDIN_SUBTYPE,Her2,0.0005824592,LumB,LumA,test +MB-0472,CLAUDIN_SUBTYPE,LumA,0.9881144,LumB,LumA,test +MB-0472,CLAUDIN_SUBTYPE,LumB,0.0028337394,LumB,LumA,test +MB-0472,CLAUDIN_SUBTYPE,NC,0.0014645314,LumB,LumA,test +MB-0472,CLAUDIN_SUBTYPE,Normal,0.005022286,LumB,LumA,test +MB-0472,CLAUDIN_SUBTYPE,claudin-low,0.001203951,LumB,LumA,test +MB-5338,CLAUDIN_SUBTYPE,Basal,0.030729877,LumB,LumB,test +MB-5338,CLAUDIN_SUBTYPE,Her2,0.023416564,LumB,LumB,test +MB-5338,CLAUDIN_SUBTYPE,LumA,0.0007048371,LumB,LumB,test +MB-5338,CLAUDIN_SUBTYPE,LumB,0.94123095,LumB,LumB,test +MB-5338,CLAUDIN_SUBTYPE,NC,0.0016280026,LumB,LumB,test +MB-5338,CLAUDIN_SUBTYPE,Normal,0.0012956072,LumB,LumB,test +MB-5338,CLAUDIN_SUBTYPE,claudin-low,0.0009942222,LumB,LumB,test +MB-2966,CLAUDIN_SUBTYPE,Basal,0.0031380653,LumA,LumA,test +MB-2966,CLAUDIN_SUBTYPE,Her2,0.0017169772,LumA,LumA,test +MB-2966,CLAUDIN_SUBTYPE,LumA,0.9318229,LumA,LumA,test +MB-2966,CLAUDIN_SUBTYPE,LumB,0.031810585,LumA,LumA,test +MB-2966,CLAUDIN_SUBTYPE,NC,0.005932116,LumA,LumA,test +MB-2966,CLAUDIN_SUBTYPE,Normal,0.024215288,LumA,LumA,test +MB-2966,CLAUDIN_SUBTYPE,claudin-low,0.0013640913,LumA,LumA,test +MB-0551,CLAUDIN_SUBTYPE,Basal,0.016118636,Normal,Normal,test +MB-0551,CLAUDIN_SUBTYPE,Her2,0.023752917,Normal,Normal,test +MB-0551,CLAUDIN_SUBTYPE,LumA,0.007736333,Normal,Normal,test +MB-0551,CLAUDIN_SUBTYPE,LumB,0.00031910927,Normal,Normal,test +MB-0551,CLAUDIN_SUBTYPE,NC,0.0024857637,Normal,Normal,test +MB-0551,CLAUDIN_SUBTYPE,Normal,0.9492916,Normal,Normal,test +MB-0551,CLAUDIN_SUBTYPE,claudin-low,0.00029556343,Normal,Normal,test +MB-5404,CLAUDIN_SUBTYPE,Basal,0.0011252166,LumA,LumA,test +MB-5404,CLAUDIN_SUBTYPE,Her2,0.0008977299,LumA,LumA,test +MB-5404,CLAUDIN_SUBTYPE,LumA,0.97227895,LumA,LumA,test +MB-5404,CLAUDIN_SUBTYPE,LumB,0.0068289763,LumA,LumA,test +MB-5404,CLAUDIN_SUBTYPE,NC,0.0029075355,LumA,LumA,test +MB-5404,CLAUDIN_SUBTYPE,Normal,0.015131961,LumA,LumA,test +MB-5404,CLAUDIN_SUBTYPE,claudin-low,0.00082953234,LumA,LumA,test +MB-5540,CLAUDIN_SUBTYPE,Basal,0.003374003,LumB,LumB,test +MB-5540,CLAUDIN_SUBTYPE,Her2,0.008654103,LumB,LumB,test +MB-5540,CLAUDIN_SUBTYPE,LumA,0.0003952225,LumB,LumB,test +MB-5540,CLAUDIN_SUBTYPE,LumB,0.9866195,LumB,LumB,test +MB-5540,CLAUDIN_SUBTYPE,NC,0.0004885159,LumB,LumB,test +MB-5540,CLAUDIN_SUBTYPE,Normal,0.00019392194,LumB,LumB,test +MB-5540,CLAUDIN_SUBTYPE,claudin-low,0.00027463053,LumB,LumB,test +MB-0644,CLAUDIN_SUBTYPE,Basal,0.061044354,claudin-low,claudin-low,test +MB-0644,CLAUDIN_SUBTYPE,Her2,0.0064615575,claudin-low,claudin-low,test +MB-0644,CLAUDIN_SUBTYPE,LumA,0.14116491,claudin-low,claudin-low,test +MB-0644,CLAUDIN_SUBTYPE,LumB,0.0017587154,claudin-low,claudin-low,test +MB-0644,CLAUDIN_SUBTYPE,NC,0.010836929,claudin-low,claudin-low,test +MB-0644,CLAUDIN_SUBTYPE,Normal,0.008266854,claudin-low,claudin-low,test +MB-0644,CLAUDIN_SUBTYPE,claudin-low,0.7704666,claudin-low,claudin-low,test +MB-0618,CLAUDIN_SUBTYPE,Basal,0.008935495,LumB,LumA,test +MB-0618,CLAUDIN_SUBTYPE,Her2,0.0030788716,LumB,LumA,test +MB-0618,CLAUDIN_SUBTYPE,LumA,0.6744612,LumB,LumA,test +MB-0618,CLAUDIN_SUBTYPE,LumB,0.28637177,LumB,LumA,test +MB-0618,CLAUDIN_SUBTYPE,NC,0.008701062,LumB,LumA,test +MB-0618,CLAUDIN_SUBTYPE,Normal,0.01560719,LumB,LumA,test +MB-0618,CLAUDIN_SUBTYPE,claudin-low,0.0028445122,LumB,LumA,test +MB-3439,CLAUDIN_SUBTYPE,Basal,0.00030271732,LumA,LumA,test +MB-3439,CLAUDIN_SUBTYPE,Her2,0.00028479946,LumA,LumA,test +MB-3439,CLAUDIN_SUBTYPE,LumA,0.99017197,LumA,LumA,test +MB-3439,CLAUDIN_SUBTYPE,LumB,0.0030675149,LumA,LumA,test +MB-3439,CLAUDIN_SUBTYPE,NC,0.00087914104,LumA,LumA,test +MB-3439,CLAUDIN_SUBTYPE,Normal,0.005088835,LumA,LumA,test +MB-3439,CLAUDIN_SUBTYPE,claudin-low,0.00020505159,LumA,LumA,test +MB-3797,CLAUDIN_SUBTYPE,Basal,0.0017444948,LumA,LumA,test +MB-3797,CLAUDIN_SUBTYPE,Her2,0.00068415445,LumA,LumA,test +MB-3797,CLAUDIN_SUBTYPE,LumA,0.97528744,LumA,LumA,test +MB-3797,CLAUDIN_SUBTYPE,LumB,0.011680061,LumA,LumA,test +MB-3797,CLAUDIN_SUBTYPE,NC,0.002203974,LumA,LumA,test +MB-3797,CLAUDIN_SUBTYPE,Normal,0.00735977,LumA,LumA,test +MB-3797,CLAUDIN_SUBTYPE,claudin-low,0.0010400674,LumA,LumA,test +MB-2929,CLAUDIN_SUBTYPE,Basal,0.04076907,Her2,Her2,test +MB-2929,CLAUDIN_SUBTYPE,Her2,0.78446895,Her2,Her2,test +MB-2929,CLAUDIN_SUBTYPE,LumA,0.011662753,Her2,Her2,test +MB-2929,CLAUDIN_SUBTYPE,LumB,0.090062164,Her2,Her2,test +MB-2929,CLAUDIN_SUBTYPE,NC,0.013410253,Her2,Her2,test +MB-2929,CLAUDIN_SUBTYPE,Normal,0.028416025,Her2,Her2,test +MB-2929,CLAUDIN_SUBTYPE,claudin-low,0.031210758,Her2,Her2,test +MB-5182,CLAUDIN_SUBTYPE,Basal,3.222719e-05,LumA,LumA,test +MB-5182,CLAUDIN_SUBTYPE,Her2,2.7079406e-05,LumA,LumA,test +MB-5182,CLAUDIN_SUBTYPE,LumA,0.9967722,LumA,LumA,test +MB-5182,CLAUDIN_SUBTYPE,LumB,0.00015356342,LumA,LumA,test +MB-5182,CLAUDIN_SUBTYPE,NC,0.00021453887,LumA,LumA,test +MB-5182,CLAUDIN_SUBTYPE,Normal,0.0027737748,LumA,LumA,test +MB-5182,CLAUDIN_SUBTYPE,claudin-low,2.6615784e-05,LumA,LumA,test +MB-0642,CLAUDIN_SUBTYPE,Basal,0.00073901145,LumA,LumA,test +MB-0642,CLAUDIN_SUBTYPE,Her2,0.0006310349,LumA,LumA,test +MB-0642,CLAUDIN_SUBTYPE,LumA,0.98000413,LumA,LumA,test +MB-0642,CLAUDIN_SUBTYPE,LumB,0.005649129,LumA,LumA,test +MB-0642,CLAUDIN_SUBTYPE,NC,0.0019334203,LumA,LumA,test +MB-0642,CLAUDIN_SUBTYPE,Normal,0.010588617,LumA,LumA,test +MB-0642,CLAUDIN_SUBTYPE,claudin-low,0.00045469968,LumA,LumA,test +MB-4738,CLAUDIN_SUBTYPE,Basal,0.0006314964,Normal,LumA,test +MB-4738,CLAUDIN_SUBTYPE,Her2,0.0005564989,Normal,LumA,test +MB-4738,CLAUDIN_SUBTYPE,LumA,0.9387441,Normal,LumA,test +MB-4738,CLAUDIN_SUBTYPE,LumB,0.0005674407,Normal,LumA,test +MB-4738,CLAUDIN_SUBTYPE,NC,0.0024898474,Normal,LumA,test +MB-4738,CLAUDIN_SUBTYPE,Normal,0.056680556,Normal,LumA,test +MB-4738,CLAUDIN_SUBTYPE,claudin-low,0.00032999794,Normal,LumA,test +MB-0192,CLAUDIN_SUBTYPE,Basal,0.035434213,claudin-low,claudin-low,test +MB-0192,CLAUDIN_SUBTYPE,Her2,0.0019459148,claudin-low,claudin-low,test +MB-0192,CLAUDIN_SUBTYPE,LumA,0.013824827,claudin-low,claudin-low,test +MB-0192,CLAUDIN_SUBTYPE,LumB,0.00040362438,claudin-low,claudin-low,test +MB-0192,CLAUDIN_SUBTYPE,NC,0.0023733827,claudin-low,claudin-low,test +MB-0192,CLAUDIN_SUBTYPE,Normal,0.00082363794,claudin-low,claudin-low,test +MB-0192,CLAUDIN_SUBTYPE,claudin-low,0.9451944,claudin-low,claudin-low,test +MB-0243,CLAUDIN_SUBTYPE,Basal,0.015972668,LumB,LumA,test +MB-0243,CLAUDIN_SUBTYPE,Her2,0.010332679,LumB,LumA,test +MB-0243,CLAUDIN_SUBTYPE,LumA,0.7183024,LumB,LumA,test +MB-0243,CLAUDIN_SUBTYPE,LumB,0.17402926,LumB,LumA,test +MB-0243,CLAUDIN_SUBTYPE,NC,0.021323534,LumB,LumA,test +MB-0243,CLAUDIN_SUBTYPE,Normal,0.052631546,LumB,LumA,test +MB-0243,CLAUDIN_SUBTYPE,claudin-low,0.0074078934,LumB,LumA,test +MB-7208,CLAUDIN_SUBTYPE,Basal,0.5404998,Basal,Basal,test +MB-7208,CLAUDIN_SUBTYPE,Her2,0.32136694,Basal,Basal,test +MB-7208,CLAUDIN_SUBTYPE,LumA,0.0014117169,Basal,Basal,test +MB-7208,CLAUDIN_SUBTYPE,LumB,0.015459034,Basal,Basal,test +MB-7208,CLAUDIN_SUBTYPE,NC,0.0039291065,Basal,Basal,test +MB-7208,CLAUDIN_SUBTYPE,Normal,0.11173458,Basal,Basal,test +MB-7208,CLAUDIN_SUBTYPE,claudin-low,0.0055988133,Basal,Basal,test +MB-0343,CLAUDIN_SUBTYPE,Basal,0.0010580262,Normal,LumA,test +MB-0343,CLAUDIN_SUBTYPE,Her2,0.0008054226,Normal,LumA,test +MB-0343,CLAUDIN_SUBTYPE,LumA,0.9591148,Normal,LumA,test +MB-0343,CLAUDIN_SUBTYPE,LumB,0.0043752915,Normal,LumA,test +MB-0343,CLAUDIN_SUBTYPE,NC,0.003232325,Normal,LumA,test +MB-0343,CLAUDIN_SUBTYPE,Normal,0.030855218,Normal,LumA,test +MB-0343,CLAUDIN_SUBTYPE,claudin-low,0.0005589006,Normal,LumA,test +MB-7229,CLAUDIN_SUBTYPE,Basal,0.00064306316,LumA,LumA,test +MB-7229,CLAUDIN_SUBTYPE,Her2,0.00064171996,LumA,LumA,test +MB-7229,CLAUDIN_SUBTYPE,LumA,0.9878539,LumA,LumA,test +MB-7229,CLAUDIN_SUBTYPE,LumB,0.0041675186,LumA,LumA,test +MB-7229,CLAUDIN_SUBTYPE,NC,0.0012794778,LumA,LumA,test +MB-7229,CLAUDIN_SUBTYPE,Normal,0.0046823504,LumA,LumA,test +MB-7229,CLAUDIN_SUBTYPE,claudin-low,0.00073200173,LumA,LumA,test +MB-0575,CLAUDIN_SUBTYPE,Basal,0.08683767,LumA,Normal,test +MB-0575,CLAUDIN_SUBTYPE,Her2,0.08707564,LumA,Normal,test +MB-0575,CLAUDIN_SUBTYPE,LumA,0.23121674,LumA,Normal,test +MB-0575,CLAUDIN_SUBTYPE,LumB,0.10548585,LumA,Normal,test +MB-0575,CLAUDIN_SUBTYPE,NC,0.061849684,LumA,Normal,test +MB-0575,CLAUDIN_SUBTYPE,Normal,0.39993745,LumA,Normal,test +MB-0575,CLAUDIN_SUBTYPE,claudin-low,0.027596926,LumA,Normal,test +MB-7091,CLAUDIN_SUBTYPE,Basal,0.005865344,LumA,LumA,test +MB-7091,CLAUDIN_SUBTYPE,Her2,0.0050462442,LumA,LumA,test +MB-7091,CLAUDIN_SUBTYPE,LumA,0.88545346,LumA,LumA,test +MB-7091,CLAUDIN_SUBTYPE,LumB,0.016431637,LumA,LumA,test +MB-7091,CLAUDIN_SUBTYPE,NC,0.012374588,LumA,LumA,test +MB-7091,CLAUDIN_SUBTYPE,Normal,0.07106886,LumA,LumA,test +MB-7091,CLAUDIN_SUBTYPE,claudin-low,0.0037599609,LumA,LumA,test +MB-0176,CLAUDIN_SUBTYPE,Basal,0.038080536,LumA,LumA,test +MB-0176,CLAUDIN_SUBTYPE,Her2,0.02837146,LumA,LumA,test +MB-0176,CLAUDIN_SUBTYPE,LumA,0.4942919,LumA,LumA,test +MB-0176,CLAUDIN_SUBTYPE,LumB,0.18353668,LumA,LumA,test +MB-0176,CLAUDIN_SUBTYPE,NC,0.047271788,LumA,LumA,test +MB-0176,CLAUDIN_SUBTYPE,Normal,0.19307849,LumA,LumA,test +MB-0176,CLAUDIN_SUBTYPE,claudin-low,0.015369191,LumA,LumA,test +MB-6103,CLAUDIN_SUBTYPE,Basal,0.02262877,Normal,LumA,test +MB-6103,CLAUDIN_SUBTYPE,Her2,0.036490705,Normal,LumA,test +MB-6103,CLAUDIN_SUBTYPE,LumA,0.5892713,Normal,LumA,test +MB-6103,CLAUDIN_SUBTYPE,LumB,0.012682543,Normal,LumA,test +MB-6103,CLAUDIN_SUBTYPE,NC,0.02431783,Normal,LumA,test +MB-6103,CLAUDIN_SUBTYPE,Normal,0.30587867,Normal,LumA,test +MB-6103,CLAUDIN_SUBTYPE,claudin-low,0.008730169,Normal,LumA,test +MB-0589,CLAUDIN_SUBTYPE,Basal,0.011077246,LumB,LumB,test +MB-0589,CLAUDIN_SUBTYPE,Her2,0.009102092,LumB,LumB,test +MB-0589,CLAUDIN_SUBTYPE,LumA,0.037723836,LumB,LumB,test +MB-0589,CLAUDIN_SUBTYPE,LumB,0.929064,LumB,LumB,test +MB-0589,CLAUDIN_SUBTYPE,NC,0.0057970304,LumB,LumB,test +MB-0589,CLAUDIN_SUBTYPE,Normal,0.0041057384,LumB,LumB,test +MB-0589,CLAUDIN_SUBTYPE,claudin-low,0.0031301128,LumB,LumB,test +MB-5061,CLAUDIN_SUBTYPE,Basal,0.043176465,LumB,LumA,test +MB-5061,CLAUDIN_SUBTYPE,Her2,0.085720174,LumB,LumA,test +MB-5061,CLAUDIN_SUBTYPE,LumA,0.5462248,LumB,LumA,test +MB-5061,CLAUDIN_SUBTYPE,LumB,0.17880414,LumB,LumA,test +MB-5061,CLAUDIN_SUBTYPE,NC,0.022508493,LumB,LumA,test +MB-5061,CLAUDIN_SUBTYPE,Normal,0.019958103,LumB,LumA,test +MB-5061,CLAUDIN_SUBTYPE,claudin-low,0.10360784,LumB,LumA,test +MB-6058,CLAUDIN_SUBTYPE,Basal,0.66850376,Basal,Basal,test +MB-6058,CLAUDIN_SUBTYPE,Her2,0.00051581167,Basal,Basal,test +MB-6058,CLAUDIN_SUBTYPE,LumA,0.0020438526,Basal,Basal,test +MB-6058,CLAUDIN_SUBTYPE,LumB,0.0005263329,Basal,Basal,test +MB-6058,CLAUDIN_SUBTYPE,NC,0.00067389366,Basal,Basal,test +MB-6058,CLAUDIN_SUBTYPE,Normal,0.0005386354,Basal,Basal,test +MB-6058,CLAUDIN_SUBTYPE,claudin-low,0.32719764,Basal,Basal,test +MB-7009,CLAUDIN_SUBTYPE,Basal,0.7792922,Basal,Basal,test +MB-7009,CLAUDIN_SUBTYPE,Her2,0.0010623139,Basal,Basal,test +MB-7009,CLAUDIN_SUBTYPE,LumA,0.0033867746,Basal,Basal,test +MB-7009,CLAUDIN_SUBTYPE,LumB,0.0016315421,Basal,Basal,test +MB-7009,CLAUDIN_SUBTYPE,NC,0.0013537677,Basal,Basal,test +MB-7009,CLAUDIN_SUBTYPE,Normal,0.0014000817,Basal,Basal,test +MB-7009,CLAUDIN_SUBTYPE,claudin-low,0.21187323,Basal,Basal,test +MB-2814,CLAUDIN_SUBTYPE,Basal,0.015165181,LumB,LumB,test +MB-2814,CLAUDIN_SUBTYPE,Her2,0.0039517754,LumB,LumB,test +MB-2814,CLAUDIN_SUBTYPE,LumA,0.15806338,LumB,LumB,test +MB-2814,CLAUDIN_SUBTYPE,LumB,0.80044216,LumB,LumB,test +MB-2814,CLAUDIN_SUBTYPE,NC,0.009208188,LumB,LumB,test +MB-2814,CLAUDIN_SUBTYPE,Normal,0.010176519,LumB,LumB,test +MB-2814,CLAUDIN_SUBTYPE,claudin-low,0.0029927627,LumB,LumB,test +MB-4653,CLAUDIN_SUBTYPE,Basal,0.009771683,Normal,Normal,test +MB-4653,CLAUDIN_SUBTYPE,Her2,0.010024962,Normal,Normal,test +MB-4653,CLAUDIN_SUBTYPE,LumA,0.04908282,Normal,Normal,test +MB-4653,CLAUDIN_SUBTYPE,LumB,0.0006216074,Normal,Normal,test +MB-4653,CLAUDIN_SUBTYPE,NC,0.005866634,Normal,Normal,test +MB-4653,CLAUDIN_SUBTYPE,Normal,0.9240287,Normal,Normal,test +MB-4653,CLAUDIN_SUBTYPE,claudin-low,0.00060358737,Normal,Normal,test +MB-5571,CLAUDIN_SUBTYPE,Basal,0.0055585974,LumA,LumA,test +MB-5571,CLAUDIN_SUBTYPE,Her2,0.008972782,LumA,LumA,test +MB-5571,CLAUDIN_SUBTYPE,LumA,0.8291742,LumA,LumA,test +MB-5571,CLAUDIN_SUBTYPE,LumB,0.114806235,LumA,LumA,test +MB-5571,CLAUDIN_SUBTYPE,NC,0.010823761,LumA,LumA,test +MB-5571,CLAUDIN_SUBTYPE,Normal,0.026464455,LumA,LumA,test +MB-5571,CLAUDIN_SUBTYPE,claudin-low,0.004200055,LumA,LumA,test +MB-5224,CLAUDIN_SUBTYPE,Basal,0.001968088,LumA,LumA,test +MB-5224,CLAUDIN_SUBTYPE,Her2,0.0022232921,LumA,LumA,test +MB-5224,CLAUDIN_SUBTYPE,LumA,0.96492183,LumA,LumA,test +MB-5224,CLAUDIN_SUBTYPE,LumB,0.0077275797,LumA,LumA,test +MB-5224,CLAUDIN_SUBTYPE,NC,0.0041146167,LumA,LumA,test +MB-5224,CLAUDIN_SUBTYPE,Normal,0.016923174,LumA,LumA,test +MB-5224,CLAUDIN_SUBTYPE,claudin-low,0.0021213263,LumA,LumA,test +MB-4796,CLAUDIN_SUBTYPE,Basal,0.002353539,LumB,LumB,test +MB-4796,CLAUDIN_SUBTYPE,Her2,0.0030635954,LumB,LumB,test +MB-4796,CLAUDIN_SUBTYPE,LumA,0.0049916115,LumB,LumB,test +MB-4796,CLAUDIN_SUBTYPE,LumB,0.98776066,LumB,LumB,test +MB-4796,CLAUDIN_SUBTYPE,NC,0.0009539681,LumB,LumB,test +MB-4796,CLAUDIN_SUBTYPE,Normal,0.00039807567,LumB,LumB,test +MB-4796,CLAUDIN_SUBTYPE,claudin-low,0.0004783908,LumB,LumB,test +MB-7238,CLAUDIN_SUBTYPE,Basal,0.24624525,Her2,LumB,test +MB-7238,CLAUDIN_SUBTYPE,Her2,0.052358698,Her2,LumB,test +MB-7238,CLAUDIN_SUBTYPE,LumA,0.03875851,Her2,LumB,test +MB-7238,CLAUDIN_SUBTYPE,LumB,0.58622956,Her2,LumB,test +MB-7238,CLAUDIN_SUBTYPE,NC,0.020017982,Her2,LumB,test +MB-7238,CLAUDIN_SUBTYPE,Normal,0.020407755,Her2,LumB,test +MB-7238,CLAUDIN_SUBTYPE,claudin-low,0.03598221,Her2,LumB,test +MB-4931,CLAUDIN_SUBTYPE,Basal,0.011187982,claudin-low,claudin-low,test +MB-4931,CLAUDIN_SUBTYPE,Her2,0.00020954342,claudin-low,claudin-low,test +MB-4931,CLAUDIN_SUBTYPE,LumA,0.0019202635,claudin-low,claudin-low,test +MB-4931,CLAUDIN_SUBTYPE,LumB,1.9125098e-05,claudin-low,claudin-low,test +MB-4931,CLAUDIN_SUBTYPE,NC,0.00021892713,claudin-low,claudin-low,test +MB-4931,CLAUDIN_SUBTYPE,Normal,3.7579026e-05,claudin-low,claudin-low,test +MB-4931,CLAUDIN_SUBTYPE,claudin-low,0.9864066,claudin-low,claudin-low,test +MB-0627,CLAUDIN_SUBTYPE,Basal,0.020750402,claudin-low,claudin-low,test +MB-0627,CLAUDIN_SUBTYPE,Her2,0.0012719609,claudin-low,claudin-low,test +MB-0627,CLAUDIN_SUBTYPE,LumA,0.0051257415,claudin-low,claudin-low,test +MB-0627,CLAUDIN_SUBTYPE,LumB,0.0001703981,claudin-low,claudin-low,test +MB-0627,CLAUDIN_SUBTYPE,NC,0.0009676965,claudin-low,claudin-low,test +MB-0627,CLAUDIN_SUBTYPE,Normal,0.00022090702,claudin-low,claudin-low,test +MB-0627,CLAUDIN_SUBTYPE,claudin-low,0.9714929,claudin-low,claudin-low,test +MB-2764,CLAUDIN_SUBTYPE,Basal,0.036022753,claudin-low,claudin-low,test +MB-2764,CLAUDIN_SUBTYPE,Her2,0.0016025014,claudin-low,claudin-low,test +MB-2764,CLAUDIN_SUBTYPE,LumA,0.00423647,claudin-low,claudin-low,test +MB-2764,CLAUDIN_SUBTYPE,LumB,0.00011455154,claudin-low,claudin-low,test +MB-2764,CLAUDIN_SUBTYPE,NC,0.000867523,claudin-low,claudin-low,test +MB-2764,CLAUDIN_SUBTYPE,Normal,0.00034884925,claudin-low,claudin-low,test +MB-2764,CLAUDIN_SUBTYPE,claudin-low,0.95680743,claudin-low,claudin-low,test +MB-3450,CLAUDIN_SUBTYPE,Basal,0.013241612,LumA,LumA,test +MB-3450,CLAUDIN_SUBTYPE,Her2,0.007773319,LumA,LumA,test +MB-3450,CLAUDIN_SUBTYPE,LumA,0.8297477,LumA,LumA,test +MB-3450,CLAUDIN_SUBTYPE,LumB,0.10690636,LumA,LumA,test +MB-3450,CLAUDIN_SUBTYPE,NC,0.011702657,LumA,LumA,test +MB-3450,CLAUDIN_SUBTYPE,Normal,0.018681236,LumA,LumA,test +MB-3450,CLAUDIN_SUBTYPE,claudin-low,0.011947215,LumA,LumA,test +MB-3824,CLAUDIN_SUBTYPE,Basal,0.009530319,LumB,LumB,test +MB-3824,CLAUDIN_SUBTYPE,Her2,0.004625703,LumB,LumB,test +MB-3824,CLAUDIN_SUBTYPE,LumA,0.04014909,LumB,LumB,test +MB-3824,CLAUDIN_SUBTYPE,LumB,0.93582416,LumB,LumB,test +MB-3824,CLAUDIN_SUBTYPE,NC,0.0045609726,LumB,LumB,test +MB-3824,CLAUDIN_SUBTYPE,Normal,0.0032499502,LumB,LumB,test +MB-3824,CLAUDIN_SUBTYPE,claudin-low,0.0020598008,LumB,LumB,test +MB-0022,CLAUDIN_SUBTYPE,Basal,0.12542996,claudin-low,claudin-low,test +MB-0022,CLAUDIN_SUBTYPE,Her2,0.07650821,claudin-low,claudin-low,test +MB-0022,CLAUDIN_SUBTYPE,LumA,0.20438926,claudin-low,claudin-low,test +MB-0022,CLAUDIN_SUBTYPE,LumB,0.16598016,claudin-low,claudin-low,test +MB-0022,CLAUDIN_SUBTYPE,NC,0.065553784,claudin-low,claudin-low,test +MB-0022,CLAUDIN_SUBTYPE,Normal,0.05504696,claudin-low,claudin-low,test +MB-0022,CLAUDIN_SUBTYPE,claudin-low,0.30709162,claudin-low,claudin-low,test +MB-4648,CLAUDIN_SUBTYPE,Basal,0.01299259,LumB,LumB,test +MB-4648,CLAUDIN_SUBTYPE,Her2,0.0056821653,LumB,LumB,test +MB-4648,CLAUDIN_SUBTYPE,LumA,0.006378649,LumB,LumB,test +MB-4648,CLAUDIN_SUBTYPE,LumB,0.96945703,LumB,LumB,test +MB-4648,CLAUDIN_SUBTYPE,NC,0.0023176214,LumB,LumB,test +MB-4648,CLAUDIN_SUBTYPE,Normal,0.0022580407,LumB,LumB,test +MB-4648,CLAUDIN_SUBTYPE,claudin-low,0.0009139541,LumB,LumB,test +MB-4607,CLAUDIN_SUBTYPE,Basal,0.0003763551,LumA,LumA,test +MB-4607,CLAUDIN_SUBTYPE,Her2,0.00027307845,LumA,LumA,test +MB-4607,CLAUDIN_SUBTYPE,LumA,0.9903385,LumA,LumA,test +MB-4607,CLAUDIN_SUBTYPE,LumB,0.0020289181,LumA,LumA,test +MB-4607,CLAUDIN_SUBTYPE,NC,0.00097253814,LumA,LumA,test +MB-4607,CLAUDIN_SUBTYPE,Normal,0.0057194927,LumA,LumA,test +MB-4607,CLAUDIN_SUBTYPE,claudin-low,0.00029102308,LumA,LumA,test +MB-0336,CLAUDIN_SUBTYPE,Basal,0.021422965,LumB,LumA,test +MB-0336,CLAUDIN_SUBTYPE,Her2,0.026144687,LumB,LumA,test +MB-0336,CLAUDIN_SUBTYPE,LumA,0.55499446,LumB,LumA,test +MB-0336,CLAUDIN_SUBTYPE,LumB,0.29034016,LumB,LumA,test +MB-0336,CLAUDIN_SUBTYPE,NC,0.03195602,LumB,LumA,test +MB-0336,CLAUDIN_SUBTYPE,Normal,0.05643516,LumB,LumA,test +MB-0336,CLAUDIN_SUBTYPE,claudin-low,0.018706419,LumB,LumA,test +MB-0373,CLAUDIN_SUBTYPE,Basal,0.014387095,LumB,LumB,test +MB-0373,CLAUDIN_SUBTYPE,Her2,0.029310577,LumB,LumB,test +MB-0373,CLAUDIN_SUBTYPE,LumA,0.38510934,LumB,LumB,test +MB-0373,CLAUDIN_SUBTYPE,LumB,0.5440556,LumB,LumB,test +MB-0373,CLAUDIN_SUBTYPE,NC,0.009671236,LumB,LumB,test +MB-0373,CLAUDIN_SUBTYPE,Normal,0.011146984,LumB,LumB,test +MB-0373,CLAUDIN_SUBTYPE,claudin-low,0.0063191014,LumB,LumB,test +MB-5521,CLAUDIN_SUBTYPE,Basal,0.087127276,LumB,claudin-low,test +MB-5521,CLAUDIN_SUBTYPE,Her2,0.05070497,LumB,claudin-low,test +MB-5521,CLAUDIN_SUBTYPE,LumA,0.16359404,LumB,claudin-low,test +MB-5521,CLAUDIN_SUBTYPE,LumB,0.00807642,LumB,claudin-low,test +MB-5521,CLAUDIN_SUBTYPE,NC,0.01983819,LumB,claudin-low,test +MB-5521,CLAUDIN_SUBTYPE,Normal,0.015758675,LumB,claudin-low,test +MB-5521,CLAUDIN_SUBTYPE,claudin-low,0.65490043,LumB,claudin-low,test +MB-3874,CLAUDIN_SUBTYPE,Basal,0.0016836161,LumA,LumA,test +MB-3874,CLAUDIN_SUBTYPE,Her2,0.0012980159,LumA,LumA,test +MB-3874,CLAUDIN_SUBTYPE,LumA,0.97220945,LumA,LumA,test +MB-3874,CLAUDIN_SUBTYPE,LumB,0.010106356,LumA,LumA,test +MB-3874,CLAUDIN_SUBTYPE,NC,0.003066919,LumA,LumA,test +MB-3874,CLAUDIN_SUBTYPE,Normal,0.009704882,LumA,LumA,test +MB-3874,CLAUDIN_SUBTYPE,claudin-low,0.0019306253,LumA,LumA,test +MB-5027,CLAUDIN_SUBTYPE,Basal,0.0014528902,LumA,LumA,test +MB-5027,CLAUDIN_SUBTYPE,Her2,0.0012269176,LumA,LumA,test +MB-5027,CLAUDIN_SUBTYPE,LumA,0.93390715,LumA,LumA,test +MB-5027,CLAUDIN_SUBTYPE,LumB,0.002001271,LumA,LumA,test +MB-5027,CLAUDIN_SUBTYPE,NC,0.003656211,LumA,LumA,test +MB-5027,CLAUDIN_SUBTYPE,Normal,0.05712867,LumA,LumA,test +MB-5027,CLAUDIN_SUBTYPE,claudin-low,0.0006269163,LumA,LumA,test +MB-0468,CLAUDIN_SUBTYPE,Basal,0.012990673,LumA,LumA,test +MB-0468,CLAUDIN_SUBTYPE,Her2,0.009133603,LumA,LumA,test +MB-0468,CLAUDIN_SUBTYPE,LumA,0.67511016,LumA,LumA,test +MB-0468,CLAUDIN_SUBTYPE,LumB,0.23245832,LumA,LumA,test +MB-0468,CLAUDIN_SUBTYPE,NC,0.020510169,LumA,LumA,test +MB-0468,CLAUDIN_SUBTYPE,Normal,0.04086844,LumA,LumA,test +MB-0468,CLAUDIN_SUBTYPE,claudin-low,0.008928693,LumA,LumA,test +MB-4696,CLAUDIN_SUBTYPE,Basal,0.5342888,claudin-low,Basal,test +MB-4696,CLAUDIN_SUBTYPE,Her2,0.020873046,claudin-low,Basal,test +MB-4696,CLAUDIN_SUBTYPE,LumA,0.013555169,claudin-low,Basal,test +MB-4696,CLAUDIN_SUBTYPE,LumB,0.003037242,claudin-low,Basal,test +MB-4696,CLAUDIN_SUBTYPE,NC,0.0066049076,claudin-low,Basal,test +MB-4696,CLAUDIN_SUBTYPE,Normal,0.015825186,claudin-low,Basal,test +MB-4696,CLAUDIN_SUBTYPE,claudin-low,0.40581557,claudin-low,Basal,test +MB-0148,CLAUDIN_SUBTYPE,Basal,0.105911985,Her2,Her2,test +MB-0148,CLAUDIN_SUBTYPE,Her2,0.68061477,Her2,Her2,test +MB-0148,CLAUDIN_SUBTYPE,LumA,0.016936218,Her2,Her2,test +MB-0148,CLAUDIN_SUBTYPE,LumB,0.020902403,Her2,Her2,test +MB-0148,CLAUDIN_SUBTYPE,NC,0.014811079,Her2,Her2,test +MB-0148,CLAUDIN_SUBTYPE,Normal,0.13562647,Her2,Her2,test +MB-0148,CLAUDIN_SUBTYPE,claudin-low,0.025197051,Her2,Her2,test +MB-0259,CLAUDIN_SUBTYPE,Basal,0.9655916,Basal,Basal,test +MB-0259,CLAUDIN_SUBTYPE,Her2,0.0017921418,Basal,Basal,test +MB-0259,CLAUDIN_SUBTYPE,LumA,0.00095415226,Basal,Basal,test +MB-0259,CLAUDIN_SUBTYPE,LumB,0.0194893,Basal,Basal,test +MB-0259,CLAUDIN_SUBTYPE,NC,0.0014253741,Basal,Basal,test +MB-0259,CLAUDIN_SUBTYPE,Normal,0.0053133294,Basal,Basal,test +MB-0259,CLAUDIN_SUBTYPE,claudin-low,0.005434054,Basal,Basal,test +MB-3576,CLAUDIN_SUBTYPE,Basal,0.014085304,Her2,LumB,test +MB-3576,CLAUDIN_SUBTYPE,Her2,0.030395169,Her2,LumB,test +MB-3576,CLAUDIN_SUBTYPE,LumA,0.008119377,Her2,LumB,test +MB-3576,CLAUDIN_SUBTYPE,LumB,0.9385239,Her2,LumB,test +MB-3576,CLAUDIN_SUBTYPE,NC,0.003706021,Her2,LumB,test +MB-3576,CLAUDIN_SUBTYPE,Normal,0.0024388966,Her2,LumB,test +MB-3576,CLAUDIN_SUBTYPE,claudin-low,0.0027313004,Her2,LumB,test +MB-6023,CLAUDIN_SUBTYPE,Basal,0.10552781,Normal,LumB,test +MB-6023,CLAUDIN_SUBTYPE,Her2,0.04281883,Normal,LumB,test +MB-6023,CLAUDIN_SUBTYPE,LumA,0.21033262,Normal,LumB,test +MB-6023,CLAUDIN_SUBTYPE,LumB,0.5202838,Normal,LumB,test +MB-6023,CLAUDIN_SUBTYPE,NC,0.028433282,Normal,LumB,test +MB-6023,CLAUDIN_SUBTYPE,Normal,0.07933291,Normal,LumB,test +MB-6023,CLAUDIN_SUBTYPE,claudin-low,0.013270646,Normal,LumB,test +MB-0531,CLAUDIN_SUBTYPE,Basal,0.21022493,Normal,Normal,test +MB-0531,CLAUDIN_SUBTYPE,Her2,0.11467583,Normal,Normal,test +MB-0531,CLAUDIN_SUBTYPE,LumA,0.07477027,Normal,Normal,test +MB-0531,CLAUDIN_SUBTYPE,LumB,0.006319668,Normal,Normal,test +MB-0531,CLAUDIN_SUBTYPE,NC,0.026580822,Normal,Normal,test +MB-0531,CLAUDIN_SUBTYPE,Normal,0.5091072,Normal,Normal,test +MB-0531,CLAUDIN_SUBTYPE,claudin-low,0.058321252,Normal,Normal,test +MB-7082,CLAUDIN_SUBTYPE,Basal,0.1157247,Her2,Her2,test +MB-7082,CLAUDIN_SUBTYPE,Her2,0.77621144,Her2,Her2,test +MB-7082,CLAUDIN_SUBTYPE,LumA,0.004608397,Her2,Her2,test +MB-7082,CLAUDIN_SUBTYPE,LumB,0.058663946,Her2,Her2,test +MB-7082,CLAUDIN_SUBTYPE,NC,0.006175034,Her2,Her2,test +MB-7082,CLAUDIN_SUBTYPE,Normal,0.022010837,Her2,Her2,test +MB-7082,CLAUDIN_SUBTYPE,claudin-low,0.016605757,Her2,Her2,test +MB-0292,CLAUDIN_SUBTYPE,Basal,0.8121689,Her2,Basal,test +MB-0292,CLAUDIN_SUBTYPE,Her2,0.069875725,Her2,Basal,test +MB-0292,CLAUDIN_SUBTYPE,LumA,0.0041141114,Her2,Basal,test +MB-0292,CLAUDIN_SUBTYPE,LumB,0.0611763,Her2,Basal,test +MB-0292,CLAUDIN_SUBTYPE,NC,0.0060262005,Her2,Basal,test +MB-0292,CLAUDIN_SUBTYPE,Normal,0.024384115,Her2,Basal,test +MB-0292,CLAUDIN_SUBTYPE,claudin-low,0.022254616,Her2,Basal,test +MB-0370,CLAUDIN_SUBTYPE,Basal,0.012829374,LumB,LumB,test +MB-0370,CLAUDIN_SUBTYPE,Her2,0.012013363,LumB,LumB,test +MB-0370,CLAUDIN_SUBTYPE,LumA,0.0067393836,LumB,LumB,test +MB-0370,CLAUDIN_SUBTYPE,LumB,0.96028435,LumB,LumB,test +MB-0370,CLAUDIN_SUBTYPE,NC,0.0037324743,LumB,LumB,test +MB-0370,CLAUDIN_SUBTYPE,Normal,0.0023109657,LumB,LumB,test +MB-0370,CLAUDIN_SUBTYPE,claudin-low,0.0020900585,LumB,LumB,test +MB-2933,CLAUDIN_SUBTYPE,Basal,0.00011494752,LumA,LumA,test +MB-2933,CLAUDIN_SUBTYPE,Her2,9.151891e-05,LumA,LumA,test +MB-2933,CLAUDIN_SUBTYPE,LumA,0.99400467,LumA,LumA,test +MB-2933,CLAUDIN_SUBTYPE,LumB,0.0005756249,LumA,LumA,test +MB-2933,CLAUDIN_SUBTYPE,NC,0.0005238338,LumA,LumA,test +MB-2933,CLAUDIN_SUBTYPE,Normal,0.004588087,LumA,LumA,test +MB-2933,CLAUDIN_SUBTYPE,claudin-low,0.00010130268,LumA,LumA,test +MB-3032,CLAUDIN_SUBTYPE,Basal,0.0031415077,LumA,LumA,test +MB-3032,CLAUDIN_SUBTYPE,Her2,0.0018050711,LumA,LumA,test +MB-3032,CLAUDIN_SUBTYPE,LumA,0.961053,LumA,LumA,test +MB-3032,CLAUDIN_SUBTYPE,LumB,0.0058364016,LumA,LumA,test +MB-3032,CLAUDIN_SUBTYPE,NC,0.0051372284,LumA,LumA,test +MB-3032,CLAUDIN_SUBTYPE,Normal,0.018474808,LumA,LumA,test +MB-3032,CLAUDIN_SUBTYPE,claudin-low,0.004551961,LumA,LumA,test +MB-2993,CLAUDIN_SUBTYPE,Basal,0.2695349,claudin-low,claudin-low,test +MB-2993,CLAUDIN_SUBTYPE,Her2,0.019920966,claudin-low,claudin-low,test +MB-2993,CLAUDIN_SUBTYPE,LumA,0.040396433,claudin-low,claudin-low,test +MB-2993,CLAUDIN_SUBTYPE,LumB,0.0016600321,claudin-low,claudin-low,test +MB-2993,CLAUDIN_SUBTYPE,NC,0.009523453,claudin-low,claudin-low,test +MB-2993,CLAUDIN_SUBTYPE,Normal,0.024829185,claudin-low,claudin-low,test +MB-2993,CLAUDIN_SUBTYPE,claudin-low,0.63413507,claudin-low,claudin-low,test +MB-6145,CLAUDIN_SUBTYPE,Basal,0.07892807,LumB,LumB,test +MB-6145,CLAUDIN_SUBTYPE,Her2,0.008111882,LumB,LumB,test +MB-6145,CLAUDIN_SUBTYPE,LumA,0.0050011,LumB,LumB,test +MB-6145,CLAUDIN_SUBTYPE,LumB,0.889813,LumB,LumB,test +MB-6145,CLAUDIN_SUBTYPE,NC,0.0052889027,LumB,LumB,test +MB-6145,CLAUDIN_SUBTYPE,Normal,0.011442315,LumB,LumB,test +MB-6145,CLAUDIN_SUBTYPE,claudin-low,0.0014147157,LumB,LumB,test +MB-7020,CLAUDIN_SUBTYPE,Basal,0.84614384,Her2,Basal,test +MB-7020,CLAUDIN_SUBTYPE,Her2,0.04755993,Her2,Basal,test +MB-7020,CLAUDIN_SUBTYPE,LumA,0.0060741375,Her2,Basal,test +MB-7020,CLAUDIN_SUBTYPE,LumB,0.023944391,Her2,Basal,test +MB-7020,CLAUDIN_SUBTYPE,NC,0.0069465516,Her2,Basal,test +MB-7020,CLAUDIN_SUBTYPE,Normal,0.040154915,Her2,Basal,test +MB-7020,CLAUDIN_SUBTYPE,claudin-low,0.029176125,Her2,Basal,test +MB-7122,CLAUDIN_SUBTYPE,Basal,0.08474028,Basal,Her2,test +MB-7122,CLAUDIN_SUBTYPE,Her2,0.4987373,Basal,Her2,test +MB-7122,CLAUDIN_SUBTYPE,LumA,0.011731912,Basal,Her2,test +MB-7122,CLAUDIN_SUBTYPE,LumB,0.008514522,Basal,Her2,test +MB-7122,CLAUDIN_SUBTYPE,NC,0.010443091,Basal,Her2,test +MB-7122,CLAUDIN_SUBTYPE,Normal,0.3794443,Basal,Her2,test +MB-7122,CLAUDIN_SUBTYPE,claudin-low,0.006388456,Basal,Her2,test +MB-7094,CLAUDIN_SUBTYPE,Basal,0.023922758,LumB,LumB,test +MB-7094,CLAUDIN_SUBTYPE,Her2,0.003619703,LumB,LumB,test +MB-7094,CLAUDIN_SUBTYPE,LumA,0.007338201,LumB,LumB,test +MB-7094,CLAUDIN_SUBTYPE,LumB,0.95778316,LumB,LumB,test +MB-7094,CLAUDIN_SUBTYPE,NC,0.0031036981,LumB,LumB,test +MB-7094,CLAUDIN_SUBTYPE,Normal,0.0031249668,LumB,LumB,test +MB-7094,CLAUDIN_SUBTYPE,claudin-low,0.00110747,LumB,LumB,test +MB-5306,CLAUDIN_SUBTYPE,Basal,0.021731438,LumA,Her2,test +MB-5306,CLAUDIN_SUBTYPE,Her2,0.91775525,LumA,Her2,test +MB-5306,CLAUDIN_SUBTYPE,LumA,0.004902402,LumA,Her2,test +MB-5306,CLAUDIN_SUBTYPE,LumB,0.021081677,LumA,Her2,test +MB-5306,CLAUDIN_SUBTYPE,NC,0.0036092622,LumA,Her2,test +MB-5306,CLAUDIN_SUBTYPE,Normal,0.025588432,LumA,Her2,test +MB-5306,CLAUDIN_SUBTYPE,claudin-low,0.0053315195,LumA,Her2,test +MB-5617,CLAUDIN_SUBTYPE,Basal,0.0030630203,LumA,LumA,test +MB-5617,CLAUDIN_SUBTYPE,Her2,0.001955523,LumA,LumA,test +MB-5617,CLAUDIN_SUBTYPE,LumA,0.94538075,LumA,LumA,test +MB-5617,CLAUDIN_SUBTYPE,LumB,0.021000806,LumA,LumA,test +MB-5617,CLAUDIN_SUBTYPE,NC,0.005717375,LumA,LumA,test +MB-5617,CLAUDIN_SUBTYPE,Normal,0.020743294,LumA,LumA,test +MB-5617,CLAUDIN_SUBTYPE,claudin-low,0.002139106,LumA,LumA,test +MB-0621,CLAUDIN_SUBTYPE,Basal,0.006565549,LumA,Normal,test +MB-0621,CLAUDIN_SUBTYPE,Her2,0.006360891,LumA,Normal,test +MB-0621,CLAUDIN_SUBTYPE,LumA,0.3304193,LumA,Normal,test +MB-0621,CLAUDIN_SUBTYPE,LumB,0.0012692043,LumA,Normal,test +MB-0621,CLAUDIN_SUBTYPE,NC,0.009304548,LumA,Normal,test +MB-0621,CLAUDIN_SUBTYPE,Normal,0.64509386,LumA,Normal,test +MB-0621,CLAUDIN_SUBTYPE,claudin-low,0.0009866556,LumA,Normal,test +MB-5477,CLAUDIN_SUBTYPE,Basal,0.008328521,LumB,LumB,test +MB-5477,CLAUDIN_SUBTYPE,Her2,0.0019549099,LumB,LumB,test +MB-5477,CLAUDIN_SUBTYPE,LumA,0.0036153146,LumB,LumB,test +MB-5477,CLAUDIN_SUBTYPE,LumB,0.98296285,LumB,LumB,test +MB-5477,CLAUDIN_SUBTYPE,NC,0.001642929,LumB,LumB,test +MB-5477,CLAUDIN_SUBTYPE,Normal,0.00085779413,LumB,LumB,test +MB-5477,CLAUDIN_SUBTYPE,claudin-low,0.00063765055,LumB,LumB,test +MB-6098,CLAUDIN_SUBTYPE,Basal,0.99172467,Basal,Basal,test +MB-6098,CLAUDIN_SUBTYPE,Her2,0.000513123,Basal,Basal,test +MB-6098,CLAUDIN_SUBTYPE,LumA,0.00020588536,Basal,Basal,test +MB-6098,CLAUDIN_SUBTYPE,LumB,0.0013674272,Basal,Basal,test +MB-6098,CLAUDIN_SUBTYPE,NC,0.00025615178,Basal,Basal,test +MB-6098,CLAUDIN_SUBTYPE,Normal,0.0016619669,Basal,Basal,test +MB-6098,CLAUDIN_SUBTYPE,claudin-low,0.0042706784,Basal,Basal,test +MB-7291,CLAUDIN_SUBTYPE,Basal,0.3002563,claudin-low,claudin-low,test +MB-7291,CLAUDIN_SUBTYPE,Her2,0.05882606,claudin-low,claudin-low,test +MB-7291,CLAUDIN_SUBTYPE,LumA,0.01891297,claudin-low,claudin-low,test +MB-7291,CLAUDIN_SUBTYPE,LumB,0.0041538556,claudin-low,claudin-low,test +MB-7291,CLAUDIN_SUBTYPE,NC,0.008713774,claudin-low,claudin-low,test +MB-7291,CLAUDIN_SUBTYPE,Normal,0.014741183,claudin-low,claudin-low,test +MB-7291,CLAUDIN_SUBTYPE,claudin-low,0.5943959,claudin-low,claudin-low,test +MB-6317,CLAUDIN_SUBTYPE,Basal,0.012958962,LumB,LumB,test +MB-6317,CLAUDIN_SUBTYPE,Her2,0.0020572403,LumB,LumB,test +MB-6317,CLAUDIN_SUBTYPE,LumA,0.025314307,LumB,LumB,test +MB-6317,CLAUDIN_SUBTYPE,LumB,0.95072824,LumB,LumB,test +MB-6317,CLAUDIN_SUBTYPE,NC,0.0043597072,LumB,LumB,test +MB-6317,CLAUDIN_SUBTYPE,Normal,0.0029214416,LumB,LumB,test +MB-6317,CLAUDIN_SUBTYPE,claudin-low,0.0016601809,LumB,LumB,test +MB-0636,CLAUDIN_SUBTYPE,Basal,0.12887633,LumA,LumA,test +MB-0636,CLAUDIN_SUBTYPE,Her2,0.02171,LumA,LumA,test +MB-0636,CLAUDIN_SUBTYPE,LumA,0.46709418,LumA,LumA,test +MB-0636,CLAUDIN_SUBTYPE,LumB,0.062577456,LumA,LumA,test +MB-0636,CLAUDIN_SUBTYPE,NC,0.038612284,LumA,LumA,test +MB-0636,CLAUDIN_SUBTYPE,Normal,0.04212916,LumA,LumA,test +MB-0636,CLAUDIN_SUBTYPE,claudin-low,0.2390007,LumA,LumA,test +MB-2896,CLAUDIN_SUBTYPE,Basal,0.002299165,claudin-low,LumA,test +MB-2896,CLAUDIN_SUBTYPE,Her2,0.0007781012,claudin-low,LumA,test +MB-2896,CLAUDIN_SUBTYPE,LumA,0.9757245,claudin-low,LumA,test +MB-2896,CLAUDIN_SUBTYPE,LumB,0.0011249594,claudin-low,LumA,test +MB-2896,CLAUDIN_SUBTYPE,NC,0.0029280025,claudin-low,LumA,test +MB-2896,CLAUDIN_SUBTYPE,Normal,0.009309344,claudin-low,LumA,test +MB-2896,CLAUDIN_SUBTYPE,claudin-low,0.007835951,claudin-low,LumA,test +MB-2616,CLAUDIN_SUBTYPE,Basal,0.06496,claudin-low,LumA,test +MB-2616,CLAUDIN_SUBTYPE,Her2,0.016235162,claudin-low,LumA,test +MB-2616,CLAUDIN_SUBTYPE,LumA,0.6097361,claudin-low,LumA,test +MB-2616,CLAUDIN_SUBTYPE,LumB,0.0042911847,claudin-low,LumA,test +MB-2616,CLAUDIN_SUBTYPE,NC,0.028379207,claudin-low,LumA,test +MB-2616,CLAUDIN_SUBTYPE,Normal,0.09773979,claudin-low,LumA,test +MB-2616,CLAUDIN_SUBTYPE,claudin-low,0.17865847,claudin-low,LumA,test +MB-5272,CLAUDIN_SUBTYPE,Basal,0.14369744,claudin-low,claudin-low,test +MB-5272,CLAUDIN_SUBTYPE,Her2,0.040493555,claudin-low,claudin-low,test +MB-5272,CLAUDIN_SUBTYPE,LumA,0.102554604,claudin-low,claudin-low,test +MB-5272,CLAUDIN_SUBTYPE,LumB,0.0080627585,claudin-low,claudin-low,test +MB-5272,CLAUDIN_SUBTYPE,NC,0.024186026,claudin-low,claudin-low,test +MB-5272,CLAUDIN_SUBTYPE,Normal,0.03038734,claudin-low,claudin-low,test +MB-5272,CLAUDIN_SUBTYPE,claudin-low,0.6506183,claudin-low,claudin-low,test +MB-5614,CLAUDIN_SUBTYPE,Basal,0.07408259,LumA,LumA,test +MB-5614,CLAUDIN_SUBTYPE,Her2,0.027301216,LumA,LumA,test +MB-5614,CLAUDIN_SUBTYPE,LumA,0.54836744,LumA,LumA,test +MB-5614,CLAUDIN_SUBTYPE,LumB,0.018616602,LumA,LumA,test +MB-5614,CLAUDIN_SUBTYPE,NC,0.049900148,LumA,LumA,test +MB-5614,CLAUDIN_SUBTYPE,Normal,0.1298033,LumA,LumA,test +MB-5614,CLAUDIN_SUBTYPE,claudin-low,0.15192871,LumA,LumA,test +MB-0261,CLAUDIN_SUBTYPE,Basal,0.014635003,LumB,LumB,test +MB-0261,CLAUDIN_SUBTYPE,Her2,0.0037229585,LumB,LumB,test +MB-0261,CLAUDIN_SUBTYPE,LumA,0.25503373,LumB,LumB,test +MB-0261,CLAUDIN_SUBTYPE,LumB,0.7036156,LumB,LumB,test +MB-0261,CLAUDIN_SUBTYPE,NC,0.008994171,LumB,LumB,test +MB-0261,CLAUDIN_SUBTYPE,Normal,0.011267811,LumB,LumB,test +MB-0261,CLAUDIN_SUBTYPE,claudin-low,0.002730723,LumB,LumB,test +MB-4818,CLAUDIN_SUBTYPE,Basal,0.007473252,LumB,LumA,test +MB-4818,CLAUDIN_SUBTYPE,Her2,0.0026798449,LumB,LumA,test +MB-4818,CLAUDIN_SUBTYPE,LumA,0.8582904,LumB,LumA,test +MB-4818,CLAUDIN_SUBTYPE,LumB,0.095787935,LumB,LumA,test +MB-4818,CLAUDIN_SUBTYPE,NC,0.008535205,LumB,LumA,test +MB-4818,CLAUDIN_SUBTYPE,Normal,0.025076509,LumB,LumA,test +MB-4818,CLAUDIN_SUBTYPE,claudin-low,0.0021569587,LumB,LumA,test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/labels_scatter.csv Tue Jun 24 05:55:40 2025 +0000 @@ -0,0 +1,561 @@ +sample_id,variable,class_label,probability,known_label,predicted_label,split +MB-0177,CLAUDIN_SUBTYPE,Basal,0.00065193686,0.538765685135181,0.972321861629101,test +MB-5115,CLAUDIN_SUBTYPE,Basal,0.996806,0.773755799156275,0.69668865583791,test +MB-3781,CLAUDIN_SUBTYPE,Basal,0.002550664,0.103112168552565,0.468559871729238,test +MB-5271,CLAUDIN_SUBTYPE,Basal,0.019927176,0.654873482633503,0.321079223394425,test +MB-6179,CLAUDIN_SUBTYPE,Basal,0.027884316,0.229694183436779,0.119303330351763,test +MB-0492,CLAUDIN_SUBTYPE,Basal,0.018194975,0.615004839717517,0.471383670080275,test +MB-5135,CLAUDIN_SUBTYPE,Basal,0.9942643,0.922977242099418,0.225834863895414,test +MB-5079,CLAUDIN_SUBTYPE,Basal,0.00039439273,0.534191254111959,0.936803468999052,test +MB-5243,CLAUDIN_SUBTYPE,Basal,0.040594183,0.436692839492028,0.60770748981312,test +MB-2984,CLAUDIN_SUBTYPE,Basal,0.004155519,0.0958561677092834,0.36055698663967,test +MB-4017,CLAUDIN_SUBTYPE,Basal,0.005148993,0.307745858743577,0.848468854748048,test +MB-5447,CLAUDIN_SUBTYPE,Basal,0.019656463,0.639867402633728,0.012061549644095,test +MB-5616,CLAUDIN_SUBTYPE,Basal,0.17296688,0.912049220967967,0.894911547757386,test +MB-3021,CLAUDIN_SUBTYPE,Basal,0.0047936346,0.933459642189237,0.0261584236237407,test +MB-0872,CLAUDIN_SUBTYPE,Basal,0.008130632,0.743861075168871,0.033341616860178,test +MB-3386,CLAUDIN_SUBTYPE,Basal,0.012321706,0.672581291497599,0.418350899757299,test +MB-7080,CLAUDIN_SUBTYPE,Basal,0.00022694626,0.822836881696739,0.0284213443101353,test +MB-5405,CLAUDIN_SUBTYPE,Basal,0.068026006,0.470667045207968,0.362595625106613,test +MB-4357,CLAUDIN_SUBTYPE,Basal,0.06376728,0.448712840431707,0.0460698271044052,test +MB-6286,CLAUDIN_SUBTYPE,Basal,0.00011293625,0.592703092678562,0.874407194516703,test +MB-5134,CLAUDIN_SUBTYPE,Basal,0.000034737288,0.433157189175717,0.989437443788809,test +MB-4942,CLAUDIN_SUBTYPE,Basal,0.0806648,0.0027781196062971,0.380280439590155,test +MB-6238,CLAUDIN_SUBTYPE,Basal,0.004182132,0.461895554513627,0.792907756330366,test +MB-0127,CLAUDIN_SUBTYPE,Basal,0.14812747,0.0667397562362506,0.811237218753761,test +MB-7277,CLAUDIN_SUBTYPE,Basal,0.00010833181,0.734151177346663,0.765459204119,test +MB-0060,CLAUDIN_SUBTYPE,Basal,0.42745838,0.57692869465675,0.491750945034112,test +MB-4721,CLAUDIN_SUBTYPE,Basal,0.0001352974,0.190105127465303,0.402842160778761,test +MB-0882,CLAUDIN_SUBTYPE,Basal,0.004198095,0.809379899744063,0.0553232215618101,test +MB-3271,CLAUDIN_SUBTYPE,Basal,0.7585569,0.675703770761042,0.187989598988555,test +MB-4746,CLAUDIN_SUBTYPE,Basal,0.023426726,0.571544361948107,0.924707400014598,test +MB-6069,CLAUDIN_SUBTYPE,Basal,0.011962601,0.331808256707687,0.668458861871782,test +MB-6044,CLAUDIN_SUBTYPE,Basal,0.091202796,0.679592423901629,0.724260110896608,test +MB-0601,CLAUDIN_SUBTYPE,Basal,0.09948703,0.911106207819084,0.00483366336869152,test +MB-4887,CLAUDIN_SUBTYPE,Basal,0.045928933,0.476257775127865,0.135369016567125,test +MB-7111,CLAUDIN_SUBTYPE,Basal,0.68688107,0.810487560193184,0.216068346765086,test +MB-7174,CLAUDIN_SUBTYPE,Basal,0.037639856,0.106401900968868,0.636746290299386,test +MB-0317,CLAUDIN_SUBTYPE,Basal,0.0013807476,0.688179800989634,0.347660444953098,test +MB-4712,CLAUDIN_SUBTYPE,Basal,0.04694011,0.635269531249685,0.652991223497237,test +MB-7263,CLAUDIN_SUBTYPE,Basal,0.008590267,0.875502437263308,0.649153177558533,test +MB-5582,CLAUDIN_SUBTYPE,Basal,0.00032956575,0.0516932548722687,0.23230092396236,test +MB-5420,CLAUDIN_SUBTYPE,Basal,0.14000916,0.274000112819961,0.716221427568446,test +MB-2718,CLAUDIN_SUBTYPE,Basal,0.9568239,0.0353525369432944,0.742227491251913,test +MB-5268,CLAUDIN_SUBTYPE,Basal,0.00022492505,0.832424839215813,0.244023029845609,test +MB-5514,CLAUDIN_SUBTYPE,Basal,0.011733811,0.753546161496848,0.385435044406807,test +MB-7053,CLAUDIN_SUBTYPE,Basal,0.054197155,0.977318962366569,0.237598711728155,test +MB-5348,CLAUDIN_SUBTYPE,Basal,0.31805244,0.319359223188422,0.292036766063516,test +MB-0901,CLAUDIN_SUBTYPE,Basal,0.91394204,0.594671956877581,0.412298017395635,test +MB-5381,CLAUDIN_SUBTYPE,Basal,0.14966057,0.558709043192928,0.679592156146556,test +MB-3153,CLAUDIN_SUBTYPE,Basal,0.54439086,0.768126529101167,0.502967178535164,test +MB-5366,CLAUDIN_SUBTYPE,Basal,0.03821787,0.53662560225541,0.134971042214036,test +MB-7107,CLAUDIN_SUBTYPE,Basal,0.011886511,0.956384541735149,0.424912555015729,test +MB-4697,CLAUDIN_SUBTYPE,Basal,0.02601451,0.159979346624961,0.47951175936242,test +MB-5070,CLAUDIN_SUBTYPE,Basal,0.55893034,0.485489118335065,0.715206536195044,test +MB-0598,CLAUDIN_SUBTYPE,Basal,0.025924109,0.0402055966956609,0.817391102492606,test +MB-4374,CLAUDIN_SUBTYPE,Basal,0.00005950361,0.923862190381015,0.366112575624947,test +MB-0264,CLAUDIN_SUBTYPE,Basal,0.064288855,0.674679302695533,0.121086371477402,test +MB-4688,CLAUDIN_SUBTYPE,Basal,0.020050965,0.211741317900613,0.220815766076866,test +MB-7003,CLAUDIN_SUBTYPE,Basal,0.0070154336,0.62877380028372,0.00724930365424901,test +MB-2964,CLAUDIN_SUBTYPE,Basal,0.22110376,0.684592472692258,0.648341090766916,test +MB-6237,CLAUDIN_SUBTYPE,Basal,0.79525214,0.592387583787763,0.101900296544652,test +MB-4977,CLAUDIN_SUBTYPE,Basal,0.008476745,0.479042242358346,0.739004222730522,test +MB-4329,CLAUDIN_SUBTYPE,Basal,0.0005693444,0.551964164273032,0.985018129855343,test +MB-4001,CLAUDIN_SUBTYPE,Basal,0.040497895,0.144140753059113,0.0480353731666699,test +MB-6163,CLAUDIN_SUBTYPE,Basal,0.01724588,0.0456347369881465,0.966866290739064,test +MB-7151,CLAUDIN_SUBTYPE,Basal,0.99036413,0.755184096215683,0.511775196406995,test +MB-3341,CLAUDIN_SUBTYPE,Basal,0.00052954024,0.867258799522286,0.945986091442646,test +MB-5378,CLAUDIN_SUBTYPE,Basal,0.99011266,0.949835247101226,0.519198814863026,test +MB-0458,CLAUDIN_SUBTYPE,Basal,0.023540689,0.920227016043002,0.786144318393002,test +MB-0197,CLAUDIN_SUBTYPE,Basal,0.011809357,0.175256319277853,0.840465492949779,test +MB-3002,CLAUDIN_SUBTYPE,Basal,0.004542802,0.157793871607326,0.821121299749014,test +MB-0411,CLAUDIN_SUBTYPE,Basal,0.033319343,0.575124325045139,0.607861457000032,test +MB-0230,CLAUDIN_SUBTYPE,Basal,0.0413835,0.572110969640788,0.956677679112499,test +MB-0188,CLAUDIN_SUBTYPE,Basal,0.04173352,0.180352143209764,0.602590415471472,test +MB-4911,CLAUDIN_SUBTYPE,Basal,0.99012136,0.415811611962587,0.776337488373441,test +MB-0428,CLAUDIN_SUBTYPE,Basal,0.089249864,0.0575320236194094,0.269872075646781,test +MB-5068,CLAUDIN_SUBTYPE,Basal,0.0002629537,0.209988150244701,0.694178888306287,test +MB-5518,CLAUDIN_SUBTYPE,Basal,0.017793423,0.872770106423506,0.987882335951355,test +MB-5185,CLAUDIN_SUBTYPE,Basal,0.008536392,0.995784701400265,0.506560081342501,test +MB-4836,CLAUDIN_SUBTYPE,Basal,0.25713205,0.452731335620843,0.0356305617497709,test +MB-6125,CLAUDIN_SUBTYPE,Basal,0.042460058,0.658474828321265,0.240372107873119,test +MB-2932,CLAUDIN_SUBTYPE,Basal,0.010055175,0.934112698152244,0.123443629673291,test +MB-0095,CLAUDIN_SUBTYPE,Basal,0.0011303613,0.468988842280344,0.4441540409682,test +MB-2564,CLAUDIN_SUBTYPE,Basal,0.00018593732,0.83184148822229,0.455375079889349,test +MB-7155,CLAUDIN_SUBTYPE,Basal,0.90355,0.213550320473657,0.157825560182372,test +MB-4603,CLAUDIN_SUBTYPE,Basal,0.0017825573,0.0776356820691351,0.95344553146745,test +MB-4173,CLAUDIN_SUBTYPE,Basal,0.00006163649,0.965875339510969,0.120009540247821,test +MB-0578,CLAUDIN_SUBTYPE,Basal,0.013469911,0.18136331409503,0.0362224612808332,test +MB-3272,CLAUDIN_SUBTYPE,Basal,0.033196483,0.582920029321961,0.431322728744303,test +MB-4695,CLAUDIN_SUBTYPE,Basal,0.0014625929,0.735023192517132,0.852608055952913,test +MB-0455,CLAUDIN_SUBTYPE,Basal,0.12362967,0.0633750622021775,0.599947037570935,test +MB-2863,CLAUDIN_SUBTYPE,Basal,0.00010688343,0.325666508407505,0.567317402149709,test +MB-0346,CLAUDIN_SUBTYPE,Basal,0.010869512,0.474107751512782,0.129836229380199,test +MB-4709,CLAUDIN_SUBTYPE,Basal,0.00011124542,0.465236162555579,0.801603138833451,test +MB-5057,CLAUDIN_SUBTYPE,Basal,0.82365197,0.283304158757239,0.760450094552461,test +MB-4724,CLAUDIN_SUBTYPE,Basal,0.02104304,0.658173141132169,0.570311648326617,test +MB-6217,CLAUDIN_SUBTYPE,Basal,0.01368638,0.760083466212131,0.751984618423523,test +MB-7160,CLAUDIN_SUBTYPE,Basal,0.63306177,0.473178834847227,0.886676676126785,test +MB-4548,CLAUDIN_SUBTYPE,Basal,0.7617707,0.810477164033397,0.864471273376427,test +MB-5222,CLAUDIN_SUBTYPE,Basal,0.040132806,0.958659306784894,0.486558670772057,test +MB-5422,CLAUDIN_SUBTYPE,Basal,0.00061716465,0.914367547113834,0.0744882484188454,test +MB-0384,CLAUDIN_SUBTYPE,Basal,0.008731177,0.162850263250862,0.829416484799937,test +MB-5335,CLAUDIN_SUBTYPE,Basal,0.98229927,0.116996514476567,0.782248319801082,test +MB-0157,CLAUDIN_SUBTYPE,Basal,0.021822063,0.169434534353104,0.178954815341916,test +MB-5324,CLAUDIN_SUBTYPE,Basal,0.00030340505,0.426680776789164,0.00819499419700242,test +MB-5150,CLAUDIN_SUBTYPE,Basal,0.0014000323,0.561205967905908,0.447864569198937,test +MB-7073,CLAUDIN_SUBTYPE,Basal,0.8283376,0.934865330006297,0.204885952707649,test +MB-0136,CLAUDIN_SUBTYPE,Basal,0.006129607,0.0850597818337014,0.301087880912686,test +MB-0163,CLAUDIN_SUBTYPE,Basal,0.99020535,0.2760274273804,0.434650044749915,test 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+MB-0235,CLAUDIN_SUBTYPE,Basal,0.00012883723,0.860624129756165,0.162472636246045,test +MB-0349,CLAUDIN_SUBTYPE,Basal,0.004910741,0.533809306990838,0.284389040383387,test +MB-3013,CLAUDIN_SUBTYPE,Basal,0.008502817,0.308583835124357,0.303367096295307,test +MB-0559,CLAUDIN_SUBTYPE,Basal,0.014843292,0.50693266292074,0.320407254262618,test +MB-5227,CLAUDIN_SUBTYPE,Basal,0.012661014,0.244924270118846,0.0202328487739021,test +MB-5084,CLAUDIN_SUBTYPE,Basal,0.00004069903,0.319769419364725,0.926448207801622,test +MB-4234,CLAUDIN_SUBTYPE,Basal,0.0006037344,0.335861221547207,0.104342070921928,test +MB-4641,CLAUDIN_SUBTYPE,Basal,0.00005447803,0.0874704630134172,0.372334321448184,test +MB-0286,CLAUDIN_SUBTYPE,Basal,0.045152564,0.484475385557862,0.508036943459549,test +MB-3014,CLAUDIN_SUBTYPE,Basal,0.9668346,0.10877581876303,0.93289600213874,test +MB-2796,CLAUDIN_SUBTYPE,Basal,0.0099408,0.610846935629103,0.985026915517205,test +MB-7058,CLAUDIN_SUBTYPE,Basal,0.004823737,0.167073512954056,0.0962562471509563,test +MB-5287,CLAUDIN_SUBTYPE,Basal,0.00011211436,0.172521498832679,0.479483562833087,test +MB-7281,CLAUDIN_SUBTYPE,Basal,0.13046472,0.945118484770153,0.584111923757987,test +MB-4011,CLAUDIN_SUBTYPE,Basal,0.013587133,0.288318864482452,0.898790486022543,test +MB-3102,CLAUDIN_SUBTYPE,Basal,0.006243442,0.0978471972931045,0.456101120775363,test +MB-6194,CLAUDIN_SUBTYPE,Basal,0.23802574,0.931732602777996,0.783029660119431,test +MB-3026,CLAUDIN_SUBTYPE,Basal,0.008249727,0.127699803362252,0.8888662409818,test +MB-7052,CLAUDIN_SUBTYPE,Basal,0.58712304,0.613677427596097,0.968574526952069,test +MB-5291,CLAUDIN_SUBTYPE,Basal,0.005792461,0.358405268470571,0.756854389395088,test +MB-4767,CLAUDIN_SUBTYPE,Basal,0.11165398,0.296987818602036,0.0614110025645691,test +MB-7043,CLAUDIN_SUBTYPE,Basal,0.115664475,0.0428474223606018,0.975246448692524,test +MB-0472,CLAUDIN_SUBTYPE,Basal,0.0007786848,0.119985717693098,0.770880815232391,test +MB-5338,CLAUDIN_SUBTYPE,Basal,0.030729877,0.95704112876801,0.813894932737194,test +MB-2966,CLAUDIN_SUBTYPE,Basal,0.0031380653,0.483126381572316,0.65694844703083,test +MB-0551,CLAUDIN_SUBTYPE,Basal,0.016118636,0.10537684657426,0.652578076073672,test +MB-5404,CLAUDIN_SUBTYPE,Basal,0.0011252166,0.814010447279065,0.975590200239067,test +MB-5540,CLAUDIN_SUBTYPE,Basal,0.003374003,0.056769263976135,0.631319371789989,test +MB-0644,CLAUDIN_SUBTYPE,Basal,0.061044354,0.383971173340051,0.771226168349101,test +MB-0618,CLAUDIN_SUBTYPE,Basal,0.008935495,0.76076715392949,0.17298396466503,test +MB-3439,CLAUDIN_SUBTYPE,Basal,0.00030271732,0.055591842308563,0.485572802861853,test +MB-3797,CLAUDIN_SUBTYPE,Basal,0.0017444948,0.779751472977302,0.568746058470295,test +MB-2929,CLAUDIN_SUBTYPE,Basal,0.04076907,0.882140769310428,0.94177657106859,test +MB-5182,CLAUDIN_SUBTYPE,Basal,0.00003222719,0.481098757322346,0.509675684989371,test +MB-0642,CLAUDIN_SUBTYPE,Basal,0.00073901145,0.564012568989754,0.165062635493404,test +MB-4738,CLAUDIN_SUBTYPE,Basal,0.0006314964,0.0534446151680114,0.787720646976592,test +MB-0192,CLAUDIN_SUBTYPE,Basal,0.035434213,0.234643396918984,0.663248932431999,test +MB-0243,CLAUDIN_SUBTYPE,Basal,0.015972668,0.310685865278066,0.885853224257435,test +MB-7208,CLAUDIN_SUBTYPE,Basal,0.5404998,0.354656361829797,0.242990095503478,test +MB-0343,CLAUDIN_SUBTYPE,Basal,0.0010580262,0.129114228023668,0.313054938731777,test +MB-7229,CLAUDIN_SUBTYPE,Basal,0.00064306316,0.996374286284691,0.633019307509032,test +MB-0575,CLAUDIN_SUBTYPE,Basal,0.08683767,0.121867773609498,0.205305103782433,test +MB-7091,CLAUDIN_SUBTYPE,Basal,0.005865344,0.440878612284111,0.944572832792479,test +MB-0176,CLAUDIN_SUBTYPE,Basal,0.038080536,0.254638848136554,0.850901277383173,test +MB-6103,CLAUDIN_SUBTYPE,Basal,0.02262877,0.0576491824718058,0.987120876701608,test +MB-0589,CLAUDIN_SUBTYPE,Basal,0.011077246,0.341798808131415,0.60840779445762,test +MB-5061,CLAUDIN_SUBTYPE,Basal,0.043176465,0.0384890195759937,0.693263066897134,test +MB-6058,CLAUDIN_SUBTYPE,Basal,0.66850376,0.240196959394224,0.625324111224012,test +MB-7009,CLAUDIN_SUBTYPE,Basal,0.7792922,0.138981570750916,0.274758449514135,test +MB-2814,CLAUDIN_SUBTYPE,Basal,0.015165181,0.82518730484964,0.350255882534714,test +MB-4653,CLAUDIN_SUBTYPE,Basal,0.009771683,0.134024174187687,0.904584470087493,test +MB-5571,CLAUDIN_SUBTYPE,Basal,0.0055585974,0.23260830377921,0.805541539760581,test +MB-5224,CLAUDIN_SUBTYPE,Basal,0.001968088,0.594346229035486,0.35801377845514,test +MB-4796,CLAUDIN_SUBTYPE,Basal,0.002353539,0.75468559038313,0.663296839570855,test +MB-7238,CLAUDIN_SUBTYPE,Basal,0.24624525,0.172959370415784,0.638871581109743,test +MB-4931,CLAUDIN_SUBTYPE,Basal,0.011187982,0.272239489016321,0.0245358429654267,test +MB-0627,CLAUDIN_SUBTYPE,Basal,0.020750402,0.966635301817588,0.65632433083211,test +MB-2764,CLAUDIN_SUBTYPE,Basal,0.036022753,0.193818415071677,0.470394116473101,test +MB-3450,CLAUDIN_SUBTYPE,Basal,0.013241612,0.119612698193582,0.0415887305369768,test +MB-3824,CLAUDIN_SUBTYPE,Basal,0.009530319,0.505219891505541,0.549804702808641,test +MB-0022,CLAUDIN_SUBTYPE,Basal,0.12542996,0.920842998728781,0.574230148343263,test +MB-4648,CLAUDIN_SUBTYPE,Basal,0.01299259,0.204564954054718,0.851327220295579,test +MB-4607,CLAUDIN_SUBTYPE,Basal,0.0003763551,0.364227943854935,0.978216998134251,test +MB-0336,CLAUDIN_SUBTYPE,Basal,0.021422965,0.890985738066562,0.559891155826585,test +MB-0373,CLAUDIN_SUBTYPE,Basal,0.014387095,0.375862034162401,0.373368468691206,test +MB-5521,CLAUDIN_SUBTYPE,Basal,0.087127276,0.677324496957088,0.766681899002205,test +MB-3874,CLAUDIN_SUBTYPE,Basal,0.0016836161,0.809906871957315,0.477781552431746,test +MB-5027,CLAUDIN_SUBTYPE,Basal,0.0014528902,0.648608946842753,0.629865390443516,test +MB-0468,CLAUDIN_SUBTYPE,Basal,0.012990673,0.125422608767086,0.824118538472175,test +MB-4696,CLAUDIN_SUBTYPE,Basal,0.5342888,0.0416804187190757,0.0757433447671714,test +MB-0148,CLAUDIN_SUBTYPE,Basal,0.105911985,0.695605150589128,0.874540697643398,test +MB-0259,CLAUDIN_SUBTYPE,Basal,0.9655916,0.0931229925666362,0.984674676038986,test +MB-3576,CLAUDIN_SUBTYPE,Basal,0.014085304,0.614765173321363,0.487185133866051,test +MB-6023,CLAUDIN_SUBTYPE,Basal,0.10552781,0.21013724591277,0.95104795444201,test +MB-0531,CLAUDIN_SUBTYPE,Basal,0.21022493,0.745116288368098,0.0485028531226679,test +MB-7082,CLAUDIN_SUBTYPE,Basal,0.1157247,0.0865989377458949,0.541176608397724,test +MB-0292,CLAUDIN_SUBTYPE,Basal,0.8121689,0.528115237716387,0.24931419924717,test +MB-0370,CLAUDIN_SUBTYPE,Basal,0.012829374,0.231379589993094,0.85472289114145,test +MB-2933,CLAUDIN_SUBTYPE,Basal,0.00011494752,0.343830034538316,0.212064616016061,test +MB-3032,CLAUDIN_SUBTYPE,Basal,0.0031415077,0.454087121338497,0.925790846679658,test +MB-2993,CLAUDIN_SUBTYPE,Basal,0.2695349,0.75580118293037,0.0464801078894475,test +MB-6145,CLAUDIN_SUBTYPE,Basal,0.07892807,0.108101176695306,0.431474921990265,test +MB-7020,CLAUDIN_SUBTYPE,Basal,0.84614384,0.101260968630039,0.408246200398893,test +MB-7122,CLAUDIN_SUBTYPE,Basal,0.08474028,0.521990161633348,0.653671282401926,test +MB-7094,CLAUDIN_SUBTYPE,Basal,0.023922758,0.085961181583144,0.120787463044007,test +MB-5306,CLAUDIN_SUBTYPE,Basal,0.021731438,0.968407469519939,0.729326333534007,test +MB-5617,CLAUDIN_SUBTYPE,Basal,0.0030630203,0.437537955671113,0.268105367166734,test +MB-0621,CLAUDIN_SUBTYPE,Basal,0.006565549,0.581242790413579,0.798339608785112,test +MB-5477,CLAUDIN_SUBTYPE,Basal,0.008328521,0.377339180411873,0.904599633423992,test +MB-6098,CLAUDIN_SUBTYPE,Basal,0.99172467,0.21396314126133,0.344969180882548,test +MB-7291,CLAUDIN_SUBTYPE,Basal,0.3002563,0.323456121159745,0.439280589340438,test +MB-6317,CLAUDIN_SUBTYPE,Basal,0.012958962,0.561475815704227,0.98584451243204,test +MB-0636,CLAUDIN_SUBTYPE,Basal,0.12887633,0.403375975989401,0.0143828288351394,test +MB-2896,CLAUDIN_SUBTYPE,Basal,0.002299165,0.144106424746212,0.699092322866917,test +MB-2616,CLAUDIN_SUBTYPE,Basal,0.06496,0.657131571866378,0.195940427630711,test +MB-5272,CLAUDIN_SUBTYPE,Basal,0.14369744,0.160773513971314,0.776892459913046,test +MB-5614,CLAUDIN_SUBTYPE,Basal,0.07408259,0.313349720353266,0.027573650009806,test +MB-0261,CLAUDIN_SUBTYPE,Basal,0.014635003,0.531841397516879,0.16895446841995,test +MB-4818,CLAUDIN_SUBTYPE,Basal,0.007473252,0.73950719800203,0.168426272601709,test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/loc.sample Tue Jun 24 05:55:40 2025 +0000 @@ -0,0 +1,1 @@ +lgg_tcga lgg_tcga 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mut.tabular Tue Jun 24 05:55:40 2025 +0000 @@ -0,0 +1,2000 @@ +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Hotspot gc_content ref_context +NOS1 4842 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 117669890 117669890 + synonymous_variant Silent SNP G G A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 19 ENST00000338101.4:c.3384C>T p.Thr1128= p.T1128= ENST00000338101 1128 acC/acT 0 0.592 CCTGGAAGATGGTGCAGGGCG +NPAS3 64067 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 34263252 34263252 + splice_donor_variant Splice_Site SNP T T G TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 26 ENST00000356141.4:c.1301+2T>G p.X434_splice ENST00000356141 0 0.333 CCTTCTTAGGTATATTTTCTA +JAG2 3714 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 105615619 105615619 + synonymous_variant Silent SNP G G A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 48 ENST00000331782.3:c.1641C>T p.Asn547= p.N547= ENST00000331782 NM_002226.4 547 aaC/aaT 0 0.662 AGCGAGCGCCGTTCCGGCAGG +ENKD1 84080 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 67700039 67700039 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 8 ENST00000243878.4:c.215G>A p.Arg72His p.R72H ENST00000243878 NM_032140.1 72 cGc/cAc 0 0.662 CCCGACGCCGCGCTGGCCGCG +FKBP8 23770 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 18650228 18650228 + synonymous_variant Silent SNP C C T TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 51 ENST00000608443.1:c.504G>A p.Thr168= p.T168= ENST00000608443 168 acG/acA 0 0.637 TGACCATGGCCGTCTCCCCCA +IRF2BP1 26145 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 46387378 46387378 + missense_variant Missense_Mutation SNP C C A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 4 15 ENST00000302165.3:c.1655G>T p.Cys552Phe p.C552F ENST00000302165 NM_015649.1 552 tGc/tTc 0 0.642 GACCAGCGGGCACTTGTCTCC +PHACTR3 116154 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 58381107 58381107 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 287 69 ENST00000371015.1:c.1186C>T p.Arg396Trp p.R396W ENST00000371015 NM_080672.4 396 Cgg/Tgg 0 0.547 AACACTGCCACGGAAATGCAA +KRTAP13-1 140258 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 31768834 31768834 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 17 ENST00000355459.2:c.430G>A p.Val144Ile p.V144I ENST00000355459 NM_181599.2 144 Gtt/Att 0 0.542 GGGCTATGGCGTTGGATTCTG +PWP2 5822 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 45540355 45540355 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 81 ENST00000291576.7:c.1315G>A p.Val439Met p.V439M ENST00000291576 NM_005049.2 439 Gtg/Atg 0 0.597 GGACGGGACCGTGCGAGCCTT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 26 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +TXK 7294 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 48114404 48114404 + synonymous_variant Silent SNP A A G TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 148 27 ENST00000264316.4:c.300T>C p.Asn100= p.N100= ENST00000264316 NM_003328.2 100 aaT/aaC 0 0.468 TTAAGGCTAAATTACAGGGTT +NPY1R 4886 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 164247119 164247119 + synonymous_variant Silent SNP G G A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 35 ENST00000296533.2:c.588C>T p.Tyr196= p.Y196= ENST00000296533 NM_000909.5 196 taC/taT 0 0.408 CAAAGCACACGTATTTGTCTT +PLEKHG4B 153478 hgsc.bcm.edu;broad.mit.edu GRCh37 5 143249 143249 + missense_variant Missense_Mutation SNP G G A rs115149634 byFrequency TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 74 22 ENST00000283426.6:c.497G>A p.Arg166Gln p.R166Q ENST00000283426 NM_052909.3 166 cGg/cAg 0 0.647 GTGCCTGCCCGGCAGCCACAC +ZDHHC11 79844 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 814876 814876 + missense_variant,splice_region_variant Missense_Mutation SNP C C G rs138424733 TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 26 ENST00000283441.8:c.1181G>C p.Gly394Ala p.G394A ENST00000283441 NM_024786.2 394 gGg/gCg 0 0.378 ACGAACTTACCCAAGTGTAGA +DNAH8 1769 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 38690599 38690599 + upstream_gene_variant 5'Flank SNP C C T TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 11 ENST00000359357 0 0.532 GAGAAGGATGCTGAAGATGGC +THEMIS 387357 hgsc.bcm.edu;broad.mit.edu GRCh37 6 128135074 128135074 + stop_gained,splice_region_variant Nonsense_Mutation SNP G G A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 40 ENST00000543064.1:c.712C>T p.Arg238Ter p.R238* ENST00000543064 NM_001164685.1 238 Cga/Tga 0 0.333 ATATCTTTTCGAACTAAAAAG +ZNF782 158431 hgsc.bcm.edu;broad.mit.edu GRCh37 9 99581580 99581580 + missense_variant Missense_Mutation SNP G G C TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 8 ENST00000481138.1:c.725C>G p.Ser242Cys p.S242C ENST00000481138 NM_001001662.1 242 tCt/tGt 0 0.333 GAAATTGTAAGATTTTCCTTT +FRMPD4 9758 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 12701668 12701668 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 3 28 ENST00000380682.1:c.535C>T p.Arg179Cys p.R179C ENST00000380682 NM_014728.3 179 Cgc/Tgc 0 0.423 TGTCAAAGTACGCTTCTCTGA +CEP104 9731 broad.mit.edu;ucsc.edu GRCh37 1 3768869 3768869 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 3 ENST00000378230.3:c.103C>T p.Arg35Trp p.R35W ENST00000378230 NM_014704.3 35 Cgg/Tgg 0 0.622 CTAGGTGACCGCCACCCACTG +NF1 4763 broad.mit.edu;ucsc.edu GRCh37 17 29670155 29670155 + splice_donor_variant Splice_Site SNP T T A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 5 ENST00000358273.4:c.7189+2T>A p.X2397_splice ENST00000358273 NM_001042492.2 0 0.318 TTTTAAAAGGTAAAAAAGCCT +HLA-J 3137 broad.mit.edu;ucsc.edu GRCh37 6 29977359 29977359 + non_coding_transcript_exon_variant,non_coding_transcript_variant RNA SNP G G A rs3831361 by1000genomes TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 7 ENST00000462773.1:n.932G>A *311* ENST00000462773 0 0.453 ATTTGTTCATGCCTTCCCTTT +TRBV7-6 28592 broad.mit.edu;ucsc.edu GRCh37 7 142139349 142139349 + synonymous_variant Silent SNP G G A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 96 26 ENST00000390374.3:c.276C>T p.Ser92= p.S92= ENST00000390374 92 tcC/tcT 0 0.567 GAGTGGAGACGGATCCCTCAG +HLA-J 3137 broad.mit.edu;ucsc.edu GRCh37 6 29977358 29977358 + non_coding_transcript_exon_variant,non_coding_transcript_variant RNA SNP T T C rs146982767 by1000genomes TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 7 ENST00000462773.1:n.931T>C *311* ENST00000462773 0 0.448 GATTTGTTCATGCCTTCCCTT +NPTX1 4884 broad.mit.edu;ucsc.edu GRCh37 17 78444660 78444660 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 7 ENST00000306773.4:c.1252G>A p.Gly418Arg p.G418R ENST00000306773 NM_002522.3 418 Gga/Aga 0 0.662 GTGGCCCCTCCGTAGATCTCG +NT5C 30833 broad.mit.edu;ucsc.edu GRCh37 17 73126675 73126675 + missense_variant Missense_Mutation SNP C C A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 30 ENST00000245552.2:c.514G>T p.Val172Phe p.V172F ENST00000245552 NM_014595.2 172 Gtc/Ttc 0 0.607 GGGGGCAGGACCAGGTGCCGA +SMC4 10051 broad.mit.edu;ucsc.edu GRCh37 3 160137299 160137299 + missense_variant Missense_Mutation SNP T T A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 35 ENST00000357388.3:c.1825T>A p.Ser609Thr p.S609T ENST00000357388 NM_001002800.1 609 Tct/Act 0 0.343 AGAAAAAAAATCTGGCAGGAT +FUBP1 8880 broad.mit.edu;hgsc.bcm.edu GRCh37 1 78433848 78433851 + splice_donor_variant,coding_sequence_variant Splice_Site DEL CAGT CAGT - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 11 20 ENST00000370768.2:c.248_250+1delACTG p.X83_splice ENST00000370768 NM_003902.3 83 0 0.319 GGAATACTTACAGTCATTTTGAGG +HGD 3081 broad.mit.edu;hgsc.bcm.edu GRCh37 3 120357338 120357338 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 23 ENST00000283871.5:c.970delG p.Val324LeufsTer16 p.V324Lfs*16 ENST00000283871 NM_000187.3 324 Gtt/tt 0 0.483 TTATCAGCAACCCCCCATCGA +WDFY3 23001 broad.mit.edu;hgsc.bcm.edu GRCh37 4 85731329 85731331 + inframe_deletion In_Frame_Del DEL GAA GAA - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 28 ENST00000295888.4:c.2054_2056delTTC p.Leu685del p.L685del ENST00000295888 NM_014991.4 685 cTTCac/cac 0 0.448 AACACAGTGTGAAGAAGTTCAAA +MAN2A1 4124 broad.mit.edu;hgsc.bcm.edu GRCh37 5 109049430 109049433 + frameshift_variant Frame_Shift_Del DEL CTGT CTGT - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 133 38 ENST00000261483.4:c.349_352delCTGT p.Phe118LeufsTer19 p.F118Lfs*19 ENST00000261483 NM_002372.2 115 gaCTGT/ga 0 0.407 ACACTGCAGACTGTCTGTTTGCTT +HDAC2 3066 broad.mit.edu;hgsc.bcm.edu GRCh37 6 114277842 114277844 + inframe_deletion In_Frame_Del DEL TCT TCT - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 15 ENST00000519065.1:c.297_299delAGA p.Glu99del p.E99del ENST00000519065 99 gaAGAt/gat 0 0.35 CACTGGACAATCTTCTCCAACAT +NOTCH1 4851 broad.mit.edu;hgsc.bcm.edu GRCh37 9 139391997 139391998 + frameshift_variant Frame_Shift_Del DEL AG AG - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 14 17 ENST00000277541.6:c.6193_6194delCT p.Leu2065ValfsTer202 p.L2065Vfs*202 ENST00000277541 NM_017617.3 2065 CTg/g 0 0.683 GGCCAGAAACAGGGGTGTCTCC +NOTCH1 4851 broad.mit.edu;hgsc.bcm.edu GRCh37 9 139395163 139395166 + frameshift_variant Frame_Shift_Del DEL GTCT GTCT - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 136 41 ENST00000277541.6:c.5772_5775delAGAC p.Asp1925AlafsTer55 p.D1925Afs*55 ENST00000277541 NM_017617.3 1924 acAGAC/ac 0 0.686 CGCCCGTGCGGTCTGTCTGGTTGT +PHLPP2 23035 broad.mit.edu;hgsc.bcm.edu GRCh37 16 71692597 71692599 + inframe_deletion In_Frame_Del DEL TGT TGT - rs145938775 TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 133 25 ENST00000568954.1:c.2105_2107delACA p.Asn702del p.N702del ENST00000568954 702 aACAtc/atc 0 0.458 AAAATGCTGATGTTGTTGGAGTG +PLIN4 729359 broad.mit.edu;hgsc.bcm.edu GRCh37 19 4510914 4510916 + inframe_deletion In_Frame_Del DEL TGG TGG - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 22 ENST00000301286.3:c.3014_3016delCCA p.Thr1005del p.T1005del ENST00000301286 NM_001080400.1 1005 aCCAag/aag 0 0.626 AGCACTGTCTTGGTGGTGTCCAG +NF1 4763 broad.mit.edu GRCh37 17 29546036 29546037 + frameshift_variant Frame_Shift_Del DEL AG AG - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 7 ENST00000358273.4:c.1541_1542delAG p.Gln514ArgfsTer43 p.Q514Rfs*43 ENST00000358273 NM_001042492.2 514 cAG/c 0 0.426 CCAAGAAAACAGGGGCCCGAAA +PIK3R1 5295 broad.mit.edu GRCh37 5 67591105 67591107 + inframe_deletion In_Frame_Del DEL TAA TAA - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 108 16 ENST00000274335.5:c.1698_1700delTAA p.Lys567del p.K567del ENST00000274335 566 atTAAa/ata 0 0.369 TGAACAGCATTAAACCAGACCTT +NF1 4763 broad.mit.edu GRCh37 17 29652976 29652979 + frameshift_variant Frame_Shift_Del DEL TCTC TCTC - TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 168 11 ENST00000358273.4:c.4977_4980delCTCT p.Lys1661GlyfsTer36 p.K1661Gfs*36 ENST00000358273 NM_001042492.2 1658 ttTCTC/tt 0 0.422 AAACAGACTTTCTCTCTAAGTGGT +NF1 4763 broad.mit.edu GRCh37 17 29553697 29553697 + stop_gained Nonsense_Mutation SNP C C A TCGA-DU-6394-01 TCGA-DU-6394-10 Untested Somatic Phase_I WXS none Illumina GAIIx 162 7 ENST00000358273.4:c.2246C>A p.Ser749Ter p.S749* ENST00000358273 NM_001042492.2 749 tCa/tAa 0 0.403 AATATGATGTCAACAGGTAAA +CUBN 8029 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 16992025 16992025 + synonymous_variant Silent SNP G G A TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 16 ENST00000377833.4:c.5055C>T p.Gly1685= p.G1685= ENST00000377833 NM_001081.3 1685 ggC/ggT 0 0.448 CTTCGTGGCCGCCATCCAAAA +OR8K1 390157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 56114203 56114203 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 27 ENST00000279783.2:c.689C>T p.Ala230Val p.A230V ENST00000279783 NM_001002907.1 230 gCc/gTc 0 0.383 ATTCTAGTGGCCATTCTCAGA +PBX4 80714 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 19672911 19672911 + stop_gained Nonsense_Mutation SNP G G A TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 4 ENST00000251203.9:c.1048C>T p.Gln350Ter p.Q350* ENST00000251203 NM_025245.2 350 Cag/Tag 0 0.597 GTGGCCCCCTGCCAGCTACCC +FAM89A 375061 hgsc.bcm.edu;broad.mit.edu GRCh37 1 231155648 231155648 + synonymous_variant Silent SNP G G A TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 3 ENST00000366654.4:c.516C>T p.Ser172= p.S172= ENST00000366654 NM_198552.2 172 tcC/tcT 0 0.567 TGGAGAGGGAGGAGACAGGCA +RIPK4 54101 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 43166845 43166845 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 96 69 ENST00000332512.3:c.760G>A p.Ala254Thr p.A254T ENST00000332512 NM_020639.2 254 Gcc/Acc 0 0.672 TGGCTGCAGGCGCGCGGCCGG +MYO7B 4648 hgsc.bcm.edu;ucsc.edu GRCh37 2 128367552 128367552 + synonymous_variant Silent SNP G G A TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 4 ENST00000428314.1:c.3153G>A p.Glu1051= p.E1051= ENST00000428314 NM_001080527.1 1051 gaG/gaA 0 0.642 TGGGCAGGGAGCACGGTGCCC +HOXD3 3232 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 177034190 177034190 + synonymous_variant Silent SNP A A G TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 17 ENST00000468418.3:c.348A>G p.Pro116= p.P116= ENST00000468418 116 ccA/ccG 0 0.642 AGCAGCAGccaccacaacccc +ZDBF2 57683 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 207175936 207175936 + synonymous_variant Silent SNP G G A TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 10 ENST00000374423.3:c.6684G>A p.Ser2228= p.S2228= ENST00000374423 NM_020923.1 2228 tcG/tcA 0 0.363 AGTATATTTCGAAATACTCTG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 121 44 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +PIK3CA 5290 hgsc.bcm.edu;broad.mit.edu GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 109 8 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 0 0.378 AATGATGCACATCATGGTGGC +CERCAM 51148 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 131186792 131186792 + missense_variant Missense_Mutation SNP G G A TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 39 ENST00000372838.4:c.665G>A p.Arg222Gln p.R222Q ENST00000372838 NM_016174.4 222 cGg/cAg 0 0.617 GCATCCCTGCGGGCTGAAGGG +KCNQ4 9132 broad.mit.edu;ucsc.edu GRCh37 1 41283890 41283890 + missense_variant Missense_Mutation SNP G G A TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 23 ENST00000347132.5:c.460G>A p.Ala154Thr p.A154T ENST00000347132 NM_004700.3 154 Gcc/Acc 0 0.612 GGTCTGGTCCGCCGGATGCTG +SLC9A7P1 121456 broad.mit.edu;ucsc.edu GRCh37 12 98850610 98850610 + non_coding_transcript_exon_variant RNA SNP C C A TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 5 ENST00000554295.1:n.314G>T *105* ENST00000554295 0 0.602 AAAGTGCACCCGGCAGTACTT +TEKT1 83659 broad.mit.edu;ucsc.edu GRCh37 17 6703471 6703471 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8187-01 TCGA-FG-8187-10 Untested Somatic Phase_I WXS none Illumina GAIIx 135 12 ENST00000338694.2:c.1132G>A p.Val378Ile p.V378I ENST00000338694 NM_053285.1 378 Gtc/Atc 0 0.527 TTCTCTTTGACCTGGATCTCC +GPR114 221188 hgsc.bcm.edu;ucsc.edu GRCh37 16 57601804 57601804 + missense_variant Missense_Mutation SNP C C A rs146006750 TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 5 ENST00000340339.4:c.858C>A p.Asn286Lys p.N286K ENST00000340339 NM_153837.1 286 aaC/aaA 0 0.612 TCCACATGAACCTGCATGCCT +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 86 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 0 0.577 ATGGGCCTCCGGTTCATGCCG +C3 718 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 6686853 6686853 + stop_gained Nonsense_Mutation SNP G G A TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 127 21 ENST00000245907.6:c.3550C>T p.Gln1184Ter p.Q1184* ENST00000245907 NM_000064.2 1184 Cag/Tag 0 0.512 TAGGATCTCTGTAGGTTCATG +KLK10 5655 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 51518742 51518742 + synonymous_variant Silent SNP G G A TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 258 124 ENST00000309958.3:c.609C>T p.Val203= p.V203= ENST00000309958 NM_002776.4 203 gtC/gtT 0 0.552 CAGGGTAGAAGACCTCACACT +ANXA9 8416 hgsc.bcm.edu;broad.mit.edu GRCh37 1 150955565 150955565 + splice_acceptor_variant Splice_Site SNP G G A TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 6 ENST00000368947.4:c.-16-1G>A p.X6_splice ENST00000368947 NM_003568.2 0 0.622 TCCTTCCCCAGGGCAACCAGT +TPO 7173 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 1499888 1499888 + missense_variant Missense_Mutation SNP G G A TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 10 ENST00000345913.4:c.2134G>A p.Gly712Ser p.G712S ENST00000345913 NM_000547.5 712 Ggc/Agc 0 0.562 CTTCCAAGTCGGCAAATTCCC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 29 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +LEPREL1 55214 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 189705423 189705423 + missense_variant Missense_Mutation SNP C C A TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 106 30 ENST00000319332.5:c.991G>T p.Ala331Ser p.A331S ENST00000319332 NM_018192.3 331 Gcc/Tcc 0 0.468 AGAAGATAGGCTTTGGCACAC +FGF5 2250 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 81207632 81207632 + missense_variant Missense_Mutation SNP C C G TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 49 ENST00000312465.7:c.613C>G p.Arg205Gly p.R205G ENST00000312465 NM_004464.3 205 Cgg/Ggg 0 0.463 GTGCAGCCCCCGGGTTAAACC +ENPEP 2028 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 111441429 111441429 + missense_variant Missense_Mutation SNP C C G TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 34 ENST00000265162.5:c.1634C>G p.Pro545Arg p.P545R ENST00000265162 NM_001977.3 545 cCt/cGt 0 0.428 ATGGGTTATCCTGTGCTTAAC +ADAD1 132612 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 123336616 123336616 + synonymous_variant Silent SNP A A T TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 116 70 ENST00000296513.2:c.1332A>T p.Pro444= p.P444= ENST00000296513 NM_139243.3 444 ccA/ccT 0 0.378 CAAAACTTCCAATGTTTTACT +TKTL2 84076 hgsc.bcm.edu;broad.mit.edu GRCh37 4 164393959 164393959 + missense_variant Missense_Mutation SNP G G C TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 228 14 ENST00000280605.3:c.928C>G p.Pro310Ala p.P310A ENST00000280605 NM_032136.4 310 Cca/Gca 0 0.408 taagcaggtggggaggtcatt +ADAM22 53616 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 87757957 87757957 + missense_variant Missense_Mutation SNP A A G TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 146 16 ENST00000265727.7:c.719A>G p.Tyr240Cys p.Y240C ENST00000265727 240 tAc/tGc 0 0.403 GAAACCAAATACATTGAACTG +KDM7A 80853 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 139824520 139824520 + missense_variant Missense_Mutation SNP T T G TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 18 ENST00000397560.2:c.952A>C p.Ser318Arg p.S318R ENST00000397560 NM_030647.1 318 Agt/Cgt 0 0.358 ACAGATGAACTCCAAGATTCA +ACTRT1 139741 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 127186136 127186136 + missense_variant Missense_Mutation SNP C C A TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 40 ENST00000371124.3:c.50G>T p.Gly17Val p.G17V ENST00000371124 NM_138289.3 17 gGt/gTt 0 0.433 GAGTCCTGAACCATTGTCAAA +ZNF185 7739 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 152083048 152083048 + synonymous_variant Silent SNP T T C TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 8 ENST00000535861.1:c.15T>C p.Ala5= p.A5= ENST00000535861 NM_001178106.1 5 gcT/gcC 0 0.547 GTATCTCAGCTCTTGGAGGCC +TTLL7 79739 broad.mit.edu;ucsc.edu GRCh37 1 84356051 84356051 + synonymous_variant Silent SNP T T C TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 29 ENST00000260505.8:c.2322A>G p.Leu774= p.L774= ENST00000260505 NM_024686.4 774 ttA/ttG 0 0.378 GACTCCAGAGTAAGCGATTAA +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76939674 76939674 + frameshift_variant Frame_Shift_Del DEL T T - TCGA-CS-4938-01 TCGA-CS-4938-10 Untested Somatic Phase_I WXS none Illumina GAIIx 143 100 ENST00000373344.5:c.1074delA p.Lys358AsnfsTer2 p.K358Nfs*2 ENST00000373344 NM_000489.3 358 aaA/aa 0 0.368 TCTCAATCAGTTTTTTTGCCT +RPP30 10556 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 92631801 92631801 + missense_variant Missense_Mutation SNP G G A TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 94 69 ENST00000413330.1:c.58G>A p.Gly20Arg p.G20R ENST00000413330 NM_001104546.1 20 Gga/Aga 0 0.637 GGCTCTGCGCGGACTTGTGGA +SPA17 53340 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 124564278 124564278 + missense_variant Missense_Mutation SNP G G A TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 98 17 ENST00000532692.1:c.392G>A p.Arg131Lys p.R131K ENST00000532692 131 aGa/aAa 0 0.408 CACATAGCCAGAGAGGAGGCA +M6PR 4074 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 9094479 9094479 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 449 57 ENST00000000412.3:c.769G>A p.Gly257Ser p.G257S ENST00000000412 NM_002355.3 257 Ggt/Agt 0 0.468 TCCCCCACACCACGATATGCT +GPRC5D 55507 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 13102595 13102595 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 15 ENST00000228887.1:c.724G>A p.Val242Ile p.V242I ENST00000228887 NM_018654.1 242 Gtc/Atc 0 0.567 GCAATGCAGACGACCGGGTCG +DNAH10 196385 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 124332564 124332564 + synonymous_variant Silent SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 57 ENST00000409039.3:c.5517C>T p.Thr1839= p.T1839= ENST00000409039 NM_207437.3 1839 acC/acT 0 0.552 CCGGCAAAACCGAGACCACCA +COL4A2 1284 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 111147702 111147702 + synonymous_variant Silent SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 111 12 ENST00000360467.5:c.3648C>T p.His1216= p.H1216= ENST00000360467 NM_001846.2 1216 caC/caT 0 0.557 CTGACATCCACGGAGACCCAG +NPAP1 23742 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 24921762 24921762 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 12 ENST00000329468.2:c.748C>T p.Arg250Trp p.R250W ENST00000329468 NM_018958.2 250 Cgg/Tgg 0 0.622 CGGATGTGCCCGGCATCTTGG +GPR139 124274 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 20043246 20043246 + synonymous_variant Silent SNP C C G TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 132 21 ENST00000570682.1:c.873G>C p.Arg291= p.R291= ENST00000570682 NM_001002911.2 291 cgG/cgC 0 0.502 TGGTGCGGAACCGCTTGCTGA +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7579311 7579311 + splice_donor_variant Splice_Site SNP C C G rs68140816 TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 56 ENST00000269305.4:c.375+1G>C p.X125_splice ENST00000269305 NM_001126112.2 0 0.532 GGGCAACTGACCGTGCAAGTC +HELZ 9931 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 65105453 65105453 + missense_variant Missense_Mutation SNP T T C TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 29 ENST00000358691.5:c.4268A>G p.Tyr1423Cys p.Y1423C ENST00000358691 NM_014877.3 1423 tAt/tGt 0 0.527 TCCCGCCTGATATGCAGGAGA +TTYH2 94015 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 72246149 72246149 + synonymous_variant Silent SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 38 ENST00000269346.4:c.1005C>T p.Pro335= p.P335= ENST00000269346 NM_032646.5 335 ccC/ccT 0 0.652 TTGCCGTGCCCCTCTTCTCCA +ACER1 125981 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 6307219 6307219 + missense_variant Missense_Mutation SNP G G A TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 12 ENST00000301452.4:c.571C>T p.Arg191Cys p.R191C ENST00000301452 NM_133492.2 191 Cgt/Tgt 0 0.542 CAAAGCAGACGGTCACTGATC +GPR32 2854 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 51273893 51273893 + missense_variant Missense_Mutation SNP T T A TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 7 ENST00000270590.4:c.36T>A p.Ser12Arg p.S12R ENST00000270590 NM_001506.2 12 agT/agA 0 0.498 GAGGCTGCAGTGACAGGCAAC +BSDC1 55108 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 32842101 32842101 + synonymous_variant Silent SNP G G T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 42 ENST00000446293.2:c.969C>A p.Ser323= p.S323= ENST00000446293 323 tcC/tcA 0 0.597 GCAGCTTTTGGGACAGGTCCT +PCIF1 63935 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 44567656 44567656 + synonymous_variant Silent SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 90 14 ENST00000372409.3:c.18C>T p.His6= p.H6= ENST00000372409 NM_022104.3 6 caC/caT 0 0.602 ATGAGAATCACGGCAGCCCCC +APOBEC3H 164668 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 39497965 39497965 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 29 ENST00000401756.1:c.461C>T p.Pro154Leu p.P154L ENST00000401756 NM_001166003.1 154 cCg/cTg 0 0.537 CACGAGAAACCGCTTTCCTTC +TTN 7273 hgsc.bcm.edu;ucsc.edu GRCh37 2 179613099 179613099 + intron_variant Intron SNP A A C TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 124 23 ENST00000589042.1:c.11311+4752T>G *3771* ENST00000589042 NM_001267550.1 0 0.333 GACTGGAAGAAATTTCTTGAC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 29 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +CNTN3 5067 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 74419100 74419100 + missense_variant Missense_Mutation SNP G G C TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 12 ENST00000263665.6:c.701C>G p.Pro234Arg p.P234R ENST00000263665 NM_020872.1 234 cCa/cGa 0 0.333 AAGAGTTTCTGGAAACTGAAC +STX19 415117 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 93733522 93733522 + synonymous_variant Silent SNP A A G TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 11 ENST00000315099.2:c.592T>C p.Leu198= p.L198= ENST00000315099 NM_001001850.2 198 Tta/Cta 0 0.328 TCTGTAAGTAAGCTTTCATTA +PLCH1 23007 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 155198970 155198970 + synonymous_variant Silent SNP G G A TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 10 ENST00000340059.7:c.4869C>T p.Thr1623= p.T1623= ENST00000340059 NM_001130960.1 1623 acC/acT 0 0.577 TCACTGCAGGGGTGGGTGCTG +ZBBX 79740 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 166960403 166960403 + synonymous_variant Silent SNP G G T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 9 ENST00000455345.2:c.2283C>A p.Thr761= p.T761= ENST00000455345 761 acC/acA 0 0.368 ACTCTTCTGAGGTTAAGCTGT +SKP2 6502 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 36152899 36152899 + missense_variant Missense_Mutation SNP T T A TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 17 ENST00000274255.6:c.35T>A p.Leu12Gln p.L12Q ENST00000274255 NM_005983.3 12 cTg/cAg 0 0.517 ATTCCAGACCTGAGTAGCAAC +GABRA6 2559 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 161118969 161118969 + missense_variant Missense_Mutation SNP G G A TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 10 ENST00000274545.5:c.849G>A p.Met283Ile p.M283I ENST00000274545 283 atG/atA 0 0.403 TTTTAACTATGACCACTTTGA +DLX5 1749 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 96651603 96651603 + missense_variant Missense_Mutation SNP G G C TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 47 ENST00000222598.4:c.434C>G p.Ser145Cys p.S145C ENST00000222598 NM_005221.5 145 tCc/tGc 0 0.498 CTGAAAGCTGGAATAAATAGT +PAX4 5078 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 127255046 127255046 + missense_variant Missense_Mutation SNP G G C TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 46 ENST00000341640.2:c.224C>G p.Pro75Arg p.P75R ENST00000341640 NM_006193.2 75 cCt/cGt 0 0.582 AGCCACCACAGGGGGTGTAGC +KEL 3792 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 142655011 142655011 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 16 ENST00000355265.2:c.575G>A p.Arg192Gln p.R192Q ENST00000355265 NM_000420.2 192 cGa/cAa 0 0.522 TCTCAGCGTTCGGTTAAAGTT +BICD2 23299 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 95481306 95481306 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 22 ENST00000356884.6:c.1621G>A p.Val541Met p.V541M ENST00000356884 NM_001003800.1 541 Gtg/Atg 0 0.657 CACATGCACACGTGGTGGTAG +DBH 1621 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 136501814 136501814 + synonymous_variant Silent SNP G G A TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 7 ENST00000393056.2:c.321G>A p.Gly107= p.G107= ENST00000393056 NM_000787.3 107 ggG/ggA 0 0.617 GGACCGATGGGGACACTGCCT +COL4A5 1287 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 107938508 107938508 + synonymous_variant Silent SNP A A T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 19 ENST00000328300.6:c.4833A>T p.Ala1611= p.A1611= ENST00000328300 NM_033380.2 1611 gcA/gcT 0 0.488 ATACAAGTGCAGGGGCAGAAG +ZNF629 23361 broad.mit.edu;ucsc.edu GRCh37 16 30795077 30795077 + missense_variant Missense_Mutation SNP G G A TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 4 ENST00000262525.4:c.572C>T p.Ser191Leu p.S191L ENST00000262525 NM_001080417.1 191 tCg/tTg 0 0.657 CACCAGGTGCGAGCTCTGCGT +OLFM3 118427 broad.mit.edu;ucsc.edu GRCh37 1 102290602 102290602 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 7 ENST00000370103.4:c.572G>A p.Arg191His p.R191H ENST00000370103 NM_058170.2 191 cGt/cAt 0 0.373 CATGCAGTCACGAAGTCTTGT +MUC17 140453 broad.mit.edu;ucsc.edu GRCh37 7 100679309 100679309 + missense_variant Missense_Mutation SNP C C G TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 257 46 ENST00000306151.4:c.4612C>G p.Pro1538Ala p.P1538A ENST00000306151 NM_001040105.1 1538 Cct/Gct 0 0.473 TTCAACAACTCCTGCTGTCAC +COL14A1 7373 broad.mit.edu;ucsc.edu GRCh37 8 121290392 121290392 + stop_gained Nonsense_Mutation SNP A A T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 52 ENST00000297848.3:c.3256A>T p.Lys1086Ter p.K1086* ENST00000297848 NM_021110.2 1086 Aaa/Taa 0 0.378 AACAGAATTTAAACTAAATGC +CXXC4 80319 broad.mit.edu;ucsc.edu GRCh37 4 105412082 105412082 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 13 ENST00000394767.2:c.878G>A p.Gly293Glu p.G293E ENST00000394767 NM_025212.2 293 gGg/gAg 0 0.602 GCCAGCTCCCCCTGAGGAGGA +CCDC33 80125 broad.mit.edu;ucsc.edu GRCh37 15 74554908 74554908 + stop_gained Nonsense_Mutation SNP C C T TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 4 ENST00000398814.3:c.313C>T p.Gln105Ter p.Q105* ENST00000398814 NM_025055.4 105 Caa/Taa 0 0.597 GGATGCAGGGCAAGAAGGTAA +ROS1 6098 broad.mit.edu;hgsc.bcm.edu GRCh37 6 117746774 117746774 + frameshift_variant Frame_Shift_Del DEL T T - TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 90 60 ENST00000368508.3:c.46delA p.Thr16LeufsTer15 p.T16Lfs*15 ENST00000368508 NM_002944.2 16 Act/ct 0 0.378 CAGCCAAGAGTTGCAAAATTG +METAP2 10988 broad.mit.edu;hgsc.bcm.edu GRCh37 12 95868076 95868078 + inframe_deletion In_Frame_Del DEL AAG AAG - TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 11 ENST00000323666.5:c.131_133delAGA p.Lys44del p.K44del ENST00000323666 NM_006838.3 41 AAG/- 0 0.557 AAAAAGACGAAAGAAGAAGAAGA +ATRX 546 broad.mit.edu GRCh37 X 76814313 76814313 + stop_gained Nonsense_Mutation SNP G G A TCGA-DU-7007-01 TCGA-DU-7007-10 Untested Somatic Phase_I WXS none Illumina GAIIx 6 15 ENST00000373344.5:c.6331C>T p.Arg2111Ter p.R2111* ENST00000373344 NM_000489.3 2111 Cga/Tga 0 0.274 ATAAATAATCGTCCTCTGAAA +CD163 9332 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 7635248 7635248 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 124 55 ENST00000359156.4:c.3238C>T p.Arg1080Trp p.R1080W ENST00000359156 NM_004244.5 1080 Cgg/Tgg 0 0.428 CCTGCAAGCCGCTGTCTCTGT +KERA 11081 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 91449544 91449544 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 160 49 ENST00000266719.3:c.515A>G p.Asp172Gly p.D172G ENST00000266719 NM_007035.3 172 gAc/gGc 0 0.413 GTTCTGTAGGTCAAGAAGGGT +FSCB 84075 hgsc.bcm.edu;broad.mit.edu GRCh37 14 44975038 44975038 + synonymous_variant Silent SNP G G T TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 144 12 ENST00000340446.4:c.1153C>A p.Arg385= p.R385= ENST00000340446 NM_032135.3 385 Cgg/Agg 0 0.532 GAGGGAGACCGAATTTCACCA +NETO1 81832 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 70417415 70417415 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 13 ENST00000327305.6:c.1423A>G p.Ile475Val p.I475V ENST00000327305 NM_138966.3 475 Atc/Gtc 0 0.507 ATGACAAGGATATTTCTTCTG +NLRP2 55655 hgsc.bcm.edu;broad.mit.edu GRCh37 19 55494669 55494669 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 4 ENST00000543010.1:c.1603G>A p.Val535Ile p.V535I ENST00000543010 NM_001174081.1 535 Gta/Ata 0 0.557 CATTGGGGACGTACAGAAGCT +FUBP1 8880 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 78420962 78420962 + stop_gained Nonsense_Mutation SNP C C T TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 11 ENST00000370768.2:c.1758G>A p.Trp586Ter p.W586* ENST00000370768 NM_003902.3 586 tgG/tgA 0 0.318 AGTACTCTTCCCAAGCCTTGG +HRNR 388697 hgsc.bcm.edu;broad.mit.edu GRCh37 1 152191242 152191242 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 319 96 ENST00000368801.2:c.2863T>C p.Ser955Pro p.S955P ENST00000368801 NM_001009931.2 955 Tcc/Ccc 0 0.542 TCGTAGCTGGAGGAGTGACCT +FLRT3 23767 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 14306271 14306271 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 141 18 ENST00000378053.3:c.1882A>G p.Ser628Gly p.S628G ENST00000378053 NM_013281.3 628 Agt/Ggt 0 0.413 CTGCTTTCACTGTGATTGTTT +TSHZ2 128553 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 51873020 51873020 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 19 ENST00000371497.5:c.3023C>T p.Ala1008Val p.A1008V ENST00000371497 NM_173485.5 1008 gCg/gTg 0 0.468 AGCAAACATGCGGTAAAACTC +DNMT3A 1788 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 25470985 25470985 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 24 ENST00000264709.3:c.776C>G p.Ala259Gly p.A259G ENST00000264709 NM_175629.2 259 gCt/gGt 0 0.647 AGGCGTGGTAGCCACAGTGGG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 16 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +PIK3CA 5290 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 178917478 178917478 + missense_variant,splice_region_variant Missense_Mutation SNP G G A TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 82 14 ENST00000263967.3:c.353G>A p.Gly118Asp p.G118D ENST00000263967 NM_006218.2 118 gGt/gAt 0 0.338 TTTATTAAAGGTTTTGCTATC +PIK3CA 5290 hgsc.bcm.edu;broad.mit.edu GRCh37 3 178952072 178952072 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 7 ENST00000263967.3:c.3127A>G p.Met1043Val p.M1043V ENST00000263967 NM_006218.2 1043 Atg/Gtg 0 0.368 CATGAAACAAATGAATGATGC +LMLN 89782 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 197751579 197751579 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 96 12 ENST00000420910.2:c.1687C>G p.Leu563Val p.L563V ENST00000420910 NM_001136049.2 563 Cta/Gta 0 0.393 TTCCGTTTGTCTAATTCAGAA +CPEB2 132864 hgsc.bcm.edu;broad.mit.edu GRCh37 4 15060817 15060817 + missense_variant Missense_Mutation SNP A A T TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 5 ENST00000538197.1:c.2587A>T p.Ile863Leu p.I863L ENST00000538197 NM_001177382.1 863 Ata/Tta 0 0.348 ATAGGTTCAAATACGTCCTTG +UGT2B28 54490 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 70155435 70155435 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 31 ENST00000335568.5:c.1055G>A p.Arg352Gln p.R352Q ENST00000335568 NM_053039.1 352 cGg/cAg 0 0.363 CTCAATACTCGGCTGTATAAG +GK2 2712 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 80328636 80328636 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 100 37 ENST00000358842.3:c.719A>G p.Tyr240Cys p.Y240C ENST00000358842 NM_033214.2 240 tAt/tGt 0 0.423 AATTAGGCCATAGATCTCAGA +NUP155 9631 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 37309323 37309323 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 9 ENST00000231498.3:c.2675A>G p.Glu892Gly p.E892G ENST00000231498 NM_153485.2 892 gAa/gGa 0 0.343 TCTTTCTTTTTCAGTCTTATT +KIF6 221458 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 39513390 39513390 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 32 ENST00000287152.7:c.1256G>A p.Arg419His p.R419H ENST00000287152 NM_145027.4 419 cGt/cAt 0 0.358 ATGAACTTTACGCATATCCGC +DLK2 65989 hgsc.bcm.edu;broad.mit.edu GRCh37 6 43418774 43418774 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 5 ENST00000357338.3:c.655C>T p.Arg219Cys p.R219C ENST00000357338 NM_206539.1 219 Cgc/Tgc 0 0.622 TGGCATGGGCGGCTGGCACAG +FRK 2444 hgsc.bcm.edu;broad.mit.edu GRCh37 6 116265543 116265543 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 4 ENST00000606080.1:c.1004C>T p.Ala335Val p.A335V ENST00000606080 NM_002031.2 335 gCg/gTg 0 0.418 AACCTGTGCCGCCATGTCTAC +MAP3K4 4216 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 161470895 161470895 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 100 13 ENST00000392142.4:c.1591G>C p.Asp531His p.D531H ENST00000392142 NM_005922.2 531 Gac/Cac 0 0.423 ACCATTTGTAGACAAAGCACT +RAB11FIP1 80223 hgsc.bcm.edu;broad.mit.edu GRCh37 8 37734856 37734856 + synonymous_variant Silent SNP G G A TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 173 13 ENST00000330843.4:c.585C>T p.Ser195= p.S195= ENST00000330843 NM_001002814.2 195 agC/agT 0 0.448 AAGGTGTCGTGCTAGGGATGA +WISP2 8839 broad.mit.edu;ucsc.edu GRCh37 20 43348625 43348625 + missense_variant Missense_Mutation SNP T T G TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 5 ENST00000372868.2:c.148T>G p.Cys50Gly p.C50G ENST00000372868 50 Tgt/Ggt 0 0.697 GCTGGATGGCTGTGGCTGCTG +HIST1H2BF 8343 broad.mit.edu;hgsc.bcm.edu GRCh37 6 26199854 26199856 + inframe_deletion In_Frame_Del DEL AGA AGA - rs150784470 TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 61 ENST00000359985.1:c.73_75delAAG p.Lys25del p.K25del ENST00000359985 NM_003522.3 23 cAGAag/cag 0 0.522 ACCAAGGCGCAGAAGAAGGATGG +BACH2 60468 broad.mit.edu;hgsc.bcm.edu GRCh37 6 90660233 90660235 + inframe_deletion In_Frame_Del DEL TCC TCC - TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 19 ENST00000257749.4:c.1590_1592delGGA p.Glu530del p.E530del ENST00000257749 NM_021813.2 530 gaGGAc/gac 0 0.616 CCCGCTCCCGTCCTCCGCGTAGG +NOTCH1 4851 broad.mit.edu GRCh37 9 139413067 139413069 + inframe_deletion In_Frame_Del DEL AGT AGT - TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 7 ENST00000277541.6:c.1073_1075delACT p.Tyr358del p.Y358del ENST00000277541 NM_017617.3 358 tACTgc/tgc 0 0.655 GGACACTCGCAGTAGAAGGAGGC +PIK3CA 5290 broad.mit.edu GRCh37 3 178928078 178928080 + inframe_deletion In_Frame_Del DEL AGA AGA - TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 102 8 ENST00000263967.3:c.1359_1361delAGA p.Glu453del p.E453del ENST00000263967 NM_006218.2 452 ttAGAa/tta 0 0.35 CTCATGGATTAGAAGATTTGCTG +PIK3R1 5295 broad.mit.edu GRCh37 5 67589147 67589149 + inframe_deletion In_Frame_Del DEL AAA AAA - TCGA-HT-7481-01 TCGA-HT-7481-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 11 ENST00000274335.5:c.1135_1137delAAA p.Lys379del p.K379del ENST00000274335 379 AAA/- 0 0.31 GGGAAATAACAAATTAATCAAAA +TRIM51 84767 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 55655604 55655604 + stop_gained Nonsense_Mutation SNP C C T TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 22 ENST00000449290.2:c.604C>T p.Arg202Ter p.R202* ENST00000449290 NM_032681.3 202 Cga/Tga 0 0.433 GGAAAGGCTGCGAAAGGAGGG +PRICKLE1 144165 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 42858963 42858963 + synonymous_variant Silent SNP A A G TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 19 ENST00000455697.1:c.873T>C p.Cys291= p.C291= ENST00000455697 NM_001144883.1 291 tgT/tgC 0 0.522 GAAGGAAGGGACATCCCAACA +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578394 7578394 + missense_variant Missense_Mutation SNP T T C TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 45 ENST00000269305.4:c.536A>G p.His179Arg p.H179R ENST00000269305 NM_001126112.2 179 cAt/cGt 0 0.642 GCAGCGCTCATGGTGGGGGCA +PSMD12 5718 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 65341917 65341917 + synonymous_variant Silent SNP T T A TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 27 ENST00000356126.3:c.852A>T p.Ser284= p.S284= ENST00000356126 NM_002816.3 284 tcA/tcT 0 0.358 GAACCAAATCTGACTGTTCAT +LAMA3 3909 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 21425086 21425086 + splice_region_variant,synonymous_variant Splice_Region SNP T T G TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 16 ENST00000313654.9:c.3717T>G p.Leu1239= p.L1239= ENST00000313654 NM_198129.1 1239 ctT/ctG 0 0.493 GCTTTTACCTTGAGTGAGTAT +RERE 473 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 8421423 8421423 + missense_variant Missense_Mutation SNP A A G TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 23 ENST00000337907.3:c.2144T>C p.Ile715Thr p.I715T ENST00000337907 NM_012102.3 715 aTc/aCc 0 0.627 GGGGCTGGGGATGCTCGGGGA +TAS1R2 80834 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 19166820 19166820 + stop_gained Nonsense_Mutation SNP G G T TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 26 ENST00000375371.3:c.1793C>A p.Ser598Ter p.S598* ENST00000375371 NM_152232.2 598 tCg/tAg 0 0.647 GCCCCCAGCCGAGCGAACTAT +COL11A1 1301 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 103380351 103380351 + missense_variant Missense_Mutation SNP C C T TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 12 ENST00000370096.3:c.3833G>A p.Arg1278Lys p.R1278K ENST00000370096 NM_001854.3 1278 aGa/aAa 0 0.453 TTTCTCTCCTCTTTCTCCTTT +PIAS3 10401 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 145585437 145585437 + missense_variant Missense_Mutation SNP C C G TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 52 ENST00000393045.2:c.1702C>G p.His568Asp p.H568D ENST00000393045 NM_006099.3 568 Cac/Gac 0 0.637 GACCCCTTCTCACTTTCTGGG +FAM161A 84140 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 62067511 62067511 + missense_variant Missense_Mutation SNP C C A TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 118 68 ENST00000404929.1:c.628G>T p.Asp210Tyr p.D210Y ENST00000404929 NM_001201543.1 210 Gat/Tat 0 0.408 CGAATATAATCCTCAACACAA +BUB1 699 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 111423902 111423902 + missense_variant Missense_Mutation SNP T T C TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 12 ENST00000302759.6:c.895A>G p.Lys299Glu p.K299E ENST00000302759 NM_004336.4 299 Aag/Gag 0 0.428 TGATGCAACTTCTTATGAAGT +WDR33 55339 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 128522748 128522748 + missense_variant,splice_region_variant Missense_Mutation SNP C C G TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 13 ENST00000322313.4:c.474G>C p.Gln158His p.Q158H ENST00000322313 NM_018383.4 158 caG/caC 0 0.398 TTATCATTACCTGTAATATTG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 32 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +SPP2 6694 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 234969077 234969077 + missense_variant Missense_Mutation SNP G G A TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 23 ENST00000168148.3:c.398G>A p.Arg133His p.R133H ENST00000168148 NM_006944.2 133 cGc/cAc 0 0.577 GTGCATGCTCGCTGCAGCTGG +HDAC4 9759 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 239976491 239976491 + synonymous_variant Silent SNP G G A TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 37 ENST00000345617.3:c.3027C>T p.Pro1009= p.P1009= ENST00000345617 NM_006037.3 1009 ccC/ccT 0 0.507 CGTTTGCATTGGGTCTTTGCT +PROS1 5627 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 93624931 93624931 + missense_variant Missense_Mutation SNP T T C TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 107 69 ENST00000394236.3:c.403A>G p.Lys135Glu p.K135E ENST00000394236 NM_000313.3 135 Aaa/Gaa 0 0.408 TTTCCATCTTTGCAGCTCATA +PLCH1 23007 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 155200741 155200741 + missense_variant Missense_Mutation SNP A A G TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 28 ENST00000340059.7:c.3098T>C p.Leu1033Pro p.L1033P ENST00000340059 NM_001130960.1 1033 cTc/cCc 0 0.453 ATCTTTGTGGAGCAGAGCACT +SPATA16 83893 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 172631478 172631478 + synonymous_variant Silent SNP A A G TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 26 ENST00000351008.3:c.1560T>C p.Asn520= p.N520= ENST00000351008 NM_031955.5 520 aaT/aaC 0 0.373 ACACACGTTCATTATTGTTTC +TRRAP 8295 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 98545941 98545941 + missense_variant Missense_Mutation SNP C C T TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 34 ENST00000359863.4:c.4625C>T p.Thr1542Met p.T1542M ENST00000359863 NM_001244580.1 1542 aCg/aTg 0 0.498 GTCATGAAAACGGAGCGGGCG +CRYGN 155051 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 151135095 151135095 + missense_variant Missense_Mutation SNP C C T rs148445096 TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 27 ENST00000337323.2:c.257G>A p.Arg86Gln p.R86Q ENST00000337323 NM_144727.1 86 cGg/cAg 0 0.627 TCCTACAGGCCGACAGGAGCC +CA9 768 hgsc.bcm.edu;ucsc.edu GRCh37 9 35674208 35674208 + synonymous_variant Silent SNP T T C rs137897809 by1000genomes TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 7 ENST00000378357.4:c.252T>C p.Pro84= p.P84= ENST00000378357 NM_001216.2 84 ccT/ccC 0 0.542 AGGATCTACCTGGAGAGGAGG +RORB 6096 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 77257427 77257427 + missense_variant Missense_Mutation SNP G G C TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 11 ENST00000376896.3:c.333G>C p.Gln111His p.Q111H ENST00000376896 NM_006914.3 111 caG/caC 0 0.592 ggcagcagcagAGTGGGGAGG +SETX 23064 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 135205145 135205145 + missense_variant Missense_Mutation SNP T T C TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 28 ENST00000224140.5:c.1840A>G p.Ile614Val p.I614V ENST00000224140 NM_015046.5 614 Atc/Gtc 0 0.353 GCAGGAGAGATTTTACATGCA +CCDC160 347475 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 133379653 133379653 + missense_variant Missense_Mutation SNP C C T TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 9 ENST00000517294.1:c.823C>T p.Arg275Cys p.R275C ENST00000517294 275 Cgc/Tgc 0 0.383 GGCAAAGATCCGCGGAGAGCT +PLXNA3 55558 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 153688767 153688767 + missense_variant Missense_Mutation SNP A A G rs142949704 TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 10 ENST00000369682.3:c.244A>G p.Ser82Gly p.S82G ENST00000369682 NM_017514.3 82 Agc/Ggc 0 0.672 CCCGCCCCCCAGCATGCGCGT +ZNF451 26036 broad.mit.edu;ucsc.edu GRCh37 6 57012701 57012701 + stop_gained Nonsense_Mutation SNP G G A TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 40 ENST00000370706.4:c.1818G>A p.Trp606Ter p.W606* ENST00000370706 NM_001031623.2 606 tgG/tgA 0 0.418 GGGGTAAATGGCAATGCCGGA +CPO 130749 broad.mit.edu;ucsc.edu GRCh37 2 207814342 207814342 + missense_variant,splice_region_variant Missense_Mutation SNP T T C TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 25 ENST00000272852.3:c.70T>C p.Ser24Pro p.S24P ENST00000272852 NM_173077.2 24 Tcc/Ccc 0 0.473 CCTTTGCAGATCCTTAGCCCA +AKAP4 8852 broad.mit.edu;ucsc.edu GRCh37 X 49957597 49957597 + synonymous_variant Silent SNP A A G TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 31 ENST00000358526.2:c.1767T>C p.Gly589= p.G589= ENST00000358526 NM_003886.2 589 ggT/ggC 0 0.488 CACTTTGGCCACCTCCACACT +ATRX 546 broad.mit.edu;ucsc.edu GRCh37 X 76813106 76813106 + missense_variant Missense_Mutation SNP T T G TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 35 ENST00000373344.5:c.6515A>C p.Glu2172Ala p.E2172A ENST00000373344 NM_000489.3 2172 gAa/gCa 0 0.338 AATCTTATCTTCCATGGTTCC +COL1A2 1278 broad.mit.edu;ucsc.edu GRCh37 7 94057712 94057712 + missense_variant Missense_Mutation SNP C C T TCGA-DU-5872-01 TCGA-DU-5872-10 Untested Somatic Phase_I WXS none Illumina GAIIx 100 34 ENST00000297268.6:c.3634C>T p.Pro1212Ser p.P1212S ENST00000297268 NM_000089.3 1212 Cca/Tca 0 0.488 TGAAAACATCCCAGCCAAGAA +SLCO1B1 10599 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 21329781 21329781 + missense_variant Missense_Mutation SNP T T C TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 39 ENST00000256958.2:c.431T>C p.Ile144Thr p.I144T ENST00000256958 NM_006446.4 144 aTt/aCt 0 0.274 ACTTGTTTAATTAATCAAATT +DYNC1H1 1778 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 102508452 102508452 + missense_variant Missense_Mutation SNP A A G TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 18 12 ENST00000360184.4:c.12205A>G p.Ile4069Val p.I4069V ENST00000360184 NM_001376.4 4069 Att/Gtt 0 0.537 GATCACTTCAATTGCAATCGG +ITGAD 3681 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 31419095 31419095 + synonymous_variant Silent SNP C C T TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 17 ENST00000389202.2:c.867C>T p.His289= p.H289= ENST00000389202 NM_005353.2 289 caC/caT 0 0.617 AGGTGGGACACGCTTTCCAGG +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7574018 7574018 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 8 20 ENST00000269305.4:c.1009C>T p.Arg337Cys p.R337C ENST00000269305 NM_001126112.2 337 Cgc/Tgc 0 0.522 ATCTCGAAGCGCTCACGCCCA +TMC6 11322 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 76116777 76116777 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 109 29 ENST00000590602.1:c.1672G>A p.Val558Ile p.V558I ENST00000590602 558 Gtc/Atc 0 0.637 AACATGAGGACGAAGTCCATC +CEACAM5 1048 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 42224879 42224879 + synonymous_variant Silent SNP G G A TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 45 ENST00000221992.6:c.1809G>A p.Ser603= p.S603= ENST00000221992 NM_004363.2 603 tcG/tcA 0 0.547 CCCCAGACTCGTCTTACCTTT +DHDDS 79947 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 26772898 26772898 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 46 ENST00000360009.2:c.415G>A p.Val139Ile p.V139I ENST00000360009 NM_024887.3 139 Gta/Ata 0 0.517 TGCACAAGCTGTACAGGCCAC +CELSR1 9620 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 46929726 46929726 + missense_variant Missense_Mutation SNP G G C TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 82 ENST00000262738.3:c.3342C>G p.Asn1114Lys p.N1114K ENST00000262738 NM_014246.1 1114 aaC/aaG 0 0.592 TGTTGGACTTGTTGGTGACAT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113113 209113113 + missense_variant Missense_Mutation SNP G G T rs121913499 TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 28 ENST00000345146.2:c.394C>A p.Arg132Ser p.R132S ENST00000345146 NM_005896.2 132 Cgt/Agt 0 0.398 TAAGCATGACGACCTATGATG +SLIT2 9353 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 20490510 20490510 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 180 35 ENST00000504154.1:c.680G>A p.Arg227Lys p.R227K ENST00000504154 NM_004787.1 227 aGg/aAg 0 0.498 CTTCGCCAAAGGCCTCGGGTT +LAMA2 3908 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 129419503 129419503 + synonymous_variant Silent SNP T T C TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 9 ENST00000421865.2:c.582T>C p.Asp194= p.D194= ENST00000421865 NM_001079823.1 194 gaT/gaC 0 0.443 ATGCCAAAGATGATGAGGTCA +TNFAIP3 7128 hgsc.bcm.edu;broad.mit.edu GRCh37 6 138199814 138199814 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 7 ENST00000237289.4:c.1232G>A p.Arg411Gln p.R411Q ENST00000237289 NM_001270507.1 411 cGg/cAg 0 0.557 TCAGAGAGGCGGCAAAAGAAT +ENPP2 5168 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 120596283 120596283 + synonymous_variant Silent SNP A A G TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 66 ENST00000259486.6:c.1530T>C p.Pro510= p.P510= ENST00000259486 NM_006209.4 510 ccT/ccC 0 0.348 AAACATCCAAAGGTTTCCTAA +KCNT1 57582 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 138657002 138657002 + missense_variant Missense_Mutation SNP G G T TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 98 11 ENST00000371757.2:c.1161G>T p.Met387Ile p.M387I ENST00000371757 NM_020822.2 387 atG/atT 0 0.642 ACCTTCTCATGGACTTCCTGA +CXorf23 256643 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 19983583 19983583 + missense_variant Missense_Mutation SNP G G T TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 41 ENST00000379687.3:c.853C>A p.Arg285Ser p.R285S ENST00000379687 NM_198279.3 285 Cgt/Agt 0 0.458 AGCTTAGGACGTTTGTGACGA +HDAC6 10013 hgsc.bcm.edu;broad.mit.edu GRCh37 X 48682452 48682452 + missense_variant Missense_Mutation SNP A A G TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 6 ENST00000334136.5:c.3424A>G p.Asn1142Asp p.N1142D ENST00000334136 1142 Aat/Gat 0 0.592 AATCCAAGAGAATTGGGTGTG +GLUD2 2747 hgsc.bcm.edu;broad.mit.edu GRCh37 X 120182836 120182836 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 214 22 ENST00000328078.1:c.1298G>A p.Gly433Glu p.G433E ENST00000328078 NM_012084.3 433 gGa/gAa 0 0.418 TTGAATGCTGGAGGAGTGACA +ZFYVE26 23503 broad.mit.edu;ucsc.edu GRCh37 14 68251787 68251787 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 111 75 ENST00000347230.4:c.3512G>A p.Ser1171Asn p.S1171N ENST00000347230 NM_015346.3 1171 aGc/aAc 0 0.502 AGGCTCAGAGCTCAAACTTTG +MAP2K3 5606 broad.mit.edu;ucsc.edu GRCh37 17 21217496 21217496 + missense_variant Missense_Mutation SNP C C T rs35755743 TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 317 65 ENST00000342679.4:c.998C>T p.Thr333Met p.T333M ENST00000342679 NM_145109.2 333 aCg/aTg 0 0.617 ACCAAGAAGACGGACATTGCT +LPAR4 2846 broad.mit.edu;ucsc.edu GRCh37 X 78010568 78010568 + missense_variant Missense_Mutation SNP A A G TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 260 50 ENST00000435339.3:c.202A>G p.Met68Val p.M68V ENST00000435339 NM_005296.2 68 Atg/Gtg 0 0.358 CTGTTTCCGCATGAAAATGAG +PTCD1 26024 broad.mit.edu;ucsc.edu GRCh37 7 99026819 99026819 + synonymous_variant Silent SNP G G A TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 10 ENST00000413834.1:c.969C>T p.Ile323= p.I323= ENST00000413834 323 atC/atT 0 0.557 GCCCTTTGTGGATGATTTCCT +XPO6 23214 broad.mit.edu;ucsc.edu GRCh37 16 28137080 28137080 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 117 29 ENST00000304658.5:c.1696C>T p.Arg566Cys p.R566C ENST00000304658 NM_015171.3 566 Cgc/Tgc 0 0.582 TCGGCCAGGCGGCCCACGGCC +ESCO2 157570 broad.mit.edu;hgsc.bcm.edu GRCh37 8 27634263 27634266 + frameshift_variant Frame_Shift_Del DEL TAAG TAAG - TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 23 ENST00000305188.8:c.440_443delAGTA p.Lys147IlefsTer23 p.K147Ifs*23 ENST00000305188 NM_001017420.2 146 gcTAAG/gc 0 0.353 GTTTAACTGCTAAGTATCAACCAA +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76939673 76939674 + frameshift_variant Frame_Shift_Ins INS - - T TCGA-DU-6401-01 TCGA-DU-6401-10 Untested Somatic Phase_I WXS none Illumina GAIIx 94 52 ENST00000373344.5:c.1074dupA p.Leu359ThrfsTer3 p.L359Tfs*3 ENST00000373344 NM_000489.3 358 -/A 0 0.366 GTCTCAATCAGTTTTTTTGCCT +ANK3 288 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 61958113 61958113 + synonymous_variant Silent SNP T T C TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 14 ENST00000280772.2:c.1674A>G p.Leu558= p.L558= ENST00000280772 NM_020987.3 558 ttA/ttG 0 0.498 TTGTTATAGATAAAGACGCTC +OR2AG2 338755 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 6789589 6789589 + synonymous_variant Silent SNP G G A TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 18 10 ENST00000338569.2:c.600C>T p.Tyr200= p.Y200= ENST00000338569 NM_001004490.1 200 taC/taT 0 0.493 CACCTGTCACGTATATTATAA +SIPA1 6494 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 65408733 65408733 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 67 ENST00000394224.3:c.341G>A p.Arg114Gln p.R114Q ENST00000394224 NM_153253.29 114 cGa/cAa 0 0.632 CTTGAGCCTCGATGGTTTGCC +PLEKHA5 54477 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 19489486 19489486 + missense_variant Missense_Mutation SNP A A C TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 26 ENST00000429027.2:c.2486A>C p.Glu829Ala p.E829A ENST00000429027 NM_001256470.1 829 gAa/gCa 0 0.348 GATAAGTTAGAATACGATGTA +LRRK1 79705 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 101588788 101588788 + synonymous_variant Silent SNP A A G TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 58 ENST00000388948.3:c.3225A>G p.Thr1075= p.T1075= ENST00000388948 NM_024652.3 1075 acA/acG 0 0.448 GCTGTAGCACATTCAGAGTGA +TP53 7157 hgsc.bcm.edu;broad.mit.edu GRCh37 17 7577121 7577121 + missense_variant Missense_Mutation SNP G G A rs121913343 TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 0 9 ENST00000269305.4:c.817C>T p.Arg273Cys p.R273C ENST00000269305 NM_001126112.2 273 Cgt/Tgt 0 0.542 GCACAAACACGCACCTCAAAG +GAS2L2 246176 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 34079638 34079638 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 23 ENST00000254466.6:c.232G>A p.Ala78Thr p.A78T ENST00000254466 NM_139285.3 78 Gcc/Acc 0 0.652 GCCAGGAAGGCCAGGGCAGCG +HELZ 9931 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 65174991 65174991 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 17 ENST00000358691.5:c.1214G>A p.Arg405His p.R405H ENST00000358691 NM_014877.3 405 cGt/cAt 0 0.348 AGAATCCCAACGTTTAGCTGT +EPS15L1 58513 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 16487940 16487940 + synonymous_variant Silent SNP C C T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 15 ENST00000455140.2:c.2373G>A p.Pro791= p.P791= ENST00000455140 NM_001258374.1 791 ccG/ccA 0 0.612 GACCGCTGGGCGGTTTAGGCC +FGR 2268 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 27943402 27943402 + synonymous_variant Silent SNP G G A TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 141 70 ENST00000374005.3:c.648C>T p.Phe216= p.F216= ENST00000374005 NM_005248.2 216 ttC/ttT 0 0.562 GCACCGAGTTGAACTGAACCC +ZSCAN20 7579 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 33960425 33960425 + synonymous_variant Silent SNP T T G TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 154 93 ENST00000361328.3:c.2481T>G p.Pro827= p.P827= ENST00000361328 NM_145238.3 827 ccT/ccG 0 0.448 GTAGTGAGCCTGGGGGAAACT +LRRC8D 55144 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 90400076 90400076 + synonymous_variant Silent SNP C C T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 13 ENST00000337338.5:c.1449C>T p.Pro483= p.P483= ENST00000337338 NM_001134479.1 483 ccC/ccT 0 0.468 CGGGGGTGCCCGATGCTGTCT +CFHR5 81494 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 196953247 196953247 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 21 ENST00000256785.4:c.410C>T p.Pro137Leu p.P137L ENST00000256785 137 cCt/cTt 0 0.348 TGGTCCACTCCTCCCATATGC +ASPM 259266 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 197091601 197091601 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 11 ENST00000367409.4:c.3515C>T p.Thr1172Met p.T1172M ENST00000367409 NM_018136.4 1172 aCg/aTg 0 0.413 ACCAGTTTGCGTACATTCCAC +SLC25A1 6576 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 19164192 19164192 + missense_variant Missense_Mutation SNP T T G TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 12 ENST00000215882.5:c.646A>C p.Lys216Gln p.K216Q ENST00000215882 NM_005984.3 216 Aag/Cag 0 0.592 TTCATGGGCTTGTTGGGGTTG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 35 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +VIL1 7429 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 219295519 219295519 + synonymous_variant Silent SNP C C T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 19 ENST00000248444.5:c.1020C>T p.Ala340= p.A340= ENST00000248444 NM_007127.2 340 gcC/gcT 0 0.597 CTGAGTCGGCCGTCTTTCAGC +PCDHA11 56138 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 140249016 140249016 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 171 147 ENST00000398640.2:c.328G>A p.Val110Met p.V110M ENST00000398640 NM_018902.3 110 Gtg/Atg 0 0.552 GGAGGTGATCGTGGACAGGCC +DUSP22 56940 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 348774 348774 + synonymous_variant Silent SNP G G T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 24 ENST00000344450.5:c.441G>T p.Arg147= p.R147= ENST00000344450 NM_020185.3 147 cgG/cgT 0 0.522 TCCAGTATCGGCAGTGGCTGA +FIGNL1 63979 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 50513534 50513534 + synonymous_variant Silent SNP T T C TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 50 ENST00000419119.1:c.1452A>G p.Ala484= p.A484= ENST00000419119 484 gcA/gcG 0 0.443 CAGCAAACAATGCACGGACCA +ZNF138 7697 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 64292367 64292367 + missense_variant Missense_Mutation SNP A A C TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 16 ENST00000440155.2:c.669A>C p.Lys223Asn p.K223N ENST00000440155 NM_006524.3 223 aaA/aaC 0 0.368 CTGGAGAAAAACCCTATAAAT +SEMA3C 10512 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 80374454 80374454 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 24 ENST00000265361.3:c.2012C>T p.Thr671Met p.T671M ENST00000265361 NM_006379.3 671 aCg/aTg 0 0.478 CCATTTGTCCGTCACAACAGC +JPH1 56704 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 75171665 75171665 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 18 ENST00000342232.4:c.1213G>A p.Ala405Thr p.A405T ENST00000342232 NM_020647.2 405 Gcg/Acg 0 0.607 ACAGCTCTCGCGATGTCGCAC +NUDCD1 84955 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 110287672 110287672 + missense_variant Missense_Mutation SNP A A C TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 11 ENST00000239690.4:c.1082T>G p.Val361Gly p.V361G ENST00000239690 NM_032869.3 361 gTa/gGa 0 0.383 ATCTCCAATTACTAGCTCTGG +EPPK1 83481 hgsc.bcm.edu;broad.mit.edu GRCh37 8 144940576 144940576 + synonymous_variant Silent SNP C C T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 4 ENST00000525985.1:c.6846G>A p.Ser2282= p.S2282= ENST00000525985 NM_031308.2 2282 tcG/tcA 0 0.736 CCTCCTCCACCGACAGCCTCA +ZFP37 7539 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 115811700 115811700 + synonymous_variant Silent SNP T T C TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 27 ENST00000374227.3:c.291A>G p.Arg97= p.R97= ENST00000374227 97 agA/agG 0 0.403 CTTGACTGGGTCTTTTCCCCT +DDX31 64794 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 135522404 135522404 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 60 40 ENST00000372159.3:c.1324A>G p.Ser442Gly p.S442G ENST00000372159 NM_022779.7 442 Agt/Ggt 0 0.493 ACAGAAATACTGACTGGATCA +GSPT2 23708 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 51488448 51488448 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 24 ENST00000340438.4:c.1726G>A p.Val576Met p.V576M ENST00000340438 NM_018094.4 576 Gtg/Atg 0 0.418 ACCCCGCTTCGTGAAACAAGA +ZCCHC5 203430 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 77912924 77912924 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 9 ENST00000321110.1:c.994C>A p.Leu332Ile p.L332I ENST00000321110 NM_152694.2 332 Ctc/Atc 0 0.463 CCTTGGCAGAGTTGATGGATG +TENM1 10178 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 123525932 123525932 + synonymous_variant Silent SNP C C T TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 8 15 ENST00000422452.2:c.5658G>A p.Gly1886= p.G1886= ENST00000422452 NM_001163279.1 1886 ggG/ggA 0 0.378 TCCAAATTTTCCCATCAGCCC +KCNJ8 3764 broad.mit.edu;ucsc.edu GRCh37 12 21926252 21926252 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 34 ENST00000240662.2:c.299A>G p.Asp100Gly p.D100G ENST00000240662 NM_004982.3 100 gAc/gGc 0 0.507 AGCATAGATGTCCCCATGGGC +SMARCA4 6597 broad.mit.edu;ucsc.edu GRCh37 19 11132434 11132434 + missense_variant Missense_Mutation SNP C C A TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 14 ENST00000344626.4:c.2650C>A p.His884Asn p.H884N ENST00000344626 NM_003072.3 884 Cac/Aac 0 0.622 GGACGAAGGTCACCGCATGAA +PCDH18 54510 broad.mit.edu;ucsc.edu GRCh37 4 138452008 138452008 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 3 ENST00000344876.4:c.1235A>G p.Glu412Gly p.E412G ENST00000344876 NM_019035.3 412 gAa/gGa 0 0.403 ATAATTGTTTTCATATGTCTT +RBM41 55285 broad.mit.edu;hgsc.bcm.edu GRCh37 X 106331986 106331986 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-HT-7606-01 TCGA-HT-7606-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 15 ENST00000372479.3:c.607delG p.Glu203LysfsTer6 p.E203Kfs*6 ENST00000372479 NM_018301.3 203 Gaa/aa 0 0.428 TGAAACTCTTCAAGACGTTTT +ARMC3 219681 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 23292319 23292319 + synonymous_variant Silent SNP C C T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 59 ENST00000298032.5:c.1707C>T p.Asn569= p.N569= ENST00000298032 NM_173081.3 569 aaC/aaT 0 0.323 ACATAATTAACGATGGATTCT +ATG16L2 89849 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 72528829 72528829 + missense_variant Missense_Mutation SNP G G C TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 15 ENST00000321297.5:c.247G>C p.Val83Leu p.V83L ENST00000321297 NM_033388.1 83 Gtc/Ctc 0 0.587 CTCAGACCAAGTCCCATCACT +BCL9L 283149 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 118772576 118772576 + missense_variant Missense_Mutation SNP T T C TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 14 ENST00000334801.3:c.1876A>G p.Met626Val p.M626V ENST00000334801 NM_182557.2 626 Atg/Gtg 0 0.622 ATGGCATTCATGGGCACCTCC +WNK1 65125 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 994382 994382 + missense_variant Missense_Mutation SNP C C T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 29 ENST00000315939.6:c.4412C>T p.Pro1471Leu p.P1471L ENST00000315939 NM_018979.3 1471 cCt/cTt 0 0.507 GGTCCTAAGCCTCCAGCTGTA +PSMC6 5706 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 53175072 53175072 + missense_variant Missense_Mutation SNP A A G TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 25 ENST00000445930.2:c.173A>G p.Glu58Gly p.E58G ENST00000445930 58 gAa/gGa 0 0.353 GAAAAGTCTGAAAATGATCTG +COPS2 9318 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 49447771 49447771 + missense_variant Missense_Mutation SNP G G C TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 49 ENST00000299259.6:c.5C>G p.Ser2Cys p.S2C ENST00000299259 2 tCt/tGt 0 0.557 CTCCATGTCAGACATCTTGGC +PDE8A 5151 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 85610300 85610300 + missense_variant Missense_Mutation SNP G G A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 45 ENST00000310298.4:c.299G>A p.Cys100Tyr p.C100Y ENST00000310298 100 tGt/tAt 0 0.383 TGCAGGGCATGTGAAAAAGCA +DHX38 9785 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 72132924 72132924 + missense_variant Missense_Mutation SNP C C T rs148934675 TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 20 ENST00000268482.3:c.863C>T p.Pro288Leu p.P288L ENST00000268482 NM_014003.3 288 cCg/cTg 0 0.617 GGGTCCACCCCGCGTCTGTCC +ZFHX3 463 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 72993684 72993684 + missense_variant Missense_Mutation SNP C C A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 117 23 ENST00000268489.5:c.361G>T p.Asp121Tyr p.D121Y ENST00000268489 NM_006885.3 121 Gac/Tac 0 0.687 CTCTCCTCGTCCCCCTCCTCA +PLCG2 5336 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 81953235 81953235 + missense_variant Missense_Mutation SNP C C A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 28 ENST00000359376.3:c.2201C>A p.Pro734His p.P734H ENST00000359376 NM_002661.3 734 cCc/cAc 0 0.517 CTGCGCTACCCCGTGACCCCC +METTL16 79066 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 2324130 2324130 + synonymous_variant Silent SNP G G A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 237 104 ENST00000263092.6:c.957C>T p.Ser319= p.S319= ENST00000263092 NM_024086.3 319 tcC/tcT 0 0.453 CCTTCATCACGGACGCCAGCA +ALDH4A1 8659 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 19209803 19209803 + synonymous_variant Silent SNP G G A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 21 ENST00000375341.3:c.573C>T p.Ser191= p.S191= ENST00000375341 NM_003748.3 191 agC/agT 0 0.647 TGCTGTTGGTGCTCGGGGGCA +ALDH4A1 8659 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 19209838 19209838 + missense_variant Missense_Mutation SNP G G C TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 24 ENST00000375341.3:c.538C>G p.Leu180Val p.L180V ENST00000375341 NM_003748.3 180 Ctg/Gtg 0 0.642 TGCCCCTCCAGCTCCACCGCA +TMEM39B 55116 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 32542835 32542835 + missense_variant Missense_Mutation SNP C C T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 187 19 ENST00000336294.5:c.506C>T p.Thr169Met p.T169M ENST00000336294 NM_018056.2 169 aCg/aTg 0 0.592 ACCGTTCTCACGGCAACAGGC +TOR1AIP1 26092 hgsc.bcm.edu;ucsc.edu GRCh37 1 179876983 179876983 + missense_variant Missense_Mutation SNP G G C TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 4 ENST00000606911.2:c.822G>C p.Lys274Asn p.K274N ENST00000606911 274 aaG/aaC 0 0.328 CTCATGATAAGCAACCTTCAG +BRINP3 339479 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 190067492 190067492 + missense_variant Missense_Mutation SNP C C T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 38 ENST00000367462.3:c.1957G>A p.Asp653Asn p.D653N ENST00000367462 NM_199051.1 653 Gac/Aac 0 0.428 CGGGAAGGGTCAATAAACTCC +HSPA13 6782 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 15748040 15748040 + synonymous_variant Silent SNP G G A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 116 37 ENST00000285667.3:c.681C>T p.Gly227= p.G227= ENST00000285667 NM_006948.4 227 ggC/ggT 0 0.483 GAGTTCCTCCGCCCAAGTCTA +BCR 613 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 23631729 23631729 + synonymous_variant Silent SNP C C G TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 24 ENST00000305877.8:c.2628C>G p.Ser876= p.S876= ENST00000305877 NM_004327.3 876 tcC/tcG 0 0.572 CCCTGACATCCGTGGAGCTGC +LRP1B 53353 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 141274478 141274478 + missense_variant Missense_Mutation SNP C C G TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 35 ENST00000389484.3:c.8129G>C p.Gly2710Ala p.G2710A ENST00000389484 NM_018557.2 2710 gGa/gCa 0 0.328 TTCATCACGTCCATCCTCACA +DNAH7 56171 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 196877622 196877622 + missense_variant Missense_Mutation SNP C C T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 20 ENST00000312428.6:c.878G>A p.Arg293His p.R293H ENST00000312428 NM_018897.2 293 cGt/cAt 0 0.279 ATCAACTAAACGTAATTTTCT +CACNA1D 776 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 53837571 53837571 + missense_variant Missense_Mutation SNP G G C TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 215 97 ENST00000288139.4:c.5617G>C p.Glu1873Gln p.E1873Q ENST00000288139 NM_000720.3 1873 Gag/Cag 0 0.617 GGAATGCTACGAGGATGACAG +SLITRK3 22865 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 164906713 164906713 + missense_variant Missense_Mutation SNP G G T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 11 ENST00000475390.1:c.1906C>A p.Pro636Thr p.P636T ENST00000475390 636 Cca/Aca 0 0.527 GCACTGGTTGGTGCCCCAATA +GABRA1 2554 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 161324195 161324195 + missense_variant Missense_Mutation SNP G G C TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 138 44 ENST00000428797.2:c.1138G>C p.Ala380Pro p.A380P ENST00000428797 NM_001127643.1 380 Gcc/Ccc 0 0.458 CCCTAATTTGGCCAGGGGCGA +EGFR 1956 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 55211008 55211008 + missense_variant Missense_Mutation SNP A A T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 90 32 ENST00000275493.2:c.251A>T p.Glu84Val p.E84V ENST00000275493 NM_005228.3 84 gAg/gTg 0 0.448 ACCATCCAGGAGGTGGCTGGT +SEMA3E 9723 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 83119551 83119551 + missense_variant Missense_Mutation SNP G G T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 20 ENST00000307792.3:c.155C>A p.Pro52His p.P52H ENST00000307792 NM_012431.2 52 cCt/cAt 0 0.413 AAATCCAAAAGGGCTATGAAA +RNF19A 25897 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 101287238 101287238 + missense_variant Missense_Mutation SNP G G A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 27 ENST00000519449.1:c.826C>T p.Arg276Cys p.R276C ENST00000519449 NM_015435.4 276 Cgt/Tgt 0 0.418 GTTCTCAAACGTAAGCTCTGG +SLC45A4 57210 hgsc.bcm.edu;broad.mit.edu GRCh37 8 142231748 142231748 + missense_variant Missense_Mutation SNP G G A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 6 ENST00000024061.3:c.205C>T p.Arg69Trp p.R69W ENST00000024061 NM_001080431.1 69 Cgg/Tgg 0 0.617 ATGAAGGGCCGCCGGCGGCCC +EPPK1 83481 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 144945911 144945911 + missense_variant Missense_Mutation SNP C C T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 8 ENST00000525985.1:c.1511G>A p.Arg504Gln p.R504Q ENST00000525985 NM_031308.2 504 cGg/cAg 0 0.677 GGGCCGGCCCCGGAACTTCCC +APBA1 320 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 72131516 72131516 + missense_variant Missense_Mutation SNP G G T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 15 ENST00000265381.4:c.611C>A p.Ala204Glu p.A204E ENST00000265381 NM_001163.3 204 gCg/gAg 0 0.721 CAGCTCGGGCGCGTCCCCTAT +APOO 79135 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 23899066 23899066 + missense_variant Missense_Mutation SNP T T A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 36 ENST00000379226.4:c.13A>T p.Ile5Phe p.I5F ENST00000379226 NM_024122.4 5 Att/Ttt 0 0.478 GACCTCTGAATTACCTGAAAT +HLTF 6596 broad.mit.edu;ucsc.edu GRCh37 3 148792096 148792096 + synonymous_variant Silent SNP A A C TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 34 ENST00000310053.5:c.435T>G p.Pro145= p.P145= ENST00000310053 NM_003071.3 145 ccT/ccG 0 0.363 TCATATGCAGAGGCATGGTAA +LUZP4 51213 broad.mit.edu;ucsc.edu GRCh37 X 114541268 114541268 + missense_variant Missense_Mutation SNP G G A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 114 23 ENST00000371920.3:c.841G>A p.Val281Met p.V281M ENST00000371920 NM_016383.3 281 Gtg/Atg 0 0.428 GAGAGATCTCGTGGCCACTGA +PGM3 5238 broad.mit.edu;ucsc.edu GRCh37 6 83884095 83884095 + missense_variant,splice_region_variant Missense_Mutation SNP G G T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 3 ENST00000506587.1:c.1324C>A p.Gln442Lys p.Q442K ENST00000506587 NM_001199917.1 442 Cag/Aag 0 0.383 GTTCTGACCTGGTTAAACAAG +KIF1B 23095 broad.mit.edu;ucsc.edu GRCh37 1 10386237 10386237 + missense_variant Missense_Mutation SNP C C T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 250 21 ENST00000263934.6:c.2606C>T p.Thr869Met p.T869M ENST00000263934 NM_015074.3 869 aCg/aTg 0 0.572 ACTTTTTCCACGGCCGATTCC +DNAH11 8701 broad.mit.edu;ucsc.edu GRCh37 7 21640450 21640450 + missense_variant Missense_Mutation SNP C C T TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 160 57 ENST00000328843.6:c.3157C>T p.Leu1053Phe p.L1053F ENST00000328843 1053 Ctc/Ttc 0 0.438 GAAGCATTTTCTCTTGTATGG +KIF19 124602 broad.mit.edu;ucsc.edu GRCh37 17 72343952 72343952 + missense_variant Missense_Mutation SNP G G A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 8 3 ENST00000389916.4:c.961G>A p.Ala321Thr p.A321T ENST00000389916 NM_153209.3 321 Gct/Act 0 0.627 AGTGATGATCGCTCACATCAG +DCAF12L1 139170 broad.mit.edu;ucsc.edu GRCh37 X 125686452 125686452 + missense_variant Missense_Mutation SNP G G A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 21 ENST00000371126.1:c.140C>T p.Thr47Met p.T47M ENST00000371126 NM_178470.4 47 aCg/aTg 0 0.721 CGAGCGATACGTCGCCGGCCG +PTEN 5728 broad.mit.edu;hgsc.bcm.edu GRCh37 10 89717715 89717716 + frameshift_variant Frame_Shift_Ins INS - - A TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 48 ENST00000371953.3:c.741dupA p.Pro248ThrfsTer5 p.P248Tfs*5 ENST00000371953 NM_000314.4 247 tta/ttAa 0 0.406 CCTCAGCCGTTACCTGTGTGTG +BACH1 571 broad.mit.edu;hgsc.bcm.edu GRCh37 21 30699512 30699513 + frameshift_variant Frame_Shift_Del DEL TA TA - rs145991657 TCGA-DU-8158-01 TCGA-DU-8158-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 29 ENST00000399921.1:c.1367_1368delTA p.Leu456Ter p.L456* ENST00000399921 NM_206866.1 456 tTA/t 0 0.436 TTCACAACATTAAGTTCTGTCA +CUBN 8029 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 16990512 16990512 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 15 ENST00000377833.4:c.5174G>C p.Gly1725Ala p.G1725A ENST00000377833 NM_001081.3 1725 gGg/gCg 0 0.512 GTGGAAACCCCCAGCACTGAT +OR52E8 390079 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 5878264 5878264 + stop_gained Nonsense_Mutation SNP A A C TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 12 ENST00000537935.1:c.669T>G p.Tyr223Ter p.Y223* ENST00000537935 NM_001005168.1 223 taT/taG 0 0.463 GGATCCTGACATAGGAGAGAA +LRP4 4038 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 46893136 46893136 + synonymous_variant Silent SNP G G A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 18 ENST00000378623.1:c.4632C>T p.Leu1544= p.L1544= ENST00000378623 NM_002334.3 1544 ctC/ctT 0 0.557 GTTTCCCATTGAGGTCAGCAC +HTR3B 9177 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 113803068 113803068 + synonymous_variant Silent SNP C C A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 192 19 ENST00000260191.2:c.426C>A p.Thr142= p.T142= ENST00000260191 NM_006028.4 142 acC/acA 0 0.433 CATCTGGGACCATTGAGAACT +SNX19 399979 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 130750571 130750571 + stop_gained Nonsense_Mutation SNP G G A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 263 52 ENST00000265909.4:c.2704C>T p.Gln902Ter p.Q902* ENST00000265909 NM_014758.2 902 Cag/Tag 0 0.517 GCCAGTTTCTGCTCTTGGGTC +HMGA2 8091 hgsc.bcm.edu;broad.mit.edu GRCh37 12 66221789 66221789 + synonymous_variant Silent SNP C C T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 5 ENST00000403681.2:c.120C>T p.Thr40= p.T40= ENST00000403681 NM_003483.4 40 acC/acT 0 0.448 AGGAACCAACCGGTGAGCCCT +PTPRB 5787 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 70954486 70954486 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 9 ENST00000334414.6:c.4397A>G p.Asp1466Gly p.D1466G ENST00000334414 NM_001109754.2 1466 gAt/gGt 0 0.512 ATTGCTGAGATCTCCACTGTG +SHF 90525 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 45470424 45470424 + synonymous_variant Silent SNP T T C TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 16 ENST00000290894.8:c.384A>G p.Pro128= p.P128= ENST00000290894 NM_138356.2 128 ccA/ccG 0 0.567 GGACCTTCTCTGGGGCTCCTG +RHBDF1 64285 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 111434 111434 + synonymous_variant Silent SNP G G A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 7 ENST00000262316.6:c.1344C>T p.Tyr448= p.Y448= ENST00000262316 NM_022450.3 448 taC/taT 0 0.716 TGACGTTCTCGTAGACCCCGC +PRSS22 64063 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 2906139 2906139 + synonymous_variant Silent SNP G G A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 99 17 ENST00000161006.3:c.225C>T p.Cys75= p.C75= ENST00000161006 NM_022119.3 75 tgC/tgT 0 0.617 GAGAACCTGCGCAGTGGTGGG +ERCC4 2072 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 14031642 14031642 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 22 ENST00000311895.7:c.1831G>A p.Gly611Arg p.G611R ENST00000311895 NM_005236.2 611 Gga/Aga 0 0.363 TCTTATATACGGAGGTTCAAC +ANKRD11 29123 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 89348104 89348104 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 110 23 ENST00000301030.4:c.4846G>A p.Gly1616Arg p.G1616R ENST00000301030 NM_001256183.1 1616 Gga/Aga 0 0.607 TTGGGGTCTCCGGACCGGTGC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577121 7577121 + missense_variant Missense_Mutation SNP G G A rs121913343 TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 28 ENST00000269305.4:c.817C>T p.Arg273Cys p.R273C ENST00000269305 NM_001126112.2 273 Cgt/Tgt 0 0.542 GCACAAACACGCACCTCAAAG +MYO19 80179 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 34866651 34866651 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 7 ENST00000431794.3:c.1091G>A p.Arg364Gln p.R364Q ENST00000431794 NM_001163735.1 364 cGg/cAg 0 0.627 GCAGGGCTTCCGGAACACCTG +FCGBP 8857 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 40357728 40357728 + synonymous_variant Silent SNP G G A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 12 ENST00000221347.6:c.15585C>T p.Ser5195= p.S5195= ENST00000221347 NM_003890.2 5195 agC/agT 0 0.587 AACAGCGCTCGCTGCAGTCTG +PPP1R12C 54776 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 55605714 55605714 + missense_variant,splice_region_variant Missense_Mutation SNP T T G TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 135 27 ENST00000263433.3:c.1682A>C p.Gln561Pro p.Q561P ENST00000263433 NM_017607.3 561 cAg/cCg 0 0.657 ACCCCACACCTGTGTGGACCT +AGL 178 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 100346642 100346642 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 17 ENST00000294724.4:c.1910C>T p.Ala637Val p.A637V ENST00000294724 NM_000028.2 637 gCg/gTg 0 0.353 CATAGATCAGCGTATGATGCT +CEPT1 10390 hgsc.bcm.edu;broad.mit.edu GRCh37 1 111726868 111726868 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 121 6 ENST00000545121.1:c.1187C>T p.Ala396Val p.A396V ENST00000545121 NM_001007794.1 396 gCg/gTg 0 0.398 AATCAGATTGCGTCTCACCTG +TCHH 7062 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 152080904 152080904 + missense_variant Missense_Mutation SNP A A T rs71585886 TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 35 ENST00000368804.1:c.4789T>A p.Phe1597Ile p.F1597I ENST00000368804 NM_007113.3 1597 Ttc/Atc 0 0.582 TCCTCCATGAATTTTCTCTCT +CFH 3075 hgsc.bcm.edu;broad.mit.edu GRCh37 1 196642210 196642210 + missense_variant Missense_Mutation SNP C C A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 117 9 ENST00000367429.4:c.161C>A p.Pro54His p.P54H ENST00000367429 NM_000186.3 54 cCt/cAt 0 0.403 AAATGCCGCCCTGGATATAGA +RYR2 6262 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 237872820 237872820 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 12 10 ENST00000366574.2:c.10183C>T p.Leu3395Phe p.L3395F ENST00000366574 NM_001035.2 3395 Ctc/Ttc 0 0.418 AGCAGAGGAGCTCTTCCGCAT +ZNF638 27332 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 71590305 71590305 + missense_variant Missense_Mutation SNP A A C TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 26 ENST00000409544.1:c.1402A>C p.Ile468Leu p.I468L ENST00000409544 NM_001252612.1 468 Atc/Ctc 0 0.264 GAATCCTGAGATCCTCCCATC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113113 209113113 + missense_variant Missense_Mutation SNP G G T rs121913499 TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 107 34 ENST00000345146.2:c.394C>A p.Arg132Ser p.R132S ENST00000345146 NM_005896.2 132 Cgt/Agt 0 0.398 TAAGCATGACGACCTATGATG +TRPM8 79054 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 234905020 234905020 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 82 9 ENST00000324695.4:c.2990A>G p.Gln997Arg p.Q997R ENST00000324695 NM_024080.4 997 cAg/cGg 0 0.537 TGGAAGTTCCAGAGGTACTTC +KCNH8 131096 hgsc.bcm.edu;broad.mit.edu GRCh37 3 19575424 19575424 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 5 ENST00000328405.2:c.3157G>T p.Gly1053Cys p.G1053C ENST00000328405 NM_144633.2 1053 Ggc/Tgc 0 0.488 ATCAGAGGAGGGCAGCTTCAG +ABI3BP 25890 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 100489774 100489774 + synonymous_variant Silent SNP T T C TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 158 21 ENST00000284322.5:c.2421A>G p.Gln807= p.Q807= ENST00000284322 NM_015429.3 807 caA/caG 0 0.468 TGTCAGGCTTTTGGATGTATC +GPR149 344758 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 154146852 154146852 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 7 ENST00000389740.2:c.553G>A p.Asp185Asn p.D185N ENST00000389740 NM_001038705.1 185 Gac/Aac 0 0.657 CTGGAGCAGTCCACCAGGCAG +STATH 6779 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 70866654 70866654 + synonymous_variant Silent SNP A A G TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 167 46 ENST00000246895.4:c.177A>G p.Gln59= p.Q59= ENST00000246895 NM_003154.2 59 caA/caG 0 0.373 AATACCAACAATATACCTTTT +CAPSL 133690 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 35910530 35910530 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 89 18 ENST00000397367.2:c.253C>T p.Arg85Trp p.R85W ENST00000397367 NM_144647.3 85 Cgg/Tgg 0 0.358 TCAAACCTCCGGAAAAGTTCT +SPOCK1 6695 hgsc.bcm.edu;ucsc.edu GRCh37 5 136324179 136324179 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 139 46 ENST00000394945.1:c.860C>T p.Ser287Leu p.S287L ENST00000394945 NM_004598.3 287 tCg/tTg 0 0.498 GGAGTCACACGAGTTGAAAAG +RNF145 153830 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 158621725 158621725 + missense_variant,splice_region_variant Missense_Mutation SNP T T C TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 155 65 ENST00000518802.1:c.382A>G p.Arg128Gly p.R128G ENST00000518802 NM_001199380.1 128 Agg/Ggg 0 0.363 TATTCTTACCTGGAAATTTGA +COL19A1 1310 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 70877920 70877920 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 15 ENST00000322773.4:c.2449A>G p.Ile817Val p.I817V ENST00000322773 NM_001858.4 817 Att/Gtt 0 0.279 TCCTAAGGGTATTCCATTTAA +PRDM1 639 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 106555167 106555167 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 28 ENST00000369096.4:c.2284G>A p.Val762Met p.V762M ENST00000369096 NM_001198.3 762 Gtg/Atg 0 0.478 AATTCTGGCCGTGGTCAGAAA +MICAL1 64780 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 109770958 109770958 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 159 17 ENST00000358807.3:c.1336A>G p.Thr446Ala p.T446A ENST00000358807 NM_022765.3 446 Aca/Gca 0 0.607 TCTGGGGATGTCTGTGACAGA +FOXB2 442425 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 79635448 79635448 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 17 ENST00000376708.1:c.878C>T p.Ser293Phe p.S293F ENST00000376708 NM_001013735.1 293 tCc/tTc 0 0.662 CCCTTGGCGTCCGTCATGCAC +AKAP4 8852 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 49958837 49958837 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 49 ENST00000358526.2:c.527G>A p.Arg176His p.R176H ENST00000358526 NM_003886.2 176 cGt/cAt 0 0.443 CATTTCTAGACGTAGGTTTTG +DOPEY1 23033 broad.mit.edu;ucsc.edu GRCh37 6 83839856 83839856 + stop_gained Nonsense_Mutation SNP C C T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 23 ENST00000349129.2:c.2356C>T p.Gln786Ter p.Q786* ENST00000349129 NM_015018.3 786 Cag/Tag 0 0.418 TGAGCATGTGCAGCCTCCACA +NOTCH1 4851 broad.mit.edu;ucsc.edu GRCh37 9 139411837 139411837 + missense_variant,splice_region_variant Missense_Mutation SNP C C A TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 4 ENST00000277541.6:c.1442G>T p.Gly481Val p.G481V ENST00000277541 NM_017617.3 481 gGc/gTc 0 0.647 ACCCTCGTAGCCTGTGGGGTG +SRPK2 6733 broad.mit.edu;ucsc.edu GRCh37 7 104782648 104782648 + synonymous_variant Silent SNP T T C rs56003957 byFrequency TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 23 ENST00000393651.3:c.1350A>G p.Pro450= p.P450= ENST00000393651 NM_182692.2 450 ccA/ccG 0 0.443 GTCGTCCATTTGGCAATTCAC +TRAPPC11 60684 broad.mit.edu;ucsc.edu GRCh37 4 184628079 184628079 + missense_variant Missense_Mutation SNP T T G TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 8 ENST00000334690.6:c.3175T>G p.Ser1059Ala p.S1059A ENST00000334690 NM_021942.5 1059 Tca/Gca 0 0.418 CTTCATGTTCTCAGGTCTCAA +LRRTM4 80059 broad.mit.edu;ucsc.edu GRCh37 2 76975874 76975874 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 169 49 ENST00000409093.1:c.1720A>G p.Thr574Ala p.T574A ENST00000409093 574 Acc/Gcc 0 0.617 CTGGCGATGGTGGCGATGAAG +ZW10 9183 broad.mit.edu;hgsc.bcm.edu GRCh37 11 113614641 113614641 + frameshift_variant Frame_Shift_Del DEL T T - TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 153 64 ENST00000200135.3:c.1394delA p.Asn465IlefsTer19 p.N465Ifs*19 ENST00000200135 NM_004724.3 465 aAt/at 0 0.418 GTCCAATGTATTTTCAGGCTC +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76874329 76874330 + frameshift_variant Frame_Shift_Ins INS - - T TCGA-HT-7470-01 TCGA-HT-7470-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 82 ENST00000373344.5:c.5392dupA p.Arg1798LysfsTer12 p.R1798Kfs*12 ENST00000373344 NM_000489.3 1798 aga/aAga 0 0.322 TTTCATCACTCTGACATCTACC +INTS4 92105 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 77639508 77639508 + synonymous_variant Silent SNP A A T TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 47 ENST00000534064.1:c.1251T>A p.Val417= p.V417= ENST00000534064 NM_033547.3 417 gtT/gtA 0 0.443 TGAACATGTCAACTAGGAAAT +MAML2 84441 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 95712904 95712904 + missense_variant Missense_Mutation SNP C C G TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 114 ENST00000524717.1:c.2679G>C p.Gln893His p.Q893H ENST00000524717 NM_032427.1 893 caG/caC 0 0.408 TTGGGTTTCTCTGTTGGGTCA +ATN1 1822 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 7046127 7046127 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 216 17 ENST00000356654.4:c.1697C>T p.Pro566Leu p.P566L ENST00000356654 NM_001007026.1 566 cCt/cTt 0 0.637 CCCAATGGCCCTCCAGTCTCT +SPTBN5 51332 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 42172441 42172441 + synonymous_variant Silent SNP A A G TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 18 8 ENST00000320955.6:c.2728T>C p.Leu910= p.L910= ENST00000320955 NM_016642.3 910 Ttg/Ctg 0 0.632 TCCAGCCACAACTGGAGCTCC +ACAN 176 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 89398499 89398499 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 40 ENST00000439576.2:c.2683C>T p.Pro895Ser p.P895S ENST00000439576 NM_013227.3 895 Ccc/Tcc 0 0.572 AAGTGGACTGCCCTCTGGAGA +SLX4 84464 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 3640690 3640690 + synonymous_variant Silent SNP G G A TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 123 130 ENST00000294008.3:c.2949C>T p.Tyr983= p.Y983= ENST00000294008 NM_032444.2 983 taC/taT 0 0.572 AGAGCTGTTCGTAATCCCCGG +ABCC12 94160 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 48174762 48174762 + synonymous_variant Silent SNP G G A TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 79 ENST00000311303.3:c.493C>T p.Leu165= p.L165= ENST00000311303 NM_033226.2 165 Ctg/Ttg 0 0.537 GCTATGCACAGTCCAATGCCA +TP53 7157 hgsc.bcm.edu;broad.mit.edu GRCh37 17 7574035 7574035 + splice_acceptor_variant Splice_Site SNP T T G TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 15 ENST00000269305.4:c.994-2A>C p.X332_splice ENST00000269305 NM_001126112.2 0 0.507 CCCACGGATCTGCAGCAACAG +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577572 7577572 + missense_variant Missense_Mutation SNP T T C TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 45 ENST00000269305.4:c.709A>G p.Met237Val p.M237V ENST00000269305 NM_001126112.2 237 Atg/Gtg 0 0.572 CTGTTACACATGTAGTTGTAG +NF1 4763 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 29556166 29556166 + missense_variant Missense_Mutation SNP T T C TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 12 101 ENST00000358273.4:c.2533T>C p.Cys845Arg p.C845R ENST00000358273 NM_001042492.2 845 Tgt/Cgt 0 0.512 TGGCTTCCTTTGTGCCCTTGG +CCDC40 55036 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 78032380 78032380 + missense_variant Missense_Mutation SNP G G A TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 12 120 ENST00000397545.4:c.1247G>A p.Arg416His p.R416H ENST00000397545 NM_017950.3 416 cGc/cAc 0 0.537 GACGACATCCGCGTGATGACA +PLIN4 729359 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 4511095 4511095 + synonymous_variant Silent SNP G G A TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 83 34 ENST00000301286.3:c.2835C>T p.Gly945= p.G945= ENST00000301286 NM_001080400.1 945 ggC/ggT 0 0.592 CATCCTTAGCGCCACTCAGCA +NOTCH3 4854 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 15281250 15281250 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 45 ENST00000263388.2:c.5006G>A p.Arg1669His p.R1669H ENST00000263388 NM_000435.2 1669 cGc/cAc 0 0.677 GCTGTGCTCGCGCTTGCGCCG +SLC7A9 11136 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 33350866 33350866 + missense_variant Missense_Mutation SNP G G T TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 21 ENST00000023064.4:c.754C>A p.Leu252Met p.L252M ENST00000023064 NM_014270.4 252 Ctg/Atg 0 0.602 GCCAAAGGCAGGTTTCTGGGA +LPHN2 23266 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 82456736 82456736 + synonymous_variant Silent SNP T T C TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 48 ENST00000319517.6:c.4119T>C p.Asn1373= p.N1373= ENST00000319517 NM_012302.2 1373 aaT/aaC 0 0.428 gcaggggcaatagtgatggtt +RFWD2 64326 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 176132075 176132075 + missense_variant Missense_Mutation SNP T T C TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 99 85 ENST00000367669.3:c.692A>G p.Asp231Gly p.D231G ENST00000367669 NM_022457.5 231 gAt/gGt 0 0.358 ATCAAGGTTATCTTGGTCAGT +RBM11 54033 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 15599378 15599378 + missense_variant Missense_Mutation SNP G G A TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 373 100 ENST00000400577.3:c.610G>A p.Ala204Thr p.A204T ENST00000400577 NM_144770.3 204 Gct/Act 0 0.463 TCAGATGACAGCTCCACTTCC +APOB 338 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 21228172 21228172 + synonymous_variant Silent SNP G G A TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 110 ENST00000233242.1:c.11568C>T p.Ile3856= p.I3856= ENST00000233242 NM_000384.2 3856 atC/atT 0 0.473 GCTCAGGCACGATGATGGTGG +ACOXL 55289 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 111562956 111562956 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 121 76 ENST00000439055.1:c.737C>T p.Ala246Val p.A246V ENST00000439055 NM_001142807.1 246 gCt/gTt 0 0.453 GCTTTCCAAGCTATGGGTGCC +NDUFAF3 25915 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 49059582 49059582 + missense_variant Missense_Mutation SNP C C G TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 13 ENST00000326925.6:c.5C>G p.Ala2Gly p.A2G ENST00000326925 NM_199069.1 2 gCc/gGc 0 0.716 TCAGCCATGGCCACCGCTCTC +UBXN7 26043 hgsc.bcm.edu;broad.mit.edu GRCh37 3 196094958 196094958 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 243 20 ENST00000296328.4:c.775G>A p.Gly259Ser p.G259S ENST00000296328 NM_015562.1 259 Ggt/Agt 0 0.398 CCATGTTCACCCAGAAATCCC +HIST1H4G 8369 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 26247163 26247163 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 20 ENST00000244537.4:c.43G>A p.Gly15Ser p.G15S ENST00000244537 NM_003547.2 15 Ggt/Agt 0 0.517 CACTTGGCACCGCCTTTCCCA +HLA-DQA2 3118 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 32713607 32713607 + missense_variant Missense_Mutation SNP C C T rs144060347 TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 127 130 ENST00000374940.3:c.371C>T p.Thr124Met p.T124M ENST00000374940 NM_020056.4 124 aCg/aTg 0 0.507 TTTCCTGTGACGCTGGGTCAG +SLC25A40 55972 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 87466058 87466058 + synonymous_variant Silent SNP G G A TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 28 ENST00000341119.5:c.891C>T p.Ser297= p.S297= ENST00000341119 NM_018843.3 297 tcC/tcT 0 0.259 AAAATAATCCGGAAAATCCAT +CPA1 1357 hgsc.bcm.edu;broad.mit.edu GRCh37 7 130024455 130024455 + missense_variant Missense_Mutation SNP G G A TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 151 12 ENST00000011292.3:c.775G>A p.Ala259Thr p.A259T ENST00000011292 NM_001868.2 259 Gct/Act 0 0.602 GAACTGGGACGCTGGCTTTGG +ZCRB1 85437 broad.mit.edu;ucsc.edu GRCh37 12 42711595 42711595 + missense_variant Missense_Mutation SNP G G T TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 137 90 ENST00000266529.3:c.219C>A p.Asn73Lys p.N73K ENST00000266529 NM_033114.3 73 aaC/aaA 0 0.393 TTACCTGTTTGTTGTTTATTG +UGGT1 56886 broad.mit.edu;hgsc.bcm.edu GRCh37 2 128938471 128938471 + frameshift_variant Frame_Shift_Del DEL T T - TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 54 ENST00000259253.6:c.3908delT p.Ile1303AsnfsTer47 p.I1303Nfs*47 ENST00000259253 NM_020120.3 1303 aTa/aa 0 0.373 TAGGAGTTTATACCTTACATG +TP63 8626 broad.mit.edu;hgsc.bcm.edu GRCh37 3 189612149 189612149 + frameshift_variant Frame_Shift_Del DEL G G - TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 155 107 ENST00000264731.3:c.1904delG p.Gly635ValfsTer69 p.G635Vfs*69 ENST00000264731 NM_003722.4 634 cGg/cg 0 0.567 AGTGAGACCCGGGGTGAGCGT +TP53 7157 broad.mit.edu;hgsc.bcm.edu GRCh37 17 7574025 7574025 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-DH-5140-01 TCGA-DH-5140-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 19 ENST00000269305.4:c.1002delG p.Arg335ValfsTer10 p.R335Vfs*10 ENST00000269305 NM_001126112.2 334 ggG/gg 0 0.522 AGCGCTCACGCCCACGGATCT +CCKBR 887 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 6292257 6292257 + synonymous_variant Silent SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 117 14 ENST00000334619.2:c.828C>T p.Asn276= p.N276= ENST00000334619 NM_176875.3 276 aaC/aaT 0 0.662 TTCACCAGAACGGGCGTTGCC +MADD 8567 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 47304014 47304014 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 95 10 ENST00000311027.5:c.1552C>T p.Arg518Trp p.R518W ENST00000311027 NM_003682.3 518 Cgg/Tgg 0 0.562 CCTCTTTCCTCGGCCTGTGGT +OR5L1 219437 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 55579059 55579059 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 225 33 ENST00000333973.2:c.117G>T p.Leu39Phe p.L39F ENST00000333973 NM_001004738.1 39 ttG/ttT 0 0.507 GAGTCACGTTGTTAGCCAACC +DYNC2H1 79659 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 102995846 102995846 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 8 ENST00000398093.3:c.1679G>A p.Arg560Gln p.R560Q ENST00000398093 560 cGa/cAa 0 0.333 GCTAGTAGTCGAATTATGGAA +BRF1 2972 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 105688184 105688184 + synonymous_variant Silent SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 4 ENST00000546474.1:c.1116C>T p.Ala372= p.A372= ENST00000546474 NM_001519.3 372 gcC/gcT 0 0.637 GGCTGGCCGCGGCTTCCAGCT +NPAP1 23742 hgsc.bcm.edu;broad.mit.edu GRCh37 15 24921093 24921093 + missense_variant Missense_Mutation SNP C C A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 6 ENST00000329468.2:c.79C>A p.Pro27Thr p.P27T ENST00000329468 NM_018958.2 27 Ccc/Acc 0 0.701 CGCCCCCGCTCCCCTGTCCCG +ATP10A 57194 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 25959052 25959052 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 22 ENST00000356865.6:c.2113T>C p.Tyr705His p.Y705H ENST00000356865 NM_024490.3 705 Tat/Cat 0 0.662 CTGGCCGCATACACCAGTGCG +HS3ST6 64711 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 1962006 1962006 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 9 ENST00000443547.1:c.521G>A p.Arg174His p.R174H ENST00000443547 NM_001009606.2 174 cGc/cAc 0 0.716 GGCCAGGGCGCGGAAGCTGGG +LPO 4025 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 56343663 56343663 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 8 ENST00000262290.4:c.1669C>T p.Arg557Cys p.R557C ENST00000262290 NM_006151.2 557 Cgt/Tgt 0 0.502 CAACACACAGCGTTGCCGGGA +MAP1S 55201 hgsc.bcm.edu;broad.mit.edu GRCh37 19 17845112 17845112 + missense_variant Missense_Mutation SNP G G C rs71762031 TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 6 ENST00000324096.4:c.3055G>C p.Ala1019Pro p.A1019P ENST00000324096 NM_018174.4 1019 Gcc/Ccc 0 0.657 CGACTCGGTGGCCATGCATAC +ZNF536 9745 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 31040081 31040081 + synonymous_variant Silent SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 9 ENST00000355537.3:c.3555C>T p.Thr1185= p.T1185= ENST00000355537 NM_014717.1 1185 acC/acT 0 0.572 ATGTTGAAACCGAACCGGAAA +LILRB2 10288 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 54783825 54783825 + missense_variant Missense_Mutation SNP C C T rs141797988 TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 182 24 ENST00000391749.4:c.176G>A p.Arg59His p.R59H ENST00000391749 NM_001278406.1 59 cGt/cAt 0 0.547 CCTATATAGACGGTACTCCTG +LILRA3 11026 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 54803127 54803127 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 182 23 ENST00000251390.3:c.550G>A p.Val184Met p.V184M ENST00000251390 NM_006865.3 184 Gtg/Atg 0 0.567 ACGGGGCCCACGGAGAAGATG +TAS1R2 80834 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 19181133 19181133 + synonymous_variant Silent SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 6 ENST00000375371.3:c.831C>T p.Pro277= p.P277= ENST00000375371 NM_152232.2 277 ccC/ccT 0 0.632 GGGTCAGGTCGGGCGAGAACA +GLIS1 148979 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 53995560 53995560 + synonymous_variant Silent SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 11 ENST00000312233.2:c.861G>A p.Thr287= p.T287= ENST00000312233 NM_147193.2 287 acG/acA 0 0.637 GCTTCTCGCCCGTGTGGCTCC +SRSF11 9295 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 70715634 70715634 + splice_acceptor_variant Splice_Site SNP G G C TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 5 ENST00000370950.3:c.1023-1G>C p.X341_splice ENST00000370950 0 0.418 TGTGATTCTAGAGAGAGACGA +FMO3 2328 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 171079965 171079965 + synonymous_variant Silent SNP C C G TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 107 11 ENST00000367755.4:c.654C>G p.Ser218= p.S218= ENST00000367755 NM_001002294.2 218 tcC/tcG 0 0.473 GAAGTGGCTCCTGGGTGATGA +CFH 3075 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 196716352 196716352 + missense_variant Missense_Mutation SNP A A T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 89 17 ENST00000367429.4:c.3605A>T p.Lys1202Ile p.K1202I ENST00000367429 NM_000186.3 1202 aAa/aTa 0 0.383 TTTGTGTGTAAACGGGGATAT +KDM5B 10765 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 202702739 202702739 + synonymous_variant Silent SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 16 ENST00000367265.3:c.3699G>A p.Leu1233= p.L1233= ENST00000367265 NM_006618.3 1233 ctG/ctA 0 0.532 CGAGCAGGGGCAGAATTTTCT +OBSCN 84033 hgsc.bcm.edu;ucsc.edu GRCh37 1 228487678 228487678 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 10 ENST00000570156.2:c.13570G>A p.Val4524Met p.V4524M ENST00000570156 NM_001271223.2 4524 Gtg/Atg 0 0.557 GGCGGCCCCCGTGGAGTGGAG +OR13G1 441933 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 247835492 247835492 + synonymous_variant Silent SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 93 17 ENST00000359688.2:c.852G>A p.Pro284= p.P284= ENST00000359688 NM_001005487.1 284 ccG/ccA 0 0.438 TGTACACCATCGGGTTTAATG +XKR7 343702 hgsc.bcm.edu;broad.mit.edu GRCh37 20 30584347 30584347 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 7 ENST00000562532.2:c.827C>T p.Thr276Met p.T276M ENST00000562532 NM_001011718.1 276 aCg/aTg 0 0.701 CTGGCCTGGACGCTGGCCTCC +DPP10 57628 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 116497433 116497433 + synonymous_variant Silent SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 134 22 ENST00000393147.2:c.828G>A p.Ala276= p.A276= ENST00000393147 NM_001178034.1 276 gcG/gcA 0 0.458 TTACTGGAGCGTTGTATCCCA +CWC22 57703 hgsc.bcm.edu;broad.mit.edu GRCh37 2 180810177 180810177 + synonymous_variant Silent SNP A A G TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 126 9 ENST00000410053.3:c.2406T>C p.Asn802= p.N802= ENST00000410053 NM_020943.2 802 aaT/aaC 0 0.353 GGTCTCTGTCATTCGCAACTC +CEP97 79598 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 101476897 101476897 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 81 17 ENST00000341893.3:c.1447C>T p.Pro483Ser p.P483S ENST00000341893 483 Cct/Tct 0 0.378 TGGACTATTACCTTGTCCTGA +PIK3CA 5290 hgsc.bcm.edu;broad.mit.edu GRCh37 3 178922364 178922364 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 4 ENST00000263967.3:c.1133G>A p.Cys378Tyr p.C378Y ENST00000263967 NM_006218.2 378 tGt/tAt 0 0.328 AGAGTACCTTGTTCCAATCCC +B3GNT5 84002 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 182988131 182988131 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 82 19 ENST00000326505.3:c.545A>G p.Tyr182Cys p.Y182C ENST00000326505 NM_032047.4 182 tAt/tGt 0 0.333 GCAAATACCTATTGTCCACAT +PDGFRA 5156 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 55131161 55131161 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 136 551 ENST00000257290.5:c.704G>A p.Cys235Tyr p.C235Y ENST00000257290 NM_006206.4 235 tGt/tAt 0 0.443 GTGGTCACCTGTGCTGTTTTT +TET2 54790 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 106157894 106157894 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 12 ENST00000380013.4:c.2795A>G p.Asp932Gly p.D932G ENST00000380013 NM_001127208.2 932 gAc/gGc 0 0.453 CCTGTGCCTGACCAGGGAGGA +SLC6A3 6531 hgsc.bcm.edu;broad.mit.edu GRCh37 5 1406358 1406358 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 10 ENST00000270349.9:c.1544G>A p.Arg515Gln p.R515Q ENST00000270349 NM_001044.4 515 cGg/cAg 0 0.652 CAGGCTGGGCCGCTGCCCGGT +SLC6A3 6531 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 1406386 1406386 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 132 14 ENST00000270349.9:c.1516G>A p.Asp506Asn p.D506N ENST00000270349 NM_001044.4 506 Gac/Aac 0 0.642 TGGATGTCGTCGCTGAACTGC +SLCO4C1 353189 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 101582955 101582955 + splice_donor_variant Splice_Site SNP C C A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 9 ENST00000310954.6:c.1811+1G>T p.X604_splice ENST00000310954 NM_180991.4 0 0.378 GTGCTACATACCTTAGGATAG +PRSS35 167681 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 84233953 84233953 + stop_gained Nonsense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 8 ENST00000536636.1:c.793C>T p.Arg265Ter p.R265* ENST00000536636 NM_001170423.1 265 Cga/Tga 0 0.527 GGGCTGGGCACGAGGAGGCAT +SAMD3 154075 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 130497110 130497110 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 10 ENST00000368134.2:c.698G>A p.Arg233Gln p.R233Q ENST00000368134 NM_001258275.1 233 cGa/cAa 0 0.343 TATGGGTCTTCGAACATATTT +PDE7B 27115 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 136494954 136494954 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 12 ENST00000308191.6:c.731A>G p.Asn244Ser p.N244S ENST00000308191 NM_018945.3 244 aAt/aGt 0 0.428 GTGCTGGAGAATCATCACTGG +PPP1R3A 5506 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 113517983 113517983 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 162 18 ENST00000284601.3:c.3164C>T p.Pro1055Leu p.P1055L ENST00000284601 NM_002711.3 1055 cCt/cTt 0 0.363 TTCCTCAACAGGAAGACTAGT +ASZ1 136991 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 117067417 117067417 + missense_variant Missense_Mutation SNP G G A rs113501399 TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 164 25 ENST00000284629.2:c.98C>T p.Thr33Met p.T33M ENST00000284629 NM_130768.2 33 aCg/aTg 0 0.657 TACCTGAGACGTCCGGTCGAG +KDM7A 80853 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 139810958 139810958 + missense_variant Missense_Mutation SNP A A C TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 7 ENST00000397560.2:c.1365T>G p.Ile455Met p.I455M ENST00000397560 NM_030647.1 455 atT/atG 0 0.294 CATTGTCTGGAATTTCAAAGG +TAS2R40 259286 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 142919425 142919425 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 119 12 ENST00000408947.3:c.254G>A p.Arg85Gln p.R85Q ENST00000408947 NM_176882.1 85 cGa/cAa 0 0.433 CTGCTATTCCGAATTGTTTAT +EFCAB1 79645 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 49643961 49643961 + stop_gained Nonsense_Mutation SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 6 ENST00000262103.3:c.160C>T p.Arg54Ter p.R54* ENST00000262103 NM_024593.3 54 Cga/Tga 0 0.393 AGGATGTTTCGAAATGCATTA +ASS1 445 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 133333962 133333962 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 5 ENST00000372394.1:c.349G>A p.Gly117Ser p.G117S ENST00000372394 117 Ggc/Agc 0 0.657 TGTGTCCCACGGCGCCACAGG +AKAP4 8852 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 49958224 49958224 + synonymous_variant Silent SNP G G A rs140947270 TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 7 ENST00000358526.2:c.1140C>T p.Ser380= p.S380= ENST00000358526 NM_003886.2 380 tcC/tcT 0 0.463 CAATCAAATCGGACACAATCT +C6orf10 10665 broad.mit.edu;ucsc.edu GRCh37 6 32261388 32261388 + synonymous_variant Silent SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 126 21 ENST00000447241.2:c.1062G>A p.Thr354= p.T354= ENST00000447241 NM_006781.3 354 acG/acA 0 0.468 ACCCACTCTTCGTTACTTGGG +TEAD3 7005 broad.mit.edu;ucsc.edu GRCh37 6 35445110 35445110 + synonymous_variant Silent SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 3 ENST00000338863.7:c.570G>A p.Pro190= p.P190= ENST00000338863 NM_003214.3 190 ccG/ccA 0 0.627 GCGGCAGGGGCGGCTGGATGG +HCK 3055 broad.mit.edu;ucsc.edu GRCh37 20 30667667 30667667 + synonymous_variant Silent SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 4 ENST00000375852.2:c.519C>T p.Ser173= p.S173= ENST00000375852 173 agC/agT 0 0.612 TCCGGGATAGCGAGACCACTA +IGHV3-53 28420 broad.mit.edu;ucsc.edu GRCh37 14 107048694 107048694 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 241 33 ENST00000390627.2:c.326C>T p.Thr109Met p.T109M ENST00000390627 109 aCg/aTg 0 0.552 ATACACGGCCGTGTCCTCGGC +SURF2 6835 broad.mit.edu;ucsc.edu GRCh37 9 136227174 136227174 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 4 ENST00000371964.4:c.551C>T p.Thr184Met p.T184M ENST00000371964 NM_001278928.1 184 aCg/aTg 0 0.527 CTTGGAAGCACGGAGGATGGG +CDC20B 166979 broad.mit.edu;ucsc.edu GRCh37 5 54424345 54424345 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 8 ENST00000381375.2:c.798C>A p.Asn266Lys p.N266K ENST00000381375 266 aaC/aaA 0 0.448 TTAAGTCTATGTTTTCAATCC +MKI67 4288 broad.mit.edu;ucsc.edu GRCh37 10 129902797 129902797 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 25 ENST00000368654.3:c.7307A>G p.Asp2436Gly p.D2436G ENST00000368654 NM_002417.4 2436 gAc/gGc 0 0.473 GCCAACCAGGTCCTCTAGAGC +PCDH11X 27328 broad.mit.edu;ucsc.edu GRCh37 X 91133911 91133911 + missense_variant Missense_Mutation SNP C C A TCGA-HT-7882-01 TCGA-HT-7882-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 15 ENST00000373094.1:c.2672C>A p.Thr891Asn p.T891N ENST00000373094 NM_032968.3 891 aCt/aAt 0 0.373 ATTGAAGAAACTAAGGCAGAT +TTC17 55761 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 43423074 43423074 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 11 ENST00000039989.4:c.1298G>A p.Arg433His p.R433H ENST00000039989 NM_018259.5 433 cGt/cAt 0 0.373 CGCTATCATCGTGGAGATATC +FANCM 57697 hgsc.bcm.edu;ucsc.edu GRCh37 14 45645153 45645153 + missense_variant Missense_Mutation SNP C C G TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 4 ENST00000267430.5:c.3196C>G p.Leu1066Val p.L1066V ENST00000267430 NM_020937.2 1066 Ctt/Gtt 0 0.303 AAAAAGTTGCCTTTATGATAT +CRAMP1L 57585 hgsc.bcm.edu;broad.mit.edu GRCh37 16 1718033 1718033 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 22 ENST00000397412.3:c.3173C>T p.Ser1058Phe p.S1058F ENST00000397412 1058 tCc/tTc 0 0.602 ATACCGCTGTCCTCGTCAGAG +XYLT1 64131 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 17202869 17202869 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 50 ENST00000261381.6:c.2563G>A p.Ala855Thr p.A855T ENST00000261381 NM_022166.3 855 Gca/Aca 0 0.562 AGCTTCAGTGCCTCCTCTGAA +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577586 7577586 + missense_variant Missense_Mutation SNP A A C TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 10 41 ENST00000269305.4:c.695T>G p.Ile232Ser p.I232S ENST00000269305 NM_001126112.2 232 aTc/aGc 0 0.552 GTTGTAGTGGATGGTGGTACA +PLVAP 83483 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 17476154 17476154 + missense_variant Missense_Mutation SNP G G C TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 44 ENST00000252590.4:c.1120C>G p.Gln374Glu p.Q374E ENST00000252590 NM_031310.1 374 Cag/Gag 0 0.622 ATCCTGAGCTGCTCCGCCTCC +CYP2B6 1555 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 41515236 41515236 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 147 72 ENST00000324071.4:c.758G>A p.Arg253His p.R253H ENST00000324071 NM_000767.4 253 cGt/cAt 0 0.527 GAGAAGCACCGTGAAACCCTG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 19 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +EFHC2 80258 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 44120532 44120532 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 23 ENST00000420999.1:c.395G>A p.Arg132Gln p.R132Q ENST00000420999 NM_025184.3 132 cGg/cAg 0 0.413 CCGATGACGCCGGATAGAAGT +ALAS2 212 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 55052378 55052378 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 15 ENST00000330807.5:c.56C>T p.Thr19Ile p.T19I ENST00000330807 NM_000032.4 19 aCa/aTa 0 0.542 TAGGAGGCTTGTGGGGCCCCG +UBQLN2 29978 hgsc.bcm.edu;ucsc.edu GRCh37 X 56590705 56590705 + synonymous_variant Silent SNP C C T TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 8 ENST00000338222.5:c.399C>T p.Ser133= p.S133= ENST00000338222 NM_013444.3 133 tcC/tcT 0 0.572 GGAGTAACTCCACACCTATTT +ATRX 546 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 76939961 76939961 + missense_variant Missense_Mutation SNP A A G TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 109 117 ENST00000373344.5:c.787T>C p.Trp263Arg p.W263R ENST00000373344 NM_000489.3 263 Tgg/Cgg 0 0.393 TAGCAATACCATTGGTTGTTT +DCAF12L2 340578 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 125299672 125299672 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 28 ENST00000538699.1:c.236C>T p.Ala79Val p.A79V ENST00000538699 NM_001013628.2 79 gCc/gTc 0 0.706 CCTCTGGACGGCGTAGCCCCG +PLXNB3 5365 broad.mit.edu;ucsc.edu GRCh37 X 153039467 153039467 + missense_variant Missense_Mutation SNP C C A TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 28 ENST00000538966.1:c.3502C>A p.Gln1168Lys p.Q1168K ENST00000538966 NM_001163257.1 1168 Cag/Aag 0 0.672 CTTCCTGTACCAGCCCAACCC +OR1D2 4991 broad.mit.edu;ucsc.edu GRCh37 17 2995927 2995927 + missense_variant Missense_Mutation SNP G G A rs73300984 byFrequency TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 21 ENST00000331459.1:c.364C>T p.Arg122Cys p.R122C ENST00000331459 NM_002548.2 122 Cgc/Tgc 0 0.537 GCCACATAGCGGTCATATGCC +IPO8 10526 broad.mit.edu;ucsc.edu GRCh37 12 30827606 30827606 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 128 76 ENST00000256079.4:c.811C>T p.Arg271Trp p.R271W ENST00000256079 NM_006390.3 271 Cgg/Tgg 0 0.418 TCAAAGAGCCGAGCTACAATA +GRIP2 80852 broad.mit.edu;ucsc.edu GRCh37 3 14535207 14535207 + non_coding_transcript_exon_variant RNA SNP C C T TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 10 ENST00000273083.3:n.3163G>A *1055* ENST00000273083 0 0.672 GCCTGGCGATCGGGGGGCCCG +RLIM 51132 broad.mit.edu;hgsc.bcm.edu GRCh37 X 73812199 73812200 + frameshift_variant Frame_Shift_Ins INS - - G rs61752449 TCGA-HW-A5KL-01 TCGA-HW-A5KL-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 30 ENST00000332687.6:c.950dupC p.Thr318AsnfsTer5 p.T318Nfs*5 ENST00000332687 NM_016120.3 317 cca/ccCa 0 0.48 GGACTATGGTTGGAGGTCTCTG +GATA3 2625 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 8100386 8100386 + synonymous_variant Silent SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 166 101 ENST00000346208.3:c.360G>A p.Thr120= p.T120= ENST00000346208 120 acG/acA 0 0.697 TCTCCAAGACGTCCATCCACC +FRMD4A 55691 hgsc.bcm.edu;broad.mit.edu GRCh37 10 13698931 13698931 + synonymous_variant Silent SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 8 4 ENST00000357447.2:c.2658C>T p.Gly886= p.G886= ENST00000357447 NM_018027.3 886 ggC/ggT 0 0.716 CGTCGCCGCCGCCGCCGCGCC +OR4X2 119764 hgsc.bcm.edu;broad.mit.edu GRCh37 11 48267032 48267032 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 99 6 ENST00000302329.3:c.377C>G p.Thr126Ser p.T126S ENST00000302329 NM_001004727.1 126 aCc/aGc 0 0.498 AGCTACACCACCATCATGAAC +CPSF7 79869 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 61178544 61178544 + synonymous_variant Silent SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 58 ENST00000340437.4:c.1416C>T p.Ser472= p.S472= ENST00000340437 NM_024811.3 472 agC/agT 0 0.502 CCCGGGACCGGCTAGGTGACC +TYR 7299 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 88961080 88961080 + missense_variant Missense_Mutation SNP C C G rs61754389 TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 23 ENST00000263321.5:c.1126C>G p.Gln376Glu p.Q376E ENST00000263321 NM_000372.4 376 Cag/Gag 0 0.413 AACAATGTCCCAGGTACAGGG +C11orf65 160140 hgsc.bcm.edu;broad.mit.edu GRCh37 11 108256655 108256655 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 236 14 ENST00000393084.1:c.779A>G p.Asn260Ser p.N260S ENST00000393084 NM_152587.3 260 aAc/aGc 0 0.333 ACCTTTGAAGTTAGCCGAAGA +NNMT 4837 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 114182852 114182852 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 90 96 ENST00000535401.1:c.448G>A p.Gly150Arg p.G150R ENST00000535401 150 Ggg/Agg 0 0.602 CCAGCCACTGGGGGCCGTCCC +ITPR2 3709 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 26985668 26985668 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 165 33 ENST00000381340.3:c.47C>T p.Ser16Phe p.S16F ENST00000381340 NM_002223.2 16 tCc/tTc 0 0.622 CGCGTACAGGGACACGATGTC +IGDCC4 57722 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 65684524 65684524 + synonymous_variant Silent SNP C C T TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 95 59 ENST00000352385.2:c.2070G>A p.Val690= p.V690= ENST00000352385 NM_020962.1 690 gtG/gtA 0 0.622 GGACAGGCCCCACATCCCAAG +MGRN1 23295 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 4732911 4732911 + synonymous_variant Silent SNP C C T TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 14 ENST00000262370.7:c.1446C>T p.Gly482= p.G482= ENST00000262370 NM_015246.3 482 ggC/ggT 0 0.701 CACTGGGTGGCGCAGAGCTGG +IRF8 3394 hgsc.bcm.edu;broad.mit.edu GRCh37 16 85952180 85952180 + synonymous_variant Silent SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 6 16 ENST00000268638.5:c.759G>A p.Pro253= p.P253= ENST00000268638 NM_002163.2 253 ccG/ccA 0 0.741 TGCGCTTCCCGCCGGCCGACG +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577570 7577570 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 51 ENST00000269305.4:c.711G>A p.Met237Ile p.M237I ENST00000269305 NM_001126112.2 237 atG/atA 0 0.567 AACTGTTACACATGTAGTTGT +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578263 7578263 + stop_gained Nonsense_Mutation SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 24 ENST00000269305.4:c.586C>T p.Arg196Ter p.R196* ENST00000269305 NM_001126112.2 196 Cga/Tga 0 0.552 CCTTCCACTCGGATAAGATGC +CLUL1 27098 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 618009 618009 + synonymous_variant Silent SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 8 ENST00000400606.2:c.9G>A p.Pro3= p.P3= ENST00000400606 NM_014410.4 3 ccG/ccA 0 0.448 ACATGAAGCCGCCACTCTTGG +LIPG 9388 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 47107968 47107968 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 69 ENST00000261292.4:c.977T>C p.Met326Thr p.M326T ENST00000261292 NM_006033.2 326 aTg/aCg 0 0.493 GCCAAGAAAATGAGGAACAAG +NFATC1 4772 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 77227575 77227575 + synonymous_variant Silent SNP C C T TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 28 ENST00000329101.4:c.2046C>T p.Pro682= p.P682= ENST00000329101 NM_172387.2 682 ccC/ccT 0 0.532 CCTACCTTCCCGCCAACGGTA +MUC16 94025 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 9062722 9062722 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 33 ENST00000397910.4:c.24724A>G p.Thr8242Ala p.T8242A ENST00000397910 NM_024690.2 8242 Acc/Gcc 0 0.498 ACAAGAGTGGTCATCTCTGAG +HKR1 284459 hgsc.bcm.edu;broad.mit.edu GRCh37 19 37838730 37838730 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 4 ENST00000324411.4:c.269C>T p.Ala90Val p.A90V ENST00000324411 NM_181786.2 90 gCg/gTg 0 0.493 CGAGGGGAAGCGCCCTGGAGA +RYR1 6261 hgsc.bcm.edu;broad.mit.edu GRCh37 19 38995497 38995497 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 4 ENST00000359596.3:c.8177A>G p.Lys2726Arg p.K2726R ENST00000359596 2726 aAg/aGg 0 0.597 GCAGAGAAAAAGGCCACAGTG +ZC3H4 23211 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 47593321 47593321 + synonymous_variant Silent SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 45 ENST00000253048.5:c.618C>T p.Gly206= p.G206= ENST00000253048 NM_015168.1 206 ggC/ggT 0 0.577 CCTCCTCGTCGCCCTCATATT +FASLG 356 hgsc.bcm.edu;broad.mit.edu GRCh37 1 172634805 172634805 + synonymous_variant Silent SNP C C A rs80358236 TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 81 5 ENST00000367721.2:c.495C>A p.Thr165= p.T165= ENST00000367721 NM_000639.1 165 acC/acA 0 0.428 GGGAAGACACCTATGGAATTG +C20orf194 25943 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 3356865 3356865 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 50 ENST00000252032.9:c.368A>G p.His123Arg p.H123R ENST00000252032 NM_001009984.2 123 cAt/cGt 0 0.368 ATTTCTCCAATGTGCCACATA +PCK1 5105 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 56139236 56139236 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 12 ENST00000319441.4:c.973G>A p.Ala325Thr p.A325T ENST00000319441 NM_002591.3 325 Gcc/Acc 0 0.448 TCATTTAAGGGCCATCAACCC +APOB 338 hgsc.bcm.edu;broad.mit.edu GRCh37 2 21230555 21230555 + stop_gained Nonsense_Mutation SNP A A C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 6 ENST00000233242.1:c.9185T>G p.Leu3062Ter p.L3062* ENST00000233242 NM_000384.2 3062 tTa/tGa 0 0.408 TGTTAACCTTAATGGAAAACG +TEKT4 150483 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 95542422 95542422 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 23 ENST00000295201.4:c.1216G>A p.Ala406Thr p.A406T ENST00000295201 NM_144705.2 406 Gcc/Acc 0 0.592 GGACATTGCCGCCATGACCAA +ZEB2 9839 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 145147369 145147369 + synonymous_variant Silent SNP T T C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 27 ENST00000558170.2:c.3294A>G p.Lys1098= p.K1098= ENST00000558170 NM_014795.3 1098 aaA/aaG 0 0.617 CCAAGTGCCCTTTCTCGCGCG +LRP2 4036 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 170030513 170030513 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 37 ENST00000263816.3:c.10930A>G p.Asn3644Asp p.N3644D ENST00000263816 NM_004525.2 3644 Aat/Gat 0 0.542 CAGCGGCCATTAGCACACCGA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113113 209113113 + missense_variant Missense_Mutation SNP G G T rs121913499 TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 67 ENST00000345146.2:c.394C>A p.Arg132Ser p.R132S ENST00000345146 NM_005896.2 132 Cgt/Agt 0 0.398 TAAGCATGACGACCTATGATG +ZFAND2B 130617 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 220072487 220072487 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 12 ENST00000289528.5:c.268C>G p.Gln90Glu p.Q90E ENST00000289528 NM_001270999.1 90 Cag/Gag 0 0.557 TGATCCAGCACAGCAAAAACG +OR5H1 26341 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 97852349 97852349 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 41 ENST00000354565.2:c.808C>G p.Gln270Glu p.Q270E ENST00000354565 NM_001005338.1 270 Caa/Gaa 0 0.428 AGCAGATGATCAAGATATGGT +ACAD9 28976 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 128628194 128628194 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 113 57 ENST00000308982.7:c.1493C>G p.Ala498Gly p.A498G ENST00000308982 NM_014049.4 498 gCc/gGc 0 0.587 TAGGACAGTGCCAACAAGTTT +AADACL2 344752 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 151461908 151461908 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 55 ENST00000356517.3:c.389G>C p.Arg130Thr p.R130T ENST00000356517 NM_207365.3 130 aGa/aCa 0 0.358 TTCCTGAATAGATGGACGGCA +GPBP1 65056 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 56546841 56546841 + stop_gained Nonsense_Mutation SNP C C T TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 18 ENST00000264779.6:c.1054C>T p.Arg352Ter p.R352* ENST00000264779 NM_001127236.2 352 Cga/Tga 0 0.353 GGATATAAACCGAAACTTCGA +KIF6 221458 hgsc.bcm.edu;broad.mit.edu GRCh37 6 39513460 39513460 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 4 ENST00000287152.7:c.1186G>C p.Glu396Gln p.E396Q ENST00000287152 NM_145027.4 396 Gaa/Caa 0 0.338 ATTAGTTTTTCCAGCCTAAAA +C6orf118 168090 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 165715396 165715396 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 135 21 ENST00000230301.8:c.415T>C p.Ser139Pro p.S139P ENST00000230301 NM_144980.3 139 Tcc/Ccc 0 0.627 GAAGTGTGGGAAAGAGAGGCC +SDK1 221935 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 4185446 4185446 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 97 ENST00000404826.2:c.4321G>A p.Asp1441Asn p.D1441N ENST00000404826 NM_152744.3 1441 Gac/Aac 0 0.667 CACAGCCACCGACCTGGCCCC +PKD1L1 168507 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 47897211 47897211 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 14 ENST00000289672.2:c.4582C>T p.Pro1528Ser p.P1528S ENST00000289672 NM_138295.3 1528 Cct/Tct 0 0.493 ACCTGCCCAGGAGCTTGGCTC +PCLO 27445 hgsc.bcm.edu;broad.mit.edu GRCh37 7 82580131 82580131 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 153 11 ENST00000333891.9:c.9773A>G p.Glu3258Gly p.E3258G ENST00000333891 NM_033026.5 3258 gAg/gGg 0 0.453 CTGCAGCTCCTCCAACTTTTT +ABCB1 5243 hgsc.bcm.edu;broad.mit.edu GRCh37 7 87214993 87214993 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 19 ENST00000265724.3:c.121C>T p.Arg41Cys p.R41C ENST00000265724 NM_000927.4 41 Cgc/Tgc 0 0.378 TTTGAATAGCGAAACTAAAAA +DOCK4 9732 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 111617325 111617325 + missense_variant Missense_Mutation SNP T T A TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 8 11 ENST00000437633.1:c.563A>T p.His188Leu p.H188L ENST00000437633 NM_014705.3 188 cAt/cTt 0 0.502 TTTCTTCCGATGTCGATGTTC +SLC20A2 6575 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 42297083 42297083 + synonymous_variant Silent SNP C C T TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 170 122 ENST00000342228.3:c.819G>A p.Glu273= p.E273= ENST00000342228 NM_006749.4 273 gaG/gaA 0 0.517 CACCTGGTAGCTCTTTAAATA +XIAP 331 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 123034427 123034427 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 5 32 ENST00000355640.3:c.1184A>G p.Glu395Gly p.E395G ENST00000355640 395 gAa/gGa 0 0.368 ATAATGGAGGAAAAAATTCAG +VPS13D 55187 broad.mit.edu;ucsc.edu GRCh37 1 12439544 12439544 + missense_variant,splice_region_variant Missense_Mutation SNP A A G TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 60 40 ENST00000358136.3:c.11084A>G p.Tyr3695Cys p.Y3695C ENST00000358136 NM_015378.2 3695 tAc/tGc 0 0.498 TTTTCCAGATACGAGCCACTG +PBX2 5089 broad.mit.edu;ucsc.edu GRCh37 6 32157564 32157564 + synonymous_variant Silent SNP C C A rs151067717 TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 32 ENST00000375050.4:c.129G>T p.Gly43= p.G43= ENST00000375050 NM_002586.4 43 ggG/ggT 0 0.711 CTCCCGGGACCCCCCCGCTAC +C12orf55 144535 broad.mit.edu;ucsc.edu GRCh37 12 97151344 97151344 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 5 ENST00000524981.4:c.8018C>T p.Ser2673Leu p.S2673L ENST00000524981 2673 tCa/tTa 0 0.303 ATAAAAATTTCAGGATCACCA +FAM212B 55924 broad.mit.edu;ucsc.edu GRCh37 1 112270041 112270041 + missense_variant Missense_Mutation SNP C C T rs142952172 TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 35 ENST00000357260.5:c.443G>A p.Arg148Gln p.R148Q ENST00000357260 NM_019099.4 148 cGg/cAg 0 0.587 ATTCCGGCCCCGGGACATCAA +UHRF1BP1 54887 broad.mit.edu;ucsc.edu GRCh37 6 34827130 34827130 + synonymous_variant Silent SNP G G A rs73419681 by1000genomes TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 31 ENST00000192788.5:c.2997G>A p.Glu999= p.E999= ENST00000192788 NM_017754.3 999 gaG/gaA 0 0.552 CTGGCAGGGAGACTGCTGTGA +H2AFX 3014 broad.mit.edu;hgsc.bcm.edu GRCh37 11 118965808 118965809 + frameshift_variant Frame_Shift_Ins INS - - C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 191 73 ENST00000530167.1:c.296dupG p.Gly100ArgfsTer131 p.G100Rfs*131 ENST00000530167 NM_002105.2 99 ggc/ggGc 0 0.693 TCGTCACGCCGCCCAGCAGCTT +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76937745 76937745 + frameshift_variant Frame_Shift_Del DEL T T - TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 8 52 ENST00000373344.5:c.3003delA p.Val1002Ter p.V1002* ENST00000373344 NM_000489.3 1001 aaA/aa 0 0.338 TTTTAATTACTTTTTTCTTAA +PIK3R1 5295 hgsc.bcm.edu GRCh37 5 67593256 67593256 + missense_variant Missense_Mutation SNP A A C TCGA-HT-7604-01 TCGA-HT-7604-10 Untested Somatic Phase_I WXS none Illumina GAIIx 93 18 ENST00000274335.5:c.2002A>C p.Lys668Gln p.K668Q ENST00000274335 668 Aag/Cag 0 0.423 CGGCGAAGTAAAGCATTGTGT +IDI1 3422 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 1089327 1089327 + missense_variant Missense_Mutation SNP A A G TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 22 ENST00000381344.3:c.320T>C p.Leu107Ser p.L107S ENST00000381344 NM_004508.2 107 tTg/tCg 0 0.348 AGCTCGATGCAATAATCCTGA +OR4K15 81127 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 20444378 20444378 + missense_variant Missense_Mutation SNP C C T TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 100 42 ENST00000305051.5:c.701C>T p.Ser234Phe p.S234F ENST00000305051 NM_001005486.1 234 tCc/tTc 0 0.453 TCTCTGAGTTCCTTTCTCCTC +CHD8 57680 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 21868155 21868155 + missense_variant Missense_Mutation SNP C C T TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 209 80 ENST00000399982.2:c.4802G>A p.Gly1601Glu p.G1601E ENST00000399982 NM_001170629.1 1601 gGg/gAg 0 0.423 AATCGCACCCCCTAACACCTT +AHNAK2 113146 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 105420366 105420366 + synonymous_variant Silent SNP G G A TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 8 ENST00000333244.5:c.1422C>T p.Gly474= p.G474= ENST00000333244 NM_138420.2 474 ggC/ggT 0 0.522 CAATCTGTGTGCCTCCTTCGG +SPTBN5 51332 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 42164528 42164528 + missense_variant Missense_Mutation SNP G G A TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 8 ENST00000320955.6:c.5137C>T p.Arg1713Trp p.R1713W ENST00000320955 NM_016642.3 1713 Cgg/Tgg 0 0.637 TGCAGTGCCCGCAGCTGCTCC +LAMA3 3909 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 21330907 21330907 + missense_variant Missense_Mutation SNP G G A TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 100 55 ENST00000313654.9:c.710G>A p.Arg237His p.R237H ENST00000313654 NM_198129.1 237 cGt/cAt 0 0.393 ATAAACGGTCGTCCAGGTGCA +MISP 126353 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 757295 757295 + missense_variant Missense_Mutation SNP G G C TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 12 ENST00000215582.6:c.349G>C p.Glu117Gln p.E117Q ENST00000215582 NM_173481.2 117 Gag/Cag 0 0.667 AGAGGACGGGGAGGACAAGGA +CIC 23152 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 42791758 42791758 + missense_variant Missense_Mutation SNP G G A TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 21 ENST00000575354.2:c.644G>A p.Arg215Gln p.R215Q ENST00000575354 NM_015125.3 215 cGg/cAg 0 0.612 AAGCGGCACCGGGCCCTGGTC +NLRP9 338321 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 56249567 56249567 + synonymous_variant Silent SNP C C A TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 180 196 ENST00000332836.2:c.174G>T p.Leu58= p.L58= ENST00000332836 NM_176820.2 58 ctG/ctT 0 0.458 GTTTGTCCAGCAGCTTTGCTA +UMODL1 89766 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 43519136 43519136 + synonymous_variant Silent SNP C C T TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 33 ENST00000408989.2:c.1032C>T p.Val344= p.V344= ENST00000408989 NM_173568.3 344 gtC/gtT 0 0.542 CTTTCCATGTCCGGGTTTACC +TTN 7273 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 179433152 179433152 + missense_variant Missense_Mutation SNP C C T TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 8 ENST00000589042.1:c.77707G>A p.Val25903Ile p.V25903I ENST00000589042 NM_001267550.1 25903 Gtc/Atc 0 0.403 TCAGCACTGACGTCATCAAAT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 19 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +ITPR1 3708 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 4725122 4725122 + missense_variant Missense_Mutation SNP C C T TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 149 63 ENST00000302640.8:c.3169C>T p.Arg1057Cys p.R1057C ENST00000302640 NM_001168272.1 1057 Cgt/Tgt 0 0.582 AACCTTTCTCCGTGTCCTGCT +MYLK 4638 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 123419711 123419711 + synonymous_variant Silent SNP G G A TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 81 34 ENST00000360304.3:c.2604C>T p.Asp868= p.D868= ENST00000360304 NM_053025.3 868 gaC/gaT 0 0.652 CCCCTCGCACGTCCTCGCCGT +MARCH1 55016 hgsc.bcm.edu;broad.mit.edu GRCh37 4 164450155 164450155 + synonymous_variant Silent SNP G G C TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 3 ENST00000503008.1:c.615C>G p.Ala205= p.A205= ENST00000503008 NM_001166373.1 205 gcC/gcG 0 0.438 TGAAGCCAATGGCTACCACAA +TIFAB 497189 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 134785348 134785348 + synonymous_variant Silent SNP C C T TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 51 ENST00000537858.1:c.282G>A p.Leu94= p.L94= ENST00000537858 NM_001099221.1 94 ctG/ctA 0 0.607 GGACCTGCTCCAGGTACCTCA +TRPC7 57113 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 135693009 135693009 + missense_variant Missense_Mutation SNP G G A TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 37 ENST00000513104.1:c.67C>T p.Arg23Cys p.R23C ENST00000513104 NM_020389.2 23 Cgc/Tgc 0 0.587 ATGGCCTGGCGACGGCCCTTC +SSPO 23145 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 149486800 149486800 + non_coding_transcript_exon_variant RNA SNP C C T TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 15 ENST00000378016.2:n.4574C>T *1525* ENST00000378016 0 0.682 GATGAGGGGCCGGGACACTGC +CDKN2C 1031 broad.mit.edu;ucsc.edu GRCh37 1 51439758 51439758 + missense_variant Missense_Mutation SNP A A G TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 8 ENST00000262662.1:c.323A>G p.His108Arg p.H108R ENST00000262662 108 cAc/cGc 0 0.552 CTGCCCTTGCACTTGGCTGCC +DAO 1610 broad.mit.edu;ucsc.edu GRCh37 12 109294236 109294236 + synonymous_variant Silent SNP C C T TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 18 ENST00000228476.3:c.969C>T p.Ala323= p.A323= ENST00000228476 NM_001917.4 323 gcC/gcT 0 0.572 GGGGATGTGCCCTGGAGGCAG +FUBP1 8880 broad.mit.edu;hgsc.bcm.edu GRCh37 1 78426058 78426059 + stop_gained,frameshift_variant Nonsense_Mutation INS - - T TCGA-HW-7487-01 TCGA-HW-7487-10 Untested Somatic Phase_I WXS none Illumina GAIIx 6 13 ENST00000370768.2:c.1466dupA p.Tyr489Ter p.Y489* ENST00000370768 NM_003902.3 489 tat/taAt 0 0.545 GTCCAGGATTATAAGGTGCAGG +ATAD1 84896 hgsc.bcm.edu;broad.mit.edu GRCh37 10 89536119 89536119 + missense_variant Missense_Mutation SNP T T G TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 220 13 ENST00000308448.7:c.649A>C p.Met217Leu p.M217L ENST00000308448 NM_032810.2 217 Atg/Ctg 0 0.378 CAGAGACTCATAAACTGAGCT +NPAT 4863 hgsc.bcm.edu;broad.mit.edu GRCh37 11 108043929 108043929 + synonymous_variant Silent SNP A A G TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 9 ENST00000278612.8:c.1782T>C p.Asn594= p.N594= ENST00000278612 NM_002519.2 594 aaT/aaC 0 0.313 TATCTTGGCAATTTGATAGCT +NCAM1 4684 hgsc.bcm.edu;broad.mit.edu GRCh37 11 113076288 113076288 + synonymous_variant Silent SNP G G A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 100 7 ENST00000524665.1:c.567G>A p.Arg189= p.R189= ENST00000524665 NM_000615.6 189 cgG/cgA 0 0.507 AGGAGTTCCGGGAGGGGGAAG +KRT76 51350 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 53169301 53169301 + missense_variant Missense_Mutation SNP C C T TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 115 80 ENST00000332411.2:c.686G>A p.Ser229Asn p.S229N ENST00000332411 NM_015848.4 229 aGc/aAc 0 0.557 AGGCTCCAGGCTGCTGGGCCC +REM2 161253 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 23354069 23354069 + missense_variant Missense_Mutation SNP C C T TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 94 14 ENST00000267396.4:c.290C>T p.Ser97Leu p.S97L ENST00000267396 NM_173527.2 97 tCg/tTg 0 0.612 TCCTCTGGCTCGTCTGACTCC +CDC42BPB 9578 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 103430859 103430859 + synonymous_variant Silent SNP G G A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 16 ENST00000361246.2:c.2706C>T p.Asp902= p.D902= ENST00000361246 NM_006035.3 902 gaC/gaT 0 0.652 TGAGGTTGGCGTCCTTGACCT +NDN 4692 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 23932264 23932264 + missense_variant Missense_Mutation SNP G G A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 7 ENST00000331837.4:c.101C>T p.Pro34Leu p.P34L ENST00000331837 NM_002487.2 34 cCg/cTg 0 0.692 GGTCGCGGACGGAGGAACCCC +ITGA11 22801 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 68643096 68643096 + missense_variant Missense_Mutation SNP C C T TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 29 ENST00000315757.7:c.919G>A p.Gly307Arg p.G307R ENST00000315757 NM_001004439.1 307 Ggg/Agg 0 0.502 GGATTGATCCCCCTGCGGTTG +ATXN2L 11273 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 28846974 28846974 + synonymous_variant Silent SNP T T C TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 9 ENST00000395547.2:c.2790T>C p.Pro930= p.P930= ENST00000395547 NM_148414.2 930 ccT/ccC 0 0.662 CACCGGGACCTTCTGCCCAGT +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577568 7577568 + missense_variant Missense_Mutation SNP C C T TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 76 46 ENST00000269305.4:c.713G>A p.Cys238Tyr p.C238Y ENST00000269305 NM_001126112.2 238 tGt/tAt 0 0.572 GGAACTGTTACACATGTAGTT +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578263 7578263 + stop_gained Nonsense_Mutation SNP G G A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 27 ENST00000269305.4:c.586C>T p.Arg196Ter p.R196* ENST00000269305 NM_001126112.2 196 Cga/Tga 0 0.552 CCTTCCACTCGGATAAGATGC +MUC16 94025 hgsc.bcm.edu;broad.mit.edu GRCh37 19 9086351 9086351 + missense_variant Missense_Mutation SNP T T A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 137 8 ENST00000397910.4:c.5464A>T p.Thr1822Ser p.T1822S ENST00000397910 NM_024690.2 1822 Act/Tct 0 0.483 ATTGATGGAGTTGGAGATGGA +SMARCA4 6597 hgsc.bcm.edu;broad.mit.edu GRCh37 19 11098500 11098500 + missense_variant Missense_Mutation SNP G G A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 11 ENST00000344626.4:c.1018G>A p.Ala340Thr p.A340T ENST00000344626 NM_003072.3 340 Gcg/Acg 0 0.746 GGCCCAGCCCGCGCCCATGGT +ATP4A 495 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 36054521 36054521 + missense_variant,splice_region_variant Missense_Mutation SNP G G A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 9 ENST00000262623.3:c.11C>T p.Ala4Val p.A4V ENST00000262623 NM_000704.2 4 gCc/gTc 0 0.652 CCCACTCACGGCCTTCCCCAT +PANK4 55229 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 2440330 2440330 + missense_variant Missense_Mutation SNP G G A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 19 ENST00000378466.3:c.2278C>T p.Arg760Trp p.R760W ENST00000378466 NM_018216.1 760 Cgg/Tgg 0 0.622 CTGAAGAGCCGGCCGCCCAGC +ZZZ3 26009 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 78041829 78041829 + missense_variant Missense_Mutation SNP G G A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 39 ENST00000370801.3:c.2255C>T p.Pro752Leu p.P752L ENST00000370801 NM_015534.4 752 cCg/cTg 0 0.378 ATACACTGGCGGTTCATGTGA +RBMXL1 494115 hgsc.bcm.edu;broad.mit.edu GRCh37 1 89448635 89448635 + missense_variant Missense_Mutation SNP C C T TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 301 19 ENST00000399794.2:c.875G>A p.Arg292His p.R292H ENST00000399794 NM_001162536.2 292 cGt/cAt 0 0.483 TGGAGCACTACGTGAGTTACC +ZNF831 128611 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 57769660 57769660 + missense_variant Missense_Mutation SNP G G A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 25 ENST00000371030.2:c.3586G>A p.Ala1196Thr p.A1196T ENST00000371030 NM_178457.2 1196 Gcg/Acg 0 0.637 CCCTCTGCCCGCGGAGCAGAA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 24 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +MSX2 4488 hgsc.bcm.edu;broad.mit.edu GRCh37 5 174156254 174156254 + missense_variant Missense_Mutation SNP G G A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 4 ENST00000239243.6:c.472G>A p.Glu158Lys p.E158K ENST00000239243 NM_002449.4 158 Gag/Aag 0 0.552 CCTCGCCCTGGAGCGCAAGTT +DNAH8 1769 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 38976646 38976646 + missense_variant Missense_Mutation SNP A A G TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 158 87 ENST00000359357.3:c.12620A>G p.Lys4207Arg p.K4207R ENST00000359357 4207 aAa/aGa 0 0.423 ATTCAACCCAAAGAGAGTGGA +PHF10 55274 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 170112612 170112612 + missense_variant Missense_Mutation SNP T T C TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 117 10 ENST00000339209.4:c.827A>G p.Tyr276Cys p.Y276C ENST00000339209 NM_133325.2 276 tAt/tGt 0 0.438 TAATGGCAGATACCGCAGCTC +TNFSF15 9966 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 117552881 117552881 + missense_variant Missense_Mutation SNP C C T rs150498686 TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 10 ENST00000374045.4:c.607G>A p.Glu203Lys p.E203K ENST00000374045 NM_005118.3 203 Gaa/Aaa 0 0.527 CTACCTACTTCGCATACAGAC +ATRX 546 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 76939522 76939522 + stop_gained Nonsense_Mutation SNP A A T rs122445109 TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 241 ENST00000373344.5:c.1226T>A p.Leu409Ter p.L409* ENST00000373344 NM_000489.3 409 tTg/tAg 0 0.363 GTCTTCTTCCAATGCAAGATG +CCNB1IP1 57820 broad.mit.edu;ucsc.edu GRCh37 14 20779861 20779861 + missense_variant Missense_Mutation SNP C C T TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 8 ENST00000398169.3:c.682G>A p.Asp228Asn p.D228N ENST00000398169 228 Gat/Aat 0 0.398 CCATCTCCATCGCCCCGATTT +RIOK3 8780 broad.mit.edu;ucsc.edu GRCh37 18 21057190 21057190 + missense_variant Missense_Mutation SNP C C A rs56187215 TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 53 ENST00000339486.3:c.1302C>A p.His434Gln p.H434Q ENST00000339486 NM_003831.3 434 caC/caA 0 0.413 CCCACCCTCACGGCCTGGAGT +HSP90AB2P 391634 broad.mit.edu;ucsc.edu GRCh37 4 13339305 13339305 + non_coding_transcript_exon_variant RNA SNP A A T TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 6 ENST00000507090.2:n.1200A>T *400* ENST00000507090 0 0.423 AAAATCTTCAAAGTCATTCAC +MYH2 4620 broad.mit.edu;ucsc.edu GRCh37 17 10451106 10451106 + missense_variant Missense_Mutation SNP T T A TCGA-FG-6690-01 TCGA-FG-6690-10 Untested Somatic Phase_I WXS none Illumina GAIIx 122 83 ENST00000245503.5:c.132A>T p.Lys44Asn p.K44N ENST00000245503 NM_017534.5 44 aaA/aaT 0 0.537 CAAAGGATTCTTTGGGCTCCG +MS4A3 932 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 59830060 59830060 + synonymous_variant Silent SNP G G A TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 51 ENST00000278865.3:c.276G>A p.Pro92= p.P92= ENST00000278865 NM_006138.4 92 ccG/ccA 0 0.423 CAGGCTACCCGATTTGGGGTG +IL18 3606 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 112014361 112014361 + missense_variant Missense_Mutation SNP C C A TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 12 6 ENST00000280357.7:c.540G>T p.Leu180Phe p.L180F ENST00000280357 NM_001562.3 180 ttG/ttT 0 0.388 ATCTATCCCCCAATTCATCCT +CADM1 23705 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 115109342 115109342 + missense_variant Missense_Mutation SNP T T C TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 28 ENST00000452722.3:c.302A>G p.Asn101Ser p.N101S ENST00000452722 NM_014333.3 101 aAt/aGt 0 0.393 GCTAGAAAAATTCAGCAACTG +KERA 11081 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 91445220 91445220 + missense_variant Missense_Mutation SNP T T C TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 13 ENST00000266719.3:c.962A>G p.His321Arg p.H321R ENST00000266719 NM_007035.3 321 cAt/cGt 0 0.438 GTAGCGAAGATGAGGTCCATA +CDK10 8558 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 89755723 89755723 + missense_variant Missense_Mutation SNP G G A TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 30 ENST00000353379.7:c.151G>A p.Gly51Ser p.G51S ENST00000353379 NM_052988.4 51 Ggc/Agc 0 0.582 GGGTACCTACGGCATTGTGTG +GNAL 2774 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 11880999 11880999 + synonymous_variant Silent SNP G G A TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 31 ENST00000334049.6:c.1242G>A p.Thr414= p.T414= ENST00000334049 NM_182978.3 414 acG/acA 0 0.622 GGATCAGCACGGCCACCGGTG +TTN 7273 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 179593263 179593263 + missense_variant Missense_Mutation SNP C C T TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 5 ENST00000589042.1:c.19390G>A p.Gly6464Arg p.G6464R ENST00000589042 NM_001267550.1 6464 Gga/Aga 0 0.398 CTACTGCTTCCGAAGTCATTT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 35 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +EIF4A2 1974 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 186501406 186501406 + missense_variant Missense_Mutation SNP G G T TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 100 59 ENST00000323963.5:c.7G>T p.Gly3Cys p.G3C ENST00000323963 3 Ggt/Tgt 0 0.572 GATCATGTCTGGTGGCTCCGC +BBS7 55212 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 122756377 122756377 + missense_variant Missense_Mutation SNP G G T TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 18 ENST00000264499.4:c.1433C>A p.Pro478His p.P478H ENST00000264499 NM_176824.2 478 cCc/cAc 0 0.393 ACAGGTTTTGGGTTGAATTCT +ROPN1L 83853 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 10461352 10461352 + synonymous_variant Silent SNP C C T TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 99 60 ENST00000503804.1:c.474C>T p.Gly158= p.G158= ENST00000503804 158 ggC/ggT 0 0.567 ATCCGGAGGGCGGGCCCGCTC +SIM1 6492 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 100911318 100911318 + synonymous_variant Silent SNP C C T TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 162 32 ENST00000369208.3:c.27G>A p.Ala9= p.A9= ENST00000369208 9 gcG/gcA 0 0.423 TCCTAGTCCGCGCAGCATTTT +OPHN1 4983 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 67414334 67414334 + missense_variant Missense_Mutation SNP G G C TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 19 ENST00000355520.5:c.1111C>G p.His371Asp p.H371D ENST00000355520 NM_002547.2 371 Cac/Gac 0 0.348 ATAGGGCTGTGGTAGATCTAC +IRS4 8471 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 107979043 107979043 + missense_variant Missense_Mutation SNP C C G TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 30 ENST00000372129.2:c.532G>C p.Ala178Pro p.A178P ENST00000372129 NM_003604.2 178 Gcg/Ccg 0 0.612 GCCACCATCGCGAAGTATTCG +TENM1 10178 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 123518058 123518058 + synonymous_variant Silent SNP C C T TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 47 ENST00000422452.2:c.6723G>A p.Leu2241= p.L2241= ENST00000422452 NM_001163279.1 2241 ctG/ctA 0 0.458 AGGCTTTCTGCAGCAGGCCAT +RENBP 5973 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 153208518 153208518 + missense_variant Missense_Mutation SNP T T G TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 21 ENST00000393700.3:c.476A>C p.Glu159Ala p.E159A ENST00000393700 NM_002910.5 159 gAg/gCg 0 0.711 ATCCATCATCTCCACCGCTTC +SYNE1 23345 broad.mit.edu;ucsc.edu GRCh37 6 152485384 152485384 + missense_variant Missense_Mutation SNP C C T TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 57 ENST00000367255.5:c.23704G>A p.Ala7902Thr p.A7902T ENST00000367255 NM_182961.3 7902 Gct/Act 0 0.502 TCGATGTGAGCGAGCCAGGTC +IL36B 27177 broad.mit.edu;ucsc.edu GRCh37 2 113788702 113788702 + missense_variant Missense_Mutation SNP C C T TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 17 ENST00000259213.4:c.44G>A p.Arg15His p.R15H ENST00000259213 NM_014438.4 15 cGt/cAt 0 0.478 TCGAGAATCACGAATAGCATA +TP53 7157 broad.mit.edu;hgsc.bcm.edu GRCh37 17 7578471 7578471 + frameshift_variant Frame_Shift_Del DEL G G - rs137852790 TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 70 ENST00000269305.4:c.459delC p.Gly154AlafsTer16 p.G154Afs*16 ENST00000269305 NM_001126112.2 153 ccC/cc 0 0.612 CGCGGGTGCCGGGCGGGGGTG +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76813062 76813063 + frameshift_variant Frame_Shift_Ins INS - - AG TCGA-HT-8108-01 TCGA-HT-8108-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 65 ENST00000373344.5:c.6557_6558dupCT p.Phe2187LeufsTer16 p.F2187Lfs*16 ENST00000373344 NM_000489.3 2186 -/CT 0 0.347 ACAACTCGAAAAGACAGTGACT +KNDC1 85442 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 135038195 135038195 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 25 ENST00000304613.3:c.5051C>T p.Ala1684Val p.A1684V ENST00000304613 1684 gCg/gTg 0 0.597 CAGGTGCACGCGTTCCAGGAG +OR52B6 340980 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 5602864 5602864 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 340 43 ENST00000345043.2:c.758G>A p.Arg253His p.R253H ENST00000345043 NM_001005162.2 253 cGc/cAc 0 0.507 CAAGATGCCCGCTCCAAGGCC +MS4A6E 245802 hgsc.bcm.edu;broad.mit.edu GRCh37 11 60105367 60105367 + missense_variant Missense_Mutation SNP G G T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 199 14 ENST00000300182.4:c.301G>T p.Asp101Tyr p.D101Y ENST00000300182 NM_139249.2 101 Gat/Tat 0 0.403 TCTTTCTTATGATTATCATTC +AHNAK 79026 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 62299210 62299210 + synonymous_variant Silent SNP C C T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 348 280 ENST00000378024.4:c.2679G>A p.Glu893= p.E893= ENST00000378024 NM_001620.2 893 gaG/gaA 0 0.517 CTTCTGGGCCCTCTGCTTTGA +CWF19L2 143884 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 107224323 107224323 + missense_variant Missense_Mutation SNP T T C TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 50 ENST00000282251.5:c.2012A>G p.Gln671Arg p.Q671R ENST00000282251 NM_152434.2 671 cAa/cGa 0 0.393 TTTTTCCATTTGTGCAGCAAG +KSR2 283455 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 118016978 118016978 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 7 ENST00000339824.5:c.1271C>T p.Thr424Met p.T424M ENST00000339824 424 aCg/aTg 0 0.468 GACTGTGCACGTCTGAGACAT +LMO7 4008 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 76382215 76382215 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 26 ENST00000465261.2:c.1097G>A p.Gly366Glu p.G366E ENST00000465261 NM_015842.2 366 gGa/gAa 0 0.498 TGGAAACTGGGAACTACCGTG +CYP1A1 1543 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 75012968 75012968 + synonymous_variant Silent SNP G G C TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 141 35 ENST00000379727.3:c.1401C>G p.Val467= p.V467= ENST00000379727 467 gtC/gtG 0 0.542 GGAAGAGAAAGACCTCCCAGC +IDH2 3418 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 90631838 90631838 + missense_variant Missense_Mutation SNP C C A rs121913503 TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 65 ENST00000330062.3:c.515G>T p.Arg172Met p.R172M ENST00000330062 NM_002168.2 172 aGg/aTg 0 0.632 ATGGGCGTGCCTGCCAATGGT +CDH5 1003 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 66436644 66436644 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 5 ENST00000341529.3:c.1927G>A p.Val643Ile p.V643I ENST00000341529 NM_001795.3 643 Gtc/Atc 0 0.711 CGAGCAGCTGGTCACCTACGA +KRT33B 3884 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 39521763 39521763 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 27 ENST00000251646.3:c.631G>A p.Val211Met p.V211M ENST00000251646 NM_002279.4 211 Gtg/Atg 0 0.522 TCCACCTCCACGTTGAGGCGG +ELL 8178 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 18557617 18557617 + synonymous_variant Silent SNP G G A rs73923115 byFrequency TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 13 ENST00000262809.4:c.1473C>T p.Asn491= p.N491= ENST00000262809 NM_006532.3 491 aaC/aaT 0 0.572 TGCAGGTTCCGTTTAAACCTA +PRODH2 58510 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 36302867 36302867 + synonymous_variant Silent SNP C C T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 14 24 ENST00000301175.3:c.822G>A p.Gly274= p.G274= ENST00000301175 NM_021232.1 274 ggG/ggA 0 0.597 TCCTTACCTGCCCAGAGTCCA +KLK4 9622 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 51411835 51411835 + missense_variant,splice_region_variant Missense_Mutation SNP C C T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 8 ENST00000324041.1:c.475G>A p.Gly159Ser p.G159S ENST00000324041 NM_004917.3 159 Ggc/Agc 0 0.637 GTGAGCTCACCGTTCGCCAGC +HRNR 388697 hgsc.bcm.edu;broad.mit.edu GRCh37 1 152193228 152193228 + missense_variant Missense_Mutation SNP A A G TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 317 15 ENST00000368801.2:c.877T>C p.Ser293Pro p.S293P ENST00000368801 NM_001009931.2 293 Tct/Cct 0 0.607 TGGCCCAAAGACTGACGGGAA +SELE 6401 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 169698637 169698637 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 87 ENST00000333360.7:c.893C>T p.Thr298Met p.T298M ENST00000333360 NM_000450.2 298 aCg/aTg 0 0.443 ACCTTTACACGTTGGCTTCTC +IL1RL2 8808 hgsc.bcm.edu;broad.mit.edu GRCh37 2 102805614 102805614 + missense_variant Missense_Mutation SNP C C A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 151 10 ENST00000264257.2:c.137C>A p.Pro46His p.P46H ENST00000264257 NM_003854.2 46 cCc/cAc 0 0.378 ACATTCCCTCCCATAACATCT +NEB 4703 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 152521900 152521900 + missense_variant Missense_Mutation SNP T T A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 33 ENST00000397345.3:c.5185A>T p.Met1729Leu p.M1729L ENST00000397345 NM_001164508.1 1729 Atg/Ttg 0 0.507 ATTGTGTCCATGGCGTAAGTG +KLHL30 377007 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 239051515 239051515 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 18 6 ENST00000409223.1:c.850G>A p.Ala284Thr p.A284T ENST00000409223 284 Gca/Aca 0 0.672 GGAGGAGGAGGCAGGTGAGGA +SI 6476 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 164776970 164776970 + missense_variant Missense_Mutation SNP A A G rs148511215 by1000genomes TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 102 16 ENST00000264382.3:c.1264T>C p.Tyr422His p.Y422H ENST00000264382 NM_001041.3 422 Tat/Cat 0 0.323 ATGATGACATATTTCTGTCCA +FSTL5 56884 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 162577528 162577528 + stop_gained Nonsense_Mutation SNP C C T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 106 18 ENST00000306100.5:c.846G>A p.Trp282Ter p.W282* ENST00000306100 NM_001128427.2 282 tgG/tgA 0 0.353 TGTTCCTTTTCCAGATAATGG +PSD3 23362 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 18725224 18725224 + missense_variant Missense_Mutation SNP T T C rs62636654 TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 111 73 ENST00000327040.8:c.1594A>G p.Ile532Val p.I532V ENST00000327040 NM_015310.3 532 Atc/Gtc 0 0.507 TTCGTGTAGATGGAGTCGCTG +KCNU1 157855 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 36671795 36671795 + missense_variant Missense_Mutation SNP A A G TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 8 ENST00000399881.3:c.803A>G p.Tyr268Cys p.Y268C ENST00000399881 NM_001031836.2 268 tAc/tGc 0 0.433 GAGTCAATTTACCTGGTCATG +KLHL9 55958 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 21333865 21333865 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 145 91 ENST00000359039.4:c.994C>T p.Pro332Ser p.P332S ENST00000359039 332 Cca/Tca 0 0.418 GCATCCATTGGGGCTAAAGAT +SIT1 27240 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 35650242 35650242 + missense_variant,splice_region_variant Missense_Mutation SNP C C T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 55 ENST00000259608.3:c.296G>A p.Gly99Glu p.G99E ENST00000259608 NM_014450.2 99 gGa/gAa 0 0.627 AGACAGCCGTCCTGGGACGGG +ARSE 415 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 2867631 2867631 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 9 ENST00000381134.3:c.568C>T p.Arg190Cys p.R190C ENST00000381134 NM_000047.2 190 Cgt/Tgt 0 0.527 AGGTTGACACGCTTCTCTGAG +MAGEB2 4113 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 30237371 30237371 + missense_variant Missense_Mutation SNP A A T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 14 ENST00000378988.4:c.674A>T p.Glu225Val p.E225V ENST00000378988 NM_002364.4 225 gAa/gTa 0 0.483 GAGATCTGGGAATTCCTGAAT +PGRMC1 10857 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 118370561 118370561 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 16 ENST00000217971.7:c.235C>T p.Arg79Trp p.R79W ENST00000217971 NM_006667.3 79 Cgg/Tgg 0 0.711 CGCCGAGCTGCGGCGCTTCGA +LAMP2 3920 hgsc.bcm.edu;broad.mit.edu GRCh37 X 119581704 119581704 + stop_gained Nonsense_Mutation SNP G G A TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 258 19 ENST00000434600.2:c.733C>T p.Gln245Ter p.Q245* ENST00000434600 NM_001122606.1 245 Cag/Tag 0 0.403 ACCTTATCCTGAGTGATGTTC +NAIP 4671 broad.mit.edu;ucsc.edu GRCh37 5 70308387 70308387 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 98 65 ENST00000517649.1:c.356G>A p.Arg119Lys p.R119K ENST00000517649 NM_004536.2 119 aGg/aAg 0 0.473 TGGATGAAACCTCTTGTGGTC +HTR7P1 93164 broad.mit.edu;ucsc.edu GRCh37 12 13155006 13155006 + non_coding_transcript_exon_variant RNA SNP G G C TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 4 ENST00000331998.1:n.1458G>C *486* ENST00000331998 0 0.483 CGTACCCTATGAGGCAGAAGG +PDHA1 5160 broad.mit.edu;ucsc.edu GRCh37 X 19368118 19368118 + missense_variant Missense_Mutation SNP G G C TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 98 75 ENST00000379806.5:c.295G>C p.Gly99Arg p.G99R ENST00000379806 NM_001173454.1 99 Ggg/Cgg 0 0.453 CAGGGAGGATGGGCTCAAATA +BRWD1 54014 broad.mit.edu;ucsc.edu GRCh37 21 40590181 40590181 + missense_variant Missense_Mutation SNP C C T rs75547980 TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 145 23 ENST00000333229.2:c.3556G>A p.Ala1186Thr p.A1186T ENST00000333229 NM_018963.4 1186 Gca/Aca 0 0.368 ACAGGGCCTGCAAAAGCTGCT +CIC 23152 broad.mit.edu;hgsc.bcm.edu GRCh37 19 42795241 42795242 + frameshift_variant Frame_Shift_Ins INS - - GCCCCCT TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 10 ENST00000575354.2:c.2324_2330dupCCCCTGC p.Val778ProfsTer155 p.V778Pfs*155 ENST00000575354 NM_015125.3 774 gcg/gcGCCCCCTg 0 0.698 GGGGCCCCTGCGCCCCCTGCTG +BCOR 54880 broad.mit.edu;hgsc.bcm.edu GRCh37 X 39933875 39933875 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 42 ENST00000378444.4:c.724delG p.Glu242SerfsTer24 p.E242Sfs*24 ENST00000378444 NM_001123385.1 242 Gag/ag 0 0.577 AGAAAGCGCTCCCCATTGGTG +NOTCH1 4851 ucsc.edu GRCh37 9 139418186 139418186 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5318-01 TCGA-E1-5318-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 2 ENST00000277541.6:c.386G>A p.Cys129Tyr p.C129Y ENST00000277541 NM_017617.3 129 tGc/tAc 0 0.697 GCCGGGCGGGCAGCGGCACTT +KIAA1217 56243 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 24832988 24832988 + stop_gained Nonsense_Mutation SNP A A T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 122 13 ENST00000376454.3:c.4789A>T p.Lys1597Ter p.K1597* ENST00000376454 NM_019590.3 1597 Aag/Tag 0 0.463 TAAAACAGGGAAGAAGACTTT +AGAP5 729092 hgsc.bcm.edu;broad.mit.edu GRCh37 10 75457306 75457306 + stop_gained Nonsense_Mutation SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 197 15 ENST00000374094.4:c.208C>T p.Gln70Ter p.Q70* ENST00000374094 NM_001144000.1 70 Cag/Tag 0 0.592 GGCATCTCCTGGTCACGAATG +HELLS 3070 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 96352241 96352241 + synonymous_variant Silent SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 12 ENST00000348459.5:c.1941G>A p.Gly647= p.G647= ENST00000348459 NM_018063.3 647 ggG/ggA 0 0.343 GGCTTGATGGGTCCATGTCTT +SLIT1 6585 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 98764460 98764460 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 15 ENST00000266058.4:c.3700G>A p.Ala1234Thr p.A1234T ENST00000266058 NM_003061.2 1234 Gcc/Acc 0 0.602 CTGTAGATGGCAGAGCTGGGG +MAP3K12 7786 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 53877509 53877509 + splice_acceptor_variant Splice_Site SNP T T A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 8 ENST00000547035.1:c.1359-2A>T p.X453_splice ENST00000547035 0 0.507 AGGGCGTGTCTGCAACGGGCA +SMUG1 23583 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 54577582 54577582 + missense_variant Missense_Mutation SNP G G A rs149806805 byFrequency TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 6 ENST00000508394.2:c.143C>T p.Ser48Leu p.S48L ENST00000508394 NM_001243788.1 48 tCg/tTg 0 0.597 CACAGGCTCCGAAAACTGCAG +TBX5 6910 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 114793348 114793348 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 8 ENST00000310346.4:c.1546G>A p.Asp516Asn p.D516N ENST00000310346 NM_000192.3 516 Gac/Aac 0 0.517 TAGCTATTGTCGCTCCACTCT +TRPM1 4308 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 31359319 31359319 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 74 50 ENST00000542188.1:c.616G>A p.Gly206Arg p.G206R ENST00000542188 NM_001252020.1 206 Gga/Aga 0 0.453 GGAGCAATTCCTATAGCACAA +SPPL2A 84888 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 51017471 51017471 + missense_variant Missense_Mutation SNP C C G TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 120 52 ENST00000261854.5:c.1196G>C p.Ser399Thr p.S399T ENST00000261854 NM_032802.3 399 aGt/aCt 0 0.313 GAGGCACACACTCATTACTGA +TPM1 7168 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 63336271 63336271 + missense_variant Missense_Mutation SNP G G A rs104894505 TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 9 ENST00000358278.3:c.160G>A p.Glu54Lys p.E54K ENST00000358278 NM_001018006.1 54 Gaa/Aaa 0 0.562 CAAGGGCACCGAAGATGAACT +NEO1 4756 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 73428355 73428355 + missense_variant Missense_Mutation SNP G G C TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 17 ENST00000339362.5:c.1002G>C p.Glu334Asp p.E334D ENST00000339362 334 gaG/gaC 0 0.373 CTCAAGCAGAGCTTACAGTGC +SMAD2 4087 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 45422914 45422914 + missense_variant Missense_Mutation SNP T T C TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 9 ENST00000262160.6:c.214A>G p.Thr72Ala p.T72A ENST00000262160 NM_005901.5 72 Act/Gct 0 0.368 ACACATTTAGTATTACAGTTT +DAPK3 1613 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 3964722 3964722 + synonymous_variant Silent SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 133 17 ENST00000545797.2:c.330G>A p.Ser110= p.S110= ENST00000545797 110 tcG/tcA 0 0.592 CCTCCGTCAGCGACTCCTTCT +C3 718 hgsc.bcm.edu;broad.mit.edu GRCh37 19 6718386 6718386 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 148 10 ENST00000245907.6:c.305G>A p.Arg102His p.R102H ENST00000245907 NM_000064.2 102 cGc/cAc 0 0.607 GAACTTGTTGCGCCCCTTTTC +ZNF878 729747 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 12154973 12154973 + stop_gained Nonsense_Mutation SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 13 ENST00000547628.1:c.1243C>T p.Arg415Ter p.R415* ENST00000547628 NM_001080404.2 415 Cga/Tga 0 0.433 GTGTGAGTTCGTATGTGCTTT +NOTCH3 4854 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 15299837 15299837 + synonymous_variant Silent SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 9 ENST00000263388.2:c.1341C>T p.Leu447= p.L447= ENST00000263388 NM_000435.2 447 ctC/ctT 0 0.667 CTATGCGGTCGAGGCACGTGG +TEAD2 8463 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 49845721 49845721 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 27 ENST00000598810.1:c.1216G>A p.Val406Ile p.V406I ENST00000598810 NM_001256661.1 406 Gtc/Atc 0 0.572 TTTTCCAGGACGCTGTTCATC +U2AF2 11338 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 56175034 56175034 + missense_variant Missense_Mutation SNP G G C TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 106 10 ENST00000308924.4:c.666G>C p.Gln222His p.Q222H ENST00000308924 222 caG/caC 0 0.567 TCCAGGGCCAGTCACTAAAGA +PRRC2C 23215 hgsc.bcm.edu;broad.mit.edu GRCh37 1 171511013 171511013 + missense_variant Missense_Mutation SNP C C G TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 5 ENST00000338920.4:c.4402C>G p.Pro1468Ala p.P1468A ENST00000338920 NM_015172.3 1468 Cca/Gca 0 0.428 GGCTCAAGAACCAGTTAATAC +BPIFB3 359710 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 31659936 31659936 + synonymous_variant Silent SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 87 15 ENST00000375494.3:c.1287C>T p.Ser429= p.S429= ENST00000375494 NM_182658.1 429 agC/agT 0 0.532 AATGGCTCAGCCATGTGGTCG +COL18A1 80781 hgsc.bcm.edu;broad.mit.edu GRCh37 21 46909433 46909433 + missense_variant,splice_region_variant Missense_Mutation SNP A A G TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 12 10 ENST00000355480.5:c.2497A>G p.Lys833Glu p.K833E ENST00000355480 NM_030582.3 833 Aag/Gag 0 0.706 GCCGGGGGCGAAGGTAAGCGC +PARVB 29780 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 44489821 44489821 + synonymous_variant Silent SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 104 49 ENST00000406477.3:c.225G>A p.Gln75= p.Q75= ENST00000406477 NM_001003828.2 75 caG/caA 0 0.547 GTGACCTGCAGGAAGAAGGCA +TTN 7273 hgsc.bcm.edu;broad.mit.edu GRCh37 2 179634978 179634978 + missense_variant Missense_Mutation SNP C C G TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 95 8 ENST00000589042.1:c.8450G>C p.Ser2817Thr p.S2817T ENST00000589042 NM_001267550.1 2817 aGt/aCt 0 0.408 ATGGGAAACACTAACTTCAAA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 20 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +NGEF 25791 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 233759484 233759484 + missense_variant Missense_Mutation SNP A A G TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 82 31 ENST00000264051.3:c.971T>C p.Val324Ala p.V324A ENST00000264051 NM_019850.2 324 gTg/gCg 0 0.602 GACAGCCAGCACGTCCAGGAC +FLNB 2317 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 58097875 58097875 + splice_acceptor_variant Splice_Site SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 137 83 ENST00000490882.1:c.2576-1G>A p.X859_splice ENST00000490882 NM_001164317.1 0 0.522 TATCTTTCCAGGTGTGGAAAA +CRYBG3 131544 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 97596597 97596597 + stop_gained Nonsense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 12 ENST00000182096.4:c.715C>T p.Gln239Ter p.Q239* ENST00000182096 NM_153605.3 239 Cag/Tag 0 0.468 CCCTGATGACCAGGAGAGCGT +ENAM 10117 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 71508741 71508741 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 32 ENST00000396073.3:c.1598C>T p.Thr533Ile p.T533I ENST00000396073 NM_031889.2 533 aCt/aTt 0 0.413 GAATCAGAAACTAATCAGTCA +NAF1 92345 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 164050323 164050323 + missense_variant Missense_Mutation SNP T T C TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 10 ENST00000274054.2:c.1211A>G p.Gln404Arg p.Q404R ENST00000274054 NM_138386.2 404 cAg/cGg 0 0.458 TGAAGTCTCCTGAGATACCAT +FAT1 2195 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 187521295 187521295 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 6 ENST00000441802.2:c.11860G>A p.Gly3954Ser p.G3954S ENST00000441802 NM_005245.3 3954 Ggc/Agc 0 0.483 CGGATGTGGCCACCAAAAAAC +MAML1 9794 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 179192669 179192669 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 5 ENST00000292599.3:c.658C>T p.Pro220Ser p.P220S ENST00000292599 NM_014757.4 220 Cct/Tct 0 0.517 GAAGCAGGAGCCTGTCGAAGA +NOTCH4 4855 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 32166813 32166813 + synonymous_variant Silent SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 32 ENST00000375023.3:c.4425C>T p.Arg1475= p.R1475= ENST00000375023 NM_004557.3 1475 cgC/cgT 0 0.677 CATGCTCTCGGCGTCGACGCC +NOTCH4 4855 hgsc.bcm.edu;broad.mit.edu GRCh37 6 32190325 32190325 + synonymous_variant Silent SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 8 ENST00000375023.3:c.414G>A p.Ser138= p.S138= ENST00000375023 NM_004557.3 138 tcG/tcA 0 0.647 GTGGGCGGCCCGAGGCCTGGA +PNPLA1 285848 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 36262065 36262065 + synonymous_variant Silent SNP C C A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 138 24 ENST00000394571.2:c.603C>A p.Pro201= p.P201= ENST00000394571 NM_001145717.1 201 ccC/ccA 0 0.607 ACATCTGTCCCCGGGACTGCC +PPP2R5D 5528 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 42974286 42974286 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 130 76 ENST00000485511.1:c.191C>T p.Pro64Leu p.P64L ENST00000485511 NM_001270476.1 64 cCg/cTg 0 0.622 AATAGCACGCCGCCCCCCACG +TTBK1 84630 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 43251409 43251409 + synonymous_variant Silent SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 26 ENST00000259750.4:c.2931G>A p.Ala977= p.A977= ENST00000259750 NM_032538.1 977 gcG/gcA 0 0.697 GGGCCCGAGCGCCCCTGGAGA +ZNF292 23036 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 87943087 87943087 + missense_variant Missense_Mutation SNP A A G TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 9 ENST00000369577.3:c.583A>G p.Arg195Gly p.R195G ENST00000369577 NM_015021.1 195 Aga/Gga 0 0.308 GTTGGATATGAGAATTAAACA +RUNX1T1 862 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 92972658 92972658 + missense_variant Missense_Mutation SNP C C G TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 10 ENST00000436581.2:c.1660G>C p.Asp554His p.D554H ENST00000436581 554 Gac/Cac 0 0.567 TTCTCCCAGTCTTTGTGCTGG +PLEC 5339 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 144995732 144995732 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 30 ENST00000322810.4:c.8668G>A p.Ala2890Thr p.A2890T ENST00000322810 NM_201380.2 2890 Gct/Act 0 0.687 TCCTTCACAGCCTCGTTGACG +GNE 10020 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 36249251 36249251 + synonymous_variant Silent SNP G G A rs147290887 TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 9 ENST00000396594.3:c.195C>T p.Thr65= p.T65= ENST00000396594 NM_001128227.2 65 acC/acT 0 0.408 ACTCAGGTTCGGTTTTAATGC +ALDH1A1 216 hgsc.bcm.edu;ucsc.edu GRCh37 9 75520933 75520933 + synonymous_variant Silent SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 6 ENST00000297785.3:c.1374C>T p.Gly458= p.G458= ENST00000297785 NM_000689.4 458 ggC/ggT 0 0.348 CACTTACCACGCCATAGCAAT +FPGS 2356 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 130570869 130570869 + synonymous_variant Silent SNP C C G TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 20 ENST00000373247.2:c.855C>G p.Ala285= p.A285= ENST00000373247 NM_004957.4 285 gcC/gcG 0 0.687 TGCTGGAGGCCCTCGAGGAAG +NOTCH1 4851 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 139412597 139412597 + missense_variant Missense_Mutation SNP C C A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 10 9 ENST00000277541.6:c.1247G>T p.Cys416Phe p.C416F ENST00000277541 NM_017617.3 416 tGc/tTc 0 0.672 ACCCAGCGAGCACTCATCCAC +FTSJ1 24140 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 48339829 48339829 + missense_variant Missense_Mutation SNP G G T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 11 30 ENST00000348411.2:c.484G>T p.Asp162Tyr p.D162Y ENST00000348411 NM_012280.2 162 Gat/Tat 0 0.602 CCGAGGCCGGGATGTGACGCT +LHFPL1 340596 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 111914414 111914414 + missense_variant Missense_Mutation SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 36 ENST00000371968.3:c.205C>T p.Arg69Cys p.R69C ENST00000371968 NM_178175.3 69 Cgc/Tgc 0 0.592 CTGGCATAGCGCCCACATTCT +NSDHL 50814 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 152037637 152037637 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 11 ENST00000370274.3:c.1099C>T p.Arg367Cys p.R367C ENST00000370274 NM_015922.2 367 Cgc/Tgc 0 0.552 GCAGAGCTTTCGCCACCTGCG +ABI3BP 25890 broad.mit.edu;ucsc.edu GRCh37 3 100523693 100523693 + missense_variant Missense_Mutation SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 13 ENST00000284322.5:c.1690C>T p.Arg564Cys p.R564C ENST00000284322 NM_015429.3 564 Cgt/Tgt 0 0.398 GCAGTAACACGCTGGGGCACC +CRIP3 401262 broad.mit.edu;ucsc.edu GRCh37 6 43275627 43275627 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 4 ENST00000372569.3:c.146G>A p.Gly49Glu p.G49E ENST00000372569 NM_206922.2 49 gGg/gAg 0 0.607 GTATGGCCTCCCATTGTGCTG +KPRP 448834 broad.mit.edu;ucsc.edu GRCh37 1 152733157 152733157 + missense_variant Missense_Mutation SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 13 ENST00000368773.1:c.1093G>A p.Ala365Thr p.A365T ENST00000368773 NM_001025231.1 365 Gcc/Acc 0 0.662 CTCCTGGGGCGCCTCCTGCCC +TTC12 54970 broad.mit.edu;ucsc.edu GRCh37 11 113215006 113215006 + missense_variant Missense_Mutation SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 126 73 ENST00000529221.1:c.998G>A p.Arg333His p.R333H ENST00000529221 NM_017868.3 333 cGt/cAt 0 0.532 GAAAACCAGCGTGTGCTAGTG +THSD7B 80731 broad.mit.edu;ucsc.edu GRCh37 2 137814593 137814593 + stop_gained Nonsense_Mutation SNP G G A TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 39 ENST00000272643.3:c.743G>A p.Trp248Ter p.W248* ENST00000272643 248 tGg/tAg 0 0.413 GTTGGACCATGGAGTAAATGC +DIXDC1 85458 broad.mit.edu;ucsc.edu GRCh37 11 111835363 111835363 + missense_variant Missense_Mutation SNP C C T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 7 ENST00000440460.2:c.151C>T p.Arg51Trp p.R51W ENST00000440460 NM_001037954.3 51 Cgg/Tgg 0 0.517 ACAAGATCTCCGGGATGGGGT +HFM1 164045 broad.mit.edu;hgsc.bcm.edu GRCh37 1 91781979 91781980 + frameshift_variant Frame_Shift_Ins INS - - T TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 29 ENST00000370425.3:c.2866dupA p.Ile956AsnfsTer10 p.I956Nfs*10 ENST00000370425 NM_001017975.3 956 ata/aAta 0 0.292 TGTCTCTTCTATTTTTTTAAAG +KIAA1147 57189 broad.mit.edu;hgsc.bcm.edu GRCh37 7 141362626 141362626 + frameshift_variant Frame_Shift_Del DEL T T - TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 2 10 ENST00000536163.1:c.1198delA p.Ile400TyrfsTer16 p.I400Yfs*16 ENST00000536163 NM_001080392.1 400 Ata/ta 0 0.502 GTCTGAAATATCCGGTTGTTT +CIC 23152 broad.mit.edu;hgsc.bcm.edu GRCh37 19 42797750 42797750 + frameshift_variant Frame_Shift_Del DEL A A - TCGA-IK-8125-01 TCGA-IK-8125-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 25 ENST00000575354.2:c.3804delA p.Lys1268AsnfsTer34 p.K1268Nfs*34 ENST00000575354 NM_015125.3 1268 Aaa/aa 0 0.637 CCAGGCCAGCAAATTCCCCAG +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577545 7577545 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7880-01 TCGA-HT-7880-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 10 ENST00000269305.4:c.736A>G p.Met246Val p.M246V ENST00000269305 NM_001126112.2 246 Atg/Gtg 0 0.577 CTCCGGTTCATGCCGCCCATG +PTPN14 5784 hgsc.bcm.edu;broad.mit.edu GRCh37 1 214557534 214557534 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7880-01 TCGA-HT-7880-10 Untested Somatic Phase_I WXS none Illumina GAIIx 124 10 ENST00000366956.5:c.1664C>T p.Thr555Met p.T555M ENST00000366956 NM_005401.4 555 aCg/aTg 0 0.637 CATGTGGGCCGTGCTGTAGTT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-7880-01 TCGA-HT-7880-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 15 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +PKN3 29941 hgsc.bcm.edu;broad.mit.edu GRCh37 9 131475882 131475882 + synonymous_variant Silent SNP G G C TCGA-HT-7880-01 TCGA-HT-7880-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 6 ENST00000291906.4:c.1197G>C p.Leu399= p.L399= ENST00000291906 NM_013355.3 399 ctG/ctC 0 0.632 GTCACCAACTGTCCCTCAGCC +ATRX 546 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 76937900 76937900 + stop_gained Nonsense_Mutation SNP T T A TCGA-HT-7880-01 TCGA-HT-7880-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 18 ENST00000373344.5:c.2848A>T p.Lys950Ter p.K950* ENST00000373344 NM_000489.3 950 Aaa/Taa 0 0.358 GTTTTGGTTTTGAGATGCTTG +ATRX 546 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 76938788 76938788 + synonymous_variant Silent SNP G G T TCGA-HT-7880-01 TCGA-HT-7880-10 Untested Somatic Phase_I WXS none Illumina GAIIx 115 19 ENST00000373344.5:c.1960C>A p.Arg654= p.R654= ENST00000373344 NM_000489.3 654 Cga/Aga 0 0.393 GGGGATCTTCGAAGATCAGAT +AFF2 2334 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 148037448 148037448 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7880-01 TCGA-HT-7880-10 Untested Somatic Phase_I WXS none Illumina GAIIx 110 16 ENST00000370460.2:c.1873A>G p.Thr625Ala p.T625A ENST00000370460 NM_002025.3 625 Aca/Gca 0 0.443 GTCTCAAAGGACAATTGGGAA +NF1 4763 broad.mit.edu GRCh37 17 29562657 29562660 + frameshift_variant Frame_Shift_Del DEL TGTT TGTT - TCGA-HT-7880-01 TCGA-HT-7880-10 Untested Somatic Phase_I WXS none Illumina GAIIx 226 20 ENST00000358273.4:c.3739_3742delTTTG p.Phe1247IlefsTer18 p.F1247Ifs*18 ENST00000358273 NM_001042492.2 1246 cTGTTt/ct 0 0.412 CTGGTTACTCTGTTTGATTCTCGG +NAV2 89797 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 19970369 19970369 + synonymous_variant Silent SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 11 ENST00000396087.3:c.2457C>T p.Asp819= p.D819= ENST00000396087 NM_001244963.1 819 gaC/gaT 0 0.617 AAGCAGGAGACGCCCCCTCAA +ADAMTS15 170689 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 130332501 130332501 + synonymous_variant Silent SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 129 17 ENST00000299164.2:c.1368C>T p.Ser456= p.S456= ENST00000299164 NM_139055.2 456 tcC/tcT 0 0.647 GCGTGGGCTCCAAGCCCTGTC +PRB3 5544 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 11420209 11420209 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 220 36 ENST00000381842.3:c.847C>T p.Pro283Ser p.P283S ENST00000381842 NM_006249.4 283 Ccc/Tcc 0 0.622 TTTCCAGCGGGAGGTGGCAGA +MGAT4C 25834 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 86374059 86374059 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 12 ENST00000604798.1:c.445C>T p.Arg149Cys p.R149C ENST00000604798 149 Cgt/Tgt 0 0.398 ATGGCATCACGCCAGGAAGAA +SLC13A2 9058 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 26817446 26817446 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 264 40 ENST00000444914.3:c.353C>T p.Pro118Leu p.P118L ENST00000444914 NM_001145975.1 118 cCg/cTg 0 0.612 GTCTTCCCGCCGCTCAGCCAT +LRRC37B 114659 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 30349672 30349672 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 115 23 ENST00000341671.7:c.1507G>A p.Val503Met p.V503M ENST00000341671 NM_052888.2 503 Gtg/Atg 0 0.507 GGATTCATTGGTGCAGTCTGA +ZNF521 25925 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 22805969 22805969 + missense_variant Missense_Mutation SNP T T G TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 147 23 ENST00000361524.3:c.1913A>C p.Gln638Pro p.Q638P ENST00000361524 NM_015461.2 638 cAa/cCa 0 0.478 AGCACCACATTGATTACAGAT +ZNF426 79088 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 9646905 9646905 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 74 11 ENST00000535489.1:c.4G>A p.Ala2Thr p.A2T ENST00000535489 2 Gca/Aca 0 0.463 TCAGCAGCTGCCATCCCGCGA +EHD2 30846 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 48229108 48229108 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 10 ENST00000263277.3:c.542G>A p.Arg181His p.R181H ENST00000263277 NM_014601.3 181 cGc/cAc 0 0.637 TTCGCGGAGCGCGTGGACCTC +KIAA0754 23499 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 39876726 39876726 + synonymous_variant Silent SNP A A G TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 10 ENST00000530275.1:c.381A>G p.Thr127= p.T127= ENST00000530275 NM_015038.1 127 acA/acG 0 0.512 CGAGGGCCACAAAAAGTTTAG +CEP250 11190 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 34059913 34059913 + synonymous_variant Silent SNP T T C TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 186 33 ENST00000397527.1:c.987T>C p.Ser329= p.S329= ENST00000397527 NM_007186.3 329 tcT/tcC 0 0.423 ATGAAGCATCTCTTAGTAGGA +YTHDF1 54915 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 61833842 61833842 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 82 15 ENST00000370339.3:c.1450G>A p.Val484Ile p.V484I ENST00000370339 NM_017798.3 484 Gta/Ata 0 0.537 TTATTGGGTACATCCTTAACA +VAMP5 10791 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 85818866 85818866 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 102 20 ENST00000306384.4:c.22C>T p.Arg8Trp p.R8W ENST00000306384 NM_006634.2 8 Cgg/Tgg 0 0.602 AGAGTTGGAGCGGTGCCAGCA +AMER3 205147 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 131521800 131521800 + stop_gained Nonsense_Mutation SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 12 ENST00000423981.1:c.2155C>T p.Gln719Ter p.Q719* ENST00000423981 NM_001105194.1 719 Cag/Tag 0 0.632 CATGCTGGAGCAGAAACAGTC +FN1 2335 hgsc.bcm.edu;ucsc.edu GRCh37 2 216288193 216288193 + missense_variant Missense_Mutation SNP G G C TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 6 ENST00000354785.4:c.1273C>G p.Leu425Val p.L425V ENST00000354785 425 Cta/Gta 0 0.463 TTGTTGTATAGGAAGGGGAAG +RARB 5915 hgsc.bcm.edu;ucsc.edu GRCh37 3 25470378 25470378 + splice_region_variant,synonymous_variant Splice_Region SNP A A G TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 6 ENST00000330688.4:c.156A>G p.Gln52= p.Q52= ENST00000330688 NM_000965.3 52 caA/caG 0 0.433 ACACTGCTCAATGTAGGTTTA +CELSR3 1951 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 48678778 48678778 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 125 25 ENST00000164024.4:c.9004C>T p.Arg3002Trp p.R3002W ENST00000164024 NM_001407.2 3002 Cgg/Tgg 0 0.652 CGCTGGGCCCGGCCCAGAGAA +COPB2 9276 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 139085462 139085462 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 11 ENST00000333188.5:c.1832C>T p.Pro611Leu p.P611L ENST00000333188 NM_004766.2 611 cCt/cTt 0 0.398 TGGAATGGTAGGAAGGACCTT +DNAJB14 79982 hgsc.bcm.edu;ucsc.edu GRCh37 4 100822294 100822294 + missense_variant Missense_Mutation SNP T T C TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 8 ENST00000442697.2:c.1031A>G p.Tyr344Cys p.Y344C ENST00000442697 NM_001278310.1 344 tAt/tGt 0 0.373 TTTTGCTGCATACTGCATATC +ABLIM3 22885 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 148617131 148617131 + missense_variant Missense_Mutation SNP T T C TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 117 29 ENST00000506113.1:c.1009T>C p.Ser337Pro p.S337P ENST00000506113 337 Tcc/Ccc 0 0.522 CAGATACATGTCCGACGAGAT +ATP10B 23120 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 160049524 160049524 + synonymous_variant Silent SNP G G T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 89 17 ENST00000327245.5:c.1689C>A p.Thr563= p.T563= ENST00000327245 NM_025153.2 563 acC/acA 0 0.488 TGTCTGACAAGGTCTCCAACC +PKHD1 5314 hgsc.bcm.edu;ucsc.edu GRCh37 6 51897876 51897876 + missense_variant Missense_Mutation SNP A A T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 6 ENST00000371117.3:c.3316T>A p.Leu1106Ile p.L1106I ENST00000371117 NM_138694.3 1106 Tta/Ata 0 0.383 ACTGGATTTAAGGAAGAGACA +MAP7 9053 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 136710581 136710581 + stop_gained Nonsense_Mutation SNP T T A TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 135 25 ENST00000454590.1:c.385A>T p.Lys129Ter p.K129* ENST00000454590 NM_001198614.1 129 Aag/Tag 0 0.542 AACCTCTTCTTCCGCTCTTCC +SYNE1 23345 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 152651648 152651648 + synonymous_variant Silent SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 60 11 ENST00000367255.5:c.14172G>A p.Ala4724= p.A4724= ENST00000367255 NM_182961.3 4724 gcG/gcA 0 0.552 CCCCAAGGCCCGCCACCTCGT +CDK13 8621 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 40102644 40102644 + missense_variant Missense_Mutation SNP A A G TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 14 ENST00000181839.4:c.2725A>G p.Thr909Ala p.T909A ENST00000181839 NM_031267.3 909 Act/Gct 0 0.333 CGAACTCTTCACTAAAAAACC +POM121L12 285877 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 53103839 53103839 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 11 ENST00000408890.4:c.475C>T p.Arg159Cys p.R159C ENST00000408890 NM_182595.3 159 Cgc/Tgc 0 0.721 ACAGAGAgcccgccccgcagg +VDAC3 7419 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 42259491 42259491 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 9 ENST00000521158.1:c.512C>T p.Ala171Val p.A171V ENST00000521158 171 gCc/gTc 0 0.463 AATAATTTCGCCCTGGGTTAC +GSDMD 79792 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 144642132 144642132 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 9 ENST00000526406.1:c.403C>T p.His135Tyr p.H135Y ENST00000526406 NM_001166237.1 135 Cat/Tat 0 0.537 GACTCTGCTCCATGAGAGGTG +SLC24A2 25769 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 19786146 19786146 + missense_variant Missense_Mutation SNP C C G TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 10 ENST00000341998.2:c.719G>C p.Arg240Pro p.R240P ENST00000341998 NM_001193288.2 240 cGa/cCa 0 0.393 AGACACATCTCGAAAGAGCGG +EXTL1 2134 broad.mit.edu;ucsc.edu GRCh37 1 26360306 26360306 + synonymous_variant Silent SNP C C T rs137944707 byFrequency TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 17 ENST00000374280.3:c.1638C>T p.Asn546= p.N546= ENST00000374280 NM_004455.2 546 aaC/aaT 0 0.597 AGAGGACCAACGAATTCTCCA +SPRYD3 84926 broad.mit.edu;ucsc.edu GRCh37 12 53468957 53468957 + missense_variant Missense_Mutation SNP A A C TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 173 27 ENST00000301463.4:c.293T>G p.Leu98Arg p.L98R ENST00000301463 NM_032840.2 98 cTg/cGg 0 0.562 CTGAGGGACCAGCCCCACAGC +LZTR1 8216 broad.mit.edu;ucsc.edu GRCh37 22 21347144 21347144 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 12 3 ENST00000215739.8:c.1211G>A p.Gly404Glu p.G404E ENST00000215739 NM_006767.3 404 gGg/gAg 0 0.652 TACATCTTCGGGGGCACGGTG +GSDMD 79792 broad.mit.edu;ucsc.edu GRCh37 8 144645068 144645068 + synonymous_variant Silent SNP C C A TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 5 ENST00000526406.1:c.1449C>A p.Pro483= p.P483= ENST00000526406 NM_001166237.1 483 ccC/ccA 0 0.667 GCCAGGAGCCCCACTAGCCTG +BMPR1B 658 broad.mit.edu;hgsc.bcm.edu GRCh37 4 96046194 96046194 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-HW-A5KK-01 TCGA-HW-A5KK-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 15 ENST00000440890.2:c.597delC p.Tyr199Ter p.Y199* ENST00000440890 199 taC/ta 0 0.408 ATGAAACTTACATTCCTCCTG +FOLH1 2346 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 49207240 49207240 + synonymous_variant Silent SNP T T C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 14 ENST00000256999.2:c.807A>G p.Thr269= p.T269= ENST00000256999 NM_004476.1 269 acA/acG 0 0.428 GGTAACCTGGTGTGAGAGGGT +OR5D14 219436 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 55563532 55563532 + synonymous_variant Silent SNP G G T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 191 37 ENST00000335605.1:c.501G>T p.Arg167= p.R167= ENST00000335605 NM_001004735.1 167 cgG/cgT 0 0.502 ATGCTCTCCGGTTAAACTTCT +APOA1 335 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 116707048 116707048 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 23 ENST00000236850.4:c.280G>A p.Glu94Lys p.E94K ENST00000236850 NM_000039.1 94 Gag/Aag 0 0.592 TCCCAGAACTCCTGGGTCACA +IRAK3 11213 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 66638280 66638280 + missense_variant Missense_Mutation SNP T T C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 18 ENST00000261233.4:c.902T>C p.Leu301Ser p.L301S ENST00000261233 NM_007199.2 301 tTg/tCg 0 0.393 AACATCCTTTTGGATGATCAG +KERA 11081 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 91449807 91449807 + synonymous_variant Silent SNP T T C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 13 ENST00000266719.3:c.252A>G p.Glu84= p.E84= ENST00000266719 NM_007035.3 84 gaA/gaG 0 0.348 CAGGAATGGTTTCTATCAGGT +TMCC3 57458 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 94975589 94975589 + synonymous_variant Silent SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 107 24 ENST00000261226.4:c.804C>T p.Asn268= p.N268= ENST00000261226 NM_020698.2 268 aaC/aaT 0 0.592 ACTGGTTTCCGTTACTGTCGG +ATP8A2 51761 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 26411309 26411309 + synonymous_variant Silent SNP C C A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 121 61 ENST00000381655.2:c.2763C>A p.Thr921= p.T921= ENST00000381655 NM_016529.4 921 acC/acA 0 0.498 AGATTTTCACCGCTTTGCCGC +MYO16 23026 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 109318372 109318372 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 14 ENST00000356711.2:c.101G>A p.Arg34His p.R34H ENST00000356711 NM_015011.1 34 cGc/cAc 0 0.527 TACTATGAGCGCGAGAAGGCT +CASC5 57082 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 40914116 40914116 + missense_variant Missense_Mutation SNP T T C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 10 ENST00000346991.5:c.1732T>C p.Ser578Pro p.S578P ENST00000346991 578 Tca/Cca 0 0.358 GCAGAGCCTGTCAAATCCTTT +TUBGCP4 27229 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 43695930 43695930 + missense_variant Missense_Mutation SNP C C T rs149549954 by1000genomes TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 23 ENST00000564079.1:c.1781C>T p.Ser594Leu p.S594L ENST00000564079 NM_014444.2 594 tCg/tTg 0 0.527 AGTTTTTGTTCGCTGGTCAGT +AP4E1 23431 hgsc.bcm.edu;broad.mit.edu GRCh37 15 51260560 51260560 + missense_variant Missense_Mutation SNP T T G TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 6 ENST00000261842.5:c.1952T>G p.Leu651Arg p.L651R ENST00000261842 NM_001252127.1 651 cTt/cGt 0 0.373 GAGGAAAAGCTTTCTCAGGAA +ACSM1 116285 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 20635526 20635526 + synonymous_variant Silent SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 22 ENST00000307493.4:c.1539C>T p.Ala513= p.A513= ENST00000307493 NM_052956.2 513 gcC/gcT 0 0.473 GGACAATAAAGGCCTTCACCA +DNAH2 146754 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7643864 7643864 + synonymous_variant Silent SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 129 20 ENST00000572933.1:c.1503C>T p.Arg501= p.R501= ENST00000572933 501 cgC/cgT 0 0.672 TTGCCTCCCGCGAGGTGCGGC +DNAJC7 7266 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 40140910 40140910 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 96 51 ENST00000457167.4:c.758C>T p.Ala253Val p.A253V ENST00000457167 NM_003315.3 253 gCc/gTc 0 0.423 GAGTGCTTTGGCATTCTACAG +CSHL1 1444 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 61987091 61987091 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 42 ENST00000309894.5:c.649G>A p.Glu217Lys p.E217K ENST00000309894 NM_022579.1 217 Gag/Aag 0 0.632 CAGCTGCCCTCCACAGAGCGG +LGALS3BP 3959 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 76967757 76967757 + synonymous_variant Silent SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 25 ENST00000262776.3:c.1659G>A p.Ser553= p.S553= ENST00000262776 NM_005567.3 553 tcG/tcA 0 0.612 AGGTGCTCTTCGAGCTGTTGG +LAMA3 3909 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 21489195 21489195 + missense_variant Missense_Mutation SNP A A G TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 13 ENST00000313654.9:c.7094A>G p.Asn2365Ser p.N2365S ENST00000313654 NM_198129.1 2365 aAc/aGc 0 0.453 CCCTTGGGAAACATCTCTGAC +TRAPPC8 22878 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 29433858 29433858 + missense_variant Missense_Mutation SNP G G C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 10 ENST00000283351.4:c.3387C>G p.Ser1129Arg p.S1129R ENST00000283351 NM_014939.3 1129 agC/agG 0 0.328 TCCAGTGTTTGCTACTACTTG +S1PR2 9294 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 10334891 10334891 + synonymous_variant Silent SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 15 ENST00000590320.1:c.691C>T p.Leu231= p.L231= ENST00000590320 NM_004230.3 231 Ctg/Ttg 0 0.617 GTCTTGAGCAGGGCTAGCGTC +ZNF585B 92285 hgsc.bcm.edu;broad.mit.edu GRCh37 19 37676803 37676803 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 109 18 ENST00000532828.2:c.1636G>A p.Gly546Arg p.G546R ENST00000532828 NM_152279.3 546 Gga/Aga 0 0.383 TGTCTCTCTCCAGTGTGAATT +FCGBP 8857 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 40368357 40368357 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 293 32 ENST00000221347.6:c.12991G>A p.Ala4331Thr p.A4331T ENST00000221347 NM_003890.2 4331 Gcc/Acc 0 0.647 GCCTGGCAGGCGGCCACGTAG +AJAP1 55966 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 4832380 4832380 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 11 ENST00000378191.4:c.958C>T p.Arg320Trp p.R320W ENST00000378191 NM_018836.3 320 Cgg/Tgg 0 0.607 CAGCCACCAGCGGAAGACCAA +CLSTN1 22883 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 9794036 9794036 + missense_variant Missense_Mutation SNP A A C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 19 ENST00000377298.4:c.2275T>G p.Phe759Val p.F759V ENST00000377298 NM_001009566.1 759 Ttc/Gtc 0 0.612 TTACCTGTGAAGGTCATGCCC +SPRR2G 6706 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 153122438 153122438 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 120 23 ENST00000368748.4:c.149C>T p.Pro50Leu p.P50L ENST00000368748 NM_001014291.3 50 cCa/cTa 0 0.567 ATCCTGGCATGGTGGAGGTGG +CD244 51744 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 160811431 160811431 + stop_gained Nonsense_Mutation SNP C C A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 102 26 ENST00000368033.3:c.322G>T p.Glu108Ter p.E108* ENST00000368033 108 Gag/Tag 0 0.453 CTGGTGACCTCCAGGCAGTAG +RXRG 6258 hgsc.bcm.edu;broad.mit.edu GRCh37 1 165398112 165398112 + missense_variant Missense_Mutation SNP A A C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 5 ENST00000359842.5:c.141T>G p.Asp47Glu p.D47E ENST00000359842 NM_001256570.1 47 gaT/gaG 0 0.607 TCACTGGGGTATCTGTGTAGC +SELE 6401 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 169697059 169697059 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 137 34 ENST00000333360.7:c.1289G>A p.Cys430Tyr p.C430Y ENST00000333360 NM_000450.2 430 tGc/tAc 0 0.498 GACAGCATCGCATCTCACAGC +EDEM3 80267 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 184695449 184695449 + synonymous_variant Silent SNP T T C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 15 ENST00000318130.8:c.687A>G p.Ala229= p.A229= ENST00000318130 NM_025191.3 229 gcA/gcG 0 0.388 TCAAGGTACCTGCACAAGCTG +GPR137B 7107 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 236341829 236341829 + stop_gained Nonsense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 180 58 ENST00000366592.3:c.580C>T p.Arg194Ter p.R194* ENST00000366592 NM_003272.3 194 Cga/Tga 0 0.478 CGTCTCTGTGCGAGTGGCCAT +RYR2 6262 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 237804239 237804239 + missense_variant Missense_Mutation SNP C C G TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 8 ENST00000366574.2:c.7158C>G p.Asn2386Lys p.N2386K ENST00000366574 NM_001035.2 2386 aaC/aaG 0 0.443 ACATGGGGAACGCGATCATGA +BCL11A 53335 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 60679728 60679728 + downstream_gene_variant 3'Flank SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 119 38 ENST00000335712 NM_022893.3 0 0.557 TAAGGGCTCTCGAGCTTCCAT +RND3 390 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 151326607 151326607 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 125 34 ENST00000375734.2:c.629C>T p.Ser210Leu p.S210L ENST00000375734 NM_001254738.1 210 tCa/tTa 0 0.458 GGCTCTCTGTGATTTGTTCCG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 74 18 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +BSN 8927 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 49691512 49691512 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 11 ENST00000296452.4:c.4523C>T p.Thr1508Met p.T1508M ENST00000296452 NM_003458.3 1508 aCg/aTg 0 0.622 TCTACACAGACGCCAAGTCCA +BSN 8927 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 49694614 49694614 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 14 ENST00000296452.4:c.7625C>T p.Thr2542Met p.T2542M ENST00000296452 NM_003458.3 2542 aCg/aTg 0 0.632 TCACTGCAAACGGAGGAGCAG +CACNA2D3 55799 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 54596855 54596855 + missense_variant Missense_Mutation SNP G G T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 10 ENST00000474759.1:c.573G>T p.Trp191Cys p.W191C ENST00000474759 NM_018398.2 191 tgG/tgT 0 0.403 GGGTTTATTGGTCTGAATCTC +SEL1L3 23231 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 25849135 25849135 + missense_variant Missense_Mutation SNP T T C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 9 ENST00000399878.3:c.514A>G p.Ile172Val p.I172V ENST00000399878 NM_015187.3 172 Ata/Gta 0 0.408 GCGCGTACTATCACTGCAGAT +SHROOM3 57619 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 77661578 77661578 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 5 ENST00000296043.6:c.2252C>T p.Pro751Leu p.P751L ENST00000296043 NM_020859.3 751 cCg/cTg 0 0.692 CCCTCGCACCCGCACACATCC +FRAS1 80144 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 79400621 79400621 + missense_variant Missense_Mutation SNP T T G TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 15 ENST00000264895.6:c.8192T>G p.Phe2731Cys p.F2731C ENST00000264895 NM_025074.6 2731 tTt/tGt 0 0.463 GGCTCTGATTTTAAATCTAGA +USP53 54532 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 120214081 120214081 + missense_variant Missense_Mutation SNP T T A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 9 ENST00000450251.1:c.2937T>A p.Asp979Glu p.D979E ENST00000450251 979 gaT/gaA 0 0.393 ATATGAATGATGAAAGACATA +PRDM5 11107 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 121698363 121698363 + missense_variant Missense_Mutation SNP A A C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 155 35 ENST00000264808.3:c.1517T>G p.Val506Gly p.V506G ENST00000264808 NM_018699.2 506 gTt/gGt 0 0.383 CCGGATATGAACTCTGAGTGT +GMDS 2762 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 1726688 1726688 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 194 37 ENST00000380815.4:c.949G>A p.Val317Met p.V317M ENST00000380815 NM_001500.3 317 Gtg/Atg 0 0.507 TCCACAGTCACGTGAACTTTG +GPR116 221395 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 46826760 46826760 + synonymous_variant Silent SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 114 16 ENST00000283296.7:c.2880G>A p.Arg960= p.R960= ENST00000283296 NM_001098518.1 960 agG/agA 0 0.478 TGTTGGCAAGCCTGAAGTTCC +NT5E 4907 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 86203685 86203685 + missense_variant Missense_Mutation SNP T T C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 14 ENST00000257770.3:c.1688T>C p.Leu563Pro p.L563P ENST00000257770 NM_002526.3 563 cTt/cCt 0 0.353 TTAATATTTCTTTCACTTTGG +RNGTT 8732 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 89563379 89563379 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 108 13 ENST00000369485.4:c.1001G>A p.Arg334His p.R334H ENST00000369485 NM_003800.3 334 cGt/cAt 0 0.289 TAAATGCATACGAAGATCTTT +TMEM200A 114801 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 130761742 130761742 + missense_variant Missense_Mutation SNP T T C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 93 61 ENST00000392429.1:c.175T>C p.Ser59Pro p.S59P ENST00000392429 NM_052913.2 59 Tcc/Ccc 0 0.478 CCGGCTTTATTCCCCATCTGG +FOXP2 93986 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 114282537 114282537 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 35 ENST00000408937.3:c.923G>A p.Gly308Asp p.G308D ENST00000408937 NM_014491.3 308 gGc/gAc 0 0.428 GAAGACAATGGCATTAAACAT +WNT2 7472 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 116960776 116960776 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 10 ENST00000265441.3:c.155G>A p.Arg52Gln p.R52Q ENST00000265441 NM_003391.2 52 cGg/cAg 0 0.597 ACACAGCTGCCGCTGGCTGCT +AKR1B10 57016 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 134212705 134212705 + synonymous_variant Silent SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 19 ENST00000359579.4:c.42C>T p.Pro14= p.P14= ENST00000359579 NM_020299.4 14 ccC/ccT 0 0.502 CCAAGATGCCCATTGTGGGCC +POLR3D 661 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 22107627 22107627 + missense_variant Missense_Mutation SNP C C A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 36 ENST00000397802.4:c.961C>A p.Leu321Met p.L321M ENST00000397802 321 Ctg/Atg 0 0.542 CCTGGCTGACCTGACAGAGGG +DOCK5 80005 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 25154057 25154057 + missense_variant Missense_Mutation SNP G G C TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 4 ENST00000276440.7:c.499G>C p.Asp167His p.D167H ENST00000276440 NM_024940.6 167 Gat/Cat 0 0.512 GGTGGTGCGAGATGACAATGG +NRG1 3084 hgsc.bcm.edu;ucsc.edu GRCh37 8 32600199 32600199 + synonymous_variant Silent SNP A A T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 205 39 ENST00000356819.4:c.639A>T p.Pro213= p.P213= ENST00000356819 NM_013956.3 213 ccA/ccT 0 0.423 TCAGGTGCCCAAATGAGTTTA +ANK1 286 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 41543690 41543690 + missense_variant Missense_Mutation SNP C C T rs138642972 byFrequency TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 81 29 ENST00000265709.8:c.4493G>A p.Arg1498His p.R1498H ENST00000265709 NM_001142446.1 1498 cGt/cAt 0 0.522 TTGGCCTTCACGGATGACCCA +CLVS1 157807 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 62371030 62371030 + synonymous_variant Silent SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 24 ENST00000519846.1:c.906C>T p.Ser302= p.S302= ENST00000519846 302 tcC/tcT 0 0.502 CTCACACATCCTATAATGCAA +COL5A1 1289 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 137591840 137591840 + synonymous_variant Silent SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 29 ENST00000371817.3:c.363C>T p.Asn121= p.N121= ENST00000371817 NM_001278074.1 121 aaC/aaT 0 0.587 CCATCTACAACGAGCAGGGTA +GYG2 8908 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 2799186 2799186 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 7 ENST00000381163.3:c.1438C>T p.Arg480Cys p.R480C ENST00000381163 NM_001079855.1 480 Cgt/Tgt 0 0.572 GGAGGAAGGCCGTATCGACTA +PRPS2 5634 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 12838861 12838861 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 76 19 ENST00000398491.2:c.812C>T p.Ala271Val p.A271V ENST00000398491 271 gCt/gTt 0 0.483 GCCTTTGAGGCTGTTGTCGTC +RS1 6247 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 18660177 18660177 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 28 ENST00000379984.3:c.622G>A p.Val208Ile p.V208I ENST00000379984 NM_000330.3 208 Gtc/Atc 0 0.657 GCAATGCGGACGTGCCAGCCC +POLA1 5422 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 24830876 24830876 + synonymous_variant Silent SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 24 ENST00000379059.3:c.3174G>A p.Leu1058= p.L1058= ENST00000379059 NM_016937.3 1058 ctG/ctA 0 0.393 ACGCTGCTCTGGTTGTTGAGC +FAM47B 170062 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 34962025 34962025 + synonymous_variant Silent SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 60 21 ENST00000329357.5:c.1077C>T p.Asp359= p.D359= ENST00000329357 NM_152631.2 359 gaC/gaT 0 0.537 AGCTGGAAGACGCACGGGCTC +FAM120C 54954 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 54209051 54209051 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 7 ENST00000375180.2:c.581C>T p.Ala194Val p.A194V ENST00000375180 NM_017848.4 194 gCg/gTg 0 0.721 GATCAGTTGCGCTGTCTGCCG +USP51 158880 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 55514135 55514135 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 15 ENST00000500968.3:c.1238C>T p.Ser413Leu p.S413L ENST00000500968 NM_201286.3 413 tCg/tTg 0 0.438 ATGAAAAAGCGAAGACATTTC +KIAA2022 340533 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 73963361 73963361 + missense_variant Missense_Mutation SNP G G T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 17 ENST00000055682.6:c.1031C>A p.Thr344Asn p.T344N ENST00000055682 NM_001008537.2 344 aCc/aAc 0 0.463 CTTGGGGCAGGTAGTAAAGAC +AMMECR1 9949 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 109459855 109459855 + missense_variant Missense_Mutation SNP A A G TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 21 ENST00000262844.5:c.590T>C p.Leu197Pro p.L197P ENST00000262844 NM_015365.2 197 cTt/cCt 0 0.378 GCTATCTTTAAGGGCACTGTT +CFP 5199 broad.mit.edu;ucsc.edu GRCh37 X 47487019 47487019 + missense_variant Missense_Mutation SNP C C A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 7 ENST00000247153.3:c.425G>T p.Trp142Leu p.W142L ENST00000247153 NM_002621.2 142 tGg/tTg 0 0.632 CCAGGGCCCCCAGCCAGACCA +OBSCN 84033 broad.mit.edu;ucsc.edu GRCh37 1 228404888 228404888 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 113 15 ENST00000570156.2:c.2552C>T p.Thr851Met p.T851M ENST00000570156 NM_001271223.2 851 aCg/aTg 0 0.652 GATGTGGGGACGCGGCACCGG +ZDBF2 57683 broad.mit.edu;ucsc.edu GRCh37 2 207169761 207169761 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 9 ENST00000374423.3:c.509C>T p.Ala170Val p.A170V ENST00000374423 NM_020923.1 170 gCt/gTt 0 0.423 ATTGGTCAGGCTACAAATAAT +SP100 6672 broad.mit.edu;ucsc.edu GRCh37 2 231367785 231367785 + synonymous_variant Silent SNP A A G TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 18 ENST00000340126.4:c.1725A>G p.Arg575= p.R575= ENST00000340126 NM_001080391.1 575 agA/agG 0 0.289 TCTCAGGAAGAAAAGCCAACA +SERPINB11 89778 broad.mit.edu;ucsc.edu GRCh37 18 61387343 61387343 + missense_variant Missense_Mutation SNP A A T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 8 ENST00000544088.1:c.572A>T p.Lys191Ile p.K191I ENST00000544088 NM_080475.2 191 aAa/aTa 0 0.348 TGGCAAAATAAATTTCAAGTA +SELENOF 9403 broad.mit.edu;ucsc.edu GRCh37 1 87369113 87369113 + stop_gained Nonsense_Mutation SNP C C A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 12 ENST00000331835.5:c.94G>T p.Glu32Ter p.E32* ENST00000331835 NM_004261.3 32 Gag/Tag 0 0.418 GATGAAAACTCTGCCCCAAAA +OR9G1 390174 broad.mit.edu;ucsc.edu GRCh37 11 56468417 56468417 + missense_variant Missense_Mutation SNP A A G TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 130 29 ENST00000312153.1:c.554A>G p.Glu185Gly p.E185G ENST00000312153 NM_001005213.1 185 gAg/gGg 0 0.463 CCCTTGGTGGAGCTGGCCTGT +ADAMTS18 170692 broad.mit.edu;ucsc.edu GRCh37 16 77401350 77401350 + stop_gained Nonsense_Mutation SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 20 ENST00000282849.5:c.766C>T p.Arg256Ter p.R256* ENST00000282849 NM_199355.2 256 Cga/Tga 0 0.443 TTCTTGCGTCGTCCACAAAAA +PCSK2 5126 broad.mit.edu;ucsc.edu GRCh37 20 17446133 17446133 + missense_variant Missense_Mutation SNP G G T TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 6 ENST00000262545.2:c.1365G>T p.Met455Ile p.M455I ENST00000262545 NM_002594.3 455 atG/atT 0 0.567 TGGTGAAAATGGCTAAAGACT +CISH 1154 broad.mit.edu;ucsc.edu GRCh37 3 50645154 50645154 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 104 23 ENST00000443053.2:c.712C>T p.Arg238Cys p.R238C ENST00000443053 NM_013324.5 238 Cgc/Tgc 0 0.622 TGCAGGCTGCGGGCACTGCTT +HTR1E 3354 broad.mit.edu;ucsc.edu GRCh37 6 87725427 87725427 + synonymous_variant Silent SNP C C A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 129 18 ENST00000305344.5:c.375C>A p.Thr125= p.T125= ENST00000305344 NM_000865.2 125 acC/acA 0 0.562 GGGCCATCACCAATGCTATTG +TNXB 7148 broad.mit.edu;ucsc.edu GRCh37 6 32049264 32049264 + upstream_gene_variant 5'Flank SNP G G A TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 4 ENST00000516703 0 0.617 CTCATCCCCCGCAACAGGCAC +TP53 7157 broad.mit.edu;hgsc.bcm.edu GRCh37 17 7577105 7577105 + frameshift_variant Frame_Shift_Del DEL G G - TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 38 ENST00000269305.4:c.833delC p.Pro278LeufsTer67 p.P278Lfs*67 ENST00000269305 NM_001126112.2 278 cCt/ct 0 0.552 GTCTCTCCCAGGACAGGCACA +EMILIN2 84034 broad.mit.edu;hgsc.bcm.edu GRCh37 18 2891806 2891806 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 23 ENST00000254528.3:c.1682delC p.Pro561LeufsTer23 p.P561Lfs*23 ENST00000254528 NM_032048.2 561 Cct/ct 0 0.502 CCAGGGAAAGCCTCATGGGAT +CYTH4 27128 broad.mit.edu;hgsc.bcm.edu GRCh37 22 37705324 37705326 + inframe_deletion In_Frame_Del DEL CTT CTT - TCGA-CS-6665-01 TCGA-CS-6665-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 45 ENST00000248901.6:c.772_774delTTC p.Phe258del p.F258del ENST00000248901 NM_013385.3 256 acCTTc/acc 0 0.567 TCACTCACACCTTCTTCAATCCA +AK7 122481 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 96944967 96944967 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 60 43 ENST00000267584.4:c.1721T>C p.Phe574Ser p.F574S ENST00000267584 NM_152327.3 574 tTt/tCt 0 0.478 TTCAACTATTTTGATGAACTT +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 by1000genomes TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 4 14 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 0 0.542 GGCACAAACACGCACCTCAAA +MYH2 4620 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 10429940 10429940 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 195 61 ENST00000245503.5:c.4163G>A p.Arg1388His p.R1388H ENST00000245503 NM_017534.5 1388 cGc/cAc 0 0.512 CTCCTCTGTGCGCTGGATGGC +TUBG1 7283 hgsc.bcm.edu;broad.mit.edu GRCh37 17 40767042 40767042 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 4 ENST00000251413.3:c.1339G>A p.Gly447Ser p.G447S ENST00000251413 NM_001070.4 447 Ggc/Agc 0 0.582 CATCTCCTGGGGCACCCAGGA +PRDM16 63976 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 3342279 3342279 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 156 16 ENST00000270722.5:c.3074G>A p.Arg1025Gln p.R1025Q ENST00000270722 1025 cGg/cAg 0 0.662 AACCTGGACCGGCACCTCAAG +SLC16A4 9122 hgsc.bcm.edu;ucsc.edu GRCh37 1 110921952 110921952 + missense_variant Missense_Mutation SNP C C T rs35157487 byFrequency TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 16 ENST00000369779.4:c.553G>A p.Ala185Thr p.A185T ENST00000369779 NM_001201547.1 185 Gca/Aca 0 0.378 AAATTCAATGCGATAGCTCCA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 38 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +PLCH1 23007 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 155200712 155200712 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 41 ENST00000340059.7:c.3127A>G p.Ile1043Val p.I1043V ENST00000340059 NM_001130960.1 1043 Att/Gtt 0 0.458 GTAGATACAATGGTGTCCCCT +ANXA10 11199 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 169105805 169105805 + synonymous_variant Silent SNP T T C TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 96 57 ENST00000359299.3:c.879T>C p.Tyr293= p.Y293= ENST00000359299 NM_007193.4 293 taT/taC 0 0.353 AAGAGCGATATGGAAAATCCC +PRDM9 56979 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 23526872 23526872 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 31 ENST00000296682.3:c.1675C>T p.Arg559Trp p.R559W ENST00000296682 NM_020227.2 559 Cgg/Tgg 0 0.527 GGAGTGTGGGCGGGGCTTTAG +HCN1 348980 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 45262356 45262356 + synonymous_variant Silent SNP G G T TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 21 ENST00000303230.4:c.2340C>A p.Thr780= p.T780= ENST00000303230 NM_021072.3 780 acC/acA 0 0.632 TGACTTCCCGGGTCAGGTTGG +DHX29 54505 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 54577281 54577281 + synonymous_variant Silent SNP G G C TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 40 ENST00000251636.5:c.2028C>G p.Leu676= p.L676= ENST00000251636 NM_019030.2 676 ctC/ctG 0 0.393 TTGTACAATAGAGTAACCTGG +UNC5CL 222643 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 40996311 40996311 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 34 ENST00000244565.3:c.1358C>A p.Pro453His p.P453H ENST00000244565 NM_173561.2 453 cCc/cAc 0 0.672 GGCCGCTGCGGGGCTGCGCTG +ADAM28 10863 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 24201057 24201057 + synonymous_variant Silent SNP A A G TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 34 ENST00000265769.4:c.1950A>G p.Gly650= p.G650= ENST00000265769 NM_014265.4 650 ggA/ggG 0 0.498 GTGAGGAAGGATGGATCCCTC +PKHD1L1 93035 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 110408325 110408325 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 12 ENST00000378402.5:c.881T>C p.Phe294Ser p.F294S ENST00000378402 NM_177531.4 294 tTc/tCc 0 0.403 AGTGGGCGTTTCTTTGATCAG +EPPK1 83481 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 144941387 144941387 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 15 ENST00000525985.1:c.6035C>A p.Ala2012Asp p.A2012D ENST00000525985 NM_031308.2 2012 gCc/gAc 0 0.627 ACCCCCCGTGGCCACCTGCAC +CCNB3 85417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 50055581 50055581 + missense_variant Missense_Mutation SNP T T A TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 156 23 ENST00000376042.1:c.3372T>A p.Ser1124Arg p.S1124R ENST00000376042 1124 agT/agA 0 0.383 GTGATCCAAGTTTCAACCCAA +UBAP1 51271 broad.mit.edu;ucsc.edu GRCh37 9 34250662 34250662 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 19 ENST00000545103.1:c.1465G>T p.Asp489Tyr p.D489Y ENST00000545103 NM_001171201.1 489 Gac/Tac 0 0.468 TTAGATTCTCGACTATCTCTT +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76920224 76920224 + frameshift_variant Frame_Shift_Del DEL A A - TCGA-HT-7686-01 TCGA-HT-7686-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 13 ENST00000373344.5:c.3853delT p.Ser1285ProfsTer61 p.S1285Pfs*61 ENST00000373344 NM_000489.3 1285 Tcc/cc 0 0.373 TCATCAGAGGAAAGATTGGCT +MPP7 143098 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 28345529 28345529 + synonymous_variant Silent SNP T T C TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 50 ENST00000337532.5:c.1431A>G p.Leu477= p.L477= ENST00000337532 NM_173496.3 477 ctA/ctG 0 0.333 GCTTAAATTCTAGTGTCCTTA +OR52I2 143502 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 4608789 4608789 + missense_variant Missense_Mutation SNP C C G TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 64 ENST00000312614.4:c.747C>G p.Ile249Met p.I249M ENST00000312614 NM_001005170.2 249 atC/atG 0 0.488 CCTCCTATATCTTAATTCTCA +OR51L1 119682 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 5021019 5021019 + synonymous_variant Silent SNP T T C TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 5 ENST00000321543.1:c.807T>C p.His269= p.H269= ENST00000321543 NM_001004755.1 269 caT/caC 0 0.463 TTGGGAAGCATCTGTCTCCCA +MRGPRX3 117195 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 18159642 18159642 + missense_variant Missense_Mutation SNP C C T TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 11 28 ENST00000396275.2:c.893C>T p.Thr298Met p.T298M ENST00000396275 NM_054031.3 298 aCg/aTg 0 0.562 CTGCAGGACACGCCTGAGGTG +OR9G4 283189 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 56510829 56510829 + synonymous_variant Silent SNP G G A rs149257582 TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 191 15 ENST00000302957.3:c.459C>T p.Thr153= p.T153= ENST00000302957 NM_001005284.1 153 acC/acT 0 0.478 TACAGAGGGCGGTGGACATGG +PTGR2 145482 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 74347933 74347933 + missense_variant Missense_Mutation SNP A A G TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 51 ENST00000555661.1:c.877A>G p.Lys293Glu p.K293E ENST00000555661 293 Aaa/Gaa 0 0.358 ATTAAATTATAAAGACAAATT +ISLR 3671 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 74467824 74467824 + missense_variant Missense_Mutation SNP G G A TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 14 ENST00000249842.3:c.625G>A p.Ala209Thr p.A209T ENST00000249842 NM_005545.3 209 Gcc/Acc 0 0.652 GGACAACATCGCCTGCACCTC +CRAMP1L 57585 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 1706072 1706072 + synonymous_variant Silent SNP C C T TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 10 ENST00000397412.3:c.1314C>T p.Asp438= p.D438= ENST00000397412 438 gaC/gaT 0 0.706 GTGCCAAGGACGCCCACGTGC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 26 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 0 0.572 GATGGGCCTCCGGTTCATGCC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578263 7578263 + stop_gained Nonsense_Mutation SNP G G A TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 25 ENST00000269305.4:c.586C>T p.Arg196Ter p.R196* ENST00000269305 NM_001126112.2 196 Cga/Tga 0 0.552 CCTTCCACTCGGATAAGATGC +ZC3H4 23211 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 47570840 47570840 + synonymous_variant Silent SNP G G A TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 13 ENST00000253048.5:c.2685C>T p.Ala895= p.A895= ENST00000253048 NM_015168.1 895 gcC/gcT 0 0.701 AGGTGGGCAGGGCGCGAGCCA +HIVEP3 59269 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 41978828 41978828 + missense_variant Missense_Mutation SNP C C T TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 31 ENST00000372583.1:c.6064G>A p.Gly2022Ser p.G2022S ENST00000372583 NM_024503.4 2022 Ggc/Agc 0 0.632 GGGAGAGCGCCCATGCCCCTT +CD1E 913 hgsc.bcm.edu;ucsc.edu GRCh37 1 158325319 158325319 + synonymous_variant Silent SNP G G A TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 4 ENST00000368167.3:c.585G>A p.Ala195= p.A195= ENST00000368167 NM_030893.3 195 gcG/gcA 0 0.478 GATTTCTAGCGGGGCTCATGG +OR2T1 26696 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 248570030 248570030 + synonymous_variant Silent SNP C C T rs148427102 TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 36 ENST00000366474.1:c.735C>T p.Tyr245= p.Y245= ENST00000366474 NM_030904.1 245 taC/taT 0 0.493 CAGCCCTCTACGAGACAGTGA +MYH7B 57644 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 33581234 33581234 + missense_variant Missense_Mutation SNP G G A TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 14 ENST00000262873.7:c.2531G>A p.Arg844His p.R844H ENST00000262873 NM_020884.3 844 cGc/cAc 0 0.672 AGCCGTGGCCGCCTCATGCGC +DGCR2 9993 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 19026633 19026633 + splice_region_variant,synonymous_variant Splice_Region SNP G G A rs146027196 TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 14 ENST00000263196.7:c.1398C>T p.Asp466= p.D466= ENST00000263196 NM_001184781.1 466 gaC/gaT 0 0.622 AAGCATCATCGTCTGCAGGAA +APOB 338 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 21226157 21226157 + missense_variant Missense_Mutation SNP C C T rs149273387 TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 242 122 ENST00000233242.1:c.12137G>A p.Arg4046Gln p.R4046Q ENST00000233242 NM_000384.2 4046 cGg/cAg 0 0.408 ATCAGATTCCCGGACCCTCAA +SCN2A 6326 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 166211024 166211024 + missense_variant Missense_Mutation SNP G G C TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 30 ENST00000357398.3:c.3242G>C p.Ser1081Thr p.S1081T ENST00000357398 1081 aGt/aCt 0 0.388 ATAGGCAGCAGTGTAGAAAAA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 28 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +ANKRD28 23243 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 15719776 15719776 + missense_variant Missense_Mutation SNP C C T TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 17 ENST00000399451.2:c.2557G>A p.Asp853Asn p.D853N ENST00000399451 NM_015199.3 853 Gac/Aac 0 0.398 CCTGTAGAGTCCACAGAATTG +SATB1 6304 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 18435971 18435971 + missense_variant Missense_Mutation SNP C C A TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 104 47 ENST00000417717.2:c.1189G>T p.Ala397Ser p.A397S ENST00000417717 NM_001195470.1 397 Gct/Tct 0 0.433 CTGTTAAAAGCCACACGTGCA +SLC4A7 9497 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 27439832 27439832 + missense_variant Missense_Mutation SNP G G C TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 50 ENST00000295736.5:c.2413C>G p.Leu805Val p.L805V ENST00000295736 NM_003615.4 805 Ctt/Gtt 0 0.363 ACACCACGAAGTTTTTTACAT +MYH15 22989 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 108195254 108195254 + missense_variant Missense_Mutation SNP G G A TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 28 ENST00000273353.3:c.1283C>T p.Thr428Ile p.T428I ENST00000273353 NM_014981.1 428 aCt/aTt 0 0.338 CTGTTCTATAGTTTGACCTCT +HCN1 348980 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 45262407 45262407 + synonymous_variant Silent SNP C C T TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 33 ENST00000303230.4:c.2289G>A p.Pro763= p.P763= ENST00000303230 NM_021072.3 763 ccG/ccA 0 0.652 CTTCATTTTTCGGCGTGGAGC +ERAP2 64167 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 96215430 96215430 + missense_variant Missense_Mutation SNP C C T TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 8 ENST00000437043.3:c.41C>T p.Pro14Leu p.P14L ENST00000437043 NM_001130140.1 14 cCa/cTa 0 0.373 CACAGAAAACCAATGTTTAAC +LIMK1 3984 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 73511062 73511062 + missense_variant Missense_Mutation SNP C C G TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 18 ENST00000336180.2:c.263C>G p.Ser88Cys p.S88C ENST00000336180 NM_002314.3 88 tCt/tGt 0 0.597 CATGGGTGCTCTGAGCAAATC +LRRCC1 85444 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 86021973 86021973 + missense_variant Missense_Mutation SNP T T G TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 12 9 ENST00000360375.3:c.248T>G p.Leu83Arg p.L83R ENST00000360375 NM_033402.4 83 cTa/cGa 0 0.323 ATTGAAGGACTAAACACACTG +RASEF 158158 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 85607825 85607825 + missense_variant Missense_Mutation SNP G G C TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 184 82 ENST00000376447.3:c.2036C>G p.Ala679Gly p.A679G ENST00000376447 NM_152573.3 679 gCc/gGc 0 0.473 TCTTACCATGGCCAGTTTCTC +ZNF189 7743 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 104170609 104170609 + missense_variant Missense_Mutation SNP C C T TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 112 37 ENST00000339664.2:c.559C>T p.Arg187Cys p.R187C ENST00000339664 NM_001278240.1 187 Cgc/Tgc 0 0.413 AAGTTTTAGTCGCAGTTCATT +CAMSAP1 157922 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 138713009 138713009 + synonymous_variant Silent SNP G G A TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 112 107 ENST00000389532.4:c.3498C>T p.Phe1166= p.F1166= ENST00000389532 NM_015447.3 1166 ttC/ttT 0 0.567 TGTAACTGTCGAAGAGACACT +PBDC1 51260 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 75396760 75396760 + missense_variant Missense_Mutation SNP C C G TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 34 ENST00000373358.3:c.342C>G p.Asp114Glu p.D114E ENST00000373358 NM_016500.3 114 gaC/gaG 0 0.423 TTGTTGAAGACTTCAACTATG +ATRX 546 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 76940431 76940431 + missense_variant,splice_region_variant Missense_Mutation SNP C C T TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 36 ENST00000373344.5:c.662G>A p.Arg221Lys p.R221K ENST00000373344 NM_000489.3 221 aGg/aAg 0 0.328 TATTACCTACCTACATTGTTC +PLS3 5358 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 114882253 114882253 + missense_variant Missense_Mutation SNP T T G TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 108 66 ENST00000420625.2:c.1676T>G p.Ile559Ser p.I559S ENST00000420625 NM_001136025.3 559 aTt/aGt 0 0.403 GTGGATTTAATTGATGCCATC +ZNF275 10838 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 152612569 152612569 + synonymous_variant Silent SNP G G A TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 19 ENST00000370251.3:c.426G>A p.Ala142= p.A142= ENST00000370251 NM_001080485.3 142 gcG/gcA 0 0.607 GGGGGGTGGCGGAGTTTAATG +CANT1 124583 broad.mit.edu;ucsc.edu GRCh37 17 76991172 76991172 + missense_variant Missense_Mutation SNP C C T TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 3 3 ENST00000302345.2:c.763G>A p.Gly255Ser p.G255S ENST00000302345 NM_001159773.1 255 Ggc/Agc 0 0.652 TCCACGCTGCCCTTGTAGCCC +AKAP5 9495 broad.mit.edu;hgsc.bcm.edu GRCh37 14 64936370 64936374 + frameshift_variant Frame_Shift_Del DEL AATAA AATAA - TCGA-HW-8319-01 TCGA-HW-8319-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 21 ENST00000394718.4:c.1264_1268delATAAA p.Ile422GlnfsTer18 p.I422Qfs*18 ENST00000394718 NM_004857.3 420 AATAAa/a 0 0.341 CTCTGATGATAATAAAATAAACAAT +FAM186B 84070 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 49992644 49992644 + missense_variant Missense_Mutation SNP A A G rs140386687 byFrequency TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 66 ENST00000257894.2:c.2258T>C p.Ile753Thr p.I753T ENST00000257894 NM_032130.2 753 aTt/aCt 0 0.537 CAGGCGGTCAATGTTTTCCAG +VRK1 7443 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 97321577 97321577 + missense_variant Missense_Mutation SNP A A G TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 106 78 ENST00000216639.3:c.593A>G p.Tyr198Cys p.Y198C ENST00000216639 NM_003384.2 198 tAt/tGt 0 0.393 TTGGTAGATTATGGCCTTGCT +TNFAIP2 7127 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 103599762 103599762 + missense_variant Missense_Mutation SNP C C T TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 43 ENST00000560869.1:c.1609C>T p.Arg537Cys p.R537C ENST00000560869 537 Cgc/Tgc 0 0.622 CAGCAAGGGGCGCCTGGTCCT +TAT 6898 hgsc.bcm.edu;broad.mit.edu GRCh37 16 71602180 71602180 + missense_variant Missense_Mutation SNP T T C TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 3 ENST00000355962.4:c.1232A>G p.Glu411Gly p.E411G ENST00000355962 NM_000353.2 411 gAg/gGg 0 0.502 ATTCGGGTACTCAAAGCACTG +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 by1000genomes TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 30 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 0 0.542 GGCACAAACACGCACCTCAAA +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578466 7578466 + missense_variant Missense_Mutation SNP G G T TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 49 ENST00000269305.4:c.464C>A p.Thr155Asn p.T155N ENST00000269305 NM_001126112.2 155 aCc/aAc 0 0.612 GCGGACGCGGGTGCCGGGCGG +DSG4 147409 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 28983444 28983444 + missense_variant Missense_Mutation SNP C C T TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 28 ENST00000359747.4:c.1483C>T p.Pro495Ser p.P495S ENST00000359747 NM_001134453.1 495 Cca/Tca 0 0.383 TGATTATTGTCCAAACATTTT +NUMBL 9253 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 41183289 41183289 + missense_variant Missense_Mutation SNP G G C TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 18 ENST00000252891.4:c.578C>G p.Ala193Gly p.A193G ENST00000252891 NM_004756.3 193 gCc/gGc 0 0.697 CAGGCAGGCGGCAAAAGCACA +ITPKC 80271 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 41223412 41223412 + synonymous_variant Silent SNP A A C TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 42 ENST00000263370.2:c.372A>C p.Leu124= p.L124= ENST00000263370 NM_025194.2 124 ctA/ctC 0 0.607 GGACGCATCTAGAATGGAGCT +LILRA2 11027 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 55086405 55086405 + missense_variant Missense_Mutation SNP C C T rs74454618 TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 109 99 ENST00000251377.3:c.560C>T p.Pro187Leu p.P187L ENST00000251377 187 cCg/cTg 0 0.587 CCCGTGAGCCCGAGTCGCAGG +MYOM3 127294 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 24419503 24419503 + missense_variant Missense_Mutation SNP G G A TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 19 ENST00000374434.3:c.1024C>T p.Leu342Phe p.L342F ENST00000374434 NM_152372.3 342 Ctc/Ttc 0 0.637 ACCATGTAGAGCCCCTCGTCC +ZCCHC11 23318 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 52889613 52889613 + synonymous_variant Silent SNP C C T TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 16 ENST00000257177.4:c.4932G>A p.Ser1644= p.S1644= ENST00000257177 1644 tcG/tcA 0 0.507 CGCATTACTCCGACACGTTTC +FCRL3 115352 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 157665373 157665373 + missense_variant Missense_Mutation SNP G G T TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 24 ENST00000368184.3:c.1157C>A p.Thr386Asn p.T386N ENST00000368184 NM_052939.3 386 aCc/aAc 0 0.557 AGCCCTGAAGGTGAGGACAGG +FMO1 2326 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 171254528 171254528 + missense_variant Missense_Mutation SNP G G A TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 41 ENST00000354841.4:c.1444G>A p.Glu482Lys p.E482K ENST00000354841 NM_001282692.1 482 Gaa/Aaa 0 0.502 AGGAAAATGGGAAGGAGCCAG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 40 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +IL17RC 84818 hgsc.bcm.edu;broad.mit.edu GRCh37 3 9959040 9959040 + missense_variant Missense_Mutation SNP G G A rs112532783 byFrequency TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 6 ENST00000295981.3:c.41G>A p.Arg14Gln p.R14Q ENST00000295981 NM_153461.3 14 cGa/cAa 0 0.657 GCACTGGGCCGAAGCCCAGTG +HMGN3 9324 hgsc.bcm.edu;ucsc.edu GRCh37 6 79944270 79944270 + missense_variant Missense_Mutation SNP T T G TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 178 17 ENST00000344726.5:c.8A>C p.Lys3Thr p.K3T ENST00000344726 NM_004242.3 3 aAg/aCg 0 0.502 TACCTTTCTCTTCGGCATAAT +LINGO2 158038 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 27950110 27950110 + missense_variant Missense_Mutation SNP C C T TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 45 ENST00000379992.2:c.560G>A p.Cys187Tyr p.C187Y ENST00000379992 NM_152570.2 187 tGc/tAc 0 0.483 TGTTAAGTTGCATTTCTCCAG +MYO10 4651 broad.mit.edu;ucsc.edu GRCh37 5 16694555 16694555 + missense_variant Missense_Mutation SNP C C T TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 179 24 ENST00000513610.1:c.3725G>A p.Arg1242His p.R1242H ENST00000513610 NM_012334.2 1242 cGc/cAc 0 0.567 CTTGGACTGGCGGAGGACAAA +LACC1 144811 broad.mit.edu;hgsc.bcm.edu GRCh37 13 44455647 44455647 + frameshift_variant Frame_Shift_Del DEL G G - TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 51 ENST00000441843.1:c.527delG p.Gly176GlufsTer3 p.G176Efs*3 ENST00000441843 NM_001128303.1 176 Gga/ga 0 0.328 AGCACTGAGAGGAAAATTAAC +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76938749 76938765 + frameshift_variant Frame_Shift_Del DEL GTCGCCTCAAGGGTGTA GTCGCCTCAAGGGTGTA - TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 90 ENST00000373344.5:c.1983_1999delTACACCCTTGAGGCGAC p.Thr662AspfsTer4 p.T662Dfs*4 ENST00000373344 NM_000489.3 661 acTACACCCTTGAGGCGACcg/accg 0 0.373 GTTTCTGTCGGTCGCCTCAAGGGTGTAGTCTTTACAC +ATRX 546 hgsc.bcm.edu GRCh37 X 76938765 76938765 + synonymous_variant Silent SNP A A G TCGA-DB-5280-01 TCGA-DB-5280-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 6 ENST00000373344.5:c.1983T>C p.Thr661= p.T661= ENST00000373344 NM_000489.3 661 acT/acC 0 0.383 TCAAGGGTGTAGTCTTTACAC +RET 5979 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 43609023 43609023 + synonymous_variant Silent SNP A A G TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 8 ENST00000355710.3:c.1779A>G p.Gly593= p.G593= ENST00000355710 NM_020975.4 593 ggA/ggG 0 0.642 TTGTTGGGGGACACGAGCCTG +ABTB2 25841 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 34176285 34176285 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 139 108 ENST00000435224.2:c.2729C>T p.Thr910Ile p.T910I ENST00000435224 NM_145804.2 910 aCa/aTa 0 0.592 CATGGATTCTGTTCCTCCGTA +CTTN 2017 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 70261803 70261803 + missense_variant Missense_Mutation SNP A A G TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 362 212 ENST00000376561.3:c.437A>G p.Glu146Gly p.E146G ENST00000376561 NM_001184740.1 146 gAg/gGg 0 0.532 GGGAAGACTGAGAAGCATGCC +CWF19L2 143884 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 107299708 107299708 + missense_variant Missense_Mutation SNP G G T TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 527 42 ENST00000282251.5:c.1250C>A p.Thr417Lys p.T417K ENST00000282251 NM_152434.2 417 aCa/aAa 0 0.418 ACTCCATGATGTTAATCTTTC +LRIG3 121227 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 59271321 59271321 + synonymous_variant Silent SNP C C T TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 81 52 ENST00000320743.3:c.2397G>A p.Ser799= p.S799= ENST00000320743 NM_153377.4 799 tcG/tcA 0 0.562 CATCGTCTAACGATGGGGCTG +TNRC6A 27327 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 24826581 24826581 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 112 71 ENST00000395799.3:c.4786C>T p.Arg1596Cys p.R1596C ENST00000395799 NM_014494.2 1596 Cgt/Tgt 0 0.448 TGGCTGGCCACGTGCCAAATC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578442 7578442 + missense_variant Missense_Mutation SNP T T C rs148924904 TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 139 ENST00000269305.4:c.488A>G p.Tyr163Cys p.Y163C ENST00000269305 NM_001126112.2 163 tAc/tGc 0 0.622 TGACTGCTTGTAGATGGCCAT +NEK8 284086 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 27065006 27065006 + synonymous_variant Silent SNP C C T TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 45 ENST00000268766.6:c.1059C>T p.Leu353= p.L353= ENST00000268766 NM_178170.2 353 ctC/ctT 0 0.701 CTGGGCGTCTCATCCTGTGGG +SESN2 83667 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 28598956 28598956 + synonymous_variant Silent SNP C C T TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 100 63 ENST00000253063.3:c.516C>T p.Leu172= p.L172= ENST00000253063 NM_031459.4 172 ctC/ctT 0 0.652 GGCCATGGCTCATCACCAAGG +HRNR 388697 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 152192510 152192510 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 414 45 ENST00000368801.2:c.1595G>A p.Arg532Gln p.R532Q ENST00000368801 NM_001009931.2 532 cGa/cAa 0 0.567 AGACCCATGTCGGCTGTGTCC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 118 54 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +DAW1 164781 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 228750104 228750104 + missense_variant Missense_Mutation SNP G G C TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 258 19 ENST00000309931.2:c.78G>C p.Lys26Asn p.K26N ENST00000309931 NM_178821.1 26 aaG/aaC 0 0.343 GAGAATTAAAGACTAAGTCCA +OR5H6 79295 hgsc.bcm.edu;broad.mit.edu GRCh37 3 97983515 97983515 + synonymous_variant Silent SNP T T C TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 290 26 ENST00000383696.2:c.387T>C p.Phe129= p.F129= ENST00000383696 NM_001005479.1 129 ttT/ttC 0 0.368 CAGAATGTTTTCTCTTGGCAA +PDE6B 5158 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 659049 659049 + synonymous_variant Silent SNP A A G TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 21 ENST00000496514.1:c.2199A>G p.Ala733= p.A733= ENST00000496514 733 gcA/gcG 0 0.627 TCCAGGTCGCACTTCTCGTGG +FOXP4 116113 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 41554783 41554783 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 9 ENST00000373060.1:c.547C>T p.Leu183Phe p.L183F ENST00000373060 NM_001012426.1 183 Ctc/Ttc 0 0.662 CCAGCAGCAGCTCCTGCAAAT +LAMA2 3908 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 129475728 129475728 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 111 83 ENST00000421865.2:c.1106G>A p.Arg369His p.R369H ENST00000421865 NM_001079823.1 369 cGt/cAt 0 0.388 TTGAATATACGTGGAAAGTAC +MACC1 346389 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 20198861 20198861 + missense_variant Missense_Mutation SNP A A G TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 95 66 ENST00000400331.5:c.1123T>C p.Tyr375His p.Y375H ENST00000400331 NM_182762.3 375 Tat/Cat 0 0.398 TTGGGTCCATAAATTCCAATT +SH2D3C 10044 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 130507277 130507277 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 189 24 ENST00000314830.8:c.1366G>A p.Ala456Thr p.A456T ENST00000314830 NM_170600.2 456 Gcc/Acc 0 0.662 GTCTTTGGGGCACTTCCGGGA +MAP7D3 79649 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 135323365 135323365 + missense_variant Missense_Mutation SNP T T A TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 137 91 ENST00000316077.9:c.489A>T p.Arg163Ser p.R163S ENST00000316077 NM_024597.3 163 agA/agT 0 0.323 CCCATGACCATCTTTTTTGCT +FLOT1 10211 broad.mit.edu;ucsc.edu GRCh37 6 30708275 30708275 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs139987312 byFrequency TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 143 106 ENST00000376389.3:c.568C>T p.Arg190Trp p.R190W ENST00000376389 NM_005803.2 190 Cgg/Tgg 0 0.532 TCTCTCACCCGGATCCCAGCA +WNT9B 7484 broad.mit.edu;ucsc.edu GRCh37 17 44953783 44953783 + missense_variant Missense_Mutation SNP G G A rs149931425 by1000genomes TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 89 54 ENST00000290015.2:c.773G>A p.Arg258His p.R258H ENST00000290015 NM_003396.1 258 cGc/cAc 0 0.642 GCCTTGGGCCGCCTAGAGCTG +LIMCH1 22998 broad.mit.edu;ucsc.edu GRCh37 4 41646515 41646515 + splice_acceptor_variant Splice_Site SNP A A C TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 10 ENST00000313860.7:c.972-2A>C p.X324_splice ENST00000313860 NM_014988.2 0 0.672 CTCCACACTCAGGAGCACCAG +C3P1 388503 broad.mit.edu;ucsc.edu GRCh37 19 10165979 10165979 + non_coding_transcript_exon_variant RNA SNP G G A TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 116 16 ENST00000497718.1:n.2693G>A *898* ENST00000497718 0 0.592 CACCTCCAAGGGGAACCCAGG +OR2T1 26696 broad.mit.edu;hgsc.bcm.edu GRCh37 1 248570073 248570073 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 164 36 ENST00000366474.1:c.779delC p.Pro260LeufsTer4 p.P260Lfs*4 ENST00000366474 NM_030904.1 260 Cct/ct 0 0.507 GCTGCTGATTCCTTTCTCTGT +FAM208B 54906 broad.mit.edu;hgsc.bcm.edu GRCh37 10 5784139 5784140 + frameshift_variant Frame_Shift_Del DEL AA AA - TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 217 70 ENST00000328090.5:c.2407_2408delAA p.Asn803SerfsTer25 p.N803Sfs*25 ENST00000328090 NM_017782.4 803 AAt/t 0 0.396 GTTTTACAGCAATCAGAACAAA +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76944356 76944356 + frameshift_variant Frame_Shift_Del DEL T T - TCGA-E1-5322-01 TCGA-E1-5322-10 Untested Somatic Phase_I WXS none Illumina GAIIx 231 157 ENST00000373344.5:c.549delA p.Asp184IlefsTer22 p.D184Ifs*22 ENST00000373344 NM_000489.3 183 aaA/aa 0 0.353 AAATGGAATCTTTTTGAAAAT +ANKK1 255239 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 113267965 113267965 + synonymous_variant Silent SNP C C T TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 10 ENST00000303941.3:c.858C>T p.Asp286= p.D286= ENST00000303941 NM_178510.1 286 gaC/gaT 0 0.582 TCGAGACAGACATACTGCTGT +FMNL3 91010 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 50043069 50043069 + synonymous_variant Silent SNP A A G TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 99 18 ENST00000335154.5:c.2358T>C p.Tyr786= p.Y786= ENST00000335154 NM_175736.4 786 taT/taC 0 0.572 GCTTGAAGCCATACACAGCTC +PTPN11 5781 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 112888197 112888197 + missense_variant Missense_Mutation SNP T T A TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 50 ENST00000351677.2:c.213T>A p.Phe71Leu p.F71L ENST00000351677 NM_002834.3 71 ttT/ttA 0 0.418 GGGAGAAATTTGCCACTTTGG +NPAP1 23742 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 24921605 24921605 + synonymous_variant Silent SNP C C T TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 6 ENST00000329468.2:c.591C>T p.Asp197= p.D197= ENST00000329468 NM_018958.2 197 gaC/gaT 0 0.592 CCCAGGGAGACGTGGCCTCCT +VPS9D1 9605 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 89785502 89785502 + synonymous_variant Silent SNP G G A TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 114 19 ENST00000389386.3:c.108C>T p.Tyr36= p.Y36= ENST00000389386 NM_004913.2 36 taC/taT 0 0.552 GGTATTCCGTGTATGCCTCCT +NF1 4763 hgsc.bcm.edu;broad.mit.edu GRCh37 17 29576001 29576001 + splice_acceptor_variant Splice_Site SNP G G A TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 48 ENST00000358273.4:c.3975-1G>A p.X1325_splice ENST00000358273 NM_001042492.2 0 0.368 TTTTTTTGTAGGTTAGAACCA +DMRTC2 63946 hgsc.bcm.edu;ucsc.edu GRCh37 19 42354645 42354645 + synonymous_variant Silent SNP C C T TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 28 ENST00000269945.3:c.868C>T p.Leu290= p.L290= ENST00000269945 NM_001040283.1 290 Ctg/Ttg 0 0.637 AGAGTGGCAGCTGCAGCAAGA +ABCA4 24 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 94528252 94528252 + synonymous_variant Silent SNP G G T TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 10 ENST00000370225.3:c.1818C>A p.Gly606= p.G606= ENST00000370225 NM_000350.2 606 ggC/ggA 0 0.562 AGGCAAACCCGCCCCAGATGT +TET2 54790 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 106155166 106155166 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 11 ENST00000380013.4:c.67C>T p.Pro23Ser p.P23S ENST00000380013 NM_001127208.2 23 Ccc/Tcc 0 0.527 ACCATCACCTCCCATTTGCCA +NAA15 80155 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 140262069 140262069 + stop_gained Nonsense_Mutation SNP G G A TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 26 ENST00000296543.5:c.248G>A p.Trp83Ter p.W83* ENST00000296543 NM_057175.3 83 tGg/tAg 0 0.363 TCTTTAGGTTGGCACGTTTAT +DUSP22 56940 hgsc.bcm.edu;broad.mit.edu GRCh37 6 348272 348272 + stop_gained,splice_region_variant Nonsense_Mutation SNP C C T TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 140 15 ENST00000344450.5:c.433C>T p.Gln145Ter p.Q145* ENST00000344450 NM_020185.3 145 Cag/Tag 0 0.577 TGAGGTCCATCAGGTAAGCAG +DNAH8 1769 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 38810444 38810444 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 25 ENST00000359357.3:c.3959G>A p.Arg1320His p.R1320H ENST00000359357 1320 cGt/cAt 0 0.323 GAAAGATGTCGTAAACTTCCA +EXOC4 60412 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 133749244 133749244 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 21 ENST00000253861.4:c.2888A>G p.Lys963Arg p.K963R ENST00000253861 NM_021807.3 963 aAg/aGg 0 0.572 GCTGCCATCAAGCAAGCCACC +UBR5 51366 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 103266680 103266680 + synonymous_variant Silent SNP G G A TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 11 ENST00000520539.1:c.8250C>T p.Pro2750= p.P2750= ENST00000520539 NM_015902.5 2750 ccC/ccT 0 0.408 TTGTGATTGAGGGCATAGGCT +KLHL25 64410 broad.mit.edu;ucsc.edu GRCh37 15 86311637 86311637 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 140 17 ENST00000337975.5:c.1405G>A p.Glu469Lys p.E469K ENST00000337975 NM_022480.3 469 Gag/Aag 0 0.602 CACCTGTTCTCCGAGGGGTCA +OR10C1 442194 broad.mit.edu;ucsc.edu GRCh37 6 29407957 29407957 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 164 20 ENST00000444197.2:c.165G>T p.Gln55His p.Q55H ENST00000444197 NM_013941.3 55 caG/caT 0 0.567 CTGCCCTCCAGTCCCCTATGT +EMC10 284361 broad.mit.edu;ucsc.edu GRCh37 19 50981247 50981247 + stop_gained Nonsense_Mutation SNP C C G TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 3 ENST00000334976.6:c.176C>G p.Ser59Ter p.S59* ENST00000334976 NM_206538.2 59 tCa/tGa 0 0.607 CTGGAGCACTCATTTGAGATC +PSME4 23198 broad.mit.edu;hgsc.bcm.edu GRCh37 2 54148047 54148049 + inframe_deletion In_Frame_Del DEL AGG AGG - TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 22 ENST00000404125.1:c.2239_2241delCCT p.Pro747del p.P747del ENST00000404125 NM_014614.2 747 CCT/- 0 0.374 AGTATTCAGAAGGAGGCTTGTCA +PLA2G15 23659 broad.mit.edu;hgsc.bcm.edu GRCh37 16 68293167 68293171 + frameshift_variant Frame_Shift_Del DEL CGTGC CGTGC - rs142263893 TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 16 ENST00000219345.5:c.846_850delCGTGC p.Phe282LeufsTer22 p.F282Lfs*22 ENST00000219345 NM_012320.3 282 ttCGTGCag/ttag 0 0.58 AGAAGGTGTTCGTGCAGACACCCAC +ATRX 546 broad.mit.edu GRCh37 X 76814303 76814306 + frameshift_variant Frame_Shift_Del DEL ATAA ATAA - TCGA-HT-7857-01 TCGA-HT-7857-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 18 ENST00000373344.5:c.6338_6341delTTAT p.Phe2113SerfsTer9 p.F2113Sfs*9 ENST00000373344 NM_000489.3 2113 tTTATc/tc 0 0.289 AGTAGAAATGATAAATAATCGTCC +CNNM1 26507 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 101124220 101124220 + missense_variant Missense_Mutation SNP A A G TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 9 ENST00000356713.4:c.2075A>G p.Asn692Ser p.N692S ENST00000356713 NM_020348.2 692 aAt/aGt 0 0.423 CGCTTTGAAAATGGAGCCTTT +ACACB 32 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 109616926 109616926 + missense_variant Missense_Mutation SNP C C G TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 17 ENST00000338432.7:c.1471C>G p.Leu491Val p.L491V ENST00000338432 491 Ctc/Gtc 0 0.562 GCCCATCTTTCTCATGAAGCT +ACSF3 197322 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 89180794 89180794 + missense_variant Missense_Mutation SNP A A G TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 104 33 ENST00000317447.4:c.1025A>G p.Lys342Arg p.K342R ENST00000317447 NM_174917.3 342 aAg/aGg 0 0.647 GTGCTGGAGAAGTGGAAGAAC +MED24 9862 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 38188968 38188968 + missense_variant Missense_Mutation SNP G G T TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 23 ENST00000394128.2:c.870C>A p.Phe290Leu p.F290L ENST00000394128 NM_014815.3 290 ttC/ttA 0 0.577 TGAGCCCCACGAAGCAAGCTT +ARRDC5 645432 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 4891396 4891396 + missense_variant Missense_Mutation SNP G G C TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 13 ENST00000381781.2:c.691C>G p.Gln231Glu p.Q231E ENST00000381781 NM_001080523.1 231 Cag/Gag 0 0.587 CCCTCGTACTGTATGTGGGCA +PPP1R13L 10848 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 45895364 45895364 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 12 ENST00000418234.2:c.1589C>T p.Ala530Val p.A530V ENST00000418234 NM_001142502.1 530 gCc/gTc 0 0.687 CACAGCAGGGGCCTGCTCCAT +EXTL1 2134 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 26349229 26349229 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 11 31 ENST00000374280.3:c.92G>A p.Arg31His p.R31H ENST00000374280 NM_004455.2 31 cGc/cAc 0 0.657 TCCCTTCTCCGCCTGGCATTG +G0S2 50486 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 209849305 209849305 + synonymous_variant Silent SNP C C T TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 13 ENST00000367029.4:c.276C>T p.Gly92= p.G92= ENST00000367029 NM_015714.3 92 ggC/ggT 0 0.667 CGGTCCTCGGCGGCCGGGCCC +RYR2 6262 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 237957283 237957283 + synonymous_variant Silent SNP C C T TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 16 ENST00000366574.2:c.13899C>T p.Leu4633= p.L4633= ENST00000366574 NM_001035.2 4633 ctC/ctT 0 0.363 GGGATAGACTCGTAATCAACA +LAMA5 3911 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 60888747 60888747 + synonymous_variant Silent SNP G G A TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 96 76 ENST00000252999.3:c.8616C>T p.Asp2872= p.D2872= ENST00000252999 NM_005560.4 2872 gaC/gaT 0 0.662 AGACGAAGTCGTCTGGCCGCA +FZD7 8324 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 202900715 202900715 + missense_variant Missense_Mutation SNP C C T TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 41 ENST00000286201.1:c.1345C>T p.Arg449Cys p.R449C ENST00000286201 NM_003507.1 449 Cgt/Tgt 0 0.612 GTCCCTCTTCCGTATCCGCAC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 25 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +ECT2 1894 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 172501694 172501694 + missense_variant Missense_Mutation SNP C C T TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 18 ENST00000392692.3:c.1723C>T p.Leu575Phe p.L575F ENST00000392692 NM_001258315.1 575 Ctc/Ttc 0 0.274 TCATGCTTTTCTCAAGGTAAT +ABCE1 6059 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 146044497 146044497 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 41 ENST00000296577.4:c.1505G>A p.Arg502Gln p.R502Q ENST00000296577 NM_002940.2 502 cGa/cAa 0 0.383 ATGGCAGCTCGAGTTGTCAAA +PHF3 23469 hgsc.bcm.edu;broad.mit.edu GRCh37 6 64423124 64423124 + synonymous_variant Silent SNP C C G TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 155 12 ENST00000262043.3:c.5640C>G p.Gly1880= p.G1880= ENST00000262043 1880 ggC/ggG 0 0.507 GGTATATAGGCCCGCAGAATT +SLC26A4 5172 hgsc.bcm.edu;broad.mit.edu GRCh37 7 107314667 107314667 + synonymous_variant Silent SNP C C T TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 5 ENST00000265715.3:c.474C>T p.Asp158= p.D158= ENST00000265715 NM_000441.1 158 gaC/gaT 0 0.433 TGGCCCCCGACGAACACTTTC +SVEP1 79987 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 113194246 113194246 + missense_variant Missense_Mutation SNP A A G TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 29 ENST00000401783.2:c.5302T>C p.Tyr1768His p.Y1768H ENST00000401783 NM_153366.3 1768 Tac/Cac 0 0.378 GAACATATGTAGGATCCATCT +XPNPEP2 7512 broad.mit.edu;ucsc.edu GRCh37 X 128879232 128879232 + synonymous_variant Silent SNP A A T TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 3 ENST00000371106.3:c.288A>T p.Thr96= p.T96= ENST00000371106 NM_003399.5 96 acA/acT 0 0.488 CAGGCTTTACAGGGTCTGCAG +TACR3 6870 broad.mit.edu;ucsc.edu GRCh37 4 104510918 104510918 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 107 70 ENST00000304883.2:c.1319C>T p.Ser440Phe p.S440F ENST00000304883 NM_001059.2 440 tCt/tTt 0 0.478 ATTCCTGCGAGAGCAGCCATT +CREB3 10488 broad.mit.edu;ucsc.edu GRCh37 9 35736644 35736644 + missense_variant Missense_Mutation SNP A A C TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 199 75 ENST00000353704.2:c.1037A>C p.Gln346Pro p.Q346P ENST00000353704 NM_006368.4 346 cAg/cCg 0 0.567 CTCCCCCTGCAGGCAAATCTC +ITSN1 6453 broad.mit.edu;ucsc.edu GRCh37 21 35183494 35183494 + synonymous_variant Silent SNP G G A TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 40 ENST00000381318.3:c.2535G>A p.Thr845= p.T845= ENST00000381318 NM_003024.2 845 acG/acA 0 0.547 AGCCCTCCACGACCCCTAATA +SLC1A7 6512 broad.mit.edu;hgsc.bcm.edu GRCh37 1 53553683 53553684 + frameshift_variant,stop_lost Frame_Shift_Del DEL AG AG - TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 18 ENST00000371494.4:c.1680_1681delCT p.Ter561SerfsTer41 p.*561Sfs*41 ENST00000371494 NM_006671.4 560 gtCTga/gtga 0 0.663 CCGCAGGCTCAGACATTGGTCT +CTNNB1 1499 broad.mit.edu;hgsc.bcm.edu GRCh37 3 41275294 41275294 + frameshift_variant Frame_Shift_Del DEL T T - TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 164 105 ENST00000349496.5:c.1461delT p.His488ThrfsTer19 p.H488Tfs*19 ENST00000349496 NM_001904.3 487 cTt/ct 0 0.493 GCAGTTCGCCTTCACTATGGA +PRAG1 157285 broad.mit.edu;hgsc.bcm.edu GRCh37 8 8234817 8234819 + inframe_deletion In_Frame_Del DEL TCA TCA - TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 15 ENST00000520004.1:c.1100_1102delTGA p.Met367del p.M367del ENST00000520004 367 aTGAag/aag 0 0.68 GCAGGTTCCTTCATGAGGGAGCA +KAT6B 23522 broad.mit.edu;hgsc.bcm.edu GRCh37 10 76784946 76784949 + frameshift_variant Frame_Shift_Del DEL ACAA ACAA - TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 14 ENST00000287239.4:c.3606_3609delAACA p.Thr1203ArgfsTer21 p.T1203Rfs*21 ENST00000287239 NM_001256468.1 1201 agACAA/ag 0 0.451 GGAAGAAAAGACAAACAGAGGAAG +RBBP6 5930 broad.mit.edu;hgsc.bcm.edu GRCh37 16 24567746 24567747 + stop_gained,frameshift_variant Nonsense_Mutation INS - - A TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 14 ENST00000319715.4:c.653dupA p.Tyr218Ter p.Y218* ENST00000319715 NM_006910.4 218 tat/tAat 0 0.401 CACTGGAAAATATGCAATACCA +ZACN 353174 broad.mit.edu;hgsc.bcm.edu GRCh37 17 74075804 74075805 + frameshift_variant Frame_Shift_Ins INS - - CC TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 21 ENST00000334586.5:c.245_246dupCC p.Ser83ProfsTer58 p.S83Pfs*58 ENST00000334586 NM_180990.3 82 tcc/tCCcc 0 0.569 ATACACAATGTCCTCCATGCTG +CIC 23152 broad.mit.edu;hgsc.bcm.edu GRCh37 19 42797776 42797777 + frameshift_variant Frame_Shift_Del DEL GC GC - TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 10 ENST00000575354.2:c.3831_3832delCG p.Val1278ProfsTer65 p.V1278Pfs*65 ENST00000575354 NM_015125.3 1276 tgGCgc/tggc 0 0.649 CTTCAGACTGGCGCGTCCCTGG +CIC 23152 broad.mit.edu GRCh37 19 42798989 42798990 + frameshift_variant Frame_Shift_Ins INS - - A rs148444899 TCGA-QH-A65Z-01 TCGA-QH-A65Z-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 8 ENST00000575354.2:c.4473_4474insA p.Ala1492SerfsTer22 p.A1492Sfs*22 ENST00000575354 NM_015125.3 1491 -/A 0 0.574 AGGCCACAGCCGCCTTCCAGGC +CAMK1D 57118 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 12803041 12803041 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 13 ENST00000378847.3:c.394G>A p.Val132Met p.V132M ENST00000378847 NM_153498.2 132 Gtg/Atg 0 0.577 CTTGGACGCCGTGTACTATCT +MYO3A 53904 hgsc.bcm.edu;broad.mit.edu GRCh37 10 26359114 26359114 + synonymous_variant Silent SNP T T C TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 4 ENST00000265944.5:c.1245T>C p.Tyr415= p.Y415= ENST00000265944 NM_017433.4 415 taT/taC 0 0.318 ACTTAGGATATCAATCTATGA +HPS1 3257 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 100185433 100185433 + missense_variant Missense_Mutation SNP A A C TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 15 ENST00000325103.6:c.1200T>G p.Asp400Glu p.D400E ENST00000325103 NM_000195.3 400 gaT/gaG 0 0.692 TGGAGAAGCCATCCATCAGCT +CBX5 23468 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 54635636 54635636 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 45 ENST00000209875.4:c.479G>A p.Cys160Tyr p.C160Y ENST00000209875 NM_012117.2 160 tGt/tAt 0 0.398 AATTTGTGGACATTTCACATT +MIPEP 4285 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 24444199 24444199 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 54 ENST00000382172.3:c.739G>A p.Asp247Asn p.D247N ENST00000382172 NM_005932.3 247 Gat/Aat 0 0.393 ATGATATGATCCCCAGCAGAT +ZDHHC7 55625 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 85010046 85010046 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 17 ENST00000564466.1:c.941G>A p.Gly314Glu p.G314E ENST00000564466 NM_001145548.1 314 gGg/gAg 0 0.572 TGAGGGGGGCCCCCCAAAGAC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7579362 7579362 + missense_variant Missense_Mutation SNP A A C TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 54 ENST00000269305.4:c.325T>G p.Phe109Val p.F109V ENST00000269305 NM_001126112.2 109 Ttc/Gtc 0 0.612 CCCAGACGGAAACCGTAGCTG +ACACA 31 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 35640173 35640173 + missense_variant Missense_Mutation SNP T T C TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 15 ENST00000353139.5:c.605A>G p.Asn202Ser p.N202S ENST00000353139 NM_198834.1 202 aAt/aGt 0 0.408 CTCACCTGCATTGGCTTTAAG +HNF1B 6928 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 36059196 36059196 + synonymous_variant Silent SNP G G A TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 7 ENST00000225893.4:c.1539C>T p.Tyr513= p.Y513= ENST00000225893 NM_001165923.1 513 taC/taT 0 0.532 GCTTGTGTGCGTACACTGGAG +FPGT 8790 hgsc.bcm.edu;ucsc.edu GRCh37 1 74670899 74670899 + missense_variant Missense_Mutation SNP C C A TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 11 ENST00000609362.1:c.1168C>A p.Pro390Thr p.P390T ENST00000609362 390 Cca/Aca 0 0.388 TAGTATCTTTCCAGATATACC +USP25 29761 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 17246819 17246819 + missense_variant Missense_Mutation SNP T T C TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 182 34 ENST00000285679.6:c.2773T>C p.Ser925Pro p.S925P ENST00000285679 NM_013396.3 925 Tca/Cca 0 0.328 AGAATTGATATCACATTATAG +CYP26B1 56603 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 72359586 72359586 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 20 ENST00000001146.2:c.1309G>A p.Gly437Ser p.G437S ENST00000001146 NM_019885.3 437 Ggt/Agt 0 0.647 GTCCGGACACCGCCACCGAAC +SCN1A 6323 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 166872165 166872165 + missense_variant Missense_Mutation SNP C C T rs146374754 TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 87 54 ENST00000303395.4:c.3502G>A p.Val1168Ile p.V1168I ENST00000303395 1168 Gta/Ata 0 0.413 GGTTCCACTACGGGCTGTTCT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 24 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +LMCD1 29995 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 8590439 8590439 + synonymous_variant Silent SNP C C T TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 34 ENST00000157600.3:c.573C>T p.Ser191= p.S191= ENST00000157600 NM_014583.3 191 agC/agT 0 0.587 AATATAAGAGCGAGGCCCTCG +FAM134B 54463 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 16475174 16475174 + synonymous_variant Silent SNP C C T TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 38 ENST00000306320.9:c.1170G>A p.Thr390= p.T390= ENST00000306320 NM_001034850.2 390 acG/acA 0 0.493 CTGCTGATTGCGTCTCTTTGC +CHDC2 286464 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 36091355 36091355 + missense_variant Missense_Mutation SNP C C A TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 30 ENST00000313548.4:c.290C>A p.Ser97Tyr p.S97Y ENST00000313548 NM_173695.2 97 tCt/tAt 0 0.433 CAATTCCTTTCTCTTGAGGAA +HNRNPH2 3188 hgsc.bcm.edu;broad.mit.edu GRCh37 X 100667035 100667035 + missense_variant Missense_Mutation SNP G G T TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 99 5 ENST00000316594.5:c.59G>T p.Trp20Leu p.W20L ENST00000316594 NM_001199974.1 20 tGg/tTg 0 0.527 GGCCTACCCTGGTCCTGCTCA +IGF2R 3482 broad.mit.edu;ucsc.edu GRCh37 6 160501242 160501242 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 44 ENST00000356956.1:c.5768C>T p.Ala1923Val p.A1923V ENST00000356956 NM_000876.2 1923 gCg/gTg 0 0.557 GAGAGCAGGGCGAAGCTGTGG +GATA3 2625 broad.mit.edu;ucsc.edu GRCh37 10 8100437 8100437 + synonymous_variant Silent SNP G G A TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 33 ENST00000346208.3:c.411G>A p.Ser137= p.S137= ENST00000346208 137 tcG/tcA 0 0.716 CCCCGGCCTCGTCCTCCTCCT +HELZ 9931 broad.mit.edu;ucsc.edu GRCh37 17 65105677 65105677 + synonymous_variant Silent SNP A A G TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 43 ENST00000358691.5:c.4044T>C p.Ala1348= p.A1348= ENST00000358691 NM_014877.3 1348 gcT/gcC 0 0.473 GTGCGTGGGGAGCAGGAAGGG +PDK1 5163 broad.mit.edu;ucsc.edu GRCh37 2 173423525 173423525 + missense_variant Missense_Mutation SNP C C G TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 30 ENST00000282077.3:c.286C>G p.Leu96Val p.L96V ENST00000282077 96 Ctc/Gtc 0 0.393 AGAAATAAGTCTCCTTCCAGA +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76939340 76939343 + frameshift_variant Frame_Shift_Del DEL CTAC CTAC - TCGA-DU-6407-01 TCGA-DU-6407-10 Untested Somatic Phase_I WXS none Illumina GAIIx 277 132 ENST00000373344.5:c.1405_1408delGTAG p.Val469IlefsTer44 p.V469Ifs*44 ENST00000373344 NM_000489.3 469 GTAGat/at 0 0.358 TGCTCACTATCTACCTGTTTTCTT +PLAC9 219348 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 81901857 81901857 + synonymous_variant Silent SNP T T A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 10 ENST00000372263.3:c.84T>A p.Pro28= p.P28= ENST00000372263 NM_001012973.1 28 ccT/ccA 0 0.532 CCTTCAGCCCTCCGCGAGGAG +OR4S2 219431 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 55419308 55419308 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 90 62 ENST00000312422.2:c.929G>T p.Gly310Val p.G310V ENST00000312422 NM_001004059.2 310 gGg/gTg 0 0.363 GAGGCTAAAGGGAAATAGTTG +FAT3 120114 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 92624025 92624025 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 23 ENST00000298047.6:c.13516G>T p.Val4506Leu p.V4506L ENST00000298047 4506 Gtg/Ttg 0 0.582 AACGGATTTGGTGGGCCCGCC +TUBGCP3 10426 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 113181323 113181323 + synonymous_variant Silent SNP A A C TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 9 ENST00000261965.3:c.1488T>G p.Val496= p.V496= ENST00000261965 NM_006322.4 496 gtT/gtG 0 0.398 GATCATGACAAACTTGGTGCA +DLGAP5 9787 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 55643912 55643912 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 19 ENST00000247191.2:c.917C>T p.Ser306Phe p.S306F ENST00000247191 NM_014750.4 306 tCc/tTc 0 0.383 AGGTGCAAAGGAATTCTTCCC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578394 7578394 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 74 ENST00000269305.4:c.536A>G p.His179Arg p.H179R ENST00000269305 NM_001126112.2 179 cAt/cGt 0 0.642 GCAGCGCTCATGGTGGGGGCA +MYO15A 51168 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 18022907 18022907 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 41 ENST00000205890.5:c.793G>A p.Gly265Ser p.G265S ENST00000205890 NM_016239.3 265 Ggc/Agc 0 0.652 GGCGGGCCTCGGCCCCTACAG +VEZF1 7716 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 56060673 56060673 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 94 77 ENST00000581208.1:c.115G>C p.Asp39His p.D39H ENST00000581208 NM_007146.2 39 Gat/Cat 0 0.473 GGTTTCTGATCAGGGGGCTCC +DNAI2 64446 hgsc.bcm.edu;broad.mit.edu GRCh37 17 72301394 72301394 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 111 11 ENST00000446837.2:c.1024G>A p.Val342Ile p.V342I ENST00000446837 342 Gtc/Atc 0 0.577 GCAGGGCATCGTCATCTCCTG +NUDT19 390916 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 33183087 33183087 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 9 ENST00000397061.3:c.221C>T p.Ala74Val p.A74V ENST00000397061 NM_001105570.1 74 gCg/gTg 0 0.751 GACCGCTCGGCGGACTGGCTG +CROCC 9696 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 17264170 17264170 + missense_variant Missense_Mutation SNP G G C rs141704732 TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 6 ENST00000375541.5:c.1228G>C p.Glu410Gln p.E410Q ENST00000375541 NM_014675.3 410 Gag/Cag 0 0.572 GAAGCGTCTTGAGAAGCAGAA +FCRL5 83416 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 157514077 157514077 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 155 134 ENST00000361835.3:c.819C>A p.Ser273Arg p.S273R ENST00000361835 NM_001195388.1 273 agC/agA 0 0.512 AGGATCTCGGGCTGTCAGATA +PTGS2 5743 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 186643728 186643728 + synonymous_variant Silent SNP A A G TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 111 21 ENST00000367468.5:c.1572T>C p.Val524= p.V524= ENST00000367468 NM_000963.2 524 gtT/gtC 0 0.458 GAGAACATATAACATTACCCA +LAD1 3898 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 201352455 201352455 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 201 70 ENST00000391967.2:c.1238C>T p.Thr413Met p.T413M ENST00000391967 NM_005558.3 413 aCg/aTg 0 0.597 CCGTATGGCCGTGTGGTATCT +RYR2 6262 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 237804274 237804274 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 14 19 ENST00000366574.2:c.7193T>C p.Leu2398Pro p.L2398P ENST00000366574 NM_001035.2 2398 cTc/cCc 0 0.453 TTGATTGACCTCTTGGGACGC +SPATA2 9825 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 48523042 48523042 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 18 ENST00000422556.1:c.677C>T p.Ser226Leu p.S226L ENST00000422556 NM_001135773.1 226 tCa/tTa 0 0.672 TGCCACTCGTGACATGGAGGC +SCUBE1 80274 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 43606074 43606074 + synonymous_variant Silent SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 47 ENST00000360835.4:c.2556C>T p.Gly852= p.G852= ENST00000360835 NM_173050.3 852 ggC/ggT 0 0.632 CCAGAACATCGCCGCACTCAT +GPR45 11250 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 105858985 105858985 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 23 ENST00000258456.1:c.670A>G p.Lys224Glu p.K224E ENST00000258456 NM_007227.3 224 Aag/Gag 0 0.672 CACGGTCCGCAAGAACGCCGT +TTN 7273 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 179588855 179588855 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 8 13 ENST00000589042.1:c.21131C>T p.Pro7044Leu p.P7044L ENST00000589042 NM_001267550.1 7044 cCc/cTc 0 0.423 TGTGAAAGAGGGAGGAACTGC +DNAH7 56171 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 196749379 196749379 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 16 ENST00000312428.6:c.5693C>T p.Thr1898Ile p.T1898I ENST00000312428 NM_018897.2 1898 aCa/aTa 0 0.358 CTTTGAGGATGTTTGCTCAGT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 28 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +ANKMY1 51281 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 241468460 241468460 + missense_variant Missense_Mutation SNP T T G TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 124 26 ENST00000391987.1:c.680A>C p.Lys227Thr p.K227T ENST00000391987 227 aAg/aCg 0 0.522 TCACCTGAACTTGTAAGTTTG +NBEAL2 23218 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 47038035 47038035 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 7 ENST00000450053.3:c.2426T>C p.Phe809Ser p.F809S ENST00000450053 NM_015175.2 809 tTt/tCt 0 0.657 GTGGCCATCTTTCACGAAGCC +P2RY12 64805 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 151056104 151056104 + missense_variant Missense_Mutation SNP A A T TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 22 ENST00000302632.3:c.530T>A p.Phe177Tyr p.F177Y ENST00000302632 NM_022788.4 177 tTc/tAc 0 0.368 TGATTTAAGGAAAGAGCATTT +RGS12 6002 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 3318009 3318009 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 184 19 ENST00000344733.5:c.112G>A p.Gly38Arg p.G38R ENST00000344733 NM_198229.2 38 Gga/Aga 0 0.637 CACGCTTTCGGGACAGGCACC +FRYL 285527 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 48536663 48536663 + synonymous_variant Silent SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 37 ENST00000358350.4:c.6604C>T p.Leu2202= p.L2202= ENST00000358350 NM_015030.1 2202 Cta/Tta 0 0.313 ATAATCTGTAGTAATGATTGC +C4orf21 55345 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 113475127 113475127 + missense_variant Missense_Mutation SNP C C A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 133 16 ENST00000505019.1:c.5210G>T p.Gly1737Val p.G1737V ENST00000505019 NM_018392.4 1737 gGc/gTc 0 0.313 ATTTTCTGAGCCAGCATGCAA +BBS12 166379 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 123664898 123664898 + synonymous_variant Silent SNP A A G TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 16 ENST00000542236.1:c.1851A>G p.Thr617= p.T617= ENST00000542236 NM_001178007.1 617 acA/acG 0 0.363 AAGCCAGCACATACATTCAAC +TRIML2 205860 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 189018488 189018488 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 44 ENST00000512729.1:c.484T>C p.Ser162Pro p.S162P ENST00000512729 NM_173553.1 162 Tct/Cct 0 0.383 CTTTCTAAAGAGTATTTTGCA +CDH9 1007 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 26881636 26881636 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 40 ENST00000231021.4:c.1979A>G p.Asn660Ser p.N660S ENST00000231021 NM_016279.3 660 aAc/aGc 0 0.428 GCCTTCATCGTTGTAGGTCAC +EGFLAM 133584 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 38338820 38338820 + synonymous_variant Silent SNP C C T rs142461042 TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 27 ENST00000354891.3:c.228C>T p.Gly76= p.G76= ENST00000354891 NM_001205301.1 76 ggC/ggT 0 0.532 CTGAGGTTGGCGCAGATAAAT +SLC26A2 1836 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 149357883 149357883 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 49 ENST00000286298.4:c.668G>A p.Ser223Asn p.S223N ENST00000286298 NM_000112.3 223 aGc/aAc 0 0.353 ATGGTTGGCAGCACTGTAACC +PGK2 5232 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 49754106 49754106 + synonymous_variant Silent SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 143 26 ENST00000304801.3:c.795C>T p.Ile265= p.I265= ENST00000304801 NM_138733.4 265 atC/atT 0 0.418 TATCTTTAACGATCTTGGCTC +RIMS1 22999 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 72967911 72967911 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 12 ENST00000521978.1:c.2854C>T p.Arg952Cys p.R952C ENST00000521978 NM_014989.5 952 Cgt/Tgt 0 0.463 TCACCGCTCACGTTCAGTATC +TTK 7272 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 80720598 80720598 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 22 ENST00000369798.2:c.537G>A p.Met179Ile p.M179I ENST00000369798 NM_003318.4 179 atG/atA 0 0.348 CACTAGAAATGCTGGAAATTG +CARD11 84433 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 2963945 2963945 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 32 ENST00000396946.4:c.1862C>T p.Ser621Phe p.S621F ENST00000396946 NM_032415.4 621 tCc/tTc 0 0.607 TTGGTGGGAGGAGGAGGAGGA +DBNL 28988 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 44097451 44097451 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 27 ENST00000468694.1:c.545A>G p.Lys182Arg p.K182R ENST00000468694 NM_001122956.1 182 aAa/aGa 0 0.547 TTCTGGGCCAAAGCAGAGGTG +TRIP6 7205 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 100465834 100465834 + synonymous_variant Silent SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 23 ENST00000200457.4:c.342G>A p.Ala114= p.A114= ENST00000200457 NM_003302.2 114 gcG/gcA 0 0.662 GGGGTCATGCGTCACGGCGAC +LRRC4 64101 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 127668930 127668930 + synonymous_variant Silent SNP G G C rs139849197 TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 20 ENST00000249363.3:c.1764C>G p.Ser588= p.S588= ENST00000249363 NM_022143.4 588 tcC/tcG 0 0.547 CTGATACACCGGACGGAgctg +PSD3 23362 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 18729531 18729531 + synonymous_variant Silent SNP T T A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 119 24 ENST00000327040.8:c.843A>T p.Pro281= p.P281= ENST00000327040 NM_015310.3 281 ccA/ccT 0 0.567 CACATCCCCCTGGGTGCTCTC +FUT10 84750 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 33246920 33246920 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 66 ENST00000327671.5:c.773A>G p.Asn258Ser p.N258S ENST00000327671 NM_032664.3 258 aAt/aGt 0 0.438 AGAGGCTGGATTTTTCAGCTG +ADAM2 2515 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 39624672 39624672 + splice_region_variant,synonymous_variant Splice_Region SNP T T C TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 80 ENST00000265708.4:c.1311A>G p.Leu437= p.L437= ENST00000265708 NM_001464.4 437 ctA/ctG 0 0.343 AAGCTCTTACTAGACAGTTTT +FPGS 2356 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 130569293 130569293 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 151 40 ENST00000373247.2:c.428A>G p.Asn143Ser p.N143S ENST00000373247 NM_004957.4 143 aAt/aGt 0 0.657 ATCCGCATCAATGGGCAGCCC +ZER1 10444 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 131503855 131503855 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 187 39 ENST00000291900.2:c.1696C>T p.Leu566Phe p.L566F ENST00000291900 NM_006336.3 566 Ctc/Ttc 0 0.567 TTGAAATTGAGGAACATCTCG +ATRX 546 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 76940500 76940500 + splice_acceptor_variant Splice_Site SNP T T G TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 5 47 ENST00000373344.5:c.595-2A>C p.X199_splice ENST00000373344 NM_000489.3 0 0.294 AAAGCAATTCTATTAAAAGAA +ACTRT1 139741 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 127185376 127185376 + synonymous_variant Silent SNP G G T TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 49 ENST00000371124.3:c.810C>A p.Ile270= p.I270= ENST00000371124 NM_138289.3 270 atC/atA 0 0.512 CTGGGCTGTGGATGCCCAGCT +OR51D1 390038 broad.mit.edu;ucsc.edu GRCh37 11 4661741 4661741 + missense_variant Missense_Mutation SNP C C A TCGA-HT-7477-01 TCGA-HT-7477-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 17 ENST00000357605.2:c.721C>A p.Leu241Met p.L241M ENST00000357605 NM_001004751.2 241 Ctg/Atg 0 0.512 TGTTTTGGAGCTGTCCTCTCG +KCNK18 338567 hgsc.bcm.edu;broad.mit.edu GRCh37 10 118957048 118957048 + synonymous_variant Silent SNP C C T TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 76 5 ENST00000334549.1:c.49C>T p.Leu17= p.L17= ENST00000334549 NM_181840.1 17 Ctg/Ttg 0 0.632 CCCAGAGGCCCTGGGAAAGCT +PRPF40B 25766 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 50036431 50036431 + synonymous_variant Silent SNP C C G TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 29 ENST00000548825.2:c.2091C>G p.Leu697= p.L697= ENST00000548825 NM_001031698.2 697 ctC/ctG 0 0.557 GGATCCGGCTCTTCCGGGAGT +EIF2B1 1967 hgsc.bcm.edu;broad.mit.edu GRCh37 12 124111689 124111689 + synonymous_variant Silent SNP G G A rs146748240 byFrequency TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 138 9 ENST00000424014.2:c.384C>T p.His128= p.H128= ENST00000424014 NM_001414.3 128 caC/caT 0 0.562 TGGAGTAGGCGTGAGTCAATA +TSHR 7253 hgsc.bcm.edu;broad.mit.edu GRCh37 14 81609744 81609744 + missense_variant Missense_Mutation SNP G G A rs146403935 by1000genomes TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 202 14 ENST00000298171.2:c.1342G>A p.Val448Ile p.V448I ENST00000298171 NM_000369.2 448 Gtc/Atc 0 0.517 CAAACTGAACGTCCCCCGCTT +KLHL25 64410 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 86312652 86312652 + synonymous_variant Silent SNP G G A TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 60 10 ENST00000337975.5:c.390C>T p.His130= p.H130= ENST00000337975 NM_022480.3 130 caC/caT 0 0.622 CCCGCACATCGTGGAACTGCA +MYH8 4626 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 10299697 10299697 + stop_gained Nonsense_Mutation SNP G G A TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 6 ENST00000403437.2:c.4603C>T p.Gln1535Ter p.Q1535* ENST00000403437 NM_002472.2 1535 Caa/Taa 0 0.383 TGTTCTACTTGCTTCTTTATT +KRT15 3866 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 39673185 39673185 + missense_variant Missense_Mutation SNP C C T rs138271368 TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 89 14 ENST00000254043.3:c.613G>A p.Val205Ile p.V205I ENST00000254043 NM_002275.3 205 Gtt/Att 0 0.612 TCAGCCTCAACGCCCTGGCGC +DNM2 1785 hgsc.bcm.edu;ucsc.edu GRCh37 19 10908139 10908139 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 24 ENST00000389253.4:c.1280G>T p.Cys427Phe p.C427F ENST00000389253 NM_001005361.2 427 tGt/tTt 0 0.517 AGTTTGAAGTGTGTTGATCTC +AXL 558 hgsc.bcm.edu;broad.mit.edu GRCh37 19 41763470 41763470 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 116 6 ENST00000301178.4:c.2269G>A p.Glu757Lys p.E757K ENST00000301178 NM_021913.4 757 Gag/Aag 0 0.557 GGAGAACAGCGAGATTTATGA +C1orf65 164127 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 223567391 223567391 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 82 64 ENST00000366875.3:c.574C>T p.Arg192Trp p.R192W ENST00000366875 NM_152610.2 192 Cgg/Tgg 0 0.597 TCCCTCGGAGCGGTCTTCTGT +RIPK4 54101 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 43161859 43161859 + synonymous_variant Silent SNP G G A TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 136 12 ENST00000332512.3:c.1494C>T p.Asn498= p.N498= ENST00000332512 NM_020639.2 498 aaC/aaT 0 0.632 CATCCTTGGCGTTGACACTGA +TOP3B 8940 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 22322990 22322990 + splice_donor_variant Splice_Site SNP C C A TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 76 22 ENST00000398793.2:c.738+1G>T p.X246_splice ENST00000398793 NM_003935.3 0 0.552 AGGCAAGGAACCTTGGCCTGC +RASD2 23551 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 35947956 35947956 + synonymous_variant Silent SNP C C T rs144245051 TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 24 ENST00000216127.4:c.678C>T p.Asp226= p.D226= ENST00000216127 NM_014310.3 226 gaC/gaT 0 0.642 AGGAGATGGACGCCTATGGCA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 43 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +OTOP1 133060 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 4199681 4199681 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 38 ENST00000296358.4:c.880C>T p.Arg294Cys p.R294C ENST00000296358 NM_177998.1 294 Cgc/Tgc 0 0.567 TCAACTTTGCGCCCGATGTTC +IL17F 112744 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 52103580 52103580 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 35 ENST00000336123.4:c.202G>A p.Val68Ile p.V68I ENST00000336123 NM_052872.3 68 Gtt/Att 0 0.448 GACATGGAAACGCGCTGGTTT +AP1S1 1174 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 100799992 100799992 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 5 ENST00000337619.5:c.121G>C p.Ala41Pro p.A41P ENST00000337619 NM_001283.3 41 Gct/Cct 0 0.537 GGTTGTCCTGGCTCGAAAGCC +TIGIT 201633 broad.mit.edu;ucsc.edu GRCh37 3 114026861 114026861 + synonymous_variant Silent SNP A A G TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 45 ENST00000486257.1:c.618A>G p.Ala206= p.A206= ENST00000486257 206 gcA/gcG 0 0.572 CAGAAGCTGCACCTGCTGGGC +LMNA 4000 broad.mit.edu;ucsc.edu GRCh37 1 156104684 156104684 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 20 ENST00000368300.4:c.728A>G p.Asp243Gly p.D243G ENST00000368300 NM_170707.3 243 gAt/gGt 0 0.582 CGGCTGGCGGATGCGCTGCAG +FUBP1 8880 broad.mit.edu;hgsc.bcm.edu GRCh37 1 78422268 78422269 + frameshift_variant Frame_Shift_Ins INS - - T TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 54 ENST00000370768.2:c.1693dupA p.Thr565AsnfsTer2 p.T565Nfs*2 ENST00000370768 NM_003902.3 565 act/aAct 0 0.406 TTGTCCATTAGTTTGAGTTGTA +CIC 23152 broad.mit.edu GRCh37 19 42792020 42792021 + frameshift_variant Frame_Shift_Del DEL AG AG - TCGA-HT-7608-01 TCGA-HT-7608-10 Untested Somatic Phase_I WXS none Illumina GAIIx 5 5 ENST00000575354.2:c.825_826delGA p.Lys276ValfsTer38 p.K276Vfs*38 ENST00000575354 NM_015125.3 275 aAG/a 0 0.649 AAGGACCGAAAGAAGTCCAGCT +LRRC32 2615 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 76371010 76371010 + synonymous_variant Silent SNP G G A TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 14 ENST00000407242.2:c.1627C>T p.Leu543= p.L543= ENST00000407242 NM_005512.2 543 Ctg/Ttg 0 0.637 TTGTTTCGCAGGTCCAGCACC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 by1000genomes TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 3 42 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 0 0.542 GGCACAAACACGCACCTCAAA +KRI1 65095 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 10668901 10668901 + synonymous_variant Silent SNP G G A TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 23 ENST00000312962.6:c.1227C>T p.Asp409= p.D409= ENST00000312962 NM_023008.3 409 gaC/gaT 0 0.602 CGTAGTACTCGTCCCCAAAGC +CCDC105 126402 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 15133702 15133702 + missense_variant Missense_Mutation SNP G G T TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 9 ENST00000292574.3:c.1271G>T p.Cys424Phe p.C424F ENST00000292574 NM_173482.2 424 tGc/tTc 0 0.617 AAGCTGCAGTGCCACATCACG +TMCC2 9911 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 205210633 205210633 + missense_variant,splice_region_variant Missense_Mutation SNP A A G TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 40 ENST00000358024.3:c.208A>G p.Lys70Glu p.K70E ENST00000358024 NM_014858.3 70 Aaa/Gaa 0 0.557 CCCCCTTAAGAAAATCCAGCA +OR2B11 127623 hgsc.bcm.edu;broad.mit.edu GRCh37 1 247614765 247614765 + missense_variant Missense_Mutation SNP C C T TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 4 ENST00000318749.6:c.520G>A p.Gly174Arg p.G174R ENST00000318749 NM_001004492.1 174 Ggg/Agg 0 0.597 ACCTGCCGCCCGCAGAATGGC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 26 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +CDCP1 64866 hgsc.bcm.edu;broad.mit.edu GRCh37 3 45127212 45127212 + missense_variant Missense_Mutation SNP T T C TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 144 12 ENST00000296129.1:c.2429A>G p.His810Arg p.H810R ENST00000296129 NM_022842.4 810 cAt/cGt 0 0.552 ATTGTTGGGATGGGAGAAGGT +PCDHGA1 56114 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 140711256 140711256 + synonymous_variant Silent SNP C C A TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 35 ENST00000517417.1:c.1005C>A p.Ile335= p.I335= ENST00000517417 NM_018912.2 335 atC/atA 0 0.418 AGGTACTGATCAAAGTTTTGG +GABRP 2568 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 170236583 170236583 + missense_variant Missense_Mutation SNP G G A TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 83 ENST00000518525.1:c.844G>A p.Val282Met p.V282M ENST00000518525 282 Gtg/Atg 0 0.517 AGTGACGACCGTGTTATCAAT +FBXL6 26233 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 145580132 145580132 + synonymous_variant Silent SNP G G A TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 59 ENST00000331890.5:c.1053C>T p.Pro351= p.P351= ENST00000331890 NM_012162.3 351 ccC/ccT 0 0.652 AGCCTGGTCCGGGAGCCACCC +OPHN1 4983 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 67413796 67413796 + splice_acceptor_variant Splice_Site SNP T T C TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 15 ENST00000355520.5:c.1139-2A>G p.X380_splice ENST00000355520 NM_002547.2 0 0.408 TTAGCTCCACTGTTTCAAGCA +RGPD3 653489 broad.mit.edu;ucsc.edu GRCh37 2 107029596 107029596 + missense_variant Missense_Mutation SNP T T C TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 81 ENST00000409886.3:c.5210A>G p.Asn1737Ser p.N1737S ENST00000409886 NM_001144013.1 1737 aAt/aGt 0 0.438 CAACATCGTATTTATAACAGG +CYP39A1 51302 broad.mit.edu;ucsc.edu GRCh37 6 46518143 46518143 + missense_variant Missense_Mutation SNP G G A TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 19 ENST00000275016.2:c.1370C>T p.Pro457Leu p.P457L ENST00000275016 NM_001278739.1 457 cCg/cTg 0 0.458 TTGCCCTTCCGGCTGGGGGAC +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76939758 76939762 + frameshift_variant Frame_Shift_Del DEL TTTCT TTTCT - TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 23 ENST00000373344.5:c.986_990delAGAAA p.Lys329IlefsTer3 p.K329Ifs*3 ENST00000373344 NM_000489.3 329 aAGAAA/a 0 0.341 AATCATCTAATTTCTTTTCTTCTCC +MAGEA6 4105 broad.mit.edu;hgsc.bcm.edu GRCh37 X 151870011 151870011 + frameshift_variant Frame_Shift_Del DEL G G - TCGA-P5-A5EW-01 TCGA-P5-A5EW-10 Untested Somatic Phase_I WXS none Illumina GAIIx 219 144 ENST00000329342.5:c.703delG p.Glu235LysfsTer50 p.E235Kfs*50 ENST00000329342 NM_005363.2 234 aGg/ag 0 0.532 TTTGAGGGGAGGGAAGACAGT +ADARB2 105 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 1779285 1779285 + missense_variant Missense_Mutation SNP G G C TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 328 55 ENST00000381312.1:c.60C>G p.Cys20Trp p.C20W ENST00000381312 NM_018702.3 20 tgC/tgG 0 0.701 TCTTGGACTTGCATTTGAGTT +SLC17A6 57084 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 22360149 22360149 + missense_variant Missense_Mutation SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 9 ENST00000263160.3:c.70C>G p.Leu24Val p.L24V ENST00000263160 NM_020346.2 24 Ctc/Gtc 0 0.473 TGGAAAATCACTCGGCCAGAT +OR5D14 219436 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 55563737 55563737 + missense_variant Missense_Mutation SNP C C T rs145440752 byFrequency TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 35 ENST00000335605.1:c.706C>T p.Arg236Cys p.R236C ENST00000335605 NM_001004735.1 236 Cgc/Tgc 0 0.463 TGTTAGTGGGCGCCACAAAGC +MMP20 9313 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 102465488 102465488 + splice_region_variant,synonymous_variant Splice_Region SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 16 ENST00000260228.2:c.954G>C p.Arg318= p.R318= ENST00000260228 NM_004771.3 318 cgG/cgC 0 0.418 TCCAGAAAATCCTATGGGACA +MDM2 4193 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 69230521 69230521 + missense_variant Missense_Mutation SNP T T C TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 28 ENST00000462284.1:c.910T>C p.Ser304Pro p.S304P ENST00000462284 NM_002392.5 304 Tcc/Ccc 0 0.308 TCCTGAAATTTCCTTAGCTGT +GALC 2581 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 88454494 88454494 + missense_variant Missense_Mutation SNP T T A TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 18 ENST00000261304.2:c.322A>T p.Thr108Ser p.T108S ENST00000261304 NM_000153.3 108 Aca/Tca 0 0.358 CTACCTGTTGTCTGCCCATCA +LIPC 3990 hgsc.bcm.edu;broad.mit.edu GRCh37 15 58855814 58855814 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 95 7 ENST00000356113.6:c.1280C>T p.Ala427Val p.A427V ENST00000356113 427 gCc/gTc 0 0.507 GCAGTGTGGGCCAATGTCTGG +LINS 55180 hgsc.bcm.edu;broad.mit.edu GRCh37 15 101109585 101109585 + missense_variant Missense_Mutation SNP C C G rs148450316 TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 100 6 ENST00000314742.8:c.2132G>C p.Arg711Thr p.R711T ENST00000314742 NM_001040616.2 711 aGa/aCa 0 0.383 TTTTACTATTCTGTAAAATAT +ANKRD11 29123 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 89351668 89351668 + missense_variant Missense_Mutation SNP G G C TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 147 11 ENST00000301030.4:c.1282C>G p.Leu428Val p.L428V ENST00000301030 NM_001256183.1 428 Ctc/Gtc 0 0.488 TGTGCCGAGAGTCTCAGCTTC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578203 7578203 + missense_variant Missense_Mutation SNP C C A TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 28 ENST00000269305.4:c.646G>T p.Val216Leu p.V216L ENST00000269305 NM_001126112.2 216 Gtg/Ttg 0 0.537 GGCACCACCACACTATGTCGA +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A T TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 38 ENST00000269305.4:c.584T>A p.Ile195Asn p.I195N ENST00000269305 NM_001126112.2 195 aTc/aAc 0 0.552 TTCCACTCGGATAAGATGCTG +EFCAB5 374786 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 28409944 28409944 + synonymous_variant Silent SNP C C T TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 206 34 ENST00000394835.3:c.3462C>T p.Tyr1154= p.Y1154= ENST00000394835 NM_198529.3 1154 taC/taT 0 0.398 CCTATCACTACGTCCACAGCC +CCL11 6356 hgsc.bcm.edu;broad.mit.edu GRCh37 17 32612839 32612839 + synonymous_variant Silent SNP C C T TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 248 14 ENST00000305869.3:c.12C>T p.Ser4= p.S4= ENST00000305869 NM_002986.2 4 tcC/tcT 0 0.597 TGAAGGTCTCCGCAGCACTTC +LAMA1 284217 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 7023260 7023260 + synonymous_variant Silent SNP C C A TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 34 ENST00000389658.3:c.2604G>T p.Gly868= p.G868= ENST00000389658 NM_005559.3 868 ggG/ggT 0 0.602 TCAGGCACTCCCCGGTGACTG +STARD6 147323 hgsc.bcm.edu;broad.mit.edu GRCh37 18 51858176 51858176 + synonymous_variant Silent SNP G G A TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 4 ENST00000581310.1:c.321C>T p.Ser107= p.S107= ENST00000581310 107 tcC/tcT 0 0.368 AGTCTCGAGGGGAAATGGAGC +TSHZ1 10194 hgsc.bcm.edu;broad.mit.edu GRCh37 18 72999933 72999933 + synonymous_variant Silent SNP G G A TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 4 ENST00000322038.5:c.2436G>A p.Thr812= p.T812= ENST00000322038 NM_005786.5 812 acG/acA 0 0.602 AGTCCTCCACGCCCTCCACAG +CSNK1G2 1455 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 1979554 1979554 + missense_variant Missense_Mutation SNP A A G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 42 ENST00000255641.8:c.914A>G p.Tyr305Cys p.Y305C ENST00000255641 NM_001319.6 305 tAt/tGt 0 0.652 AAGCCCGACTATGACTACCTG +ICAM1 3383 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 10394873 10394873 + missense_variant Missense_Mutation SNP G G A TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 30 ENST00000264832.3:c.802G>A p.Asp268Asn p.D268N ENST00000264832 NM_000201.2 268 Gac/Aac 0 0.632 CTATGGCAACGACTCCTTCTC +AKAP8 10270 hgsc.bcm.edu;broad.mit.edu GRCh37 19 15472624 15472624 + missense_variant Missense_Mutation SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 3 ENST00000269701.2:c.1312G>C p.Val438Leu p.V438L ENST00000269701 NM_005858.3 438 Gta/Cta 0 0.458 TTTCTGTTTACAATGTATTCC +ADCK4 79934 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 41197999 41197999 + missense_variant Missense_Mutation SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 18 ENST00000324464.3:c.1576G>C p.Asp526His p.D526H ENST00000324464 NM_024876.3 526 Gac/Cac 0 0.672 GTGGCTGCGTCTGGCTGGCGA +ZNF460 10794 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 57802257 57802257 + missense_variant Missense_Mutation SNP G G C TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 38 ENST00000360338.3:c.348G>C p.Glu116Asp p.E116D ENST00000360338 NM_006635.3 116 gaG/gaC 0 0.473 CACAGAGTGAGAAACTCCATG +TCHH 7062 hgsc.bcm.edu;broad.mit.edu GRCh37 1 152084077 152084077 + missense_variant Missense_Mutation SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 290 17 ENST00000368804.1:c.1616G>C p.Arg539Thr p.R539T ENST00000368804 NM_007113.3 539 aGa/aCa 0 0.652 CTGCTCGCGTCTTAGTTGTTG +LAMC1 3915 hgsc.bcm.edu;broad.mit.edu GRCh37 1 183086809 183086809 + missense_variant Missense_Mutation SNP G G A TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 5 ENST00000258341.4:c.1828G>A p.Ala610Thr p.A610T ENST00000258341 NM_002293.3 610 Gct/Act 0 0.483 ACCCTTGATCGCTCAGGGCAA +MIA3 375056 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 222803484 222803484 + synonymous_variant Silent SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 21 ENST00000344922.5:c.2922C>G p.Val974= p.V974= ENST00000344922 NM_198551.2 974 gtC/gtG 0 0.428 TGGAAAAAGTCCTAGATAAGG +MYH7B 57644 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 33567544 33567544 + synonymous_variant Silent SNP G G A TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 90 54 ENST00000262873.7:c.405G>A p.Thr135= p.T135= ENST00000262873 NM_020884.3 135 acG/acA 0 0.637 CCATGATGACGCACCTGAACG +KCNB1 3745 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 48098819 48098819 + missense_variant Missense_Mutation SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 7 ENST00000371741.4:c.199G>C p.Asp67His p.D67H ENST00000371741 NM_004975.2 67 Gac/Cac 0 0.662 AGCAGCGAGTCGTGCGTGTTG +APOB 338 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 21228306 21228306 + missense_variant Missense_Mutation SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 77 ENST00000233242.1:c.11434G>C p.Glu3812Gln p.E3812Q ENST00000233242 NM_000384.2 3812 Gag/Cag 0 0.423 ACGGTTATCTCAAAAAAGGGA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113113 209113113 + missense_variant Missense_Mutation SNP G G A rs121913499 TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 32 ENST00000345146.2:c.394C>T p.Arg132Cys p.R132C ENST00000345146 NM_005896.2 132 Cgt/Tgt 0 0.398 TAAGCATGACGACCTATGATG +VHL 7428 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 10191622 10191622 + synonymous_variant Silent SNP C C T TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 16 ENST00000256474.2:c.615C>T p.Arg205= p.R205= ENST00000256474 NM_000551.3 205 cgC/cgT 0 0.468 CACAGGAGCGCATTGCACATC +MED23 9439 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 131929091 131929091 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 17 ENST00000368068.3:c.1198G>A p.Asp400Asn p.D400N ENST00000368068 NM_004830.3 400 Gac/Aac 0 0.343 TATAGCAAGTCGAAGAGCTTC +RBAK 57786 hgsc.bcm.edu;ucsc.edu GRCh37 7 5104674 5104674 + missense_variant Missense_Mutation SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 22 ENST00000396912.1:c.1587C>G p.His529Gln p.H529Q ENST00000396912 NM_021163.3 529 caC/caG 0 0.383 TCGATGGGCACCAGCCACTTC +HEPACAM2 253012 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 92838050 92838050 + missense_variant Missense_Mutation SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 32 ENST00000394468.2:c.855G>C p.Arg285Ser p.R285S ENST00000394468 NM_001039372.1 285 agG/agC 0 0.443 TATTGTCAGTCCTCCTAATCC +KIAA1429 25962 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 95530133 95530133 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 12 ENST00000297591.5:c.2551G>A p.Ala851Thr p.A851T ENST00000297591 NM_015496.4 851 Gca/Aca 0 0.318 AGTATGCATGCGTAATTATAA +SVEP1 79987 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 113139603 113139603 + synonymous_variant Silent SNP G G C TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 35 ENST00000401783.2:c.10452C>G p.Arg3484= p.R3484= ENST00000401783 NM_153366.3 3484 cgC/cgG 0 0.502 AAGCATTTGGGCGTTGGCAGA +CACNA1B 774 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 140946550 140946550 + synonymous_variant Silent SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 9 ENST00000371372.1:c.3717C>G p.Ser1239= p.S1239= ENST00000371372 NM_001243812.1 1239 tcC/tcG 0 0.582 CTAGAGGATCCAAAGGGAAAG +AMPD1 270 broad.mit.edu;ucsc.edu GRCh37 1 115216305 115216305 + synonymous_variant Silent SNP G G A TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 40 ENST00000520113.2:c.2139C>T p.Cys713= p.C713= ENST00000520113 713 tgC/tgT 0 0.438 TTGCCACTTCGCACATATCAC +FRMD7 90167 broad.mit.edu;ucsc.edu GRCh37 X 131214292 131214292 + missense_variant,splice_region_variant Missense_Mutation SNP C C G TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 3 ENST00000298542.4:c.908G>C p.Gly303Ala p.G303A ENST00000298542 NM_194277.2 303 gGa/gCa 0 0.373 TTGGGTTCGTCCACTATCATA +MMP24 10893 broad.mit.edu;ucsc.edu GRCh37 20 33862232 33862232 + synonymous_variant Silent SNP C C T TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 135 90 ENST00000246186.6:c.1758C>T p.Asp586= p.D586= ENST00000246186 NM_006690.3 586 gaC/gaT 0 0.657 CCCAGGACGACGTGGACATCA +GABRG2 2566 broad.mit.edu;ucsc.edu GRCh37 5 161569181 161569181 + missense_variant Missense_Mutation SNP G G T TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 36 ENST00000414552.2:c.901G>T p.Val301Phe p.V301F ENST00000414552 NM_198903.2 301 Gtc/Ttc 0 0.403 AGATTATGTGGTCATGTCTGT +TFPT 29844 broad.mit.edu;hgsc.bcm.edu GRCh37 19 54611378 54611379 + frameshift_variant Frame_Shift_Ins INS - - CCATC TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 152 30 ENST00000391759.1:c.592_596dupGATGG p.Arg200MetfsTer9 p.R200Mfs*9 ENST00000391759 NM_013342.3 199 gga/ggGATGGa 0 0.713 CTGCTCGGCGTCCATCCCGTGG +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76939914 76939915 + frameshift_variant Frame_Shift_Del DEL AG AG - TCGA-FG-8185-01 TCGA-FG-8185-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 70 ENST00000373344.5:c.833_834delCT p.Thr278SerfsTer3 p.T278Sfs*3 ENST00000373344 NM_000489.3 278 aCT/a 0 0.371 TGTTACATGCAGTGACCAAGTC +MYO3A 53904 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 26463288 26463288 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 118 21 ENST00000265944.5:c.4095G>T p.Gln1365His p.Q1365H ENST00000265944 NM_017433.4 1365 caG/caT 0 0.438 GAAGGCAGCAGTTGAGGAAGG +CYP2C19 1557 hgsc.bcm.edu;broad.mit.edu GRCh37 10 96535297 96535297 + splice_donor_variant Splice_Site SNP G G C rs77576043 TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 184 11 ENST00000371321.3:c.481+1G>C p.X161_splice ENST00000371321 NM_000769.1 0 0.498 AAAACCAAGGGTGGGTGAACA +WDR96 80217 hgsc.bcm.edu;broad.mit.edu GRCh37 10 105990460 105990460 + synonymous_variant Silent SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 87 5 ENST00000357060.3:c.207C>T p.Gly69= p.G69= ENST00000357060 NM_025145.5 69 ggC/ggT 0 0.408 TTGCCATGACGCCCACAATTC +DCHS1 8642 hgsc.bcm.edu;broad.mit.edu GRCh37 11 6645159 6645159 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 185 10 ENST00000299441.3:c.7748G>C p.Ser2583Thr p.S2583T ENST00000299441 NM_003737.2 2583 aGc/aCc 0 0.537 CACGACTGAGCTTTGGGGTGG +DCHS1 8642 hgsc.bcm.edu;broad.mit.edu GRCh37 11 6645181 6645181 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 119 6 ENST00000299441.3:c.7726G>C p.Asp2576His p.D2576H ENST00000299441 NM_003737.2 2576 Gac/Cac 0 0.562 TGCCCACGGTCAGCTGCAGCC +RPUSD4 84881 hgsc.bcm.edu;broad.mit.edu GRCh37 11 126075477 126075477 + missense_variant Missense_Mutation SNP C C T rs143531642 TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 121 9 ENST00000298317.4:c.682G>A p.Asp228Asn p.D228N ENST00000298317 NM_032795.2 228 Gat/Aat 0 0.557 ATTTTCCCATCGTCCATGCGG +CUL4A 8451 hgsc.bcm.edu;broad.mit.edu GRCh37 13 113891149 113891149 + synonymous_variant Silent SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 4 ENST00000375440.4:c.861T>C p.Ile287= p.I287= ENST00000375440 NM_001008895.2 287 atT/atC 0 0.358 AACCACTGATTGCTTGTGTGG +SUPT16H 11198 hgsc.bcm.edu;broad.mit.edu GRCh37 14 21838616 21838616 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 4 ENST00000216297.2:c.362T>C p.Met121Thr p.M121T ENST00000216297 NM_007192.3 121 aTg/aCg 0 0.383 GGCTTCAATCATTTTGTCAAA +CHD8 57680 hgsc.bcm.edu;broad.mit.edu GRCh37 14 21861840 21861840 + synonymous_variant Silent SNP T T G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 60 5 ENST00000399982.2:c.6114A>C p.Pro2038= p.P2038= ENST00000399982 NM_001170629.1 2038 ccA/ccC 0 0.547 CATAGTCTTGTGGGGTTGGTC +TRIM9 114088 hgsc.bcm.edu;broad.mit.edu GRCh37 14 51446210 51446210 + synonymous_variant Silent SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 222 13 ENST00000298355.3:c.1965A>G p.Arg655= p.R655= ENST00000298355 NM_015163.5 655 agA/agG 0 0.453 TCAAGTTTTTTCTATTTAAGT +GATM 2628 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 45658331 45658331 + synonymous_variant Silent SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 23 ENST00000396659.3:c.891A>G p.Lys297= p.K297= ENST00000396659 NM_001482.2 297 aaA/aaG 0 0.428 GATTGGGATCTTTAAAGGAGA +SEMA6D 80031 hgsc.bcm.edu;broad.mit.edu GRCh37 15 48052514 48052514 + stop_gained Nonsense_Mutation SNP T T A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 3 ENST00000316364.5:c.123T>A p.Tyr41Ter p.Y41* ENST00000316364 NM_153618.1 41 taT/taA 0 0.418 CAAGGCAATATCCGGTTTTTA +PDE8A 5151 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 85619979 85619979 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 150 14 ENST00000310298.4:c.507G>C p.Glu169Asp p.E169D ENST00000310298 169 gaG/gaC 0 0.294 ATAGAGAAGAGTTGTCCGTAA +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578394 7578394 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 65 ENST00000269305.4:c.536A>G p.His179Arg p.H179R ENST00000269305 NM_001126112.2 179 cAt/cGt 0 0.642 GCAGCGCTCATGGTGGGGGCA +ZNF207 7756 hgsc.bcm.edu;broad.mit.edu GRCh37 17 30696691 30696691 + synonymous_variant Silent SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 7 ENST00000394670.4:c.1398G>A p.Pro466= p.P466= ENST00000394670 NM_001098507.1 466 ccG/ccA 0 0.527 GGCAGGGACCGCCAATGGTGC +CCR7 1236 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 38715155 38715155 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 7 ENST00000246657.2:c.50T>C p.Val17Ala p.V17A ENST00000246657 NM_001838.3 17 gTc/gCc 0 0.498 CTGGAAAATGACAAGGAGAGC +C17orf47 5414 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 56620229 56620229 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 89 48 ENST00000321691.3:c.1319G>A p.Ser440Asn p.S440N ENST00000321691 NM_001038704.2 440 aGc/aAc 0 0.507 TGTCAGCTGGCTTTGGGGTGT +ABCA6 23460 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 67080574 67080574 + missense_variant,splice_region_variant Missense_Mutation SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 387 159 ENST00000284425.2:c.4259A>G p.Lys1420Arg p.K1420R ENST00000284425 NM_080284.2 1420 aAg/aGg 0 0.453 CGCACGTACCTTTCTCGTGAT +SLC26A11 284129 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 78199637 78199637 + missense_variant,splice_region_variant Missense_Mutation SNP A A G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 163 26 ENST00000361193.3:c.515A>G p.Asn172Ser p.N172S ENST00000361193 NM_001166347.1 172 aAc/aGc 0 0.587 TTTGGACAGAACCTGCTGGGA +ASXL3 80816 hgsc.bcm.edu;broad.mit.edu GRCh37 18 31325552 31325552 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 116 5 ENST00000269197.5:c.5740G>C p.Asp1914His p.D1914H ENST00000269197 NM_030632.1 1914 Gac/Cac 0 0.532 ATTTCATGTTGACAAGAATGG +MC4R 4160 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 58038877 58038877 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 11 ENST00000299766.3:c.706C>T p.Arg236Cys p.R236C ENST00000299766 NM_005912.2 236 Cgc/Tgc 0 0.517 GCACCTTGGCGGATGGCACCA +KRI1 65095 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 10671046 10671046 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 7 ENST00000312962.6:c.760C>T p.Arg254Cys p.R254C ENST00000312962 NM_023008.3 254 Cgc/Tgc 0 0.552 tcctcATAGCGTTTGTTGAGG +CYP4F22 126410 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 15651449 15651449 + missense_variant Missense_Mutation SNP G G A rs146265982 TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 25 ENST00000269703.3:c.860G>A p.Arg287His p.R287H ENST00000269703 NM_173483.3 287 cGt/cAt 0 0.632 CGGGCACTGCGTCAGCAGGGG +NPHS1 4868 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 36340183 36340183 + synonymous_variant Silent SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 14 ENST00000378910.5:c.795C>T p.Cys265= p.C265= ENST00000378910 NM_004646.3 265 tgC/tgT 0 0.657 CTCGGGCCACGCACGGCAGCT +SIPA1L3 23094 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 38643516 38643516 + synonymous_variant Silent SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 202 47 ENST00000222345.6:c.3570T>C p.Asp1190= p.D1190= ENST00000222345 NM_015073.1 1190 gaT/gaC 0 0.617 TATCTCTTGATCCCCACTTCA +ZNF17 7565 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 57932608 57932608 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 10 ENST00000601808.1:c.1748A>G p.Lys583Arg p.K583R ENST00000601808 NM_006959.2 583 aAa/aGa 0 0.428 AGAACTTACAAATGCAGCAAA +TAS1R2 80834 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 19181078 19181078 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 15 ENST00000375371.3:c.886G>A p.Ala296Thr p.A296T ENST00000375371 NM_152232.2 296 Gcc/Acc 0 0.637 ATCCACACGGCGCCAGTGAAG +SNRNP40 9410 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 31744294 31744294 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 7 ENST00000263694.4:c.707A>G p.Asp236Gly p.D236G ENST00000263694 NM_004814.2 236 gAt/gGt 0 0.448 AGTCACTGAATCTGCATGGCC +RLF 6018 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 40702367 40702367 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 111 51 ENST00000372771.4:c.1993C>G p.Leu665Val p.L665V ENST00000372771 NM_012421.3 665 Ctg/Gtg 0 0.418 AGATTGCCACCTGCAAGACAG +AGL 178 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 100353559 100353559 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 6 ENST00000294724.4:c.2707G>A p.Glu903Lys p.E903K ENST00000294724 NM_000028.2 903 Gag/Aag 0 0.373 AACTTTGGCTGAGCTAAATCA +SYCP1 6847 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 115487052 115487052 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 4 ENST00000369522.3:c.2019A>G p.Ile673Met p.I673M ENST00000369522 NM_003176.2 673 atA/atG 0 0.279 ACAAAAAGATATCAGAAGAAA +CD1E 913 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 158325321 158325321 + missense_variant Missense_Mutation SNP G G A rs142840776 TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 7 ENST00000368167.3:c.587G>A p.Gly196Glu p.G196E ENST00000368167 NM_030893.3 196 gGg/gAg 0 0.473 TTTCTAGCGGGGCTCATGGAA +SCYL3 57147 hgsc.bcm.edu;broad.mit.edu GRCh37 1 169823532 169823532 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 121 7 ENST00000367772.4:c.2048T>C p.Ile683Thr p.I683T ENST00000367772 NM_181093.3 683 aTt/aCt 0 0.393 AGAAGGCTTAATTTCTGGGAT +MROH9 80133 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 170928725 170928725 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 8 ENST00000367759.4:c.275T>C p.Ile92Thr p.I92T ENST00000367759 NM_001163629.1 92 aTt/aCt 0 0.363 TATGAGTACATTGAGGACATG +OR2M7 391196 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 248486965 248486965 + missense_variant Missense_Mutation SNP C C A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 8 ENST00000317965.2:c.906G>T p.Met302Ile p.M302I ENST00000317965 NM_001004691.1 302 atG/atT 0 0.403 CTAAGATTTTCATTAATGCTC +TGM6 343641 hgsc.bcm.edu;broad.mit.edu GRCh37 20 2411182 2411182 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 4 ENST00000202625.2:c.1769T>C p.Val590Ala p.V590A ENST00000202625 NM_198994.2 590 gTc/gCc 0 0.458 ATGTGCCTTGTCACCAAAGGA +TPX2 22974 hgsc.bcm.edu;broad.mit.edu GRCh37 20 30388772 30388772 + splice_acceptor_variant Splice_Site SNP G G C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 166 10 ENST00000300403.6:c.2134-1G>C p.X712_splice ENST00000300403 NM_012112.4 0 0.398 TTACTTTGCAGGTGCATAAGG +EIF2AK3 9451 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 88913303 88913303 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 137 10 ENST00000303236.3:c.377A>G p.Lys126Arg p.K126R ENST00000303236 NM_004836.5 126 aAg/aGg 0 0.353 ATCCCACTGCTTTTTACCATG +PTPN4 5775 hgsc.bcm.edu;broad.mit.edu GRCh37 2 120709680 120709680 + synonymous_variant Silent SNP A A G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 117 7 ENST00000263708.2:c.1788A>G p.Glu596= p.E596= ENST00000263708 NM_002830.3 596 gaA/gaG 0 0.403 ATTCTGGGGAACTCATGCTTC +TTN 7273 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 179463964 179463964 + synonymous_variant Silent SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 137 29 ENST00000589042.1:c.56556C>T p.Gly18852= p.G18852= ENST00000589042 NM_001267550.1 18852 ggC/ggT 0 0.428 CATATTCATGGCCTTCTAGCA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 26 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +NEK4 6787 hgsc.bcm.edu;broad.mit.edu GRCh37 3 52802575 52802575 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 127 7 ENST00000233027.5:c.139C>T p.Arg47Trp p.R47W ENST00000233027 NM_001193533.1 47 Cgg/Tgg 0 0.453 GCAGCTCGCCGCTCTCGGCTA +CWH43 80157 hgsc.bcm.edu;broad.mit.edu GRCh37 4 49000535 49000535 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 152 11 ENST00000226432.4:c.772C>G p.Arg258Gly p.R258G ENST00000226432 NM_025087.2 258 Cgt/Ggt 0 0.443 TTTGTGGTTTCGTGGTACTGG +KDR 3791 hgsc.bcm.edu;broad.mit.edu GRCh37 4 55981079 55981079 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 4 ENST00000263923.4:c.620A>G p.Glu207Gly p.E207G ENST00000263923 NM_002253.2 207 gAa/gGa 0 0.373 CTGGTAACTTTCATCATTAAT +DNAH5 1767 hgsc.bcm.edu;broad.mit.edu GRCh37 5 13792273 13792273 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 4 ENST00000265104.4:c.8278A>G p.Arg2760Gly p.R2760G ENST00000265104 NM_001369.2 2760 Aga/Gga 0 0.423 ACAGAATCTCTCACTTCTTCT +PDZD2 23037 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 32090257 32090257 + missense_variant Missense_Mutation SNP C C T rs147353592 TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 491 48 ENST00000438447.1:c.6703C>T p.Arg2235Trp p.R2235W ENST00000438447 2235 Cgg/Tgg 0 0.632 CCATTTTGGACGGGAGGGTCA +MAP1B 4131 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 71493611 71493611 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 16 ENST00000296755.7:c.4429A>G p.Lys1477Glu p.K1477E ENST00000296755 NM_005909.3 1477 Aaa/Gaa 0 0.403 CCAAGAAAAGAAAACTGATGA +AQPEP 206338 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 115298645 115298645 + synonymous_variant Silent SNP C C T TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 24 ENST00000357872.4:c.331C>T p.Leu111= p.L111= ENST00000357872 NM_173800.4 111 Ctg/Ttg 0 0.701 CGATCTGGAGCTGTGGCCGCA +FOXQ1 94234 hgsc.bcm.edu;broad.mit.edu GRCh37 6 1313391 1313391 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 4 ENST00000296839.2:c.452G>A p.Gly151Asp p.G151D ENST00000296839 NM_033260.3 151 gGc/gAc 0 0.652 TACCTCATGGGCAAGTTCCCC +TREML2 79865 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 41160191 41160191 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 7 ENST00000483722.1:c.940C>T p.Pro314Ser p.P314S ENST00000483722 NM_024807.2 314 Ccc/Tcc 0 0.587 TCCACATAGGGCTCTGGTCTT +PRDM1 639 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 106553291 106553291 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 10 ENST00000369096.4:c.1256G>A p.Gly419Asp p.G419D ENST00000369096 NM_001198.3 419 gGc/gAc 0 0.587 CCCCCCTACGGCATGAATTGT +IL6 3569 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 22769188 22769188 + missense_variant Missense_Mutation SNP A A T TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 11 ENST00000404625.1:c.380A>T p.Glu127Val p.E127V ENST00000404625 127 gAg/gTg 0 0.458 GTATACCTAGAGTACCTCCAG +GRB10 2887 hgsc.bcm.edu;broad.mit.edu GRCh37 7 50686969 50686969 + synonymous_variant Silent SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 123 6 ENST00000398812.2:c.675A>G p.Glu225= p.E225= ENST00000398812 NM_005311.4 225 gaA/gaG 0 0.443 GCTCATGGTCTTCCAAGCACC +INTS9 55756 hgsc.bcm.edu;broad.mit.edu GRCh37 8 28625815 28625815 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 196 11 ENST00000521022.1:c.1825G>C p.Glu609Gln p.E609Q ENST00000521022 NM_018250.3 609 Gag/Cag 0 0.502 GCTGTGTCCTCCACCTTAATA +TG 7038 hgsc.bcm.edu;broad.mit.edu GRCh37 8 133912511 133912511 + synonymous_variant Silent SNP G G A TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 5 ENST00000220616.4:c.3360G>A p.Ser1120= p.S1120= ENST00000220616 NM_003235.4 1120 tcG/tcA 0 0.622 TGCAGGCATCGGGGGCTGGCA +RORB 6096 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 77257632 77257632 + stop_gained Nonsense_Mutation SNP C C T TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 11 ENST00000376896.3:c.538C>T p.Gln180Ter p.Q180* ENST00000376896 NM_006914.3 180 Caa/Taa 0 0.468 ACAGATAAAGCAAGAACCTAT +MSL3 10943 hgsc.bcm.edu;ucsc.edu GRCh37 X 11783854 11783854 + splice_region_variant,intron_variant Splice_Region SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 136 25 ENST00000312196.4:c.1171+6T>C p.X391_splice ENST00000312196 NM_078629.3 0 0.587 AAAGAGTAGGTTCATTCTCGG +FMR1NB 158521 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 147084823 147084823 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 7 ENST00000370467.3:c.380A>G p.Asn127Ser p.N127S ENST00000370467 NM_152578.2 127 aAt/aGt 0 0.373 GCTTTGCTGAATTTTTTCTTT +UTY 7404 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 Y 15522901 15522901 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 22 ENST00000331397.4:c.527T>C p.Val176Ala p.V176A ENST00000331397 NM_001258267.1 176 gTg/gCg 0 0.413 GTCTGTGTTCACTTTGAACAT +TMEM175 84286 broad.mit.edu;ucsc.edu GRCh37 4 944293 944293 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 106 11 ENST00000264771.4:c.277G>C p.Ala93Pro p.A93P ENST00000264771 NM_032326.2 93 Gca/Cca 0 0.597 AGTGGCCTGGGCAGCACACAC +MKI67 4288 broad.mit.edu;ucsc.edu GRCh37 10 129923863 129923863 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 122 14 ENST00000368654.3:c.69C>G p.Ser23Arg p.S23R ENST00000368654 NM_002417.4 23 agC/agG 0 0.517 AGGTGCTGAGGCTCAGGGGAA +MBL2 4153 broad.mit.edu;ucsc.edu GRCh37 10 54531233 54531233 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 93 11 ENST00000373968.3:c.163A>G p.Thr55Ala p.T55A ENST00000373968 NM_000242.2 55 Acc/Gcc 0 0.537 TCTCCCTTGGTGCCATCACGC +HOXC4 3221 broad.mit.edu;ucsc.edu GRCh37 12 54447735 54447735 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 76 10 ENST00000430889.2:c.29C>G p.Ser10Cys p.S10C ENST00000430889 NM_153633.2 10 tCt/tGt 0 0.423 TTGATGGACTCTAACTACATC +ARID1A 8289 broad.mit.edu;hgsc.bcm.edu GRCh37 1 27100176 27100176 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 129 23 ENST00000324856.7:c.3977delC p.Pro1326ArgfsTer155 p.P1326Rfs*155 ENST00000324856 NM_006015.4 1324 taC/ta 0 0.597 CTAGCCGCTACCCCCCgcagc +CAD 790 broad.mit.edu;hgsc.bcm.edu GRCh37 2 27462334 27462334 + frameshift_variant Frame_Shift_Del DEL G G - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 25 ENST00000264705.4:c.5391delG p.Gln1798ArgfsTer33 p.Q1798Rfs*33 ENST00000264705 NM_004341.3 1797 Ggg/gg 0 0.567 CTATATCGATGGGCAGGTACG +FBN2 2201 broad.mit.edu;hgsc.bcm.edu GRCh37 5 127782200 127782203 + frameshift_variant Frame_Shift_Del DEL TGTT TGTT - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 16 ENST00000508053.1:c.923_926delAACA p.Lys308ArgfsTer42 p.K308Rfs*42 ENST00000508053 308 aAACAg/ag 0 0.426 AGTTTCACTCTGTTTGTGACCAGC +EPB41L2 2037 broad.mit.edu;hgsc.bcm.edu GRCh37 6 131229973 131229976 + frameshift_variant Frame_Shift_Del DEL TCTT TCTT - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 16 ENST00000337057.3:c.838_841delAAGA p.Lys280AspfsTer3 p.K280Dfs*3 ENST00000337057 NM_001431.3 280 AAGAga/ga 0 0.284 CTCAGTTGTCTCTTTATTTCTTTA +NCOA4 8031 broad.mit.edu;hgsc.bcm.edu GRCh37 10 51585027 51585029 + inframe_deletion In_Frame_Del DEL AAG AAG - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 13 ENST00000452682.1:c.1176_1178delGAA p.Lys393del p.K393del ENST00000452682 NM_001145260.1 392 AAG/- 0 0.522 CTTGGAGGCCAAGAAACCATTGT +ARID5B 84159 broad.mit.edu;hgsc.bcm.edu GRCh37 10 63845531 63845531 + frameshift_variant Frame_Shift_Del DEL A A - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 58 ENST00000279873.7:c.1272delA p.Lys424AsnfsTer55 p.K424Nfs*55 ENST00000279873 NM_032199.2 424 Aaa/aa 0 0.358 CAAACCTCGGAAACAGGAGAA +CDON 50937 broad.mit.edu;hgsc.bcm.edu GRCh37 11 125891236 125891237 + frameshift_variant Frame_Shift_Del DEL AA AA - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 19 ENST00000392693.3:c.255_256delTT p.Leu87GlnfsTer15 p.L87Qfs*15 ENST00000392693 NM_001243597.1 85 ctTTct/ctct 0 0.475 GAGTTGAGAGAAAGAATTGTCA +PTPRR 5801 broad.mit.edu;hgsc.bcm.edu GRCh37 12 71050530 71050532 + inframe_deletion In_Frame_Del DEL CTT CTT - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 159 43 ENST00000283228.2:c.1832_1834delAAG p.Glu611del p.E611del ENST00000283228 NM_002849.3 611 gAAGga/gga 0 0.433 TCCACAACTCCTTCTTCTTTCAG +C14orf37 145407 broad.mit.edu;hgsc.bcm.edu GRCh37 14 58605972 58605974 + inframe_deletion In_Frame_Del DEL CCT CCT - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 110 36 ENST00000267485.7:c.103_105delAGG p.Arg35del p.R35del ENST00000267485 NM_001001872.2 35 AGG/- 0 0.478 GTGCTATCTCCCTCCTCCTTTCT +SMARCA4 6597 broad.mit.edu;hgsc.bcm.edu GRCh37 19 11106926 11106928 + inframe_deletion In_Frame_Del DEL AGA AGA - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 145 29 ENST00000344626.4:c.1636_1638delAAG p.Lys546del p.K546del ENST00000344626 NM_003072.3 544 cAGAag/cag 0 0.576 CTCATCGACCAGAAGAAGGACAA +ATRX 546 broad.mit.edu GRCh37 X 76875860 76875861 + splice_donor_variant,intron_variant Splice_Site DEL CA CA - TCGA-HT-7688-01 TCGA-HT-7688-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 9 ENST00000373344.5:c.5272+2_5272+3delTG p.X1758_splice ENST00000373344 NM_000489.3 0 0.317 GATATTAACTCACACTCAATTA +ADARB2 105 hgsc.bcm.edu;broad.mit.edu GRCh37 10 1405304 1405304 + synonymous_variant Silent SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 10 ENST00000381312.1:c.996G>A p.Ala332= p.A332= ENST00000381312 NM_018702.3 332 gcG/gcA 0 0.746 GTGCGGCCTGCGCGGCCTGAC +PRF1 5551 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 72358832 72358832 + synonymous_variant Silent SNP A A C TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 30 ENST00000441259.1:c.645T>G p.Leu215= p.L215= ENST00000441259 NM_005041.4 215 ctT/ctG 0 0.662 AGTTGGAGATAAGCCTGAGGT +PDE6C 5146 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 95425134 95425134 + missense_variant Missense_Mutation SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 9 ENST00000371447.3:c.2536G>A p.Gly846Ser p.G846S ENST00000371447 NM_006204.3 846 Ggt/Agt 0 0.313 AGATTCAGGAGGTGGTGATGA +OR52B4 143496 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 4388941 4388941 + synonymous_variant Silent SNP T T C TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 28 ENST00000408920.2:c.585A>G p.Arg195= p.R195= ENST00000408920 NM_001005161.3 195 cgA/cgG 0 0.343 AAATGTTTATTCGAATGTCAT +SDS 10993 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 113830761 113830761 + synonymous_variant Silent SNP A A G TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 214 163 ENST00000257549.4:c.972T>C p.Asn324= p.N324= ENST00000257549 NM_006843.2 324 aaT/aaC 0 0.617 TGGGCAACCTATTTGTCATGC +KLF5 688 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 73636332 73636332 + missense_variant Missense_Mutation SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 46 ENST00000377687.4:c.595G>A p.Ala199Thr p.A199T ENST00000377687 NM_001730.3 199 Gca/Aca 0 0.532 ACACCAGACCGCAGCTCCAGA +CLEC14A 161198 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 38723787 38723787 + missense_variant Missense_Mutation SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 117 50 ENST00000342213.2:c.1441G>A p.Ala481Thr p.A481T ENST00000342213 NM_175060.2 481 Gcg/Acg 0 0.547 GGGGACTCCGCCAGCAAGGCA +TELO2 9894 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 1557703 1557703 + missense_variant Missense_Mutation SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 15 ENST00000262319.6:c.2393G>A p.Arg798Gln p.R798Q ENST00000262319 NM_016111.3 798 cGg/cAg 0 0.647 CTGGAAGCCCGGTCCTGGCTG +PDILT 204474 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 20387485 20387485 + stop_gained Nonsense_Mutation SNP G G A rs139247719 TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 33 ENST00000302451.4:c.448C>T p.Arg150Ter p.R150* ENST00000302451 NM_174924.1 150 Cga/Tga 0 0.463 CTAATTTGTCGTCTCAACCAA +ATXN2L 11273 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 28847394 28847394 + synonymous_variant Silent SNP A A G TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 106 71 ENST00000395547.2:c.3036A>G p.Ala1012= p.A1012= ENST00000395547 NM_148414.2 1012 gcA/gcG 0 0.687 GGGTGCCTGCACTCTCAGCTT +SEZ6L2 26470 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 29888271 29888271 + missense_variant,splice_region_variant Missense_Mutation SNP T T G TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 17 ENST00000308713.5:c.1910A>C p.Glu637Ala p.E637A ENST00000308713 NM_001114099.2 637 gAg/gCg 0 0.667 CCTCGGGACCTCTGCAGGGGA +TSNAXIP1 55815 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 67859118 67859118 + missense_variant Missense_Mutation SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 45 ENST00000388833.3:c.595G>A p.Ala199Thr p.A199T ENST00000388833 NM_018430.2 199 Gca/Aca 0 0.542 GATCCTCATCGCAGACCTGAA +NEURL4 84461 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7231068 7231068 + missense_variant Missense_Mutation SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 98 69 ENST00000399464.2:c.418C>T p.Arg140Cys p.R140C ENST00000399464 NM_032442.2 140 Cgc/Tgc 0 0.642 AACACAGAGCGTCCATCTCTC +PRKAR1A 5573 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 66526499 66526499 + missense_variant Missense_Mutation SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 74 55 ENST00000358598.2:c.1055G>A p.Arg352Gln p.R352Q ENST00000358598 NM_212471.2 352 cGa/cAa 0 0.488 AAGCTGGACCGACCTAGATTT +SMCHD1 23347 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 2732375 2732375 + missense_variant Missense_Mutation SNP A A G TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 33 ENST00000320876.6:c.3161A>G p.His1054Arg p.H1054R ENST00000320876 NM_015295.2 1054 cAt/cGt 0 0.363 CAGATCAAACATCAGGATGAG +PRSS57 400668 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 691902 691902 + missense_variant Missense_Mutation SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 21 ENST00000329267.7:c.337G>A p.Asp113Asn p.D113N ENST00000329267 NM_214710.3 113 Gac/Aac 0 0.622 GGGTGGTAGTCGGGGTGTGTG +CIC 23152 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 42791817 42791817 + missense_variant Missense_Mutation SNP G G T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 41 ENST00000575354.2:c.703G>T p.Gly235Cys p.G235C ENST00000575354 NM_015125.3 235 Ggc/Tgc 0 0.612 CAAGATCCTGGGCGAGTGGTG +RBMXL1 494115 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 89448560 89448560 + missense_variant Missense_Mutation SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 122 ENST00000399794.2:c.950G>A p.Arg317His p.R317H ENST00000399794 NM_001162536.2 317 cGt/cAt 0 0.498 ATATCCATCACGTGAGCTGCT +DENND2D 79961 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 111738675 111738675 + missense_variant Missense_Mutation SNP G G C TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 32 ENST00000357640.4:c.508C>G p.Leu170Val p.L170V ENST00000357640 NM_024901.4 170 Ctg/Gtg 0 0.552 ACTTCATCCAGGATCTGCAGG +OR6N2 81442 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 158746704 158746704 + missense_variant Missense_Mutation SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 22 ENST00000339258.1:c.722G>A p.Cys241Tyr p.C241Y ENST00000339258 NM_001005278.1 241 tGt/tAt 0 0.433 ATGTGAGGCACAGGTAGAAAA +EPRS 2058 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 220142262 220142262 + synonymous_variant Silent SNP T T A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 36 ENST00000366923.3:c.4425A>T p.Gly1475= p.G1475= ENST00000366923 NM_004446.2 1475 ggA/ggT 0 0.433 GGCTTTTAGCTCCCATGGATG +TLR5 7100 hgsc.bcm.edu;ucsc.edu GRCh37 1 223286129 223286129 + missense_variant Missense_Mutation SNP G G T rs764535 byFrequency TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 35 ENST00000540964.1:c.245C>A p.Thr82Asn p.T82N ENST00000540964 82 aCc/aAc 0 0.498 AGTCAAGGGGGTATACTGGCT +MMP9 4318 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 44641108 44641108 + missense_variant Missense_Mutation SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 37 ENST00000372330.3:c.1217C>T p.Ala406Val p.A406V ENST00000372330 NM_004994.2 406 gCg/gTg 0 0.637 TTCGGCCACGCGCTGGGCTTA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 25 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +ZBTB11 27107 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 101373567 101373567 + stop_gained Nonsense_Mutation SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 32 ENST00000312938.4:c.2290C>T p.Arg764Ter p.R764* ENST00000312938 NM_014415.3 764 Cga/Tga 0 0.363 TGATAGCCTCGAACCTCAGGC +ZBTB20 26137 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 114058129 114058129 + missense_variant Missense_Mutation SNP T T C TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 154 79 ENST00000474710.1:c.1949A>G p.Asn650Ser p.N650S ENST00000474710 NM_001164342.1 650 aAc/aGc 0 0.527 CATGTGCACGTTGAGGGAGCT +IGSF10 285313 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 151162901 151162901 + missense_variant Missense_Mutation SNP T T C TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 51 ENST00000282466.3:c.4868A>G p.Lys1623Arg p.K1623R ENST00000282466 NM_178822.4 1623 aAg/aGg 0 0.438 AACTGGTTTCTTATCAAAGTC +PIK3CA 5290 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 178936082 178936082 + missense_variant Missense_Mutation SNP G G A rs121913273 TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 17 ENST00000263967.3:c.1624G>A p.Glu542Lys p.E542K ENST00000263967 NM_006218.2 542 Gaa/Aaa 0 0.333 TCCTCTCTCTGAAATCACTGA +PCDHGC3 5098 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 140857769 140857769 + missense_variant Missense_Mutation SNP C C A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 279 208 ENST00000308177.3:c.2086C>A p.Leu696Ile p.L696I ENST00000308177 NM_002588.2 696 Ctt/Att 0 0.488 TTATCTACTTCTTTCTCTAAT +EZR 7430 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 159188410 159188410 + synonymous_variant Silent SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 104 51 ENST00000367075.3:c.1479C>T p.Gly493= p.G493= ENST00000367075 NM_001111077.1 493 ggC/ggT 0 0.642 TGGGCTCTGCGCCCTCATCCT +AGR3 155465 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 16918142 16918142 + missense_variant Missense_Mutation SNP A A G TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 19 ENST00000310398.2:c.101T>C p.Leu34Pro p.L34P ENST00000310398 NM_176813.3 34 cTc/cCc 0 0.383 ACCTCTTGAGAGTGTCTGAGG +SKAP2 8935 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 26729921 26729921 + missense_variant Missense_Mutation SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 25 ENST00000345317.2:c.857G>A p.Ser286Asn p.S286N ENST00000345317 NM_003930.3 286 aGt/aAt 0 0.378 GTGATGGACACTATCCTGACT +MCPH1 79648 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 6301937 6301937 + missense_variant Missense_Mutation SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 22 ENST00000344683.5:c.694C>T p.His232Tyr p.H232Y ENST00000344683 NM_024596.3 232 Cac/Tac 0 0.338 TGGTGGCTTACACTCATCTTT +WNK2 65268 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 96018613 96018613 + synonymous_variant Silent SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 14 7 ENST00000297954.4:c.2067C>T p.Pro689= p.P689= ENST00000297954 NM_001282394.1 689 ccC/ccT 0 0.751 TCCCGGCCCCCGCCTGCCCTC +AGPAT2 10555 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 139571516 139571516 + missense_variant Missense_Mutation SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 134 75 ENST00000371696.2:c.389G>A p.Gly130Asp p.G130D ENST00000371696 NM_006412.3 130 gGc/gAc 0 0.637 CATGATGAGGCCCACGGGCCC +ASMTL 8623 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 1551213 1551213 + missense_variant Missense_Mutation SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 33 ENST00000381317.3:c.458C>T p.Ser153Leu p.S153L ENST00000381317 NM_004192.3 153 tCg/tTg 0 0.637 GGACAGCTCCGAGAACTTCAC +NHS 4810 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 17744930 17744930 + stop_gained Nonsense_Mutation SNP G G T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 68 ENST00000380060.3:c.2641G>T p.Glu881Ter p.E881* ENST00000380060 NM_198270.2 881 Gaa/Taa 0 0.468 TTCTCGAATGGAAAACGCCAA +GK 2710 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 30739086 30739086 + missense_variant Missense_Mutation SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 23 ENST00000378943.3:c.1457G>A p.Arg486Gln p.R486Q ENST00000378943 NM_001128127.2 486 cGg/cAg 0 0.502 ACGATGGAGCGGTTTGAACCT +TRO 7216 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 54957391 54957391 + missense_variant Missense_Mutation SNP A A T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 25 ENST00000173898.7:c.4234A>T p.Thr1412Ser p.T1412S ENST00000173898 NM_001039705.2 1412 Acc/Tcc 0 0.587 TGGACCGAGCACCAGTGCTGG +PBDC1 51260 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 75397598 75397598 + missense_variant Missense_Mutation SNP A A T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 11 ENST00000373358.3:c.557A>T p.Asn186Ile p.N186I ENST00000373358 NM_016500.3 186 aAc/aTc 0 0.413 gaagaagagaacaccaagaat +USP26 83844 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 132159579 132159579 + synonymous_variant Silent SNP T T C TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 30 ENST00000511190.1:c.2670A>G p.Glu890= p.E890= ENST00000511190 NM_031907.1 890 gaA/gaG 0 0.458 TCAACATCTCTTCAAAGATCT +GPR112 139378 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 135405392 135405392 + missense_variant Missense_Mutation SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 98 85 ENST00000394143.1:c.526C>T p.Arg176Cys p.R176C ENST00000394143 NM_153834.3 176 Cgt/Tgt 0 0.448 AAGCATGATGCGTAGCTTTCC +AFF2 2334 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 148068962 148068962 + missense_variant Missense_Mutation SNP A A G TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 67 ENST00000370460.2:c.3689A>G p.Asn1230Ser p.N1230S ENST00000370460 NM_002025.3 1230 aAt/aGt 0 0.532 AACTGTAACAATGGCCCAGTC +COL8A1 1295 broad.mit.edu;ucsc.edu GRCh37 3 99513494 99513494 + missense_variant Missense_Mutation SNP C C T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 129 68 ENST00000261037.3:c.749C>T p.Ala250Val p.A250V ENST00000261037 NM_001850.4 250 gCg/gTg 0 0.642 ATGCCAGGTGCGCCAGGTGTA +HECW1 23072 broad.mit.edu;ucsc.edu GRCh37 7 43483866 43483866 + synonymous_variant Silent SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 21 ENST00000395891.2:c.1095G>A p.Gln365= p.Q365= ENST00000395891 NM_015052.3 365 caG/caA 0 0.532 CCCAAATTCAGGACAGCCCCA +TDGF1P3 6998 broad.mit.edu;ucsc.edu GRCh37 X 109764561 109764561 + non_coding_transcript_exon_variant RNA SNP G G A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 47 ENST00000602699.1:n.1022G>A *341* ENST00000602699 0 0.572 AGCGTGTGCTGCCCATGGGAA +ZCCHC10 54819 broad.mit.edu;hgsc.bcm.edu GRCh37 5 132334445 132334446 + frameshift_variant Frame_Shift_Ins INS - - T TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 12 ENST00000324170.3:c.342dupA p.Glu115ArgfsTer4 p.E115Rfs*4 ENST00000324170 NM_017665.1 114 -/A 0 0.48 TCACTGTCCTCTGAGGAGGAAG +ZNF292 23036 broad.mit.edu;hgsc.bcm.edu GRCh37 6 87964502 87964503 + frameshift_variant Frame_Shift_Ins INS - - A TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 19 ENST00000369577.3:c.1158dupA p.Arg387ThrfsTer7 p.R387Tfs*7 ENST00000369577 NM_015021.1 385 -/A 0 0.376 ATCTGGAAGTTAAACGTGCTTG +BCOR 54880 broad.mit.edu;hgsc.bcm.edu GRCh37 X 39930292 39930292 + frameshift_variant Frame_Shift_Del DEL G G - TCGA-DB-A64W-01 TCGA-DB-A64W-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 40 ENST00000378444.4:c.3172delC p.Gln1058ArgfsTer55 p.Q1058Rfs*55 ENST00000378444 NM_001123385.1 1058 Cag/ag 0 0.493 TTTTTGTCCTGATTTCCTTTC +PPFIA1 8500 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 70208264 70208264 + synonymous_variant Silent SNP G G A TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 109 71 ENST00000253925.7:c.2646G>A p.Thr882= p.T882= ENST00000253925 NM_003626.3 882 acG/acA 0 0.448 ACGGGCCAACGGTTGTGGTCT +SSH2 85464 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 27994187 27994187 + synonymous_variant Silent SNP G G A TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 114 53 ENST00000269033.3:c.783C>T p.Ile261= p.I261= ENST00000269033 NM_033389.2 261 atC/atT 0 0.383 TCTGCATCATGATCTCCCTTA +CIC 23152 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 42791718 42791718 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 54 ENST00000575354.2:c.604C>T p.Arg202Trp p.R202W ENST00000575354 NM_015125.3 202 Cgg/Tgg 0 0.622 CCACATCCGGCGGCCCATGAA +ECM1 1893 hgsc.bcm.edu;broad.mit.edu GRCh37 1 150482440 150482440 + missense_variant Missense_Mutation SNP A A G TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 207 10 ENST00000369049.4:c.347A>G p.Glu116Gly p.E116G ENST00000369049 NM_001202858.1 116 gAa/gGa 0 0.597 CTCCAACAGGAAAAGCTGCTA +PLCB1 23236 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 8862304 8862304 + missense_variant Missense_Mutation SNP A A C TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 257 167 ENST00000338037.6:c.3459A>C p.Lys1153Asn p.K1153N ENST00000338037 NM_015192.3 1153 aaA/aaC 0 0.468 ACCAAGACAAATTCAAAAGAC +TCFL5 10732 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 61488943 61488943 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 142 88 ENST00000335351.3:c.1042C>T p.Arg348Cys p.R348C ENST00000335351 NM_006602.2 348 Cgt/Tgt 0 0.463 TCCAACTGACGCATTCTACTC +HEATR5B 54497 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 37265041 37265041 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 90 56 ENST00000233099.5:c.3173C>T p.Ala1058Val p.A1058V ENST00000233099 NM_019024.1 1058 gCa/gTa 0 0.383 ATGTCGTGGTGCAAACATGTG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 94 73 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +FRAS1 80144 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 79420950 79420950 + missense_variant Missense_Mutation SNP A A G TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 150 108 ENST00000264895.6:c.9191A>G p.Asn3064Ser p.N3064S ENST00000264895 NM_025074.6 3064 aAc/aGc 0 0.532 GCGATTCTGAACATCAAGGTG +IL15 3600 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 142651106 142651106 + missense_variant Missense_Mutation SNP T T C TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 179 63 ENST00000296545.7:c.347T>C p.Ile116Thr p.I116T ENST00000296545 116 aTc/aCc 0 0.388 AATCTGATCATCCTAGCAAAC +PCDHGA3 56112 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 140724038 140724038 + synonymous_variant Silent SNP G G A TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 78 ENST00000253812.6:c.438G>A p.Thr146= p.T146= ENST00000253812 NM_018916.3 146 acG/acA 0 0.353 GTGAACTAACGGTTCCTGGAA +KIAA1324L 222223 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 86526826 86526826 + missense_variant Missense_Mutation SNP A A C TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 140 72 ENST00000450689.2:c.2681T>G p.Phe894Cys p.F894C ENST00000450689 NM_001142749.2 894 tTt/tGt 0 0.468 CCTTACCTGAAATCCTCTCTT +KCNU1 157855 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 36766859 36766859 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 395 255 ENST00000399881.3:c.2137C>T p.Arg713Trp p.R713W ENST00000399881 NM_001031836.2 713 Cgg/Tgg 0 0.468 GTATAAGTTTCGGAACCATAT +NOTCH1 4851 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 139412204 139412204 + missense_variant,splice_region_variant Missense_Mutation SNP C C G TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 43 ENST00000277541.6:c.1441G>C p.Gly481Arg p.G481R ENST00000277541 NM_017617.3 481 Ggc/Cgc 0 0.667 GCCGACGCACCGGGCATGCAG +SMC4 10051 broad.mit.edu;ucsc.edu GRCh37 3 160141575 160141575 + missense_variant Missense_Mutation SNP G G C TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 144 34 ENST00000357388.3:c.2272G>C p.Val758Leu p.V758L ENST00000357388 NM_001002800.1 758 Gta/Cta 0 0.383 TGGAAGCAAAGTAATGAAAGG +ANKRD11 29123 broad.mit.edu;ucsc.edu GRCh37 16 89350191 89350191 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 211 108 ENST00000301030.4:c.2759G>A p.Arg920Lys p.R920K ENST00000301030 NM_001256183.1 920 aGg/aAg 0 0.547 CTGCTCTTTCCTCTTCTCAGA +DNM1P46 196968 broad.mit.edu;ucsc.edu GRCh37 15 100332827 100332827 + non_coding_transcript_exon_variant RNA SNP G G A TCGA-E1-5311-01 TCGA-E1-5311-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 26 ENST00000341853.1:n.1365C>T *455* ENST00000341853 0 0.612 TGACTACAACGAGGGACACAG +ITIH2 3698 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 7780699 7780699 + synonymous_variant Silent SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 12 ENST00000358415.4:c.2073G>A p.Thr691= p.T691= ENST00000358415 NM_002216.2 691 acG/acA 0 0.562 TAGAGTCCACGCCACCCCCAC +RAG1 5896 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 36596675 36596675 + synonymous_variant Silent SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 11 ENST00000299440.5:c.1821C>T p.Asp607= p.D607= ENST00000299440 NM_000448.2 607 gaC/gaT 0 0.468 GAATGGGAGACGTGAGTGAGA +SORL1 6653 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 121421301 121421301 + missense_variant Missense_Mutation SNP A A G TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 7 ENST00000260197.7:c.2188A>G p.Lys730Glu p.K730E ENST00000260197 NM_003105.5 730 Aag/Gag 0 0.557 CAGCTACCGGAAGATTTCTGG +KCNMB4 27345 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 70824288 70824288 + missense_variant Missense_Mutation SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 152 19 ENST00000258111.4:c.488G>A p.Arg163His p.R163H ENST00000258111 NM_014505.5 163 cGc/cAc 0 0.488 CTTCTGCATCGCACTCATGAT +HECTD4 283450 hgsc.bcm.edu;broad.mit.edu GRCh37 12 112617095 112617095 + synonymous_variant Silent SNP G G C TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 14 6 ENST00000550722.1:c.10656C>G p.Val3552= p.V3552= ENST00000550722 NM_001109662.3 3552 gtC/gtG 0 0.542 AAATGTCAGAGACTCTGATGG +SOHLH2 54937 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 36776075 36776075 + synonymous_variant Silent SNP A A G TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 23 ENST00000511166.1:c.435T>C p.Val145= p.V145= ENST00000511166 NM_001198910.1 145 gtT/gtC 0 0.423 CCTTCAAGAGAACCATGTTGA +FNDC3A 22862 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 49710555 49710555 + missense_variant Missense_Mutation SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 27 ENST00000492622.2:c.578G>A p.Arg193His p.R193H ENST00000492622 NM_001079673.1 193 cGc/cAc 0 0.388 TTGAAGGATCGCCAAGGAACA +NGDN 25983 hgsc.bcm.edu;broad.mit.edu GRCh37 14 23940135 23940135 + synonymous_variant Silent SNP A A G TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 6 ENST00000408901.3:c.93A>G p.Gln31= p.Q31= ENST00000408901 NM_015514.1 31 caA/caG 0 0.368 TAACTGCACAAGTGAAATCAC +CTAGE5 4253 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 39784908 39784908 + missense_variant Missense_Mutation SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 26 ENST00000396158.2:c.1393G>A p.Ala465Thr p.A465T ENST00000396158 NM_001247989.1 465 Gca/Aca 0 0.254 TGAGAAAAAAGCACATGATAA +EIF2AK4 440275 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 40241413 40241413 + missense_variant Missense_Mutation SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 47 ENST00000263791.5:c.457C>T p.Arg153Trp p.R153W ENST00000263791 NM_001013703.2 153 Cgg/Tgg 0 0.537 GCTGGAAAGGCGGGCTCAGGA +BUB1B 701 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 40509802 40509802 + synonymous_variant Silent SNP C C T rs139066741 by1000genomes TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 305 95 ENST00000287598.6:c.2784C>T p.Ser928= p.S928= ENST00000287598 NM_001211.5 928 agC/agT 0 0.443 TTACCCTCAGCGGCTTTCGGA +TP53 7157 hgsc.bcm.edu;broad.mit.edu GRCh37 17 7577121 7577121 + missense_variant Missense_Mutation SNP G G A rs121913343 TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 3 23 ENST00000269305.4:c.817C>T p.Arg273Cys p.R273C ENST00000269305 NM_001126112.2 273 Cgt/Tgt 0 0.542 GCACAAACACGCACCTCAAAG +CTC1 80169 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 8132163 8132163 + missense_variant Missense_Mutation SNP T T C TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 4 ENST00000315684.8:c.3269A>G p.Asn1090Ser p.N1090S ENST00000315684 NM_025099.5 1090 aAt/aGt 0 0.567 CACATGGTGATTCCTACAGGT +PSMD3 5709 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 38151212 38151212 + missense_variant Missense_Mutation SNP C C G TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 19 ENST00000264639.4:c.987C>G p.His329Gln p.H329Q ENST00000264639 NM_002809.3 329 caC/caG 0 0.572 TCCAGGTGCACAAGCTTCTCA +CCR7 1236 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 38711759 38711759 + synonymous_variant Silent SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 19 ENST00000246657.2:c.372C>T p.Phe124= p.F124= ENST00000246657 NM_001838.3 124 ttC/ttT 0 0.552 AGTGGACACCGAAGACCCAGG +HDAC5 10014 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 42169818 42169818 + missense_variant Missense_Mutation SNP G G A rs138137922 TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 10 ENST00000225983.6:c.853C>T p.Arg285Cys p.R285C ENST00000225983 285 Cgc/Tgc 0 0.537 CCATCCTTGCGACGCAGGAGG +KLHL14 57565 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 30349844 30349844 + synonymous_variant Silent SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 10 ENST00000359358.4:c.711G>A p.Ala237= p.A237= ENST00000359358 NM_020805.1 237 gcG/gcA 0 0.657 TCTGGAAGAGCGCCAGCTCCG +FCGBP 8857 hgsc.bcm.edu;broad.mit.edu GRCh37 19 40408740 40408740 + missense_variant Missense_Mutation SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 16 ENST00000221347.6:c.4099G>A p.Ala1367Thr p.A1367T ENST00000221347 NM_003890.2 1367 Gcc/Acc 0 0.587 AGGTCGTAGGCCACACGCAGG +MST1L 11223 hgsc.bcm.edu;broad.mit.edu GRCh37 1 17084292 17084292 + non_coding_transcript_exon_variant RNA SNP A A G TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 181 27 ENST00000389184.2:n.1710T>C *570* ENST00000389184 0 0.587 TGGTCCCTGGAGGCACCACAT +MST1L 11223 hgsc.bcm.edu;broad.mit.edu GRCh37 1 17084293 17084293 + non_coding_transcript_exon_variant RNA SNP G G T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 179 26 ENST00000389184.2:n.1709C>A *570* ENST00000389184 0 0.587 GGTCCCTGGAGGCACCACATA +SCMH1 22955 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 41579187 41579187 + synonymous_variant Silent SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 14 ENST00000402904.2:c.483G>A p.Ser161= p.S161= ENST00000402904 NM_001031694.2 161 tcG/tcA 0 0.443 TGTGGGAAGGCGATGGTGGCT +CFHR5 81494 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 196973949 196973949 + missense_variant Missense_Mutation SNP T T C TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 25 ENST00000256785.4:c.1489T>C p.Trp497Arg p.W497R ENST00000256785 497 Tgg/Cgg 0 0.378 AAATAAACAGTGGTCAGAACC +HHIPL2 79802 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 222717481 222717481 + synonymous_variant Silent SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 159 40 ENST00000343410.6:c.372G>A p.Thr124= p.T124= ENST00000343410 NM_024746.3 124 acG/acA 0 0.597 TCCGGAGAGGCGTCTGGGTGT +PRND 23627 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 4705632 4705632 + synonymous_variant Silent SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 8 ENST00000305817.2:c.435C>T p.Cys145= p.C145= ENST00000305817 NM_012409.2 145 tgC/tgT 0 0.602 TCAAGCATTGCGAGTTTTGGT +PLCG1 5335 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 39795459 39795459 + missense_variant Missense_Mutation SNP A A G TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 33 ENST00000373272.2:c.2261A>G p.Tyr754Cys p.Y754C ENST00000373272 NM_002660.2 754 tAt/tGt 0 0.562 AAGCTGCGCTATCCCATCAAC +MAP3K19 80122 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 135744754 135744754 + missense_variant Missense_Mutation SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 98 16 ENST00000375845.3:c.1688C>T p.Thr563Ile p.T563I ENST00000375845 NM_025052.3 563 aCc/aTc 0 0.423 TTTATGCATGGTAGGCTTAAT +IFIH1 64135 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 163134056 163134056 + missense_variant Missense_Mutation SNP A A C TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 17 ENST00000263642.2:c.1913T>G p.Phe638Cys p.F638C ENST00000263642 NM_022168.3 638 tTt/tGt 0 0.353 TATGACTGCAAACTTCTTATC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 24 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +FLNB 2317 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 58094210 58094210 + missense_variant Missense_Mutation SNP A A G TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 12 ENST00000490882.1:c.1967A>G p.Glu656Gly p.E656G ENST00000490882 NM_001164317.1 656 gAg/gGg 0 0.448 CCAGGTTTGGAGAAATCTGGA +LEKR1 389170 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 156763496 156763496 + missense_variant Missense_Mutation SNP A A G TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 31 ENST00000356539.4:c.2036A>G p.Gln679Arg p.Q679R ENST00000356539 NM_001004316.2 679 cAg/cGg 0 0.547 GAGACTAGACAGAGACTGGCT +IGF2BP2 10644 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 185393095 185393095 + synonymous_variant Silent SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 134 17 ENST00000382199.2:c.1060C>T p.Leu354= p.L354= ENST00000382199 NM_006548.4 354 Ctg/Ttg 0 0.463 TTAACAGCCAGCATATCATTT +ANK2 287 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 114280346 114280346 + synonymous_variant Silent SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 17 ENST00000357077.4:c.10572C>T p.Thr3524= p.T3524= ENST00000357077 NM_001148.4 3524 acC/acT 0 0.473 CTGTTGAGACCGAGCACTCAG +SEC24D 9871 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 119649799 119649799 + synonymous_variant Silent SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 9 ENST00000280551.6:c.2875C>T p.Leu959= p.L959= ENST00000280551 959 Ctg/Ttg 0 0.303 ACTTCAGGCAGCAATGTCTTA +GFM2 84340 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 74034187 74034187 + missense_variant Missense_Mutation SNP A A C TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 83 88 ENST00000296805.3:c.1276T>G p.Ser426Ala p.S426A ENST00000296805 NM_032380.4 426 Tca/Gca 0 0.333 GCAGTCAATGAAGGGATTTCT +PCDHAC1 56135 hgsc.bcm.edu;broad.mit.edu GRCh37 5 140308171 140308171 + missense_variant Missense_Mutation SNP T T C TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 108 7 ENST00000253807.2:c.1694T>C p.Val565Ala p.V565A ENST00000253807 NM_018898.3 565 gTc/gCc 0 0.473 AATGGTTCTGTCCCAGTGGAA +STK10 6793 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 171520604 171520604 + missense_variant Missense_Mutation SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 10 ENST00000176763.5:c.1366G>A p.Ala456Thr p.A456T ENST00000176763 NM_005990.3 456 Gcc/Acc 0 0.647 GTCTCCAGGGCGCTGCTGTTG +NPC1L1 29881 hgsc.bcm.edu;ucsc.edu GRCh37 7 44579068 44579068 + missense_variant Missense_Mutation SNP C C T rs79803700 byFrequency TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 98 19 ENST00000289547.4:c.928G>A p.Ala310Thr p.A310T ENST00000289547 NM_013389.2 310 Gcc/Acc 0 0.602 TTGTCCCTGGCGGGGGCCACA +LMTK2 22853 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 97823142 97823142 + missense_variant Missense_Mutation SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 29 ENST00000297293.5:c.3365G>A p.Gly1122Glu p.G1122E ENST00000297293 NM_014916.3 1122 gGa/gAa 0 0.607 GAGGTCCCGGGAACCTCCCCA +COG5 10466 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 107204267 107204267 + synonymous_variant Silent SNP G G C TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 11 ENST00000297135.3:c.168C>G p.Val56= p.V56= ENST00000297135 NM_006348.3 56 gtC/gtG 0 0.667 GAAGTTCCCGGACTGTAGCTG +PLXNA4 91584 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 131848964 131848964 + synonymous_variant Silent SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 8 ENST00000359827.3:c.4437C>T p.Gly1479= p.G1479= ENST00000359827 1479 ggC/ggT 0 0.592 AGCGGGCCTCGCCCGTGATGG +SHH 6469 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 155599004 155599004 + missense_variant Missense_Mutation SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 25 ENST00000297261.2:c.548G>A p.Cys183Tyr p.C183Y ENST00000297261 NM_000193.2 183 tGc/tAc 0 0.622 TTTCACCGAGCAGTGGATATG +EPPK1 83481 hgsc.bcm.edu;broad.mit.edu GRCh37 8 144942235 144942235 + synonymous_variant Silent SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 35 ENST00000525985.1:c.5187C>T p.Phe1729= p.F1729= ENST00000525985 NM_031308.2 1729 ttC/ttT 0 0.622 TGTTGGGGTCGAAGAAGCCCT +SVEP1 79987 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 113139596 113139596 + missense_variant Missense_Mutation SNP C C A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 20 ENST00000401783.2:c.10459G>T p.Ala3487Ser p.A3487S ENST00000401783 NM_153366.3 3487 Gct/Tct 0 0.507 CAGGAACAAGCATTTGGGCGT +MAGEB10 139422 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 27840125 27840125 + synonymous_variant Silent SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 8 ENST00000356790.2:c.702C>T p.Asp234= p.D234= ENST00000356790 NM_182506.3 234 gaC/gaT 0 0.468 GGTTATATGACGGAATTGAGC +ARHGEF6 9459 hgsc.bcm.edu;broad.mit.edu GRCh37 X 135825810 135825810 + stop_gained Nonsense_Mutation SNP C C A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 222 13 ENST00000250617.6:c.595G>T p.Glu199Ter p.E199* ENST00000250617 NM_004840.2 199 Gaa/Taa 0 0.408 AATGTGCCTTCCCACCAGCCT +MAGEC3 139081 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 140969496 140969496 + missense_variant Missense_Mutation SNP C C A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 215 32 ENST00000298296.1:c.823C>A p.Leu275Ile p.L275I ENST00000298296 NM_138702.1 275 Ctc/Atc 0 0.502 CCAGAACCGCCTCCTGATTCT +TMEM9 252839 broad.mit.edu;ucsc.edu GRCh37 1 201112999 201112999 + missense_variant Missense_Mutation SNP G G C TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 4 ENST00000367330.1:c.348C>G p.Ile116Met p.I116M ENST00000367330 NM_001288565.1 116 atC/atG 0 0.572 CCGGCTTTCGGATCAGAGGGT +FOSB 2354 broad.mit.edu;ucsc.edu GRCh37 19 45974181 45974181 + missense_variant Missense_Mutation SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 15 ENST00000353609.3:c.421C>T p.Arg141Trp p.R141W ENST00000353609 NM_006732.2 141 Cgg/Tgg 0 0.632 AGCCCGAGCCCGGCCTAGGAG +MDM4 4194 broad.mit.edu;ucsc.edu GRCh37 1 204518349 204518349 + missense_variant Missense_Mutation SNP A A C TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 121 15 ENST00000367182.3:c.1012A>C p.Thr338Pro p.T338P ENST00000367182 NM_001278516.1 338 Acc/Ccc 0 0.428 TTCAAAGTTAACCCATTCTCT +KRT73 319101 broad.mit.edu;ucsc.edu GRCh37 12 53008406 53008406 + missense_variant Missense_Mutation SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 5 ENST00000305748.3:c.776C>T p.Ala259Val p.A259V ENST00000305748 NM_175068.2 259 gCc/gTc 0 0.542 TCCATCCAGGGCATCCACCTT +ATRX 546 broad.mit.edu;ucsc.edu GRCh37 X 76909629 76909629 + stop_gained Nonsense_Mutation SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 102 41 ENST00000373344.5:c.4276C>T p.Arg1426Ter p.R1426* ENST00000373344 NM_000489.3 1426 Cga/Tga 0 0.328 TTAATACGTCGCCTTTTCTTT +ASB9 140462 broad.mit.edu;ucsc.edu GRCh37 X 15272893 15272893 + missense_variant Missense_Mutation SNP G G A TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 205 25 ENST00000380488.4:c.248C>T p.Ser83Phe p.S83F ENST00000380488 NM_001031739.2 83 tCt/tTt 0 0.443 CTTCACACAAGAGAGATGACC +PTPRF 5792 broad.mit.edu;ucsc.edu GRCh37 1 44079328 44079328 + missense_variant Missense_Mutation SNP C C T TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 19 ENST00000359947.4:c.4013C>T p.Ala1338Val p.A1338V ENST00000359947 NM_002840.3 1338 gCg/gTg 0 0.597 ACCGACCTGGCGGACAACATC +ARID2 196528 broad.mit.edu;hgsc.bcm.edu GRCh37 12 46245951 46245960 + frameshift_variant Frame_Shift_Del DEL ATCAAAAGTG ATCAAAAGTG - TCGA-DU-5855-01 TCGA-DU-5855-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 19 ENST00000334344.6:c.4047_4056delCAAAAGTGAT p.Lys1350Ter p.K1350* ENST00000334344 NM_152641.2 1349 ATCAAAAGTGat/at 0 0.357 CATGCAAGATATCAAAAGTGATTTGAGAAA +TMX2 51075 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 57480129 57480129 + synonymous_variant Silent SNP G G A TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 7 ENST00000278422.4:c.39G>A p.Ser13= p.S13= ENST00000278422 NM_015959.3 13 tcG/tcA 0 0.627 TCGTGTATTCGGTGCCGCGAC +THBS1 7057 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 39884880 39884880 + stop_gained Nonsense_Mutation SNP C C T TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 18 ENST00000260356.5:c.2644C>T p.Gln882Ter p.Q882* ENST00000260356 NM_003246.2 882 Cag/Tag 0 0.502 CAATGCCAACCAGGCTGACCA +SPINT1 6692 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 41146276 41146276 + missense_variant Missense_Mutation SNP G G A rs138167951 TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 126 52 ENST00000344051.4:c.980G>A p.Arg327His p.R327H ENST00000344051 327 cGc/cAc 0 0.592 ATGGAAAGGCGCCATCCAGGT +ANKRD13B 124930 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 27939276 27939276 + missense_variant Missense_Mutation SNP T T G TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 32 ENST00000394859.3:c.1243T>G p.Phe415Val p.F415V ENST00000394859 NM_152345.4 415 Ttc/Gtc 0 0.622 GCCTCCTGGCTTCCCAGTTAA +ABCA9 10350 hgsc.bcm.edu;broad.mit.edu GRCh37 17 66982397 66982397 + synonymous_variant Silent SNP C C T TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 119 8 ENST00000340001.4:c.4116G>A p.Ala1372= p.A1372= ENST00000340001 NM_080283.3 1372 gcG/gcA 0 0.547 TGGGCCACAGCGCATTCTCCT +DSG2 1829 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 29126141 29126141 + missense_variant Missense_Mutation SNP G G C TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 66 ENST00000261590.8:c.2792G>C p.Arg931Thr p.R931T ENST00000261590 NM_001943.3 931 aGa/aCa 0 0.473 ATGGCTTCTAGAAATGTGATA +RTTN 25914 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 67695981 67695981 + synonymous_variant Silent SNP A A C TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 5 ENST00000255674.6:c.5802T>G p.Leu1934= p.L1934= ENST00000255674 NM_173630.3 1934 ctT/ctG 0 0.308 CATTTTGATAAAGACAGTTTC +PRODH2 58510 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 36293163 36293163 + synonymous_variant Silent SNP G G T TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 148 13 ENST00000301175.3:c.1356C>A p.Gly452= p.G452= ENST00000301175 NM_021232.1 452 ggC/ggA 0 0.542 CCAGAGGAATGCCCAGCTCCC +KCNA7 3743 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 49573516 49573516 + missense_variant Missense_Mutation SNP A A G TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 26 ENST00000221444.1:c.1175T>C p.Val392Ala p.V392A ENST00000221444 NM_031886.2 392 gTc/gCc 0 0.567 GGAGACAATGACGGGCACTGG +PRR12 57479 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 50123629 50123629 + synonymous_variant Silent SNP C C T TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 7 ENST00000418929.2:c.5518C>T p.Leu1840= p.L1840= ENST00000418929 NM_020719.1 1840 Ctg/Ttg 0 0.567 ACCTGGGCGTCTGCTCAAAAC +TTN 7273 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 179453926 179453926 + synonymous_variant Silent SNP A A G TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 54 ENST00000589042.1:c.62526T>C p.Tyr20842= p.Y20842= ENST00000589042 NM_001267550.1 20842 taT/taC 0 0.413 CCGTAACTACATATTTACCCC +TTN 7273 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 179579894 179579894 + synonymous_variant Silent SNP G G A TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 62 ENST00000589042.1:c.26019C>T p.His8673= p.H8673= ENST00000589042 NM_001267550.1 8673 caC/caT 0 0.443 ACCAAGAAACGTGAAATGGGG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 16 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +CCDC54 84692 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 107096617 107096617 + synonymous_variant Silent SNP C C T rs144553244 TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 29 ENST00000261058.1:c.183C>T p.Asp61= p.D61= ENST00000261058 NM_032600.2 61 gaC/gaT 0 0.363 ATAGTTATGACGGAAAAATGA +CAPN11 11131 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 44143857 44143857 + missense_variant Missense_Mutation SNP G G A TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 8 ENST00000398776.1:c.884G>A p.Gly295Glu p.G295E ENST00000398776 NM_007058.3 295 gGg/gAg 0 0.557 CTGGTGAGAGGGCACGCTTAC +MAGEB4 4115 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 30260295 30260295 + missense_variant Missense_Mutation SNP C C T TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 16 ENST00000378982.2:c.43C>T p.Arg15Cys p.R15C ENST00000378982 NM_002367.3 15 Cgc/Tgc 0 0.567 CCGTGAGAAACGCCAGCGGAC +ATRX 546 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 76939697 76939697 + stop_gained Nonsense_Mutation SNP C C A TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 39 ENST00000373344.5:c.1051G>T p.Glu351Ter p.E351* ENST00000373344 NM_000489.3 351 Gag/Tag 0 0.353 TTAATCATCTCTTTGGGCACA +RGAG1 57529 hgsc.bcm.edu;broad.mit.edu GRCh37 X 109694050 109694050 + missense_variant Missense_Mutation SNP C C G TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 316 26 ENST00000465301.2:c.205C>G p.Pro69Ala p.P69A ENST00000465301 NM_020769.2 69 Cca/Gca 0 0.517 GATGACATCTCCAGTCTTTGA +MCF2 4168 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 138711938 138711938 + missense_variant Missense_Mutation SNP T T A TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 147 82 ENST00000519895.1:c.534A>T p.Glu178Asp p.E178D ENST00000519895 NM_001171876.1 178 gaA/gaT 0 0.398 TCTCAGCCAGTTCAGTTCCAA +CD99L2 83692 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 149938823 149938823 + synonymous_variant Silent SNP G G A rs147156476 byFrequency TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 20 ENST00000370377.3:c.675C>T p.Tyr225= p.Y225= ENST00000370377 NM_031462.3 225 taC/taT 0 0.537 CTCCCTTCACGTAGTCTGCGT +HMGB3 3149 hgsc.bcm.edu;broad.mit.edu GRCh37 X 150156360 150156360 + synonymous_variant Silent SNP G G A TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 5 ENST00000325307.7:c.576G>A p.Glu192= p.E192= ENST00000325307 NM_005342.2 192 gaG/gaA 0 0.443 aggaagaagaggaggaggagg +KIAA1324 57535 broad.mit.edu;ucsc.edu GRCh37 1 109741239 109741239 + missense_variant Missense_Mutation SNP C C G TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 3 ENST00000369939.3:c.2444C>G p.Thr815Ser p.T815S ENST00000369939 NM_020775.4 815 aCc/aGc 0 0.532 AGATCAACCACCATCCGCGTC +CCAR1 55749 broad.mit.edu;hgsc.bcm.edu GRCh37 10 70513778 70513779 + frameshift_variant Frame_Shift_Ins INS - - A TCGA-HT-A616-01 TCGA-HT-A616-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 32 ENST00000265872.6:c.1295dupA p.Asn432LysfsTer6 p.N432Kfs*6 ENST00000265872 NM_018237.2 430 gaa/gAaa 0 0.381 AGAGTCCTTAGAAAAAAATATG +FPR3 2359 hgsc.bcm.edu;broad.mit.edu GRCh37 19 52327322 52327322 + synonymous_variant Silent SNP C C A TCGA-P5-A5EY-01 TCGA-P5-A5EY-10 Untested Somatic Phase_I WXS none Illumina GAIIx 87 7 ENST00000339223.4:c.321C>A p.Ile107= p.I107= ENST00000339223 NM_002030.3 107 atC/atA 0 0.478 TGATAGACATCAACCTGTTTG +ROM1 6094 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 62380964 62380964 + missense_variant Missense_Mutation SNP G G A TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 5 ENST00000278833.3:c.211G>A p.Ala71Thr p.A71T ENST00000278833 NM_000327.3 71 Gcg/Acg 0 0.667 GGCAGCGGGCGCGGTGGCTCT +SRPR 6734 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 126134414 126134414 + missense_variant Missense_Mutation SNP C C T TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 8 ENST00000332118.6:c.1546G>A p.Val516Met p.V516M ENST00000332118 NM_003139.3 516 Gtg/Atg 0 0.507 ACCAGCACCACGTCAAAGCCT +GAS6 2621 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 114531664 114531664 + synonymous_variant Silent SNP C C T TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 13 ENST00000327773.6:c.1164G>A p.Ala388= p.A388= ENST00000327773 NM_000820.2 388 gcG/gcA 0 0.537 CCAGATTCCGCGCCAGCTCCT +ZC3H14 79882 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 89044401 89044401 + missense_variant Missense_Mutation SNP T T C TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 28 ENST00000251038.5:c.1196T>C p.Val399Ala p.V399A ENST00000251038 NM_024824.4 399 gTc/gCc 0 0.388 GCAGAAGTGGTCCAGGGACAA +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578291 7578291 + splice_acceptor_variant Splice_Site SNP T T C TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 29 ENST00000269305.4:c.560-2A>G p.X187_splice ENST00000269305 NM_001126112.2 0 0.552 GGGCCAGACCTAAGAGCAATC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578394 7578394 + missense_variant Missense_Mutation SNP T T C TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 10 ENST00000269305.4:c.536A>G p.His179Arg p.H179R ENST00000269305 NM_001126112.2 179 cAt/cGt 0 0.642 GCAGCGCTCATGGTGGGGGCA +ZNF235 9310 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 44793178 44793178 + missense_variant Missense_Mutation SNP T T C TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 126 10 ENST00000291182.4:c.410A>G p.His137Arg p.H137R ENST00000291182 NM_004234.4 137 cAt/cGt 0 0.438 GGGGGAATCATGGTGCTTGGG +ITSN1 6453 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 35183494 35183494 + synonymous_variant Silent SNP G G A TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 113 10 ENST00000381318.3:c.2535G>A p.Thr845= p.T845= ENST00000381318 NM_003024.2 845 acG/acA 0 0.547 AGCCCTCCACGACCCCTAATA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 46 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +PCDH12 51294 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 141325159 141325159 + missense_variant Missense_Mutation SNP G G C TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 5 ENST00000231484.3:c.3342C>G p.Ser1114Arg p.S1114R ENST00000231484 NM_016580.3 1114 agC/agG 0 0.662 CCAGCAGTGAGCTCATCTCCG +FAT2 2196 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 150932869 150932869 + missense_variant Missense_Mutation SNP G G A TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 23 ENST00000261800.5:c.4025C>T p.Pro1342Leu p.P1342L ENST00000261800 NM_001447.2 1342 cCg/cTg 0 0.582 GATGGAGGACGGCCGGGGCCA +ATAD2 29028 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 124351613 124351613 + missense_variant Missense_Mutation SNP T T C TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 11 ENST00000287394.5:c.2792A>G p.Lys931Arg p.K931R ENST00000287394 NM_014109.3 931 aAa/aGa 0 0.274 TTCAAAAAATTTTGTCCGTTC +HDX 139324 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 83724060 83724060 + missense_variant Missense_Mutation SNP G G T TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 10 ENST00000297977.5:c.671C>A p.Pro224Gln p.P224Q ENST00000297977 NM_001177479.1 224 cCa/cAa 0 0.413 AATCCCAACTGGTTCAATTTT +RP11-248G5.8 broad.mit.edu;ucsc.edu GRCh37 13 52865661 52865661 + non_coding_transcript_exon_variant RNA SNP C C A TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 4 ENST00000451298.1:n.32G>T *11* ENST00000451298 0 0.289 AAGGATGACACAATTGAATGA +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76937602 76937603 + frameshift_variant Frame_Shift_Ins INS - - T TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 36 ENST00000373344.5:c.3145dupA p.Ile1049AsnfsTer4 p.I1049Nfs*4 ENST00000373344 NM_000489.3 1049 ata/aAta 0 0.327 TTTATCTCTTATTTTTTTACTT +ATRX 546 broad.mit.edu GRCh37 X 76938089 76938092 + frameshift_variant Frame_Shift_Del DEL TCTC TCTC - rs141180098 TCGA-HT-8114-01 TCGA-HT-8114-10 Untested Somatic Phase_I WXS none Illumina GAIIx 208 25 ENST00000373344.5:c.2656_2659delGAGA p.Glu886LeufsTer18 p.E886Lfs*18 ENST00000373344 NM_000489.3 886 GAGAct/ct 0 0.412 GAAGAGAAAGTCTCTCTCTCTTGT +PAPOLA 10914 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 97031339 97031339 + missense_variant Missense_Mutation SNP T T G TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 33 ENST00000216277.8:c.2190T>G p.Asn730Lys p.N730K ENST00000216277 NM_032632.4 730 aaT/aaG 0 0.373 TCCCTGCAAATCCTATTCCTG +HBZ 3050 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 202926 202926 + synonymous_variant Silent SNP T T C TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 24 ENST00000252951.2:c.18T>C p.Thr6= p.T6= ENST00000252951 NM_005332.2 6 acT/acC 0 0.612 TGACCAAGACTGAGAGGACCA +SENP3 26168 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7474041 7474041 + stop_gained Nonsense_Mutation SNP C C T TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 8 ENST00000429205.2:c.1522C>T p.Arg508Ter p.R508* ENST00000429205 508 Cga/Tga 0 0.473 AAAGAAAGACCGACTGGATTT +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577593 7577593 + missense_variant Missense_Mutation SNP T T G TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 21 ENST00000269305.4:c.688A>C p.Thr230Pro p.T230P ENST00000269305 NM_001126112.2 230 Acc/Ccc 0 0.532 TGGATGGTGGTACAGTCAGAG +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578507 7578507 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 32 ENST00000269305.4:c.423C>G p.Cys141Trp p.C141W ENST00000269305 NM_001126112.2 141 tgC/tgG 0 0.577 GCTGCACAGGGCAGGTCTTGG +KRT27 342574 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 38936093 38936093 + synonymous_variant Silent SNP G G A TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 13 ENST00000301656.3:c.705C>T p.Cys235= p.C235= ENST00000301656 NM_181537.3 235 tgC/tgT 0 0.483 CTCCAGCCGCGCACTGAAGAG +ABCG5 64240 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 44047075 44047075 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 114 21 ENST00000260645.1:c.1628T>C p.Leu543Pro p.L543P ENST00000260645 NM_022436.2 543 cTt/cCt 0 0.368 AGATCCAACAAGCACCCCCGC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 83 32 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +TRIP12 9320 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 230668911 230668911 + stop_gained Nonsense_Mutation SNP G G A TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 34 ENST00000283943.5:c.2458C>T p.Arg820Ter p.R820* ENST00000283943 NM_004238.1 820 Cga/Tga 0 0.363 AGCTGTGCTCGAGCATCATCC +ASTE1 28990 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 130732931 130732931 + synonymous_variant Silent SNP C C T TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 14 ENST00000264992.3:c.2010G>A p.Glu670= p.E670= ENST00000264992 NM_014065.2 670 gaG/gaA 0 0.393 CACTATGTTCCTCTAAGTTTT +LPHN3 23284 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 62813869 62813869 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 7 ENST00000514591.1:c.2476C>T p.Arg826Cys p.R826C ENST00000514591 826 Cgt/Tgt 0 0.388 CTACTCCAAGCGTACAATGAC +GPR124 25960 hgsc.bcm.edu;broad.mit.edu GRCh37 8 37698691 37698691 + synonymous_variant Silent SNP C C T TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 94 11 ENST00000412232.2:c.2835C>T p.Cys945= p.C945= ENST00000412232 NM_032777.9 945 tgC/tgT 0 0.627 ATTTCCTGTGCGCCGGGCTAC +SLC26A7 115111 hgsc.bcm.edu;ucsc.edu GRCh37 8 92364100 92364100 + synonymous_variant Silent SNP T T G rs10109254 byFrequency TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 125 36 ENST00000309536.2:c.1203T>G p.Leu401= p.L401= ENST00000309536 NM_134266.1 401 ctT/ctG 0 0.343 GACCTTTGCTTTACTGGCTGC +ATRX 546 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 76890083 76890083 + splice_donor_variant Splice_Site SNP A A C TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 74 38 ENST00000373344.5:c.4809+2T>G p.X1603_splice ENST00000373344 NM_000489.3 0 0.398 TTCAGCTCTTACCTGTAAAGT +STAG2 10735 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 123196967 123196967 + missense_variant,splice_region_variant Missense_Mutation SNP A A T TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 12 ENST00000218089.9:c.1733A>T p.Tyr578Phe p.Y578F ENST00000218089 NM_001042749.1 578 tAc/tTc 0 0.313 ATTTCACAGTACTCTGTAGAT +BCOR 54880 broad.mit.edu;ucsc.edu GRCh37 X 39931690 39931690 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 4 ENST00000378444.4:c.2909C>T p.Ala970Val p.A970V ENST00000378444 NM_001123385.1 970 gCg/gTg 0 0.527 CACGTAACCCGCTGAGTTGGC +F5 2153 broad.mit.edu;ucsc.edu GRCh37 1 169519050 169519050 + stop_gained Nonsense_Mutation SNP G G A TCGA-HT-7610-01 TCGA-HT-7610-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 4 ENST00000367797.3:c.1600C>T p.Gln534Ter p.Q534* ENST00000367797 NM_000130.4 534 Caa/Taa 0 0.428 TGTATTCCTTGCCTGTCCAGG +OR8I2 120586 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 55860898 55860898 + missense_variant Missense_Mutation SNP G G C TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 330 159 ENST00000302124.2:c.115G>C p.Val39Leu p.V39L ENST00000302124 NM_001003750.1 39 Gtt/Ctt 0 0.378 TCTATTCACTGTTTTGGGAAA +KIAA1377 57562 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 101818852 101818852 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 46 ENST00000263468.8:c.485G>A p.Arg162His p.R162H ENST00000263468 NM_020802.2 162 cGt/cAt 0 0.348 CCCTTTTCCCGTAGACCAACA +ARID2 196528 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 46242662 46242662 + stop_gained Nonsense_Mutation SNP C C T TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 96 46 ENST00000334344.6:c.1624C>T p.Arg542Ter p.R542* ENST00000334344 NM_152641.2 542 Cga/Tga 0 0.343 TTCTGTTTCTCGAGCAGAAAT +MED13L 23389 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 116460278 116460278 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 15 ENST00000281928.3:c.608C>T p.Ser203Leu p.S203L ENST00000281928 NM_015335.4 203 tCa/tTa 0 0.473 TGGTGCAGGTGAAGACTGAGC +OR11H4 390442 hgsc.bcm.edu;broad.mit.edu GRCh37 14 20710969 20710969 + missense_variant Missense_Mutation SNP G G C TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 5 ENST00000315409.2:c.19G>C p.Asp7His p.D7H ENST00000315409 NM_001004479.1 7 Gac/Cac 0 0.418 CTTCTTTGTAGACTTAAGACC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577099 7577099 + missense_variant Missense_Mutation SNP C C T rs121912660 TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 64 ENST00000269305.4:c.839G>A p.Arg280Lys p.R280K ENST00000269305 NM_001126112.2 280 aGa/aAa 0 0.542 GCGCCGGTCTCTCCCAGGACA +SRCIN1 80725 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 36714502 36714502 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 42 ENST00000264659.7:c.2162G>A p.Arg721His p.R721H ENST00000264659 NM_025248.2 721 cGc/cAc 0 0.701 GTTGAGATAGCGCAGCCGTTC +EMILIN2 84034 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 2913269 2913269 + missense_variant Missense_Mutation SNP T T C TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 32 ENST00000254528.3:c.3029T>C p.Leu1010Pro p.L1010P ENST00000254528 NM_032048.2 1010 cTc/cCc 0 0.592 GCATTCCACCTCATCGTGCAC +FZR1 51343 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 3532532 3532532 + missense_variant Missense_Mutation SNP G G C TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 7 ENST00000395095.3:c.1126G>C p.Gly376Arg p.G376R ENST00000395095 NM_001136198.1 376 Ggc/Cgc 0 0.652 CTCGGGGGGCGGCACAGCTGA +PLA2G4A 5321 hgsc.bcm.edu;broad.mit.edu GRCh37 1 186948459 186948459 + missense_variant Missense_Mutation SNP A A G TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 150 8 ENST00000367466.3:c.1973A>G p.Glu658Gly p.E658G ENST00000367466 NM_024420.2 658 gAa/gGa 0 0.333 GTTCCAAGGGAAACTGAGGAA +CHD6 84181 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 40045243 40045243 + synonymous_variant Silent SNP C C T TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 190 86 ENST00000373233.3:c.6471G>A p.Ala2157= p.A2157= ENST00000373233 NM_032221.4 2157 gcG/gcA 0 0.552 GGATCTGGGCCGCCAATGCTG +TTN 7273 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 179456089 179456089 + synonymous_variant Silent SNP G G A TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 593 284 ENST00000589042.1:c.60363C>T p.Thr20121= p.T20121= ENST00000589042 NM_001267550.1 20121 acC/acT 0 0.433 AGTGCTCATCGGTTTTAATCT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 108 46 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +SLC23A3 151295 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 220034279 220034279 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 269 101 ENST00000455516.2:c.284G>A p.Gly95Asp p.G95D ENST00000455516 NM_001144890.1 95 gGt/gAt 0 0.582 GGTAGACATACCACATGAAAA +SENP7 57337 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 101177814 101177814 + missense_variant Missense_Mutation SNP T T G TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 433 87 ENST00000394095.2:c.269A>C p.Lys90Thr p.K90T ENST00000394095 NM_020654.3 90 aAg/aCg 0 0.358 TGGTGATGACTTGGAAGTAAC +ZMAT3 64393 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 178748788 178748788 + splice_acceptor_variant Splice_Site SNP C C G TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 44 ENST00000311417.2:c.271-1G>C p.X91_splice ENST00000311417 NM_022470.3 0 0.398 GATTTTTACCCTAGAAATAAA +AFP 174 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 74303981 74303981 + missense_variant Missense_Mutation SNP A A C TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 121 23 ENST00000395792.2:c.228A>C p.Lys76Asn p.K76N ENST00000395792 NM_001134.1 76 aaA/aaC 0 0.363 CAATTGAGAAACCCACTggag +SPZ1 84654 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 79616896 79616896 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 130 71 ENST00000296739.4:c.862G>A p.Gly288Ser p.G288S ENST00000296739 NM_032567.3 288 Ggt/Agt 0 0.413 TAATGGAGTCGGTTTCCAAAC +GPR98 84059 hgsc.bcm.edu;ucsc.edu GRCh37 5 89914934 89914934 + missense_variant Missense_Mutation SNP C C A TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 5 ENST00000405460.2:c.389C>A p.Pro130Gln p.P130Q ENST00000405460 NM_032119.3 130 cCa/cAa 0 0.259 CTTGGATGGCCAAGGACTGTT +TRIM52 84851 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 180687093 180687093 + missense_variant Missense_Mutation SNP T T C TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 171 108 ENST00000327767.4:c.722A>G p.Asp241Gly p.D241G ENST00000327767 NM_032765.2 241 gAc/gGc 0 0.542 GGCCTCTTTGTCCACCTCACA +UTRN 7402 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 144872125 144872125 + missense_variant Missense_Mutation SNP C C T rs114254210 byFrequency TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 116 46 ENST00000367545.3:c.6835C>T p.Arg2279Cys p.R2279C ENST00000367545 NM_007124.2 2279 Cgc/Tgc 0 0.338 CTTAGAACAGCGCCATCCTCA +COG5 10466 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 107002756 107002756 + synonymous_variant Silent SNP T T C TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 12 ENST00000297135.3:c.1038A>G p.Gly346= p.G346= ENST00000297135 NM_006348.3 346 ggA/ggG 0 0.393 TATTTACCTGTCCACAAACAG +AGK 55750 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 141301025 141301025 + missense_variant Missense_Mutation SNP A A C TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 154 25 ENST00000355413.4:c.242A>C p.Glu81Ala p.E81A ENST00000355413 NM_018238.3 81 gAa/gCa 0 0.363 ACTCTATTTGAAAAAAATGCT +KCNV1 27012 hgsc.bcm.edu;broad.mit.edu GRCh37 8 110984685 110984685 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 181 12 ENST00000524391.1:c.793C>T p.Arg265Trp p.R265W ENST00000524391 265 Cgg/Tgg 0 0.532 CACCTGTCCCGCACACACAGG +C9orf114 51490 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 131586077 131586077 + missense_variant Missense_Mutation SNP G G C TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 10 4 ENST00000361256.5:c.1011C>G p.Asp337Glu p.D337E ENST00000361256 NM_016390.3 337 gaC/gaG 0 0.642 TGACGTACAGGTCAAAGAGGA +ZFX 7543 hgsc.bcm.edu;broad.mit.edu GRCh37 X 24229263 24229263 + stop_gained Nonsense_Mutation SNP C C T TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 181 11 ENST00000379177.1:c.2188C>T p.Gln730Ter p.Q730* ENST00000379177 NM_003410.3 730 Caa/Taa 0 0.408 GGGATTTAGGCAACAGAGTGA +HEATR2 54919 broad.mit.edu;ucsc.edu GRCh37 7 813720 813720 + missense_variant Missense_Mutation SNP A A G TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 158 56 ENST00000297440.6:c.1967A>G p.Asp656Gly p.D656G ENST00000297440 NM_017802.3 656 gAc/gGc 0 0.642 GTGACAAAGGACATCCTGGCC +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76939929 76939930 + frameshift_variant Frame_Shift_Ins INS - - A TCGA-E1-5303-01 TCGA-E1-5303-10 Untested Somatic Phase_I WXS none Illumina GAIIx 123 232 ENST00000373344.5:c.818dupT p.Leu273PhefsTer9 p.L273Ffs*9 ENST00000373344 NM_000489.3 273 ttg/ttTg 0 0.381 CCAAGTCCAACAAAGGCTCTGG +KIAA1462 57608 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 30316584 30316584 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 106 15 ENST00000375377.1:c.2493G>C p.Leu831Phe p.L831F ENST00000375377 NM_020848.2 831 ttG/ttC 0 0.557 ACTGACTGATCAAATCCCAGG +BRSK2 9024 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 1477653 1477653 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 11 9 ENST00000382179.1:c.1882G>A p.Val628Met p.V628M ENST00000382179 NM_001256630.1 628 Gtg/Atg 0 0.612 GGGGCCAGCCGTGTTCCAGAA +SLC6A15 55117 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 85255483 85255483 + synonymous_variant Silent SNP A A G TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 129 9 ENST00000266682.5:c.2121T>C p.Ala707= p.A707= ENST00000266682 NM_182767.5 707 gcT/gcC 0 0.423 GTCCATTGGGAGCAGTATCCA +SRL 6345 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 4242361 4242361 + synonymous_variant Silent SNP G G A TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 25 ENST00000399609.3:c.1215C>T p.Phe405= p.F405= ENST00000399609 NM_001098814.1 405 ttC/ttT 0 0.493 GATTGATGCCGAAGAAGTCCT +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578475 7578475 + missense_variant Missense_Mutation SNP G G A rs137852790 TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 17 ENST00000269305.4:c.455C>T p.Pro152Leu p.P152L ENST00000269305 NM_001126112.2 152 cCg/cTg 0 0.612 GGTGCCGGGCGGGGGTGTGGA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113113 209113113 + missense_variant Missense_Mutation SNP G G C rs121913499 TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 19 ENST00000345146.2:c.394C>G p.Arg132Gly p.R132G ENST00000345146 NM_005896.2 132 Cgt/Ggt 0 0.398 TAAGCATGACGACCTATGATG +DPPA4 55211 hgsc.bcm.edu;broad.mit.edu GRCh37 3 109049418 109049418 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 5 ENST00000335658.6:c.632C>G p.Ala211Gly p.A211G ENST00000335658 NM_018189.3 211 gCc/gGc 0 0.522 CCTCGCCCTGGCTGAAATTCT +PLXNA1 5361 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 126732904 126732904 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 120 28 ENST00000393409.2:c.2355C>G p.Asn785Lys p.N785K ENST00000393409 NM_032242.3 785 aaC/aaG 0 0.632 TGCCAGTGAACCTGTCAGTCG +KHDRBS2 202559 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 62611243 62611243 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 17 ENST00000281156.4:c.517C>T p.Arg173Cys p.R173C ENST00000281156 NM_152688.2 173 Cgt/Tgt 0 0.418 GATAATTCACGTAGTTGTTCC +SLC2A12 154091 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 134350799 134350799 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 6 ENST00000275230.5:c.164G>C p.Gly55Ala p.G55A ENST00000275230 NM_145176.2 55 gGt/gCt 0 0.517 AAGTTCATAACCCACCAGGAG +VPS41 27072 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 38796519 38796519 + synonymous_variant Silent SNP G G A rs146405914 TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 10 ENST00000310301.4:c.1614C>T p.Asp538= p.D538= ENST00000310301 NM_014396.3 538 gaC/gaT 0 0.284 ACTGAAAAACGTCTTTATGTC +MET 4233 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 116381017 116381017 + stop_gained Nonsense_Mutation SNP C C T TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 20 ENST00000397752.3:c.1639C>T p.Arg547Ter p.R547* ENST00000397752 NM_000245.2 547 Cga/Tga 0 0.512 CAAATGTGTGCGATCGGAGGA +AKR1B15 441282 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 134256364 134256364 + missense_variant Missense_Mutation SNP T T A TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 74 13 ENST00000457545.2:c.444T>A p.Asp148Glu p.D148E ENST00000457545 NM_001080538.2 148 gaT/gaA 0 0.423 AGACTGGGGATGACTTTTTCC +ATRX 546 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 76849221 76849221 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 20 ENST00000373344.5:c.6055A>G p.Lys2019Glu p.K2019E ENST00000373344 NM_000489.3 2019 Aaa/Gaa 0 0.363 AGTACCATTTTCCCAGAATGC +RBM41 55285 broad.mit.edu;ucsc.edu GRCh37 X 106310757 106310757 + stop_lost Nonstop_Mutation SNP C C A TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 161 43 ENST00000372479.3:c.1242G>T p.Ter414TyrextTer13 p.*414Yext*13 ENST00000372479 NM_018301.3 414 taG/taT 0 0.378 TATATATATTCTAGCTACCAC +TP53 7157 broad.mit.edu;ucsc.edu GRCh37 17 7577121 7577121 + missense_variant Missense_Mutation SNP G G A rs121913343 TCGA-HT-7482-01 TCGA-HT-7482-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 8 ENST00000269305.4:c.817C>T p.Arg273Cys p.R273C ENST00000269305 NM_001126112.2 273 Cgt/Tgt 0 0.542 GCACAAACACGCACCTCAAAG +ANKRD1 27063 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 92678671 92678671 + missense_variant Missense_Mutation SNP A A G TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 18 19 ENST00000371697.3:c.404T>C p.Val135Ala p.V135A ENST00000371697 NM_014391.2 135 gTa/gCa 0 0.343 TTTTTCTACTACTGGCAGTTT +TMEM180 79847 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 104233397 104233397 + synonymous_variant Silent SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 31 ENST00000238936.4:c.996C>T p.Tyr332= p.Y332= ENST00000238936 NM_024789.3 332 taC/taT 0 0.637 GGGGCGTCTACGCGGTGGTGC +TACC2 10579 hgsc.bcm.edu;broad.mit.edu GRCh37 10 123844064 123844064 + synonymous_variant Silent SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 2 4 ENST00000369005.1:c.2049C>T p.Pro683= p.P683= ENST00000369005 NM_206862.2 683 ccC/ccT 0 0.582 CCACTGTTCCCGAAGGAGCCA +MUC5B 727897 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 1271606 1271606 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 60 ENST00000529681.1:c.13496C>T p.Ser4499Phe p.S4499F ENST00000529681 NM_002458.2 4499 tCc/tTc 0 0.642 ACTCCCTCCTCCAGTCCAGGG +OR5F1 338674 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 55761801 55761801 + missense_variant Missense_Mutation SNP T T A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 32 ENST00000278409.1:c.301A>T p.Met101Leu p.M101L ENST00000278409 NM_003697.1 101 Atg/Ttg 0 0.463 AAGAAGTACATCTGTAGGAAG +PDE2A 5138 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 72289381 72289381 + splice_region_variant,synonymous_variant Splice_Region SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 27 ENST00000334456.5:c.2511G>A p.Glu837= p.E837= ENST00000334456 NM_002599.4 837 gaG/gaA 0 0.582 CCATGGCCTTCTCCTGCAGGC +OR2AT4 341152 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 74800020 74800020 + missense_variant Missense_Mutation SNP T T A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 11 ENST00000305159.3:c.739A>T p.Ser247Cys p.S247C ENST00000305159 NM_001005285.1 247 Agc/Tgc 0 0.567 AGGTGGGAGCTGCAGGTGGAG +ACSM4 341392 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 7477158 7477158 + synonymous_variant Silent SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 15 ENST00000399422.4:c.1500G>A p.Ser500= p.S500= ENST00000399422 NM_001080454.1 500 tcG/tcA 0 0.428 TTGTTGAATCGGCTGTTGTCA +GUCY2C 2984 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 14809526 14809526 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 25 ENST00000261170.3:c.1390C>T p.Arg464Cys p.R464C ENST00000261170 NM_004963.3 464 Cgt/Tgt 0 0.373 TTTTTCTGACGAAGTTCATAA +ALG5 29880 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 37569684 37569684 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 15 ENST00000239891.3:c.116G>A p.Arg39Gln p.R39Q ENST00000239891 NM_013338.4 39 cGa/cAa 0 0.383 TTCTTCATGTCGATGGAGTGC +SYNE3 161176 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 95932397 95932397 + synonymous_variant Silent SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 23 ENST00000334258.5:c.498G>A p.Gln166= p.Q166= ENST00000334258 NM_152592.3 166 caG/caA 0 0.637 GGAGCACCGCCTGGTTGTCCA +ATP8B4 79895 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 50223421 50223421 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 17 ENST00000284509.6:c.1537C>T p.Arg513Trp p.R513W ENST00000284509 NM_024837.3 513 Cgg/Tgg 0 0.398 TCTGGGGTCCGGGATTTAAAA +MYO5A 4644 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 52622646 52622646 + stop_gained Nonsense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 56 ENST00000399231.3:c.4384C>T p.Arg1462Ter p.R1462* ENST00000399231 NM_000259.3 1462 Cga/Tga 0 0.413 TTGACTGGTCGGATGGGTTCA +OR4F6 390648 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 102346763 102346763 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 23 ENST00000328882.4:c.841G>A p.Val281Ile p.V281I ENST00000328882 NM_001005326.1 281 Gtt/Att 0 0.343 TATCACTCCCGTTTTGAATCC +SPNS1 83985 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 28995597 28995597 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 9 ENST00000311008.11:c.1564C>T p.Pro522Ser p.P522S ENST00000311008 NM_032038.2 522 Ccc/Tcc 0 0.697 CACCCGCGTGCCCGTGGCCAG +CHST4 10164 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 71570880 71570880 + synonymous_variant Silent SNP C C T rs139260372 TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 22 ENST00000338482.5:c.300C>T p.Ala100= p.A100= ENST00000338482 100 gcC/gcT 0 0.582 TGATACGGGCCGTCTTCTTGT +ACLY 47 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 40040509 40040509 + missense_variant Missense_Mutation SNP G G C TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 20 ENST00000352035.2:c.2091C>G p.Phe697Leu p.F697L ENST00000352035 NM_001096.2 697 ttC/ttG 0 0.438 CATGATCCATGAATGTGGAGC +EPN3 55040 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 48616618 48616618 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 18 ENST00000268933.3:c.833G>A p.Arg278Gln p.R278Q ENST00000268933 NM_017957.2 278 cGg/cAg 0 0.597 CACCATCAGCGGGACAGAGAG +CATSPERD 257062 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 5727283 5727283 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 29 ENST00000381624.3:c.131G>A p.Arg44His p.R44H ENST00000381624 NM_152784.3 44 cGc/cAc 0 0.338 CTCTAGGACCGCCTGTATTTT +SLC8A2 6543 hgsc.bcm.edu;ucsc.edu GRCh37 19 47935494 47935494 + synonymous_variant Silent SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 11 ENST00000236877.6:c.2319C>T p.Phe773= p.F773= ENST00000236877 NM_015063.2 773 ttC/ttT 0 0.627 CGGTGCAGCCGAAGTGGGAGG +MYH14 79784 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 50750373 50750373 + synonymous_variant Silent SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 8 ENST00000601313.1:c.1323G>A p.Lys441= p.K441= ENST00000601313 NM_001145809.1 441 aaG/aaA 0 0.597 CCCAGACTAAGGAACAGGTAG +SELE 6401 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 169698637 169698637 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 39 ENST00000333360.7:c.893C>T p.Thr298Met p.T298M ENST00000333360 NM_000450.2 298 aCg/aTg 0 0.443 ACCTTTACACGTTGGCTTCTC +VSX1 30813 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 25057044 25057044 + synonymous_variant Silent SNP A A C TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 34 ENST00000376709.4:c.951T>G p.Pro317= p.P317= ENST00000376709 NM_014588.5 317 ccT/ccG 0 0.542 AGCCATTCTCAGGGCTCACTT +GREB1 9687 hgsc.bcm.edu;broad.mit.edu GRCh37 2 11725320 11725320 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 14 14 ENST00000381486.2:c.935G>A p.Arg312His p.R312H ENST00000381486 NM_014668.3 312 cGc/cAc 0 0.512 CCCAAAAAACGCCACAAAGGG +CENPA 1058 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 27016113 27016113 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 134 61 ENST00000335756.4:c.389G>A p.Arg130Gln p.R130Q ENST00000335756 NM_001809.3 130 cGg/cAg 0 0.552 CAACTGGCCCGGAGGATCCGG +G6PC2 57818 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 169764413 169764413 + missense_variant Missense_Mutation SNP T T G TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 43 ENST00000375363.3:c.892T>G p.Leu298Val p.L298V ENST00000375363 NM_021176.2 298 Ttg/Gtg 0 0.473 GCTCTGTGCCTTGACCTCATT +GPR55 9290 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 231774733 231774733 + synonymous_variant Silent SNP C C T rs146835586 TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 33 ENST00000392040.1:c.945G>A p.Thr315= p.T315= ENST00000392040 NM_005683.3 315 acG/acA 0 0.552 CCCGGGAGATCGTGGTGTCCT +COL6A3 1293 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 238275437 238275437 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 31 ENST00000295550.4:c.5393G>A p.Arg1798His p.R1798H ENST00000295550 NM_004369.3 1798 cGc/cAc 0 0.547 GTTGCCCACGCGGAACGCTGT +GPR98 84059 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 90136725 90136725 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 16 ENST00000405460.2:c.16942C>T p.Leu5648Phe p.L5648F ENST00000405460 NM_032119.3 5648 Ctc/Ttc 0 0.423 CAACAGAGTGCTCCATACCAT +PCDH12 51294 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 141335542 141335542 + missense_variant Missense_Mutation SNP A A T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 9 ENST00000231484.3:c.1875T>A p.Asp625Glu p.D625E ENST00000231484 NM_016580.3 625 gaT/gaA 0 0.582 CCGAGTCTGCATCTCTTGCCA +SH3TC2 79628 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 148411245 148411245 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 17 ENST00000515425.1:c.1007G>A p.Arg336Lys p.R336K ENST00000515425 NM_024577.3 336 aGg/aAg 0 0.522 GGCAGAGTTCCTGCTCCTGCA +GRIA1 2890 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 153056693 153056693 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 5 ENST00000518783.1:c.1031G>A p.Gly344Glu p.G344E ENST00000518783 NM_001258021.1 344 gGg/gAg 0 0.537 TGGGGCCAAGGGATCGACATC +TENM2 57451 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 167671581 167671581 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 28 ENST00000518659.1:c.5677G>A p.Val1893Met p.V1893M ENST00000518659 NM_001122679.1 1893 Gtg/Atg 0 0.597 AGCTGTCAACGTGTCATACTT +GABRP 2568 hgsc.bcm.edu;ucsc.edu GRCh37 5 170232777 170232777 + missense_variant Missense_Mutation SNP G G A rs112704076 byFrequency TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 22 ENST00000518525.1:c.599G>A p.Arg200His p.R200H ENST00000518525 200 cGt/cAt 0 0.522 GACTCTGTGCGTGGACTGGAA +HLA-DMB 3109 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 32906668 32906668 + missense_variant Missense_Mutation SNP T T G TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 21 ENST00000418107.2:c.130A>C p.Ile44Leu p.I44L ENST00000418107 NM_002118.4 44 Atc/Ctc 0 0.527 TTGAAGGAGATGCAGTATGTG +LAMA4 3910 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 112469437 112469437 + missense_variant Missense_Mutation SNP G G C TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 29 ENST00000230538.7:c.2275C>G p.Leu759Val p.L759V ENST00000230538 NM_001105206.2 759 Cta/Gta 0 0.517 CAGTTGGTTAGATTGTTGGCC +TCTE3 6991 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 170144257 170144257 + synonymous_variant Silent SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 18 ENST00000366774.3:c.234G>A p.Leu78= p.L78= ENST00000366774 NM_174910.1 78 ctG/ctA 0 0.373 TTAATTTTGCCAGGGCACTCT +DYNC1I1 1780 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 95657632 95657632 + missense_variant,splice_region_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 27 ENST00000324972.6:c.1166C>T p.Thr389Met p.T389M ENST00000324972 NM_004411.4 389 aCg/aTg 0 0.493 GCTGCACACACGGTAATGCAA +LAMB1 3912 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 107616242 107616242 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 25 ENST00000222399.6:c.1081G>A p.Val361Met p.V361M ENST00000222399 NM_002291.2 361 Gtg/Atg 0 0.517 TCATCACACACGCCTCCGCTG +DOCK5 80005 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 25198440 25198440 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 9 ENST00000276440.7:c.2375G>A p.Arg792His p.R792H ENST00000276440 NM_024940.6 792 cGc/cAc 0 0.398 AATTCAATTCGCCAGTTATTT +ASAP1 50807 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 131149272 131149272 + missense_variant Missense_Mutation SNP G G T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 31 ENST00000357668.1:c.1093C>A p.Pro365Thr p.P365T ENST00000357668 365 Cca/Aca 0 0.448 AACTTGGCTGGTTGCCTGTTA +MAMDC2 256691 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 72724721 72724721 + splice_donor_variant Splice_Site SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 48 ENST00000377182.4:c.505+1G>A p.X169_splice ENST00000377182 NM_153267.4 0 0.368 TACTGTATTGGTAAGTGGGCT +GOLGA2 2801 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 131022430 131022430 + synonymous_variant Silent SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 35 ENST00000421699.2:c.1716G>A p.Ser572= p.S572= ENST00000421699 NM_004486.4 572 tcG/tcA 0 0.592 CGTGCTGCTCCGACTGCAGTG +FAM47B 170062 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 34961315 34961315 + missense_variant Missense_Mutation SNP G G T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 33 ENST00000329357.5:c.367G>T p.Ala123Ser p.A123S ENST00000329357 NM_152631.2 123 Gcc/Tcc 0 0.537 GGAAGTGGAAGCCCAGCTGAT +MAGEB16 139604 hgsc.bcm.edu;broad.mit.edu GRCh37 X 35820491 35820491 + missense_variant Missense_Mutation SNP A A T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 1 9 ENST00000399989.1:c.178A>T p.Ser60Cys p.S60C ENST00000399989 NM_001099921.1 60 Agt/Tgt 0 0.532 TAAGGCAGAGAGTCCTCTTGA +DDX26B 203522 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 134706886 134706886 + synonymous_variant Silent SNP G G T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 30 ENST00000370752.4:c.1434G>T p.Gly478= p.G478= ENST00000370752 NM_182540.4 478 ggG/ggT 0 0.353 AAATCACAGGGGAAACTGCAC +SPANXN2 494119 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 142795437 142795437 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 17 141 ENST00000370498.1:c.241G>A p.Val81Ile p.V81I ENST00000370498 NM_001009615.1 81 Gtc/Atc 0 0.453 TCCTCTTGGACGGGATTGATG +SLC23A2 9962 broad.mit.edu;ucsc.edu GRCh37 20 4850643 4850643 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 27 ENST00000379333.1:c.1159G>A p.Val387Met p.V387M ENST00000379333 NM_203327.1 387 Gtg/Atg 0 0.602 CTGGCGACCACGGCACTGAGC +OR1N1 138883 broad.mit.edu;ucsc.edu GRCh37 9 125289214 125289214 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 4 ENST00000304880.2:c.359G>A p.Arg120His p.R120H ENST00000304880 NM_012363.1 120 cGc/cAc 0 0.512 GGCCACATAGCGGTCATACGC +HOXB5 3215 broad.mit.edu;ucsc.edu GRCh37 17 46670842 46670842 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 5 ENST00000239151.5:c.203C>T p.Ala68Val p.A68V ENST00000239151 NM_002147.3 68 gCg/gTg 0 0.687 CTCGCCCACCGCCCCAAAGTG +COL1A1 1277 broad.mit.edu;ucsc.edu GRCh37 17 48270361 48270361 + synonymous_variant Silent SNP G G A rs72651616 TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 5 ENST00000225964.5:c.1815C>T p.Gly605= p.G605= ENST00000225964 NM_000088.3 605 ggC/ggT 0 0.627 TTACGACAGCGCCAGGGGGTC +TTC21A 199223 broad.mit.edu;ucsc.edu GRCh37 3 39179140 39179140 + missense_variant Missense_Mutation SNP G G C TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 3 ENST00000431162.2:c.3635G>C p.Cys1212Ser p.C1212S ENST00000431162 1212 tGc/tCc 0 0.607 GACATTTACTGCCAGGGCAGC +FCHSD1 89848 broad.mit.edu;ucsc.edu GRCh37 5 141028985 141028985 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 151 73 ENST00000435817.2:c.352G>A p.Ala118Thr p.A118T ENST00000435817 NM_033449.2 118 Gcc/Acc 0 0.612 TGCTCCTTGGCGCTCCGCCCT +KCNS3 3790 broad.mit.edu;ucsc.edu GRCh37 2 18113040 18113040 + synonymous_variant Silent SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 37 ENST00000403915.1:c.765G>A p.Leu255= p.L255= ENST00000403915 NM_001282428.1 255 ctG/ctA 0 0.512 AAAACCCTCTGAACATCATTG +ITPR1 3708 broad.mit.edu;ucsc.edu GRCh37 3 4819013 4819013 + synonymous_variant Silent SNP C C A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 8 6 ENST00000302640.8:c.6201C>A p.Ile2067= p.I2067= ENST00000302640 NM_001168272.1 2067 atC/atA 0 0.423 TCAATGATATCAATCCTTTGG +USH2A 7399 broad.mit.edu;ucsc.edu GRCh37 1 216251647 216251647 + stop_gained Nonsense_Mutation SNP G G A TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 188 131 ENST00000307340.3:c.5356C>T p.Gln1786Ter p.Q1786* ENST00000307340 NM_206933.2 1786 Caa/Taa 0 0.348 AGATCCACTTGTGTAAAGGCA +CACNA1S 779 broad.mit.edu;ucsc.edu GRCh37 1 201047161 201047161 + missense_variant Missense_Mutation SNP G G A rs9333651 TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 26 ENST00000362061.3:c.1465C>T p.Arg489Cys p.R489C ENST00000362061 NM_000069.2 489 Cgc/Tgc 0 0.582 AAGTACTGGCGCAGGCCCAGC +NLRP9 338321 broad.mit.edu;ucsc.edu GRCh37 19 56244617 56244617 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 4 ENST00000332836.2:c.580G>A p.Ala194Thr p.A194T ENST00000332836 NM_176820.2 194 Gca/Aca 0 0.453 CTGGTCTCTGCGATACCGTTC +SEC23B 10483 broad.mit.edu;ucsc.edu GRCh37 20 18516372 18516372 + stop_gained Nonsense_Mutation SNP G G T TCGA-CS-6186-01 TCGA-CS-6186-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 4 ENST00000336714.3:c.1390G>T p.Glu464Ter p.E464* ENST00000336714 NM_032985.4 464 Gaa/Taa 0 0.433 CATCTATTTTGAAGTTGTCAA +PTEN 5728 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 89692835 89692835 + missense_variant Missense_Mutation SNP G G T rs57374291 TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 25 ENST00000371953.3:c.319G>T p.Asp107Tyr p.D107Y ENST00000371953 NM_000314.4 107 Gat/Tat 0 0.368 CTTTTGTGAAGATCTTGACCA +MS4A6E 245802 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 60107365 60107365 + synonymous_variant Silent SNP T T A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 200 76 ENST00000300182.4:c.381T>A p.Ser127= p.S127= ENST00000300182 NM_139249.2 127 tcT/tcA 0 0.493 TGCTGGTTTCTACTGTGTTGG +EXPH5 23086 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 108381685 108381685 + missense_variant Missense_Mutation SNP G G T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 8 ENST00000265843.4:c.4549C>A p.Leu1517Ile p.L1517I ENST00000265843 NM_015065.2 1517 Cta/Ata 0 0.433 CCAAGCTGTAGTTTATGCAAT +EXPH5 23086 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 108382533 108382533 + missense_variant Missense_Mutation SNP G G C TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 99 24 ENST00000265843.4:c.3701C>G p.Thr1234Arg p.T1234R ENST00000265843 NM_015065.2 1234 aCg/aGg 0 0.373 AACAGAAAACGTACTAGTCGT +FZD10 11211 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 130648631 130648631 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 18 ENST00000229030.4:c.1144G>A p.Gly382Arg p.G382R ENST00000229030 382 Ggg/Agg 0 0.647 CGAGCTCACCGGGGTCTGCTA +TICRR 90381 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 90167424 90167424 + missense_variant Missense_Mutation SNP C C A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 94 43 ENST00000268138.7:c.3883C>A p.Pro1295Thr p.P1295T ENST00000268138 1295 Cca/Aca 0 0.453 TCCAAAAAGACCAGGGAATTC +MYO15A 51168 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 18053797 18053797 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 10 ENST00000205890.5:c.7267G>A p.Gly2423Ser p.G2423S ENST00000205890 NM_016239.3 2423 Ggt/Agt 0 0.617 AGGCCAGCCCGGTGGAGGCAG +NF1 4763 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 29663747 29663747 + stop_gained Nonsense_Mutation SNP T T G TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 23 ENST00000358273.4:c.6242T>G p.Leu2081Ter p.L2081* ENST00000358273 NM_001042492.2 2081 tTa/tGa 0 0.408 ATTGCTATTTTAGCACGCTAC +ANKRD30B 374860 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 14763803 14763803 + synonymous_variant Silent SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 14 8 ENST00000358984.4:c.939G>A p.Thr313= p.T313= ENST00000358984 NM_001145029.1 313 acG/acA 0 0.478 TGGAGGGAACGTCTGCCAAAA +NEDD4L 23327 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 56008358 56008358 + missense_variant Missense_Mutation SNP A A G TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 4 ENST00000400345.3:c.1214A>G p.Asn405Ser p.N405S ENST00000400345 NM_001144967.2 405 aAt/aGt 0 0.478 TACTATGTCAATCATAACAAT +CD70 970 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 6590911 6590911 + missense_variant Missense_Mutation SNP C C T rs148772362 TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 32 ENST00000245903.3:c.103G>A p.Val35Met p.V35M ENST00000245903 NM_001252.3 35 Gtg/Atg 0 0.627 ATGCACACCACGAGGCAGATC +UBE2M 9040 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 59068093 59068093 + missense_variant Missense_Mutation SNP T T C TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 18 ENST00000253023.3:c.308A>G p.Asn103Ser p.N103S ENST00000253023 NM_003969.3 103 aAc/aGc 0 0.582 GAGGTCAATGTTGGGGTGATA +PRAMEF4 400735 hgsc.bcm.edu;broad.mit.edu GRCh37 1 12941802 12941802 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 239 83 ENST00000235349.5:c.748G>A p.Val250Ile p.V250I ENST00000235349 NM_001009611.2 250 Gtt/Att 0 0.488 TCTGGGGAAACGTAGCGAGAG +TCHH 7062 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 152082385 152082385 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 22 ENST00000368804.1:c.3308G>A p.Arg1103His p.R1103H ENST00000368804 NM_007113.3 1103 cGc/cAc 0 0.612 CCGCTCCTGGCGCCTTCTCTT +CD1E 913 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 158324220 158324220 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 90 29 ENST00000368167.3:c.112C>T p.Arg38Cys p.R38C ENST00000368167 NM_030893.3 38 Cgc/Tgc 0 0.542 GCTGTCCTTCCGCATGCTCCA +RYR2 6262 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 237777663 237777663 + missense_variant Missense_Mutation SNP A A T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 12 ENST00000366574.2:c.5235A>T p.Lys1745Asn p.K1745N ENST00000366574 NM_001035.2 1745 aaA/aaT 0 0.517 AGAACAAAAAACACGGCCTTC +PHACTR3 116154 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 58349322 58349322 + synonymous_variant Silent SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 14 ENST00000371015.1:c.951G>A p.Gly317= p.G317= ENST00000371015 NM_080672.4 317 ggG/ggA 0 0.527 AAAGTAAAGGGTCTCCAAAGA +LRRC3 81543 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 45877263 45877263 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 13 ENST00000291592.4:c.736G>A p.Ala246Thr p.A246T ENST00000291592 NM_030891.3 246 Gcc/Acc 0 0.652 TCTGCCCAGCGCCCCCGCCTC +SFI1 9814 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 32013006 32013006 + missense_variant Missense_Mutation SNP G G C rs143349198 by1000genomes TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 19 ENST00000400288.2:c.3454G>C p.Glu1152Gln p.E1152Q ENST00000400288 NM_001007467.2 1152 Gaa/Caa 0 0.567 CCTTGAGGCTGAACTTGAGGA +DEPDC5 9681 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 32302244 32302244 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 14 ENST00000382112.3:c.4546C>T p.Arg1516Trp p.R1516W ENST00000382112 NM_001136029.2 1516 Cgg/Tgg 0 0.607 AGGGCAGCAGCGGCGGCGGCG +PDIA6 10130 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 10929977 10929977 + synonymous_variant Silent SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 24 ENST00000272227.3:c.738C>T p.Gly246= p.G246= ENST00000272227 NM_005742.2 246 ggC/ggT 0 0.423 CAGGAGACTCGCCTTTCTGAA +KCNS3 3790 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 18113581 18113581 + missense_variant Missense_Mutation SNP C C A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 34 ENST00000403915.1:c.1306C>A p.Pro436Thr p.P436T ENST00000403915 NM_001282428.1 436 Cct/Act 0 0.453 TCATGAGCTACCTTACTTTAA +CLHC1 130162 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 55404777 55404777 + missense_variant Missense_Mutation SNP C C G TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 17 ENST00000401408.1:c.1525G>C p.Gly509Arg p.G509R ENST00000401408 NM_152385.2 509 Ggc/Cgc 0 0.353 AGCTTAATGCCAACTTTTTTC +B3GNT7 93010 hgsc.bcm.edu;broad.mit.edu GRCh37 2 232263412 232263412 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 18 ENST00000287590.5:c.982G>A p.Val328Ile p.V328I ENST00000287590 NM_145236.2 328 Gtc/Atc 0 0.672 GATCGACGACGTCTTTCTGGG +GIGYF2 26058 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 233681681 233681681 + missense_variant Missense_Mutation SNP G G A rs149585458 TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 108 67 ENST00000409451.3:c.2372G>A p.Arg791Gln p.R791Q ENST00000409451 791 cGg/cAg 0 0.488 GAAATTCTTCGGCGACAGCAG +PROM1 8842 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 15991422 15991422 + missense_variant Missense_Mutation SNP A A G TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 6 ENST00000510224.1:c.2009T>C p.Leu670Pro p.L670P ENST00000510224 670 cTg/cCg 0 0.413 ATCTCTTTTCAGGGAGTTCCT +CCKAR 886 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 26483467 26483467 + synonymous_variant Silent SNP G G A rs150897748 TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 93 20 ENST00000295589.3:c.1080C>T p.Tyr360= p.Y360= ENST00000295589 NM_000730.2 360 taC/taT 0 0.627 AGGAGGAGGTGTAGGACAGGA +MUC7 4589 hgsc.bcm.edu;ucsc.edu GRCh37 4 71347577 71347577 + synonymous_variant Silent SNP C C T rs41424846 byFrequency TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 19 ENST00000413702.1:c.1116C>T p.Asp372= p.D372= ENST00000413702 NM_001145006.1 372 gaC/gaT 0 0.338 GAATTATTGACGACATGGTGG +PPEF2 5470 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 76812812 76812812 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 224 99 ENST00000286719.7:c.230G>A p.Ser77Asn p.S77N ENST00000286719 NM_006239.2 77 aGc/aAc 0 0.522 GTCGTTGTGGCTGCTGGGGAT +FAT4 79633 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 126239159 126239159 + synonymous_variant Silent SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 16 ENST00000394329.3:c.1593C>T p.Leu531= p.L531= ENST00000394329 NM_024582.4 531 ctC/ctT 0 0.547 ATAGCGGCCTCGTGACCACTG +MARCH11 441061 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 16067657 16067657 + missense_variant Missense_Mutation SNP T T C TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 124 45 ENST00000332432.8:c.1132A>G p.Asn378Asp p.N378D ENST00000332432 NM_001102562.1 378 Aat/Gat 0 0.478 CTCATCCGATTGAACAGGTGC +PCDHA2 56146 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 140176070 140176070 + synonymous_variant Silent SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 13 ENST00000526136.1:c.1521C>T p.Tyr507= p.Y507= ENST00000526136 NM_018905.2 507 taC/taT 0 0.682 TGTCGAGCTACGTTTCGGTGC +PCDHB2 56133 hgsc.bcm.edu;broad.mit.edu GRCh37 5 140475880 140475880 + synonymous_variant Silent SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 116 15 ENST00000194155.4:c.1506C>T p.Leu502= p.L502= ENST00000194155 NM_018936.2 502 ctC/ctT 0 0.692 ACCTGCCCCTCGCCTCCCTGG +PKHD1 5314 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 51882309 51882309 + synonymous_variant Silent SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 110 26 ENST00000371117.3:c.5499G>A p.Ser1833= p.S1833= ENST00000371117 NM_138694.3 1833 tcG/tcA 0 0.512 GGTAAGGCCACGATTCAAGCA +DDC 1644 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 50611629 50611629 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 166 38 ENST00000444124.2:c.155C>T p.Thr52Met p.T52M ENST00000444124 NM_001082971.1 52 aCg/aTg 0 0.557 GTCCTCAAACGTGTCTGGCTC +GRM3 2913 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 86415593 86415593 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 257 69 ENST00000361669.2:c.485G>A p.Arg162Gln p.R162Q ENST00000361669 NM_000840.2 162 cGg/cAg 0 0.522 AACCTGCTGCGGCTCTTCCAG +SLC26A3 1811 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 107423751 107423751 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 21 ENST00000340010.5:c.1018G>A p.Val340Ile p.V340I ENST00000340010 NM_000111.2 340 Gta/Ata 0 0.418 CAATCTCCTACGGTGTTTTGG +BRAF 673 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 140453154 140453154 + missense_variant Missense_Mutation SNP T T C TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 90 22 ENST00000288602.6:c.1781A>G p.Asp594Gly p.D594G ENST00000288602 NM_004333.4 594 gAt/gGt 0 0.373 TAGACCAAAATCACCTATTTT +DAPK1 1612 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 90301560 90301560 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 11 10 ENST00000408954.3:c.2319G>A p.Met773Ile p.M773I ENST00000408954 NM_004938.2 773 atG/atA 0 0.577 CCAAAGGGATGCTGGAGGTGT +MUM1L1 139221 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 105449891 105449891 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 6 14 ENST00000337685.2:c.466G>A p.Ala156Thr p.A156T ENST00000337685 NM_152423.4 156 Gca/Aca 0 0.413 ATGCTTGTTAGCATCTTCAGA +HTR3C 170572 broad.mit.edu;ucsc.edu GRCh37 3 183774718 183774718 + stop_gained Nonsense_Mutation SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 104 39 ENST00000318351.1:c.445C>T p.Arg149Ter p.R149* ENST00000318351 NM_130770.2 149 Cga/Tga 0 0.478 CAGTGAAGGTCGAATTAAGTA +CLEC12A 160364 broad.mit.edu;ucsc.edu GRCh37 12 10124176 10124176 + missense_variant,splice_region_variant Missense_Mutation SNP A A G TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 19 ENST00000355690.4:c.11A>G p.Asp4Gly p.D4G ENST00000355690 NM_001207010.1 4 gAt/gGt 0 0.318 CTTTGTCAAGATTTCTTTACA +UGT2B17 7367 broad.mit.edu;ucsc.edu GRCh37 4 69434170 69434170 + synonymous_variant Silent SNP C C T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 307 47 ENST00000317746.2:c.33G>A p.Leu11= p.L11= ENST00000317746 NM_001077.3 11 ctG/ctA 0 0.423 TGAGCTGCATCAGCAGAAAGA +COBLL1 22837 broad.mit.edu;ucsc.edu GRCh37 2 165578649 165578649 + missense_variant Missense_Mutation SNP G G T TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 21 ENST00000342193.4:c.932C>A p.Ala311Glu p.A311E ENST00000342193 NM_014900.4 311 gCa/gAa 0 0.488 CTGGATGTGTGCAAGGTCTTG +RPSAP52 204010 broad.mit.edu;ucsc.edu GRCh37 12 66152273 66152273 + non_coding_transcript_exon_variant RNA SNP T T G TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 11 5 ENST00000489520.2:n.671A>C *224* ENST00000489520 0 0.498 TCTGACCCACTGAGGGAGCTC +RPL10L 140801 broad.mit.edu;ucsc.edu GRCh37 14 47120403 47120403 + synonymous_variant Silent SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 27 ENST00000298283.3:c.537C>T p.Asp179= p.D179= ENST00000298283 NM_080746.2 179 gaC/gaT 0 0.517 CTTCAAATTCGTCAGCATTAA +ACSM2A 123876 broad.mit.edu;ucsc.edu GRCh37 16 20476848 20476848 + stop_gained Nonsense_Mutation SNP C C T rs146541514 TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 6 ENST00000573854.1:c.187C>T p.Arg63Ter p.R63* ENST00000573854 NM_001010845.2 63 Cga/Tga 0 0.517 GGCTGGCAAGCGACTCCCAAG +SDK2 54549 broad.mit.edu;ucsc.edu GRCh37 17 71410870 71410870 + synonymous_variant Silent SNP G G A TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 16 ENST00000392650.3:c.2397C>T p.His799= p.H799= ENST00000392650 NM_001144952.1 799 caC/caT 0 0.597 TGGCTTCCGCGTGCACATTGC +NF1 4763 broad.mit.edu;hgsc.bcm.edu GRCh37 17 29548901 29548901 + frameshift_variant Frame_Shift_Del DEL G G - TCGA-DU-6402-01 TCGA-DU-6402-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 23 ENST00000358273.4:c.1675delG p.Asp559IlefsTer9 p.D559Ifs*9 ENST00000358273 NM_001042492.2 559 Gat/at 0 0.289 AGATAGCATTGATTTGTGGAA +NUP98 4928 hgsc.bcm.edu;broad.mit.edu GRCh37 11 3697451 3697451 + missense_variant Missense_Mutation SNP T T C TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 129 11 ENST00000324932.7:c.5341A>G p.Met1781Val p.M1781V ENST00000324932 NM_139132.3 1781 Atg/Gtg 0 0.582 AGTTCGTCCATGGCATAGTCC +FBXL3 26224 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 77581815 77581815 + missense_variant Missense_Mutation SNP C C T TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 23 ENST00000355619.5:c.752G>A p.Arg251Gln p.R251Q ENST00000355619 NM_012158.2 251 cGa/cAa 0 0.418 ATGTTCTAATCGAACATGTTT +KIAA1024 23251 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 79749239 79749239 + synonymous_variant Silent SNP C C T TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 27 ENST00000305428.3:c.750C>T p.Val250= p.V250= ENST00000305428 NM_015206.2 250 gtC/gtT 0 0.473 CATTTGTGGTCCAGTCCTGTG +BZRAP1 9256 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 56388978 56388978 + missense_variant Missense_Mutation SNP T T C TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 41 ENST00000343736.4:c.3035A>G p.Asn1012Ser p.N1012S ENST00000343736 1012 aAc/aGc 0 0.602 CCGGACACCGTTGGATGTGCC +PRX 57716 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 40901791 40901791 + missense_variant Missense_Mutation SNP G G A TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 115 11 ENST00000324001.7:c.2468C>T p.Ala823Val p.A823V ENST00000324001 NM_181882.2 823 gCg/gTg 0 0.587 CTCAGCACCCGCCTCGCCTGG +SOGA1 140710 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 35445831 35445831 + synonymous_variant Silent SNP G G T TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 6 8 ENST00000237536.4:c.1113C>A p.Ala371= p.A371= ENST00000237536 NM_080627.2 371 gcC/gcA 0 0.458 TCTTCTTATCGGCCTTCCCCA +ZC3H6 376940 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 113089666 113089666 + synonymous_variant Silent SNP A A G TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 16 ENST00000409871.1:c.3171A>G p.Ser1057= p.S1057= ENST00000409871 NM_198581.2 1057 tcA/tcG 0 0.443 ACGGTTCATCATCCACATCAG +TTN 7273 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 179410161 179410161 + synonymous_variant Silent SNP A A G TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 51 ENST00000589042.1:c.95676T>C p.Ser31892= p.S31892= ENST00000589042 NM_001267550.1 31892 agT/agC 0 0.468 CGCTGGGCTCACTGTTACCAG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 17 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +BOD1L1 259282 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 13603085 13603085 + synonymous_variant Silent SNP G G A TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 189 24 ENST00000040738.5:c.5439C>T p.Ser1813= p.S1813= ENST00000040738 NM_148894.2 1813 agC/agT 0 0.488 CAAAGCCTTCGCTGCTATCTT +NMBR 4829 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 142397180 142397180 + missense_variant Missense_Mutation SNP T T A TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 25 ENST00000258042.1:c.778A>T p.Thr260Ser p.T260S ENST00000258042 NM_002511.2 260 Aca/Tca 0 0.388 CGTTTCCGTGTTTCCATCTGC +WIPI2 26100 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 5256804 5256804 + missense_variant Missense_Mutation SNP G G A TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 20 ENST00000288828.4:c.562G>A p.Asp188Asn p.D188N ENST00000288828 NM_001278299.1 188 Gat/Aat 0 0.527 GCAGGTCTTCGATACCATTAA +COA1 55744 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 43687182 43687182 + missense_variant Missense_Mutation SNP C C T TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 37 ENST00000395879.1:c.67G>A p.Gly23Ser p.G23S ENST00000395879 23 Ggt/Agt 0 0.493 TAGAACACACCGTGGAAAAGG +CROT 54677 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 87005181 87005181 + missense_variant Missense_Mutation SNP T T C TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 11 ENST00000419147.2:c.872T>C p.Leu291Ser p.L291S ENST00000419147 NM_001143935.1 291 tTg/tCg 0 0.368 CCAGAGAACTTGGCTTTGTTA +FOXP2 93986 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 114294061 114294061 + missense_variant Missense_Mutation SNP A A T TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 31 ENST00000408937.3:c.1338A>T p.Lys446Asn p.K446N ENST00000408937 NM_014491.3 446 aaA/aaT 0 0.393 CATCTCCCAAACCtgtaagtg +KEL 3792 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 142638440 142638440 + stop_gained Nonsense_Mutation SNP G G A TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 145 60 ENST00000355265.2:c.2098C>T p.Arg700Ter p.R700* ENST00000355265 NM_000420.2 700 Cga/Tga 0 0.622 CCGTGGACTCGGAGGTGTGGA +BARX1 56033 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 96714489 96714489 + missense_variant Missense_Mutation SNP G G A TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 19 ENST00000253968.6:c.722C>T p.Ala241Val p.A241V ENST00000253968 NM_021570.3 241 gCg/gTg 0 0.682 CGGCACCTCCGCCGGTTTCTC +MAGEB1 4112 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 30269583 30269583 + missense_variant Missense_Mutation SNP C C T TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 93 43 ENST00000378981.3:c.973C>T p.Arg325Cys p.R325C ENST00000378981 NM_002363.4 325 Cgt/Tgt 0 0.527 TAGAGCCAGGCGTCGCACTAC +KIF4A 24137 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 69615591 69615591 + missense_variant Missense_Mutation SNP T T G TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 41 ENST00000374403.3:c.2303T>G p.Leu768Arg p.L768R ENST00000374403 NM_012310.4 768 cTt/cGt 0 0.438 AATGACCTCCTTGAAGATAGA +BRWD3 254065 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 79942476 79942476 + synonymous_variant Silent SNP A A G TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 14 ENST00000373275.4:c.3891T>C p.Ser1297= p.S1297= ENST00000373275 NM_153252.4 1297 tcT/tcC 0 0.383 TACACTTTAAAGACTGTCTTC +TENM1 10178 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 123519691 123519691 + missense_variant Missense_Mutation SNP G G C TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 119 63 ENST00000422452.2:c.5912C>G p.Thr1971Arg p.T1971R ENST00000422452 NM_001163279.1 1971 aCa/aGa 0 0.483 TCTGCGCCCTGTCCCCAGATG +ZNF551 90233 broad.mit.edu;ucsc.edu GRCh37 19 58197953 58197953 + missense_variant Missense_Mutation SNP A A G TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 64 ENST00000282296.5:c.310A>G p.Ser104Gly p.S104G ENST00000282296 104 Agt/Ggt 0 0.478 AACTCACCTCAGTGAGATTAA +CLDN11 5010 broad.mit.edu;ucsc.edu GRCh37 3 170141061 170141061 + missense_variant Missense_Mutation SNP G G A TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 116 54 ENST00000064724.3:c.337G>A p.Gly113Ser p.G113S ENST00000064724 NM_005602.5 113 Ggt/Agt 0 0.602 CCAGGAGCCCGGTGTGGCTAA +KIAA1429 25962 broad.mit.edu;hgsc.bcm.edu GRCh37 8 95541443 95541445 + inframe_deletion In_Frame_Del DEL TTG TTG - TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 10 ENST00000297591.5:c.733_735delCAA p.Gln245del p.Q245del ENST00000297591 NM_015496.4 245 CAA/- 0 0.438 ctccttcttcttgttgttcctct +MPRIP 23164 broad.mit.edu;hgsc.bcm.edu GRCh37 17 17046885 17046886 + frameshift_variant Frame_Shift_Ins INS - - C TCGA-P5-A5EX-01 TCGA-P5-A5EX-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 18 ENST00000395811.5:c.1058dupC p.Ala354SerfsTer43 p.A354Sfs*43 ENST00000395811 NM_015134.3 351 gcc/gCcc 0 0.649 CACCAATGAAGCCCCCCCAGCT +AKR1C3 8644 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 5144389 5144389 + stop_gained Nonsense_Mutation SNP C C T TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 18 ENST00000380554.3:c.667C>T p.Arg223Ter p.R223* ENST00000380554 NM_003739.5 223 Cga/Tga 0 0.383 GGGATCTCAACGAGACAAACG +KIAA1217 56243 hgsc.bcm.edu;broad.mit.edu GRCh37 10 24825812 24825812 + missense_variant Missense_Mutation SNP A A T TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 6 ENST00000376454.3:c.3524A>T p.Lys1175Met p.K1175M ENST00000376454 NM_019590.3 1175 aAg/aTg 0 0.507 GTGCCACCCAAGGAGAAGAAG +LRP1 4035 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 57588464 57588464 + missense_variant Missense_Mutation SNP G G A TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 13 ENST00000243077.3:c.8173G>A p.Glu2725Lys p.E2725K ENST00000243077 NM_002332.2 2725 Gag/Aag 0 0.597 TGAACATGGCGAGGACGAGAC +KLC1 3831 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 104143843 104143843 + missense_variant Missense_Mutation SNP A A G TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 23 ENST00000452929.2:c.1471A>G p.Met491Val p.M491V ENST00000452929 NM_001130107.1 491 Atg/Gtg 0 0.398 AGAAGCTGCTATGAGGTCTCG +MYO5A 4644 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 52720613 52720613 + missense_variant Missense_Mutation SNP G G C TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 92 42 ENST00000399231.3:c.292C>G p.Leu98Val p.L98V ENST00000399231 NM_000259.3 98 Ctt/Gtt 0 0.408 GTATAAATAAGTTTGGAATCA +CLCN7 1186 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 1510460 1510460 + missense_variant Missense_Mutation SNP C C T TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 32 ENST00000382745.4:c.553G>A p.Ala185Thr p.A185T ENST00000382745 NM_001287.5 185 Gcc/Acc 0 0.597 AGCACGAAGGCGGCGTTCAGC +CDH15 1013 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 89261356 89261356 + synonymous_variant Silent SNP G G A TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 9 ENST00000289746.2:c.2238G>A p.Ala746= p.A746= ENST00000289746 NM_004933.2 746 gcG/gcA 0 0.632 GCTCGGTGGCGGGGACGCTGA +CCR10 2826 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 40832563 40832563 + missense_variant Missense_Mutation SNP T T C TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 8 ENST00000332438.4:c.97A>G p.Lys33Glu p.K33E ENST00000332438 NM_016602.2 33 Aag/Gag 0 0.637 ACATCGGCCTTGTAGCAAAGC +BRINP2 57795 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 177247827 177247827 + missense_variant Missense_Mutation SNP G G A TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 48 ENST00000361539.4:c.1141G>A p.Val381Met p.V381M ENST00000361539 NM_021165.2 381 Gtg/Atg 0 0.607 TGGCTTGAAAGTGCTGTTCAA +SIPA1L2 57568 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 232607260 232607260 + synonymous_variant Silent SNP C C T TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 26 ENST00000366630.1:c.2100G>A p.Arg700= p.R700= ENST00000366630 700 agG/agA 0 0.383 TTCCTATGTGCCTTTTCCTCA +NCAPH2 29781 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 50956005 50956005 + splice_acceptor_variant Splice_Site SNP G G A TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 30 ENST00000299821.11:c.267-1G>A p.X89_splice ENST00000299821 0 0.632 TTCTCTCTCAGGCGGGCCAAG +ALMS1 7840 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 73836722 73836722 + missense_variant Missense_Mutation SNP A A G TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 81 14 ENST00000264448.6:c.12487A>G p.Lys4163Glu p.K4163E ENST00000264448 NM_015120.4 4163 Aaa/Gaa 0 0.433 TCTGGGGAGAAAAGTTCCCTG +MARCO 8685 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 119739756 119739756 + missense_variant Missense_Mutation SNP C C T TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 16 ENST00000327097.4:c.926C>T p.Pro309Leu p.P309L ENST00000327097 NM_006770.3 309 cCg/cTg 0 0.642 CAGGGTGTTCCGGGCCCTCCT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 17 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +BBS7 55212 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 122782768 122782768 + missense_variant Missense_Mutation SNP G G A TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 11 25 ENST00000264499.4:c.232C>T p.Pro78Ser p.P78S ENST00000264499 NM_176824.2 78 Cct/Tct 0 0.418 TTCTCCTGAGGTGTGTTGATA +CAST 831 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 96077000 96077000 + missense_variant Missense_Mutation SNP G G A TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 22 ENST00000395812.2:c.826G>A p.Ala276Thr p.A276T ENST00000395812 NM_001042440.2 276 Gcc/Acc 0 0.433 TGCTATAGACGCCTTGTCATC +FUCA2 2519 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 143823182 143823182 + synonymous_variant Silent SNP T T C TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 24 ENST00000002165.6:c.1041A>G p.Val347= p.V347= ENST00000002165 NM_032020.4 347 gtA/gtG 0 0.408 CCTCAAAAACTACAGAAATGG +NRCAM 4897 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 107808830 107808830 + missense_variant Missense_Mutation SNP T T C TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 6 ENST00000379028.3:c.3205A>G p.Arg1069Gly p.R1069G ENST00000379028 1069 Agg/Ggg 0 0.353 TTGCTGATCCTGGGATTTACT +RAB2A 5862 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 61484623 61484623 + missense_variant Missense_Mutation SNP G G A TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 11 ENST00000262646.7:c.137G>A p.Arg46Gln p.R46Q ENST00000262646 NM_002865.2 46 cGa/cAa 0 0.323 TTCGGTGCTCGAATGATAACT +SPANXD 64648 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 140785767 140785767 + missense_variant Missense_Mutation SNP A A G TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 78 ENST00000370515.3:c.149T>C p.Ile50Thr p.I50T ENST00000370515 NM_145665.1 50 aTa/aCa 0 0.498 AACCACTAGTATGGTCGAGGA +OR1A1 8383 broad.mit.edu;ucsc.edu GRCh37 17 3119138 3119138 + missense_variant Missense_Mutation SNP C C T TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 134 50 ENST00000304094.1:c.224C>T p.Ser75Leu p.S75L ENST00000304094 NM_014565.2 75 tCg/tTg 0 0.483 TTCTTCTCATCGGTAACCATC +HIST1H3C 8352 broad.mit.edu;ucsc.edu GRCh37 6 26045799 26045799 + missense_variant Missense_Mutation SNP G G A TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 5 ENST00000540144.1:c.161G>A p.Arg54His p.R54H ENST00000540144 NM_003531.2 54 cGc/cAc 0 0.622 GAAATCCGTCGCTACCAGAAG +OBSCN 84033 broad.mit.edu;ucsc.edu GRCh37 1 228529314 228529314 + stop_gained,splice_region_variant Nonsense_Mutation SNP G G A TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 5 ENST00000570156.2:c.20904G>A p.Trp6968Ter p.W6968* ENST00000570156 NM_001271223.2 6968 tgG/tgA 0 0.672 TGCCTGTGTGGCGTGAGTGTC +HCLS1 3059 broad.mit.edu;ucsc.edu GRCh37 3 121351926 121351926 + missense_variant Missense_Mutation SNP C C A TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 6 ENST00000314583.3:c.996G>T p.Gln332His p.Q332H ENST00000314583 NM_005335.4 332 caG/caT 0 0.587 CCGGGAGAGTCTGCCTAATGG +CLK1 1195 broad.mit.edu;hgsc.bcm.edu GRCh37 2 201726490 201726493 + frameshift_variant Frame_Shift_Del DEL CTTC CTTC - TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 165 45 ENST00000434813.2:c.219_222delGAAG p.Lys74AspfsTer30 p.K74Dfs*30 ENST00000434813 NM_001162407.1 73 agGAAG/ag 0 0.397 TATGTGATCTCTTCCTTCTTTTAT +RBPJ 3516 broad.mit.edu;hgsc.bcm.edu GRCh37 4 26426086 26426088 + inframe_deletion In_Frame_Del DEL TTT TTT - TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 28 ENST00000342295.1:c.661_663delTTT p.Phe221del p.F221del ENST00000342295 NM_005349.3 220 TTT/- 0 0.36 GTGGGGAGCCTTTTTTATTCATC +ZFHX4 79776 broad.mit.edu;hgsc.bcm.edu GRCh37 8 77776374 77776377 + frameshift_variant Frame_Shift_Del DEL CAAT CAAT - rs76951673 TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 22 ENST00000521891.2:c.10427_10430delTCAA p.Ile3476AsnfsTer4 p.I3476Nfs*4 ENST00000521891 NM_024721.4 3475 aCAATc/ac 0 0.456 AAAGAGAAAACAATCAAACAAGCA +RBM12B 389677 broad.mit.edu;hgsc.bcm.edu GRCh37 8 94745644 94745648 + frameshift_variant Frame_Shift_Del DEL TTAAC TTAAC - TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 19 ENST00000399300.2:c.2991_2995delGTTAA p.Lys997AsnfsTer10 p.K997Nfs*10 ENST00000399300 NM_203390.2 997 aaGTTAAct/aact 0 0.332 TACAGCAAAGTTAACTTAACTTTTC +C12orf65 91574 broad.mit.edu;hgsc.bcm.edu GRCh37 12 123738357 123738359 + inframe_deletion In_Frame_Del DEL AAG AAG - TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 10 ENST00000253233.1:c.139_141delAAG p.Lys47del p.K47del ENST00000253233 NM_152269.4 46 AAG/- 0 0.557 GATGGCAGGCAAGAAGGACTACC +UBL3 5412 broad.mit.edu;hgsc.bcm.edu GRCh37 13 30341404 30341406 + inframe_deletion In_Frame_Del DEL ACA ACA - TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 12 ENST00000380680.4:c.340_342delTGT p.Cys114del p.C114del ENST00000380680 NM_007106.3 114 TGT/- 0 0.433 ACAGGATTACACAACAATTACTC +TINF2 26277 broad.mit.edu;hgsc.bcm.edu GRCh37 14 24709491 24709493 + inframe_deletion In_Frame_Del DEL TAA TAA - TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 19 ENST00000267415.7:c.1105_1107delTTA p.Leu369del p.L369del ENST00000267415 NM_001099274.1 369 TTA/- 0 0.498 CCCTAGGAGGTAATAATGATAGT +PAF1 54623 broad.mit.edu;hgsc.bcm.edu GRCh37 19 39879756 39879758 + inframe_deletion In_Frame_Del DEL TCT TCT - TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 104 30 ENST00000221265.3:c.542_544delAGA p.Lys181del p.K181del ENST00000221265 NM_019088.3 181 aAGAct/act 0 0.483 TCCTCAAAAGTCTTCTCAATGGC +CIC 23152 broad.mit.edu;hgsc.bcm.edu GRCh37 19 42797980 42797981 + frameshift_variant Frame_Shift_Del DEL TG TG - TCGA-FG-5964-01 TCGA-FG-5964-10 Untested Somatic Phase_I WXS none Illumina GAIIx 35 32 ENST00000575354.2:c.4034_4035delTG p.Val1345GlyfsTer16 p.V1345Gfs*16 ENST00000575354 NM_015125.3 1344 tcTGtg/tctg 0 0.693 CCTTTGACTCTGTGGACAAGTG +YME1L1 10730 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 27420861 27420861 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 20 ENST00000326799.3:c.956G>A p.Arg319Gln p.R319Q ENST00000326799 NM_139312.2 319 cGg/cAg 0 0.373 TGTTGTTGTCCGGAAGCGGAC +HPS5 11234 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 18339305 18339305 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 12 8 ENST00000349215.3:c.101G>A p.Arg34His p.R34H ENST00000349215 NM_181507.1 34 cGt/cAt 0 0.463 CACCTTTAGACGACTGGAGTC +PLEKHG6 55200 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 6422805 6422805 + missense_variant Missense_Mutation SNP G G A TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 44 ENST00000396988.3:c.149G>A p.Arg50His p.R50H ENST00000396988 NM_001144856.1 50 cGc/cAc 0 0.637 GATCCCAGTCGCCGACGCCTC +SLC6A2 6530 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 55735794 55735794 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 40 ENST00000219833.8:c.1778C>T p.Thr593Met p.T593M ENST00000219833 NM_001172504.1 593 aCg/aTg 0 0.622 TATGGCATCACGCCAGAGAAC +TRPV2 51393 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 16321163 16321163 + stop_gained Nonsense_Mutation SNP C C T TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 14 ENST00000338560.7:c.181C>T p.Arg61Ter p.R61* ENST00000338560 NM_016113.4 61 Cga/Tga 0 0.597 CCTCAACTACCGAAAGGGAAC +UNC13D 201294 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 73832286 73832286 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 5 ENST00000207549.4:c.1441G>A p.Val481Met p.V481M ENST00000207549 NM_199242.2 481 Gtg/Atg 0 0.667 CTCACCTGCACCATGGGTTGA +UNC13A 23025 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 17752214 17752214 + missense_variant Missense_Mutation SNP T T C TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 24 ENST00000519716.2:c.2624A>G p.Tyr875Cys p.Y875C ENST00000519716 NM_001080421.2 875 tAc/tGc 0 0.592 CATGGCTTGGTAGATGGACTC +KIR2DL1 3802 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 55285048 55285048 + missense_variant Missense_Mutation SNP T T A TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 126 95 ENST00000336077.6:c.334T>A p.Ser112Thr p.S112T ENST00000336077 NM_014218.2 112 Tca/Aca 0 0.522 CTATCAGGTGTCAGCTCCCAG +FOXS1 2307 hgsc.bcm.edu;broad.mit.edu GRCh37 20 30432674 30432674 + synonymous_variant Silent SNP G G A TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 6 ENST00000375978.3:c.672C>T p.Phe224= p.F224= ENST00000375978 NM_004118.3 224 ttC/ttT 0 0.587 CAGCCTCTGAGAAGCCGGCAG +ZNF335 63925 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 44578967 44578967 + missense_variant Missense_Mutation SNP G G C TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 82 55 ENST00000322927.2:c.3378C>G p.His1126Gln p.H1126Q ENST00000322927 NM_022095.3 1126 caC/caG 0 0.582 CATCAGGACTGTGCAGCCGCT +SYNJ1 8867 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 34038343 34038343 + synonymous_variant Silent SNP G G A TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 11 ENST00000433931.2:c.2172C>T p.Phe724= p.F724= ENST00000433931 NM_003895.3 724 ttC/ttT 0 0.423 GGCTACAGACGAAGCAAAGGC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 22 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +ITIH3 3699 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 52840399 52840399 + missense_variant Missense_Mutation SNP G G A TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 13 ENST00000449956.2:c.2033G>A p.Arg678His p.R678H ENST00000449956 NM_002217.3 678 cGc/cAc 0 0.612 ACAGTGCTGCGCCTTATTCAG +SLC23A1 9963 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 138713162 138713162 + missense_variant Missense_Mutation SNP A A G TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 23 ENST00000353963.3:c.1490T>C p.Leu497Pro p.L497P ENST00000353963 NM_152685.3 497 cTg/cCg 0 0.527 CAGCACAATCAGAATCTGATC +ARID1B 57492 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 157495231 157495231 + stop_gained Nonsense_Mutation SNP C C T TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 9 ENST00000346085.5:c.3115C>T p.Gln1039Ter p.Q1039* ENST00000346085 NM_020732.3 1039 Cag/Tag 0 0.522 AGGCACTCCACAGCCCGAGAG +COL15A1 1306 broad.mit.edu;ucsc.edu GRCh37 9 101832036 101832036 + synonymous_variant Silent SNP G G A TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 123 68 ENST00000375001.3:c.4035G>A p.Ala1345= p.A1345= ENST00000375001 NM_001855.4 1345 gcG/gcA 0 0.537 GGCGAACCGCGGACACAGCGG +ASCC1 51008 broad.mit.edu;hgsc.bcm.edu GRCh37 10 73970535 73970535 + frameshift_variant Frame_Shift_Del DEL G G - TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 18 ENST00000342444.4:c.167delC p.Pro56HisfsTer8 p.P56Hfs*8 ENST00000342444 NM_001198799.2 56 cCa/ca 0 0.527 GAATCCTTGTGGGGTCTGCTC +CIC 23152 broad.mit.edu GRCh37 19 42792001 42792001 + missense_variant Missense_Mutation SNP T T C TCGA-DH-A66F-01 TCGA-DH-A66F-10 Untested Somatic Phase_I WXS none Illumina GAIIx 4 6 ENST00000575354.2:c.805T>C p.Trp269Arg p.W269R ENST00000575354 NM_015125.3 269 Tgg/Cgg 0 0.632 AGATTGGAAGTGGTGCAACAA +SERPING1 710 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 57367766 57367766 + missense_variant Missense_Mutation SNP G G A rs139035354 by1000genomes TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 57 ENST00000278407.4:c.466G>A p.Ala156Thr p.A156T ENST00000278407 NM_000062.2 156 Gcc/Acc 0 0.542 GCTCTACCACGCCTTCTCAGC +MS4A14 84689 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 60183353 60183353 + synonymous_variant Silent SNP T T C TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 27 ENST00000531783.1:c.1011T>C p.Phe337= p.F337= ENST00000531783 NM_001261828.1 337 ttT/ttC 0 0.423 TCCAAGTTTTTCCATCCCATT +TMTC1 83857 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 29659825 29659825 + missense_variant Missense_Mutation SNP C C T rs35279918 TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 33 ENST00000539277.1:c.2603G>A p.Arg868His p.R868H ENST00000539277 NM_001193451.1 868 cGc/cAc 0 0.453 TTTTTCTAGGCGATCCAATTT +DCLK1 9201 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 36686247 36686247 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 13 ENST00000255448.4:c.482G>A p.Arg161Gln p.R161Q ENST00000255448 NM_004734.4 161 cGg/cAg 0 0.522 AGACACTGCCCGAGAAGCCGA +DIS3 22894 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 73346337 73346337 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 17 ENST00000377767.4:c.1463A>G p.Asp488Gly p.D488G ENST00000377767 NM_014953.3 488 gAt/gGt 0 0.363 ATGTAGAGCATCGTCTATATC +FOXG1 2290 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 29237034 29237034 + synonymous_variant Silent SNP G G A TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 12 ENST00000382535.3:c.549G>A p.Pro183= p.P183= ENST00000382535 183 ccG/ccA 0 0.637 AGAAGCCGCCGTTCAGCTACA +ISM2 145501 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 77942239 77942239 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 8 ENST00000342219.4:c.1415C>T p.Ala472Val p.A472V ENST00000342219 NM_199296.2 472 gCg/gTg 0 0.677 GCAGAAGCGCGCCGTGGGCTG +TTYH2 94015 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 72249349 72249349 + synonymous_variant Silent SNP G G A TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 20 ENST00000269346.4:c.1389G>A p.Gln463= p.Q463= ENST00000269346 NM_032646.5 463 caG/caA 0 0.647 TGGGAAGTCAGACCAGCCTGC +EVPL 2125 hgsc.bcm.edu;broad.mit.edu GRCh37 17 74003681 74003681 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 5 ENST00000301607.3:c.5605G>A p.Val1869Met p.V1869M ENST00000301607 NM_001988.2 1869 Gtg/Atg 0 0.617 AGCAGGTCCACGATGCCCCCT +C3 718 hgsc.bcm.edu;broad.mit.edu GRCh37 19 6712560 6712560 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 206 15 ENST00000245907.6:c.1078A>G p.Thr360Ala p.T360A ENST00000245907 NM_000064.2 360 Aca/Gca 0 0.622 TACTTGGGTGTCTTGGTGAAG +ALG6 29929 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 63876858 63876858 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 152 56 ENST00000371108.4:c.536T>C p.Leu179Pro p.L179P ENST00000371108 NM_013339.3 179 cTt/cCt 0 0.363 TGGGGTGTTCTTGGAATATCT +DLGAP4 22839 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 35060961 35060961 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 8 11 ENST00000373913.3:c.841G>T p.Gly281Trp p.G281W ENST00000373913 281 Ggg/Tgg 0 0.632 CCCCAGCCTTGGGGTGGGCAC +LRP2 4036 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 170038748 170038748 + synonymous_variant Silent SNP C C T TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 95 34 ENST00000263816.3:c.9927G>A p.Gln3309= p.Q3309= ENST00000263816 NM_004525.2 3309 caG/caA 0 0.532 CCACACAGTGCTGGGCCAGCA +ANKAR 150709 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 190585366 190585366 + missense_variant Missense_Mutation SNP A A C TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 20 ENST00000520309.1:c.2488A>C p.Asn830His p.N830H ENST00000520309 NM_144708.3 830 Aat/Cat 0 0.284 AAGCCTGATAAATCTATTGAA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 38 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +SETD2 29072 hgsc.bcm.edu;broad.mit.edu GRCh37 3 47103767 47103767 + stop_gained Nonsense_Mutation SNP G G C TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 156 8 ENST00000409792.3:c.6179C>G p.Ser2060Ter p.S2060* ENST00000409792 NM_014159.6 2060 tCa/tGa 0 0.463 TCTCTCTCTTGACCTATTAGG +CCDC54 84692 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 107097101 107097101 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 27 ENST00000261058.1:c.667C>T p.Arg223Cys p.R223C ENST00000261058 NM_032600.2 223 Cgt/Tgt 0 0.378 TCTGAAGAAACGTAACCATCA +SLC9C1 285335 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 111887770 111887770 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 20 ENST00000305815.5:c.3191G>A p.Arg1064Gln p.R1064Q ENST00000305815 NM_183061.1 1064 cGa/cAa 0 0.323 ATAAGTTTTTCGTAACAGACA +TRPC7 57113 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 135561020 135561020 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 9 ENST00000513104.1:c.2285T>C p.Met762Thr p.M762T ENST00000513104 NM_020389.2 762 aTg/aCg 0 0.453 AGAATTCCTCATGCCAGCCTG +LY6G6D 58530 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 31685399 31685399 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 199 97 ENST00000375825.3:c.220G>A p.Ala74Thr p.A74T ENST00000375825 NM_021246.2 74 Gcc/Acc 0 0.577 CTGCGTCGCAGCCCATCATTG +DST 667 hgsc.bcm.edu;ucsc.edu GRCh37 6 56483529 56483529 + intron_variant Intron SNP G G A TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 21 ENST00000244364.6:c.3319-4247C>T *1107* ENST00000244364 NM_015548.4 0 0.358 ATCATTTTCAGTGATGACTTT +EEF1A1 1915 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 74229668 74229668 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 15 ENST00000316292.9:c.82A>G p.Ile28Val p.I28V ENST00000316292 NM_001402.5 28 Atc/Gtc 0 0.413 CATTTATAGATCAGATGGCCA +CD36 948 hgsc.bcm.edu;broad.mit.edu GRCh37 7 80286000 80286000 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 83 4 ENST00000435819.1:c.265G>A p.Gly89Ser p.G89S ENST00000435819 89 Ggt/Agt 0 0.398 TAAGCAAAGAGGTCCTTATAC +TBC1D2 55357 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 100991314 100991314 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 13 ENST00000375066.5:c.898C>T p.Arg300Trp p.R300W ENST00000375066 NM_018421.3 300 Cgg/Tgg 0 0.522 GTTCGGTTCCGTGTGATTCCT +OR13D1 286365 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 107456818 107456818 + missense_variant Missense_Mutation SNP C C G TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 7 ENST00000318763.5:c.116C>G p.Ser39Cys p.S39C ENST00000318763 NM_001004484.1 39 tCt/tGt 0 0.423 AGAAATTACTCTGCCATGACT +MUSK 4593 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 113562782 113562782 + missense_variant Missense_Mutation SNP G G C TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 121 32 ENST00000374448.4:c.2124G>C p.Gln708His p.Q708H ENST00000374448 NM_005592.3 708 caG/caC 0 0.567 TTGCCAGGCAGGTGGCAGCTG +PTGS1 5742 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 125154668 125154668 + missense_variant Missense_Mutation SNP T T G TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 26 ENST00000362012.2:c.1645T>G p.Phe549Val p.F549V ENST00000362012 NM_000962.3 549 Ttt/Gtt 0 0.537 GCCGAGCACATTTGGCGGCGA +HCCS 3052 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 11135492 11135492 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 43 ENST00000321143.4:c.358T>C p.Tyr120His p.Y120H ENST00000321143 NM_005333.4 120 Tac/Cac 0 0.383 AAAGTGGGTTTACCCTTCTGA +NOL8 55035 broad.mit.edu;ucsc.edu GRCh37 9 95077012 95077012 + missense_variant Missense_Mutation SNP T T C TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 11 6 ENST00000545558.1:c.1895A>G p.His632Arg p.H632R ENST00000545558 632 cAt/cGt 0 0.453 CTTCTTTGCATGTTGGCATGG +EFTUD2 9343 broad.mit.edu;ucsc.edu GRCh37 17 42931994 42931994 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 18 ENST00000426333.2:c.2189G>A p.Arg730His p.R730H ENST00000426333 NM_001142605.1 730 cGt/cAt 0 0.567 CCAGATGGAACGGGCAGCCAG +SSPO 23145 broad.mit.edu;ucsc.edu GRCh37 7 149482723 149482723 + non_coding_transcript_exon_variant RNA SNP C C G TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 5 ENST00000378016.2:n.3139C>G *1047* ENST00000378016 0 0.627 GGCCAGTGGCCTATTCACAGT +IQGAP1 8826 broad.mit.edu;ucsc.edu GRCh37 15 91034589 91034589 + stop_gained Nonsense_Mutation SNP C C T TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 4 ENST00000268182.5:c.4273C>T p.Gln1425Ter p.Q1425* ENST00000268182 NM_003870.3 1425 Cag/Tag 0 0.398 GAGAGCCATGCAGAGACGTGC +SYNE2 23224 broad.mit.edu;ucsc.edu GRCh37 14 64676802 64676802 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 8 ENST00000358025.3:c.18683A>G p.Asn6228Ser p.N6228S ENST00000358025 NM_182914.2 6228 aAc/aGc 0 0.622 CGCTGGGACAACCTTCAGAGG +KLHL28 54813 broad.mit.edu;hgsc.bcm.edu GRCh37 14 45415078 45415078 + frameshift_variant Frame_Shift_Del DEL A A - TCGA-HT-7684-01 TCGA-HT-7684-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 21 ENST00000396128.4:c.54delT p.Glu19AsnfsTer7 p.E19Nfs*7 ENST00000396128 NM_017658.3 18 tcT/tc 0 0.403 GAAGTTGTTCAGAATGCAAGT +TLL2 7093 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 98129891 98129891 + synonymous_variant Silent SNP G G A TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 11 ENST00000357947.3:c.2844C>T p.Tyr948= p.Y948= ENST00000357947 NM_012465.3 948 taC/taT 0 0.667 CCATGTAGTCGTAGCCGCAGT +OR5I1 10798 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 55703053 55703053 + missense_variant Missense_Mutation SNP A A G TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 16 ENST00000301532.3:c.824T>C p.Ile275Thr p.I275T ENST00000301532 NM_006637.1 275 aTt/aCt 0 0.408 CACTGAGATAATTTTATCAGT +LRRC55 219527 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 56949447 56949447 + missense_variant Missense_Mutation SNP A A G TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 11 ENST00000497933.1:c.80A>G p.Asp27Gly p.D27G ENST00000497933 NM_001005210.2 27 gAc/gGc 0 0.607 GATTCCATGGACACAGTCCTC +CASP1 834 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 104897057 104897057 + missense_variant Missense_Mutation SNP A A C TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 8 ENST00000533400.1:c.1143T>G p.Asp381Glu p.D381E ENST00000533400 NM_001257118.1 381 gaT/gaG 0 0.393 GCGCTCTACCATCTGGCTGCT +CLEC12A 160364 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 10131591 10131591 + missense_variant Missense_Mutation SNP C C T rs141455664 byFrequency TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 46 ENST00000355690.4:c.148C>T p.Arg50Cys p.R50C ENST00000355690 NM_001207010.1 50 Cgt/Tgt 0 0.433 TCATGTATGGCGTCCAGCAGC +SRRM4 84530 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 119592158 119592158 + missense_variant Missense_Mutation SNP C C T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 18 ENST00000267260.4:c.1502C>T p.Pro501Leu p.P501L ENST00000267260 NM_194286.3 501 cCg/cTg 0 0.632 AGAGACTCCCCGAGCCACCTG +NEMF 9147 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 50269393 50269393 + synonymous_variant Silent SNP A A C TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 6 ENST00000298310.5:c.1968T>G p.Leu656= p.L656= ENST00000298310 656 ctT/ctG 0 0.318 GTACCTTAAAAAGGAAGCTAA +SYNE2 23224 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 64683079 64683079 + missense_variant Missense_Mutation SNP T T C TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 38 ENST00000358025.3:c.19516T>C p.Ser6506Pro p.S6506P ENST00000358025 NM_182914.2 6506 Tcc/Ccc 0 0.498 TCCCCCTGCGTCCAGCACCCC +CHRNA5 1138 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 78882881 78882881 + missense_variant Missense_Mutation SNP G G A TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 34 ENST00000299565.5:c.1148G>A p.Gly383Asp p.G383D ENST00000299565 NM_000745.3 383 gGt/gAt 0 0.438 ACTGAGAGTGGTAGTGGACCA +ABR 29 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 915191 915191 + stop_gained Nonsense_Mutation SNP G G A TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 55 ENST00000302538.5:c.1996C>T p.Gln666Ter p.Q666* ENST00000302538 NM_021962.3 666 Cag/Tag 0 0.652 TCCACACACTGCCGGACGATG +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577157 7577157 + splice_acceptor_variant Splice_Site SNP T T G TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 14 11 ENST00000269305.4:c.783-2A>C p.X261_splice ENST00000269305 NM_001126112.2 0 0.512 AGATTACCACTACTCAGGATA +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577574 7577574 + missense_variant Missense_Mutation SNP T T C TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 45 ENST00000269305.4:c.707A>G p.Tyr236Cys p.Y236C ENST00000269305 NM_001126112.2 236 tAc/tGc 0 0.572 GTTACACATGTAGTTGTAGTG +HS3ST3A1 9955 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 13400056 13400056 + missense_variant Missense_Mutation SNP C C T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 177 53 ENST00000284110.1:c.679G>A p.Ala227Thr p.A227T ENST00000284110 NM_006042.1 227 Gcg/Acg 0 0.627 GAGATGCGCGCGGGGGCCTCC +SH2D1B 117157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 162381781 162381781 + missense_variant Missense_Mutation SNP C C T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 10 ENST00000367929.2:c.26G>A p.Arg9His p.R9H ENST00000367929 NM_053282.4 9 cGt/cAt 0 0.532 CTTGGTCAGACGTCCATGGTA +OR2M3 127062 hgsc.bcm.edu;broad.mit.edu GRCh37 1 248366698 248366698 + missense_variant Missense_Mutation SNP C C G TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 300 22 ENST00000456743.1:c.329C>G p.Ser110Cys p.S110C ENST00000456743 NM_001004689.1 110 tCt/tGt 0 0.458 CTGCTTGGCTCTGAGTGCTTT +SSTR3 6753 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 37603530 37603530 + missense_variant Missense_Mutation SNP C C T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 54 ENST00000328544.3:c.313G>A p.Ala105Thr p.A105T ENST00000328544 NM_001051.3 105 Gcc/Acc 0 0.622 TAGGACAGGGCGTTCTGGGCG +MPPED1 758 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 43898541 43898541 + missense_variant Missense_Mutation SNP C C A TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 158 17 ENST00000417669.2:c.766C>A p.Pro256Thr p.P256T ENST00000417669 256 Ccc/Acc 0 0.632 GGACTGGGTCCCCAAGAAGAT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 16 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +SEC61A1 29927 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 127786281 127786281 + synonymous_variant Silent SNP C C T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 111 59 ENST00000243253.3:c.993C>T p.Gly331= p.G331= ENST00000243253 NM_013336.3 331 ggC/ggT 0 0.483 CTTCTGGGGGCCCAGCACGTG +PIK3R4 30849 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 130463923 130463923 + missense_variant Missense_Mutation SNP T T C TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 18 ENST00000356763.3:c.140A>G p.Glu47Gly p.E47G ENST00000356763 NM_014602.2 47 gAa/gGa 0 0.408 GACCAGGCCTTCTCGGTGCTT +SMIM43 132332 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 122681459 122681459 + missense_variant Missense_Mutation SNP T T A TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 16 ENST00000337677.5:c.383A>T p.Lys128Met p.K128M ENST00000337677 NM_152399.2 128 aAg/aTg 0 0.403 tcagacaatcttgcagatagc +HOXA7 3204 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 27196035 27196035 + missense_variant Missense_Mutation SNP C C T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 160 25 ENST00000242159.3:c.130G>A p.Ala44Thr p.A44T ENST00000242159 NM_006896.3 44 Gcc/Acc 0 0.607 AAGGCGCCGGCGCCCGCCCCG +LETM2 137994 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 38262000 38262000 + synonymous_variant Silent SNP G G A TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 11 ENST00000523983.2:c.1053G>A p.Pro351= p.P351= ENST00000523983 351 ccG/ccA 0 0.557 AGCCCAAGCCGATTGAGATAC +XKR4 114786 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 56436610 56436610 + missense_variant Missense_Mutation SNP T T C TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 37 ENST00000327381.6:c.1777T>C p.Ser593Pro p.S593P ENST00000327381 NM_052898.1 593 Tca/Cca 0 0.488 GATTGAAGAATCAGTCATTAA +FAM154A 158297 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 18928550 18928550 + missense_variant Missense_Mutation SNP C C T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 68 52 ENST00000380534.4:c.925G>A p.Ala309Thr p.A309T ENST00000380534 NM_153707.2 309 Gcc/Acc 0 0.547 GTGTAATGGGCCTGCACTGTT +ZNF81 347344 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 47774744 47774744 + synonymous_variant Silent SNP T T C TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 9 ENST00000376954.1:c.699T>C p.Tyr233= p.Y233= ENST00000376954 233 taT/taC 0 0.363 ACTCTTCTTATAGTCACCACG +GRIPAP1 56850 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 48831681 48831681 + synonymous_variant Silent SNP C C G TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 22 ENST00000376441.1:c.2319G>C p.Leu773= p.L773= ENST00000376441 NM_020137.3 773 ctG/ctC 0 0.607 GGACGCTGCCCAGCCCGCTGC +RGAG4 340526 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 71350423 71350423 + missense_variant Missense_Mutation SNP C C T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 129 66 ENST00000545866.1:c.968G>A p.Arg323Gln p.R323Q ENST00000545866 NM_001024455.3 323 cGa/cAa 0 0.493 GATGATATTTCGAACTCCAGG +CSTF2 1478 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 100077401 100077401 + missense_variant Missense_Mutation SNP A A T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 21 ENST00000372972.2:c.299A>T p.Glu100Val p.E100V ENST00000372972 NM_001325.2 100 gAg/gTg 0 0.418 AACAAAGAAGAGCTGAAGAGT +DRP2 1821 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 100490939 100490939 + missense_variant Missense_Mutation SNP G G A TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 211 103 ENST00000395209.3:c.208G>A p.Ala70Thr p.A70T ENST00000395209 NM_001939.2 70 Gcc/Acc 0 0.517 GTCTGTTGGTGCCTCTGGACC +SERPINA7 6906 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 105280487 105280487 + missense_variant Missense_Mutation SNP A A C TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 116 60 ENST00000327674.4:c.563T>G p.Leu188Arg p.L188R ENST00000327674 188 cTa/cGa 0 0.413 GTCTTGAATTAGACCCACAAC +DOCK11 139818 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 117773444 117773444 + missense_variant Missense_Mutation SNP T T A TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 17 ENST00000276202.7:c.4048T>A p.Ser1350Thr p.S1350T ENST00000276202 NM_144658.3 1350 Tcg/Acg 0 0.413 AGACCGAAAATCGCAAACCAT +GPR112 139378 hgsc.bcm.edu;broad.mit.edu GRCh37 X 135428469 135428469 + synonymous_variant Silent SNP G G C TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 251 22 ENST00000394143.1:c.2604G>C p.Leu868= p.L868= ENST00000394143 NM_153834.3 868 ctG/ctC 0 0.398 CAACAATGCTGGAAGTGACAG +NAA10 8260 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 153195616 153195616 + missense_variant Missense_Mutation SNP T T C TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 89 74 ENST00000464845.1:c.532A>G p.Asn178Asp p.N178D ENST00000464845 NM_003491.3 178 Aac/Gac 0 0.627 TCCACCTTGTTCTCGATGGCA +TAZ 6901 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 153640435 153640435 + missense_variant Missense_Mutation SNP A A T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 17 ENST00000299328.5:c.122A>T p.His41Leu p.H41L ENST00000299328 NM_000116.3 41 cAc/cTc 0 0.677 TACATGAACCACCTGACCGTG +LATS2 26524 broad.mit.edu;ucsc.edu GRCh37 13 21562142 21562142 + missense_variant Missense_Mutation SNP G G A TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 107 18 ENST00000382592.4:c.1777C>T p.Arg593Cys p.R593C ENST00000382592 NM_014572.2 593 Cgc/Tgc 0 0.512 CTCTTGATGCGTGACTCTCTC +OGT 8473 broad.mit.edu;ucsc.edu GRCh37 X 70776956 70776956 + splice_donor_variant Splice_Site SNP G G T TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 4 ENST00000373719.3:c.1320+1G>T p.X440_splice ENST00000373719 NM_181673.2 0 0.368 CATTCATAAGGTACTACTGTT +CPZ 8532 broad.mit.edu;ucsc.edu GRCh37 4 8603122 8603122 + missense_variant Missense_Mutation SNP G G A TCGA-FG-A60J-01 TCGA-FG-A60J-10 Untested Somatic Phase_I WXS none Illumina GAIIx 10 5 ENST00000360986.4:c.394G>A p.Ala132Thr p.A132T ENST00000360986 NM_001014447.2 132 Gcc/Acc 0 0.677 CTGCCAGCCCGCCTTCGACGC +SVIL 6840 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 29770516 29770516 + missense_variant Missense_Mutation SNP G G T TCGA-DB-5278-01 TCGA-DB-5278-10 Untested Somatic Phase_I WXS none Illumina GAIIx 365 192 ENST00000375398.2:c.5097C>A p.His1699Gln p.H1699Q ENST00000375398 1699 caC/caA 0 0.463 GGAATACCTTGTGCTGGGCAA +SLC7A9 11136 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 33355655 33355655 + missense_variant Missense_Mutation SNP T T G TCGA-DB-5278-01 TCGA-DB-5278-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 83 ENST00000023064.4:c.115A>C p.Ile39Leu p.I39L ENST00000023064 NM_014270.4 39 Atc/Ctc 0 0.622 GTGCCCACGATGATGGAGATG +CIC 23152 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 42791743 42791743 + missense_variant Missense_Mutation SNP T T G TCGA-DB-5278-01 TCGA-DB-5278-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 39 ENST00000575354.2:c.629T>G p.Phe210Cys p.F210C ENST00000575354 NM_015125.3 210 tTc/tGc 0 0.627 TTCATGATCTTCAGCAAGCGG +RAB3GAP2 25782 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 220387224 220387224 + missense_variant Missense_Mutation SNP C C T TCGA-DB-5278-01 TCGA-DB-5278-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 25 ENST00000358951.2:c.278G>A p.Arg93Gln p.R93Q ENST00000358951 NM_012414.3 93 cGa/cAa 0 0.363 TTTTTGCTCTCGAGCTATCAC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DB-5278-01 TCGA-DB-5278-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 46 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +GIMAP6 474344 broad.mit.edu;ucsc.edu GRCh37 7 150325310 150325310 + missense_variant Missense_Mutation SNP C C T rs138521615 byFrequency TCGA-DB-5278-01 TCGA-DB-5278-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 36 ENST00000328902.5:c.376G>A p.Val126Met p.V126M ENST00000328902 NM_024711.5 126 Gtg/Atg 0 0.622 ACCAGGAGCACGGCGTGGGGC +CIC 23152 broad.mit.edu GRCh37 19 42799060 42799060 + missense_variant Missense_Mutation SNP G G A TCGA-DB-5278-01 TCGA-DB-5278-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 4 ENST00000575354.2:c.4544G>A p.Arg1515His p.R1515H ENST00000575354 NM_015125.3 1515 cGc/cAc 0 0.632 CGTGAGGTGCGCCAGAAGATC +CTSG 1511 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 25043508 25043508 + synonymous_variant Silent SNP G G A TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 19 ENST00000216336.2:c.537C>T p.Tyr179= p.Y179= ENST00000216336 NM_001911.2 179 taC/taT 0 0.627 TTCGGGGGTCGTAGGAACCGA +FPR1 2357 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 52250087 52250087 + missense_variant Missense_Mutation SNP C C T rs145808420 TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 18 ENST00000595042.1:c.161G>A p.Arg54Gln p.R54Q ENST00000595042 NM_001193306.1 54 cGg/cAg 0 0.527 GTGTGTCATCCGGAATCCAGC +FMNL2 114793 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 153473700 153473700 + synonymous_variant Silent SNP C C T TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 18 ENST00000288670.9:c.1308C>T p.Val436= p.V436= ENST00000288670 NM_052905.3 436 gtC/gtT 0 0.473 AGCTGGATGTCGTTCGGGTAA +ACOX3 8310 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 8396382 8396382 + stop_gained Nonsense_Mutation SNP G G A rs142042116 TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 10 17 ENST00000356406.5:c.1144C>T p.Arg382Ter p.R382* ENST00000356406 NM_003501.2 382 Cga/Tga 0 0.542 GCAAGTCCTCGCTGGAGCTCC +SPP1 6696 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 88901213 88901213 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 26 ENST00000395080.3:c.109C>T p.Pro37Ser p.P37S ENST00000395080 NM_001040058.1 37 Cca/Tca 0 0.363 CAACAAATACCCAGATGCTGT +TRO 7216 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 54953051 54953051 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 83 55 ENST00000173898.7:c.1693C>T p.Arg565Cys p.R565C ENST00000173898 NM_001039705.2 565 Cgc/Tgc 0 0.577 GTTGGGGCTGCGCCCTGGGTA +GDPD2 54857 hgsc.bcm.edu;broad.mit.edu GRCh37 X 69652187 69652187 + missense_variant Missense_Mutation SNP C C A TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 148 12 ENST00000453994.2:c.1491C>A p.Asn497Lys p.N497K ENST00000453994 NM_001171192.1 497 aaC/aaA 0 0.527 TCTCGGTGAACCTATTTGTAG +TRBV11-1 28582 broad.mit.edu;ucsc.edu GRCh37 7 142224222 142224222 + missense_variant Missense_Mutation SNP C C A TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 20 ENST00000390367.3:c.46G>T p.Ala16Ser p.A16S ENST00000390367 16 Gca/Tca 0 0.498 GACACACCTGCCCCCAGGAGA +G6PD 2539 broad.mit.edu;ucsc.edu GRCh37 X 153761826 153761826 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 4 ENST00000393562.2:c.919G>A p.Ala307Thr p.A307T ENST00000393562 NM_000402.3 307 Gcc/Acc 0 0.637 TTGGTGGAGGCGGGCTTCTCC +SLC25A19 60386 broad.mit.edu;ucsc.edu GRCh37 17 73282427 73282427 + synonymous_variant Silent SNP G G A TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 40 ENST00000402418.3:c.246C>T p.His82= p.H82= ENST00000402418 82 caC/caT 0 0.592 GAGCTGGGACGTGTCCTTTCC +ATG5 9474 broad.mit.edu;ucsc.edu GRCh37 6 106764059 106764059 + stop_gained Nonsense_Mutation SNP G G A TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 43 ENST00000369076.3:c.25C>T p.Arg9Ter p.R9* ENST00000369076 NM_004849.2 9 Cga/Tga 0 0.368 CACACATCTCGAAGCACATCT +KLHL13 90293 broad.mit.edu;ucsc.edu GRCh37 X 117043975 117043975 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 120 20 ENST00000539496.1:c.664G>A p.Val222Ile p.V222I ENST00000539496 NM_001168299.1 222 Gtc/Atc 0 0.423 TTCTTCAAGACGAAACTGTTA +KALRN 8997 broad.mit.edu;ucsc.edu GRCh37 3 124053129 124053129 + missense_variant Missense_Mutation SNP A A C TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 38 ENST00000240874.3:c.1428A>C p.Lys476Asn p.K476N ENST00000240874 NM_003947.4 476 aaA/aaC 0 0.572 AGGATGGCAAAGCACTACTTG +MAGI3 260425 broad.mit.edu;ucsc.edu GRCh37 1 114123223 114123223 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6404-01 TCGA-DU-6404-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 20 ENST00000307546.9:c.493G>A p.Val165Ile p.V165I ENST00000307546 NM_001142782.1 165 Gtt/Att 0 0.393 TTTCATTTCCGTTGAACAGTT +PWWP2B 170394 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 134218474 134218474 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 14 ENST00000305233.5:c.470G>A p.Arg157His p.R157H ENST00000305233 NM_138499.3 157 cGc/cAc 0 0.726 CGTCTGTCCCGCAACCGCGAC +OR5AS1 219447 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 55798589 55798589 + missense_variant Missense_Mutation SNP G G T TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 115 67 ENST00000313555.1:c.695G>T p.Gly232Val p.G232V ENST00000313555 NM_001001921.1 232 gGt/gTt 0 0.453 AAGTCCTCAGGTGGCAGAAGC +ZC3H13 23091 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 46619598 46619598 + synonymous_variant Silent SNP A A G TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 107 53 ENST00000282007.3:c.45T>C p.Thr15= p.T15= ENST00000282007 NM_015070.3 15 acT/acC 0 0.413 TATCAGATATAGTCTTGGTAT +C15orf43 145645 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 45248953 45248953 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 87 33 ENST00000340827.3:c.37G>A p.Val13Ile p.V13I ENST00000340827 NM_152448.2 13 Gtt/Att 0 0.582 TTGCGGCAGCGTTAGCCAGGA +LONP2 83752 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 48296697 48296697 + missense_variant Missense_Mutation SNP A A C TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 9 ENST00000285737.4:c.896A>C p.Lys299Thr p.K299T ENST00000285737 NM_031490.2 299 aAa/aCa 0 0.348 AGACTCAAAAAAATGCCTCAG +PSME3 10197 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 40990763 40990763 + stop_gained Nonsense_Mutation SNP C C T TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 31 ENST00000293362.3:c.460C>T p.Gln154Ter p.Q154* ENST00000293362 NM_176863.2 154 Cag/Tag 0 0.463 AATGTGGGTACAGCTCCTGAT +KCNAB2 8514 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 6155592 6155592 + missense_variant,splice_region_variant Missense_Mutation SNP G G T TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 48 ENST00000378083.3:c.856G>T p.Val286Leu p.V286L ENST00000378083 NM_001199862.1 286 Gtg/Ttg 0 0.632 CTCTTCAGGAGTGGGCGCCAT +CD40 958 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 44751286 44751286 + synonymous_variant Silent SNP A A G TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 87 41 ENST00000372285.3:c.294A>G p.Glu98= p.E98= ENST00000372285 NM_001250.4 98 gaA/gaG 0 0.607 GCACCTCAGAAACAGACACCA +NCKAP1 10787 hgsc.bcm.edu;broad.mit.edu GRCh37 2 183866755 183866755 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 8 ENST00000360982.2:c.547C>T p.Arg183Cys p.R183C ENST00000360982 NM_013436.4 183 Cgc/Tgc 0 0.363 TGGCCAAGGCGTGGGTATTCT +ZC3H15 55854 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 187371527 187371527 + missense_variant Missense_Mutation SNP C C G TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 24 ENST00000337859.6:c.1054C>G p.Leu352Val p.L352V ENST00000337859 NM_018471.2 352 Ctt/Gtt 0 0.348 TGTAGCCAGTCTTGAAAGATT +COL5A2 1290 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 189898826 189898826 + synonymous_variant Silent SNP G G A rs142895373 TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 24 ENST00000374866.3:c.4470C>T p.Gly1490= p.G1490= ENST00000374866 NM_000393.3 1490 ggC/ggT 0 0.473 CAATTTCAACGCCGAATTCCT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 23 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +SCAND3 114821 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 28540332 28540332 + missense_variant Missense_Mutation SNP A A G TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 20 ENST00000452236.2:c.3334T>C p.Phe1112Leu p.F1112L ENST00000452236 NM_052923.1 1112 Ttt/Ctt 0 0.353 agatcattaaaaatactgaag +PCLO 27445 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 82578793 82578793 + missense_variant,splice_region_variant Missense_Mutation SNP G G A TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 171 68 ENST00000333891.9:c.11111C>T p.Thr3704Met p.T3704M ENST00000333891 NM_033026.5 3704 aCg/aTg 0 0.463 CACTCTTACCGTATAGCCCTC +SND1 27044 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 127631024 127631024 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 13 ENST00000354725.3:c.1694G>A p.Arg565Gln p.R565Q ENST00000354725 NM_014390.2 565 cGa/cAa 0 0.542 AGAGGAGCCCGAAACCTCCCA +TNC 3371 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 117848575 117848575 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 201 92 ENST00000350763.4:c.1435C>T p.Arg479Cys p.R479C ENST00000350763 NM_002160.3 479 Cgc/Tgc 0 0.582 TTCACACAGCGGCCGTGCTGG +MID1IP1 58526 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 38664318 38664318 + missense_variant Missense_Mutation SNP A A T TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 32 ENST00000336949.6:c.119A>T p.Asp40Val p.D40V ENST00000336949 NM_021242.4 40 gAc/gTc 0 0.632 TTGCTGCGCGACGTGCCCCTG +NOTCH2 4853 broad.mit.edu;ucsc.edu GRCh37 1 120491184 120491184 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 33 29 ENST00000256646.2:c.2605C>T p.Arg869Trp p.R869W ENST00000256646 NM_024408.3 869 Cgg/Tgg 0 0.512 ATGGTACACCGCTGACCTAGG +UNC13D 201294 broad.mit.edu;ucsc.edu GRCh37 17 73826535 73826535 + missense_variant Missense_Mutation SNP G G A TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 5 ENST00000207549.4:c.2738C>T p.Ala913Val p.A913V ENST00000207549 NM_199242.2 913 gCt/gTt 0 0.682 GACTGTCACAGCCCCCAGCTC +TRPV6 55503 broad.mit.edu;ucsc.edu GRCh37 7 142571891 142571891 + missense_variant Missense_Mutation SNP A A G TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 5 ENST00000359396.3:c.1457T>C p.Ile486Thr p.I486T ENST00000359396 NM_018646.4 486 aTt/aCt 0 0.547 GTCGCCAAAAATCATCTAGAA +HYLS1 219844 broad.mit.edu;ucsc.edu GRCh37 11 125770123 125770123 + missense_variant Missense_Mutation SNP T T C TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 28 ENST00000425380.2:c.860T>C p.Val287Ala p.V287A ENST00000425380 NM_001134793.1 287 gTc/gCc 0 0.403 GCAAATGGTGTCATACCCAGG +STAG3L4 64940 broad.mit.edu;ucsc.edu GRCh37 7 66771046 66771046 + non_coding_transcript_exon_variant RNA SNP T T G TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 52 ENST00000416602.2:n.338T>G *113* ENST00000416602 0 0.388 TGTTAACTTTTTCATCTGATC +CIC 23152 broad.mit.edu;ucsc.edu GRCh37 19 42799059 42799059 + missense_variant Missense_Mutation SNP C C T TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 23 ENST00000575354.2:c.4543C>T p.Arg1515Cys p.R1515C ENST00000575354 NM_015125.3 1515 Cgc/Tgc 0 0.632 CCGTGAGGTGCGCCAGAAGAT +XG 7499 broad.mit.edu;hgsc.bcm.edu GRCh37 X 2670333 2670333 + frameshift_variant Frame_Shift_Del DEL A A - TCGA-QH-A65V-01 TCGA-QH-A65V-10 Untested Somatic Phase_I WXS none Illumina GAIIx 127 47 ENST00000419513.2:c.18delA p.Leu7PhefsTer10 p.L7Ffs*10 ENST00000419513 NM_001141919.1 6 ggA/gg 0 0.532 GCTGGTGGGGACTTCCCTGTC +OR10A4 283297 hgsc.bcm.edu;broad.mit.edu GRCh37 11 6898019 6898019 + missense_variant Missense_Mutation SNP C C G TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 143 10 ENST00000379829.2:c.141C>G p.Ile47Met p.I47M ENST00000379829 NM_207186.2 47 atC/atG 0 0.453 TCCTCATCATCCTGGTCACTA +GLI1 2735 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 57861814 57861814 + missense_variant Missense_Mutation SNP G G A TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 114 12 ENST00000228682.2:c.1115G>A p.Arg372His p.R372H ENST00000228682 NM_005269.2 372 cGc/cAc 0 0.542 TGCACCAAACGCTATACAGAT +TJP1 7082 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 30001004 30001004 + stop_gained Nonsense_Mutation SNP G G A TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 202 82 ENST00000346128.6:c.4609C>T p.Arg1537Ter p.R1537* ENST00000346128 NM_175610.2 1537 Cga/Tga 0 0.403 TCAAATGGTCGGGCAGAACTT +GCNT3 9245 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 59911328 59911328 + synonymous_variant Silent SNP G G A rs139760962 TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 173 25 ENST00000396065.1:c.891G>A p.Ala297= p.A297= ENST00000396065 NM_004751.2 297 gcG/gcA 0 0.408 CAGGGAATGCGTACATTGTGG +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C A rs28934576 by1000genomes TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 11 15 ENST00000269305.4:c.818G>T p.Arg273Leu p.R273L ENST00000269305 NM_001126112.2 273 cGt/cTt 0 0.542 GGCACAAACACGCACCTCAAA +MAPK7 5598 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 19283952 19283952 + missense_variant Missense_Mutation SNP C C G TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 112 20 ENST00000308406.5:c.430C>G p.Leu144Val p.L144V ENST00000308406 NM_139033.2 144 Ctg/Gtg 0 0.582 GGAAAGCGACCTGCACCAGAT +MAPK7 5598 hgsc.bcm.edu;broad.mit.edu GRCh37 17 19284535 19284535 + missense_variant Missense_Mutation SNP C C T TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 81 6 ENST00000308406.5:c.1013C>T p.Ala338Val p.A338V ENST00000308406 NM_139033.2 338 gCa/gTa 0 0.622 CGCATCTCAGCAGCTGCTGCC +MYO18A 399687 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 27434129 27434129 + missense_variant Missense_Mutation SNP C C T TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 150 52 ENST00000527372.1:c.3410G>A p.Gly1137Glu p.G1137E ENST00000527372 NM_078471.3 1137 gGg/gAg 0 0.612 GTAGTTACGCCCGTGTTTCTT +CLCNKA 1187 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 16352610 16352610 + synonymous_variant Silent SNP A A G TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 433 67 ENST00000331433.4:c.366A>G p.Gly122= p.G122= ENST00000331433 122 ggA/ggG 0 0.552 AAGGTTCTGGAATCCCGGAGC +CAPN2 824 hgsc.bcm.edu;broad.mit.edu GRCh37 1 223900426 223900426 + synonymous_variant Silent SNP C C G TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 11 ENST00000295006.5:c.84C>G p.Leu28= p.L28= ENST00000295006 NM_001748.4 28 ctC/ctG 0 0.716 TCAAGTACCTCAACCAGGACT +OR2T12 127064 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 248458716 248458716 + synonymous_variant Silent SNP C C T TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 41 8 ENST00000317996.1:c.165G>A p.Arg55= p.R55= ENST00000317996 NM_001004692.1 55 agG/agA 0 0.527 AGTACATGGGCCTGTGGAGCC +DYNC2LI1 51626 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 44028017 44028017 + missense_variant Missense_Mutation SNP G G A rs141895414 TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 6 ENST00000260605.8:c.692G>A p.Arg231His p.R231H ENST00000260605 NM_001193464.1 231 cGt/cAt 0 0.313 CTAAAAATACGTGGAGTTATC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 79 26 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +XIRP1 165904 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 39227182 39227182 + missense_variant Missense_Mutation SNP G G A TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 10 ENST00000340369.3:c.3755C>T p.Ala1252Val p.A1252V ENST00000340369 NM_194293.2 1252 gCc/gTc 0 0.622 AGGAACAAAGGCATTATGGGG +RUNX2 860 hgsc.bcm.edu;broad.mit.edu GRCh37 6 45390466 45390466 + synonymous_variant Silent SNP A A G TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 4 ENST00000371438.1:c.195A>G p.Gln65= p.Q65= ENST00000371438 NM_001024630.3 65 caA/caG 0 0.731 agcagcagcaacagcagcagc +ATRX 546 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 76814188 76814188 + stop_gained Nonsense_Mutation SNP A A C TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 10 ENST00000373344.5:c.6456T>G p.Tyr2152Ter p.Y2152* ENST00000373344 NM_000489.3 2152 taT/taG 0 0.338 GTCCAAAGCGATAAACTCTGA +ATRX 546 hgsc.bcm.edu;ucsc.edu GRCh37 X 76944328 76944328 + stop_gained Nonsense_Mutation SNP G G A TCGA-DU-8163-01 TCGA-DU-8163-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 10 ENST00000373344.5:c.577C>T p.Gln193Ter p.Q193* ENST00000373344 NM_000489.3 193 Caa/Taa 0 0.383 ATAAGAACTTGCAATGAAGGG +PCDH15 65217 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 55581631 55581631 + missense_variant Missense_Mutation SNP G G C TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 125 23 ENST00000361849.3:c.5861C>G p.Ser1954Cys p.S1954C ENST00000361849 NM_001142768.1 1954 tCt/tGt 0 0.363 CAGTGAAGTAGATTGACTGTG +OR6Q1 219952 hgsc.bcm.edu;broad.mit.edu GRCh37 11 57798711 57798711 + missense_variant Missense_Mutation SNP T T C TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 149 10 ENST00000302622.3:c.287T>C p.Ile96Thr p.I96T ENST00000302622 NM_001005186.2 96 aTc/aCc 0 0.483 GGCAAGAATATCTCTTATGCT +COQ5 84274 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 120947837 120947837 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 15 ENST00000288532.6:c.664G>A p.Val222Ile p.V222I ENST00000288532 NM_032314.3 222 Gtc/Atc 0 0.433 ATGTGTGTGACATTCCGGATC +CEBPE 1053 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 23588124 23588124 + synonymous_variant Silent SNP G G A rs141320203 TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 163 28 ENST00000206513.5:c.177C>T p.Ala59= p.A59= ENST00000206513 NM_001805.3 59 gcC/gcT 0 0.647 CTGGCTTCACGGCAAAGAGAT +OTX2 5015 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 57268721 57268721 + missense_variant Missense_Mutation SNP C C A TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 83 22 ENST00000339475.5:c.626G>T p.Cys209Phe p.C209F ENST00000339475 NM_001270524.1 209 tGt/tTt 0 0.522 ATATGATCCACAGTCCATGCC +PLIN1 5346 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 90212791 90212791 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 23 ENST00000300055.5:c.711G>A p.Met237Ile p.M237I ENST00000300055 NM_002666.4 237 atG/atA 0 0.642 GGGCCCGGGCCATGGTCTGCA +WDR24 84219 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 739166 739166 + missense_variant Missense_Mutation SNP A A T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 102 44 ENST00000293883.4:c.475T>A p.Phe159Ile p.F159I ENST00000293883 NM_032259.2 159 Ttc/Atc 0 0.632 TCACCCGAGAAGGTGCTGACA +CYP4F12 66002 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 15807863 15807863 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 120 24 ENST00000550308.1:c.1543C>T p.Arg515Trp p.R515W ENST00000550308 NM_023944.3 515 Cgg/Tgg 0 0.567 GCTTTGGCTGCGGGTGGAGCC +ZNF676 163223 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 22363763 22363763 + synonymous_variant Silent SNP G G A TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 30 ENST00000397121.2:c.756C>T p.Pro252= p.P252= ENST00000397121 NM_001001411.2 252 ccC/ccT 0 0.373 CACATTTGTAGGGTTTCTCTC +ZNF644 84146 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 91405999 91405999 + synonymous_variant Silent SNP G G T rs144274015 byFrequency TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 10 ENST00000370440.1:c.912C>A p.Thr304= p.T304= ENST00000370440 304 acC/acA 0 0.343 AGCAATCCTCGGTATAACGAG +INSRR 3645 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 156815851 156815851 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 18 ENST00000368195.3:c.1871G>A p.Arg624His p.R624H ENST00000368195 NM_014215.2 624 cGc/cAc 0 0.622 TGGCTTCCAGCGCACCAGGAG +FCRL2 79368 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 157738222 157738222 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 104 19 ENST00000361516.3:c.865G>A p.Val289Met p.V289M ENST00000361516 NM_030764.3 289 Gtg/Atg 0 0.478 GGGATATTCACCACCTTGCTC +ABL2 27 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 179084144 179084144 + missense_variant Missense_Mutation SNP T T A TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 20 ENST00000502732.1:c.1430A>T p.Glu477Val p.E477V ENST00000502732 NM_001168237.1 477 gAa/gTa 0 0.378 GGTAGCAATTTCCCACAACAA +RD3 343035 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 211652456 211652456 + synonymous_variant Silent SNP G G A TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 6 ENST00000367002.4:c.510C>T p.Ser170= p.S170= ENST00000367002 NM_001164688.1 170 tcC/tcT 0 0.716 CCACGTCCTCGGAGATGGTCC +CHRM3 1131 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 240071128 240071128 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 20 ENST00000255380.4:c.377C>T p.Thr126Met p.T126M ENST00000255380 NM_000740.2 126 aCg/aTg 0 0.468 AATCTGTTTACGACCTACATC +CHAF1B 8208 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 37775114 37775114 + missense_variant Missense_Mutation SNP G G C TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 265 55 ENST00000314103.5:c.722G>C p.Ser241Thr p.S241T ENST00000314103 NM_005441.2 241 aGt/aCt 0 0.443 CGTAGACTGAGTTTCACTCCC +MORC2 22880 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 31330834 31330834 + synonymous_variant Silent SNP A A C TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 220 70 ENST00000215862.4:c.1941T>G p.Val647= p.V647= ENST00000215862 NM_014941.1 647 gtT/gtG 0 0.552 TGGGAGAAGGAACCTCCCGAG +NLRC4 58484 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 32449596 32449596 + synonymous_variant Silent SNP A A G TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 47 ENST00000404025.2:c.3021T>C p.Phe1007= p.F1007= ENST00000404025 1007 ttT/ttC 0 0.378 CATCATCATCAAATTGCCACC +IFIH1 64135 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 163133214 163133214 + missense_variant Missense_Mutation SNP A A C TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 12 ENST00000263642.2:c.2287T>G p.Phe763Val p.F763V ENST00000263642 NM_022168.3 763 Ttc/Gtc 0 0.398 ATGGGTTTGAACTCACTGCTG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 22 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +CCDC13 152206 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 42750573 42750573 + missense_variant Missense_Mutation SNP G G A TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 21 ENST00000310232.6:c.2047C>T p.Arg683Trp p.R683W ENST00000310232 NM_144719.3 683 Cgg/Tgg 0 0.592 TCCTTTCCCCGCAGGGCACTG +TRAIP 10293 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 49867117 49867117 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 29 ENST00000331456.2:c.1169G>A p.Arg390Gln p.R390Q ENST00000331456 NM_005879.2 390 cGg/cAg 0 0.587 GATGGCATTCCGGACAAAAAT +WDR17 116966 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 177032847 177032847 + missense_variant Missense_Mutation SNP T T C TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 16 ENST00000280190.4:c.188T>C p.Ile63Thr p.I63T ENST00000280190 63 aTt/aCt 0 0.343 GCTATCTATATTTATCAGGTA +ITPR3 3710 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 33632727 33632727 + missense_variant Missense_Mutation SNP A A G TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 25 ENST00000374316.5:c.1229A>G p.Glu410Gly p.E410G ENST00000374316 410 gAg/gGg 0 0.667 ATCGAGGAGGAGCGGCCCATC +PKHD1 5314 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 51768522 51768522 + missense_variant Missense_Mutation SNP C C G TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 18 ENST00000371117.3:c.6869G>C p.Trp2290Ser p.W2290S ENST00000371117 NM_138694.3 2290 tGg/tCg 0 0.393 ATGTCCTGACCAGTCTAATGT +TNS3 64759 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 47407972 47407972 + synonymous_variant Silent SNP G G A TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 258 74 ENST00000398879.1:c.2271C>T p.Thr757= p.T757= ENST00000398879 757 acC/acT 0 0.632 CTTGCCGCCCGGTGGCCCTGC +COBL 23242 hgsc.bcm.edu;ucsc.edu GRCh37 7 51093066 51093066 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 14 ENST00000265136.7:c.3508G>A p.Ala1170Thr p.A1170T ENST00000265136 NM_015198.3 1170 Gca/Aca 0 0.517 GCAGAGGATGCCACCTGGCAA +CYP3A4 1576 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 99364768 99364768 + missense_variant Missense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 15 ENST00000336411.2:c.784G>A p.Glu262Lys p.E262K ENST00000336411 NM_001202855.2 262 Gaa/Aaa 0 0.308 TGTGTATCTTCGAGGCGACTT +PTPRZ1 5803 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 121693973 121693973 + stop_gained Nonsense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 82 51 ENST00000393386.2:c.6262C>T p.Gln2088Ter p.Q2088* ENST00000393386 NM_001206838.1 2088 Cag/Tag 0 0.403 GGGCTATTACCAGAGCAATGA +CRISPLD1 83690 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 75932115 75932115 + missense_variant Missense_Mutation SNP T T C TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 24 ENST00000262207.4:c.1138T>C p.Ser380Pro p.S380P ENST00000262207 NM_031461.5 380 Tct/Cct 0 0.333 CAAATATCAGTCTGCTAATTC +SPATA31C1 441452 hgsc.bcm.edu;broad.mit.edu GRCh37 9 90535986 90535986 + non_coding_transcript_exon_variant RNA SNP G G A TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 356 66 ENST00000420021.2:n.1461G>A *487* ENST00000420021 0 0.517 GCCCTGCGTCGCAGAATAAAG +RGS3 5998 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 116224037 116224037 + missense_variant Missense_Mutation SNP G G A TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 125 26 ENST00000374140.2:c.131G>A p.Arg44His p.R44H ENST00000374140 NM_144488.5 44 cGt/cAt 0 0.537 GGATCTCACCGTCCTGAGTGT +KIF2B 84643 broad.mit.edu;ucsc.edu GRCh37 17 51902246 51902246 + missense_variant Missense_Mutation SNP C C A TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 109 24 ENST00000268919.4:c.1852C>A p.Gln618Lys p.Q618K ENST00000268919 NM_032559.4 618 Caa/Aaa 0 0.443 GGGATCTAGCCAATGGCTGGA +MAP2K5 5607 broad.mit.edu;ucsc.edu GRCh37 15 67878228 67878228 + missense_variant,splice_region_variant Missense_Mutation SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 9 ENST00000178640.5:c.323C>T p.Ala108Val p.A108V ENST00000178640 NM_145160.2 108 gCc/gTc 0 0.373 ACTGTTTCAGCCTGCAAGCCT +APIP 51074 broad.mit.edu;ucsc.edu GRCh37 11 34909891 34909891 + missense_variant Missense_Mutation SNP T T C TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 74 22 ENST00000395787.3:c.410A>G p.His137Arg p.H137R ENST00000395787 NM_015957.2 137 cAt/cGt 0 0.373 CATCTCTTGATGTGTAATTTT +PCDHB4 56131 broad.mit.edu;ucsc.edu GRCh37 5 140502918 140502918 + synonymous_variant Silent SNP C C T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 117 115 ENST00000194152.1:c.1338C>T p.Asn446= p.N446= ENST00000194152 NM_018938.2 446 aaC/aaT 0 0.602 TCAATGACAACGCCCCCGCCT +NOTCH1 4851 broad.mit.edu;ucsc.edu GRCh37 9 139412302 139412302 + missense_variant Missense_Mutation SNP C C A TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 83 24 ENST00000277541.6:c.1343G>T p.Arg448Leu p.R448L ENST00000277541 NM_017617.3 448 cGa/cTa 0 0.647 GATCTCGCATCGGGGGCCCGT +EIF4G3 8672 broad.mit.edu;hgsc.bcm.edu GRCh37 1 21183987 21183987 + frameshift_variant Frame_Shift_Del DEL A A - TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 222 51 ENST00000602326.1:c.3098delT p.Val1033AlafsTer27 p.V1033Afs*27 ENST00000602326 NM_001198802.1 1033 gTc/gc 0 0.463 CACTCTCTGGACACCTGCAGG +ATF2 1386 broad.mit.edu;hgsc.bcm.edu GRCh37 2 175957831 175957833 + inframe_deletion In_Frame_Del DEL CTC CTC - TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 95 38 ENST00000264110.2:c.1141_1143delGAG p.Glu381del p.E381del ENST00000264110 NM_001256091.1 381 GAG/- 0 0.35 CAGCTTTCTTCTCTAAAGACTGA +SCRIB 23513 broad.mit.edu;hgsc.bcm.edu GRCh37 8 144886879 144886882 + frameshift_variant Frame_Shift_Del DEL GGGA GGGA - TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 10 ENST00000356994.2:c.2865_2868delTCCC p.Pro956AlafsTer18 p.P956Afs*18 ENST00000356994 NM_182706.4 955 ccTCCC/cc 0 0.696 GCAGAGGGCTGGGAGGAAGAGGGC +MALAT1 378938 broad.mit.edu;hgsc.bcm.edu GRCh37 11 65270886 65270887 + non_coding_transcript_exon_variant RNA INS - - TA TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 12 ENST00000534336.1:n.5655_5656dupTA *1885* ENST00000534336 0 0.371 ATTTGCATCTTTAAATAATTTC +RXFP2 122042 broad.mit.edu;hgsc.bcm.edu GRCh37 13 32371470 32371471 + frameshift_variant Frame_Shift_Del DEL TC TC - TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 45 ENST00000298386.2:c.1920_1921delCT p.Phe642TyrfsTer5 p.F642Yfs*5 ENST00000298386 NM_130806.3 640 tTC/t 0 0.396 GCAAATCGTTTCTTTTTTATAG +DNAJA2 10294 broad.mit.edu;hgsc.bcm.edu GRCh37 16 46991039 46991040 + frameshift_variant Frame_Shift_Del DEL CT CT - TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 304 156 ENST00000317089.5:c.1140_1141delAG p.Gly381LeufsTer8 p.G381Lfs*8 ENST00000317089 NM_005880.3 380 cgAGgc/cggc 0 0.465 CCTCCTGAGCCTCGAGTGCTAT +TP53 7157 broad.mit.edu;hgsc.bcm.edu GRCh37 17 7576886 7576887 + frameshift_variant Frame_Shift_Ins INS - - T TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 83 ENST00000269305.4:c.959dupA p.Lys321GlufsTer16 p.K321Efs*16 ENST00000269305 NM_001126112.2 320 aag/aaAg 0 0.46 CCAGTGGTTTCTTCTTTGGCTG +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76938097 76938100 + frameshift_variant Frame_Shift_Del DEL TCTT TCTT - TCGA-DH-A66B-01 TCGA-DH-A66B-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 79 ENST00000373344.5:c.2648_2651delAAGA p.Gln883ArgfsTer21 p.Q883Rfs*21 ENST00000373344 NM_000489.3 883 cAAGAg/cg 0 0.407 AGTCTCTCTCTCTTGTTTTCTTTC +LRRC18 474354 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 50122058 50122058 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 25 ENST00000374160.3:c.143G>A p.Arg48His p.R48H ENST00000374160 NM_001006939.3 48 cGc/cAc 0 0.507 GTCACTAAGGCGCAGAATACA +CDH23 64072 hgsc.bcm.edu;broad.mit.edu GRCh37 10 73544798 73544798 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 124 11 ENST00000224721.6:c.5668C>T p.Arg1890Cys p.R1890C ENST00000224721 NM_022124.5 1890 Cgc/Tgc 0 0.602 CTGCAATGCACGCCTCACCTT +CCDC89 220388 hgsc.bcm.edu;broad.mit.edu GRCh37 11 85397064 85397064 + missense_variant Missense_Mutation SNP G G A TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 5 ENST00000316398.3:c.110C>T p.Thr37Met p.T37M ENST00000316398 NM_152723.1 37 aCg/aTg 0 0.552 CTTAAACTCCGTCTCCTCTTC +KCNJ1 3758 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 128710111 128710111 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 106 11 ENST00000392664.2:c.85G>A p.Val29Ile p.V29I ENST00000392664 NM_000220.4 29 Gtc/Atc 0 0.408 AAGCGAGTGACGACCCATTTC +VWF 7450 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 6128787 6128787 + missense_variant Missense_Mutation SNP G G A rs61749370 TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 26 ENST00000261405.5:c.3797C>T p.Pro1266Leu p.P1266L ENST00000261405 NM_000552.3 1266 cCg/cTg 0 0.612 ATCGTGCAACGGCGGTTCCGA +GATC 283459 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 120894951 120894951 + synonymous_variant Silent SNP C C T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 19 ENST00000551765.1:c.327C>T p.Arg109= p.R109= ENST00000551765 NM_176818.2 109 cgC/cgT 0 0.478 ACTCCCATCGCGTCGTGGAGG +TGM7 116179 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 43584939 43584939 + missense_variant Missense_Mutation SNP G G A TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 70 ENST00000452443.2:c.407C>T p.Thr136Ile p.T136I ENST00000452443 NM_052955.2 136 aCt/aTt 0 0.478 TAGGATGAAAGTTCCCAGCGG +ACSBG1 23205 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 78475123 78475123 + stop_gained Nonsense_Mutation SNP C C T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 24 ENST00000258873.4:c.668G>A p.Trp223Ter p.W223* ENST00000258873 NM_001199377.1 223 tGg/tAg 0 0.463 CAACTGTTTCCAGATCTGCAT +TMEM8A 58986 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 427459 427459 + synonymous_variant Silent SNP G G A TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 14 ENST00000431232.2:c.426C>T p.Ser142= p.S142= ENST00000431232 NM_021259.2 142 tcC/tcT 0 0.677 AAACGTTGACGGAGGCATTGC +CES3 23491 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 66997813 66997813 + missense_variant Missense_Mutation SNP C C T rs148620443 byFrequency TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 75 ENST00000303334.4:c.535C>T p.Arg179Cys p.R179C ENST00000303334 NM_024922.5 179 Cgc/Tgc 0 0.607 AGTCCAGTACCGCCTTGGGGT +RFXANK 8625 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 19307810 19307810 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 241 31 ENST00000303088.4:c.226C>T p.Arg76Trp p.R76W ENST00000303088 NM_003721.3 76 Cgg/Tgg 0 0.617 TCTCACCAACCGGCAGCGAGG +FASLG 356 hgsc.bcm.edu;broad.mit.edu GRCh37 1 172628634 172628634 + missense_variant Missense_Mutation SNP G G T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 5 ENST00000367721.2:c.293G>T p.Gly98Val p.G98V ENST00000367721 NM_000639.1 98 gGc/gTc 0 0.572 GTAGGATTGGGCCTGGGGATG +ADCY3 109 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 25062839 25062839 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 132 18 ENST00000260600.5:c.1258G>A p.Val420Met p.V420M ENST00000260600 NM_004036.3 420 Gtg/Atg 0 0.642 CCCCCCAGCACGGTGCCCGTG +TRIM54 57159 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 27522276 27522276 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 16 ENST00000296098.4:c.505C>T p.Arg169Cys p.R169C ENST00000296098 NM_032546.3 169 Cgc/Tgc 0 0.522 CATTTACAAACGCCAGAAGGT +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 41 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +FLNB 2317 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 58095050 58095050 + splice_donor_variant Splice_Site SNP G G C TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 8 ENST00000490882.1:c.2199+1G>C p.X733_splice ENST00000490882 NM_001164317.1 0 0.552 CCCCTACAGGGTAGGTTGTGA +SUMF2 25870 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 56145816 56145816 + stop_gained Nonsense_Mutation SNP A A T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 156 17 ENST00000342190.6:c.670A>T p.Lys224Ter p.K224* ENST00000342190 NM_001130069.2 224 Aaa/Taa 0 0.532 CAAGGGAGACAAAGCTGAGGA +KLHL15 80311 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 24006740 24006740 + synonymous_variant Silent SNP T T C TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 135 103 ENST00000328046.8:c.1113A>G p.Glu371= p.E371= ENST00000328046 NM_030624.2 371 gaA/gaG 0 0.458 CTACAGCAAATTCAGAGCGTG +SOX3 6658 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 139586763 139586763 + missense_variant Missense_Mutation SNP G G A TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 39 ENST00000370536.2:c.463C>T p.Arg155Cys p.R155C ENST00000370536 NM_005634.2 155 Cgc/Tgc 0 0.632 GCCATTTTGCGCCGCTGCCCG +FLNA 2316 hgsc.bcm.edu;broad.mit.edu GRCh37 X 153593776 153593776 + missense_variant Missense_Mutation SNP A A T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 9 ENST00000369850.3:c.1508T>A p.Phe503Tyr p.F503Y ENST00000369850 NM_001110556.1 503 tTc/tAc 0 0.672 GTACACCTTGAAGTCAGCTGT +APOB 338 broad.mit.edu;ucsc.edu GRCh37 2 21227213 21227213 + synonymous_variant Silent SNP G G A TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 38 ENST00000233242.1:c.12015C>T p.Ala4005= p.A4005= ENST00000233242 NM_000384.2 4005 gcC/gcT 0 0.507 CGGTGCCTACGGCTGGGGAGG +KRT16P2 400578 broad.mit.edu;ucsc.edu GRCh37 17 16734855 16734855 + non_coding_transcript_exon_variant,non_coding_transcript_variant RNA SNP C C T rs688852 by1000genomes TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 6 ENST00000399048.2:n.720G>A *240* ENST00000399048 0 0.632 CACAGTCTGCCGCAGGGCCAG +MYH2 4620 broad.mit.edu;ucsc.edu GRCh37 17 10432336 10432336 + missense_variant Missense_Mutation SNP C C T TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 74 33 ENST00000245503.5:c.3415G>A p.Glu1139Lys p.E1139K ENST00000245503 NM_017534.5 1139 Gag/Aag 0 0.582 CGCTGCTTCTCTGCTTTGGCC +ZNF292 23036 broad.mit.edu;hgsc.bcm.edu GRCh37 6 87966376 87966377 + frameshift_variant Frame_Shift_Del DEL CT CT - TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 11 ENST00000369577.3:c.3032_3033delTC p.Leu1011GlnfsTer4 p.L1011Qfs*4 ENST00000369577 NM_015021.1 1010 aCT/a 0 0.356 AATTCAGAAACTCTCAAAATAG +SPDYE1 285955 broad.mit.edu;hgsc.bcm.edu GRCh37 7 44042300 44042301 + frameshift_variant Frame_Shift_Del DEL CT CT - TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 19 ENST00000258704.3:c.371_372delCT p.Pro124ArgfsTer3 p.P124Rfs*3 ENST00000258704 NM_175064.2 124 cCT/c 0 0.614 GTGCTCGCCCCTGAGCCTGAGG +GNAI1 2770 broad.mit.edu;hgsc.bcm.edu GRCh37 7 79846804 79846805 + frameshift_variant Frame_Shift_Del DEL TT TT - TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 13 ENST00000351004.3:c.1062_1063delTT p.Phe354LeufsTer15 p.F354Lfs*15 ENST00000351004 NM_002069.5 354 TTt/t 0 0.342 TTGTGGTCTCTTTTAAGTTTTG +NOTCH1 4851 broad.mit.edu;hgsc.bcm.edu GRCh37 9 139413070 139413072 + inframe_deletion In_Frame_Del DEL AGA AGA - TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 20 10 ENST00000277541.6:c.1070_1072delTCT p.Phe357del p.F357del ENST00000277541 NM_017617.3 357 tTCTac/tac 0 0.655 CACTCGCAGTAGAAGGAGGCCAC +ANO9 338440 broad.mit.edu;hgsc.bcm.edu GRCh37 11 418481 418483 + inframe_deletion In_Frame_Del DEL TCT TCT - TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 51 ENST00000332826.6:c.2237_2239delAGA p.Lys746del p.K746del ENST00000332826 NM_001012302.2 746 aAGAtg/atg 0 0.621 CCATGCCACATCTTCTCACGCAG +CLUH 23277 broad.mit.edu;hgsc.bcm.edu GRCh37 17 2601759 2601761 + inframe_deletion In_Frame_Del DEL GAA GAA - TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 11 ENST00000570628.2:c.1276_1278delTTC p.Phe426del p.F426del ENST00000570628 426 TTC/- 0 0.611 AGCCCAGGCTGAAGAAGATGTTG +CIC 23152 broad.mit.edu;hgsc.bcm.edu GRCh37 19 42798099 42798100 + frameshift_variant Frame_Shift_Del DEL AG AG - TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 64 ENST00000575354.2:c.4054_4055delGA p.Glu1352SerfsTer9 p.E1352Sfs*9 ENST00000575354 NM_015125.3 1351 tcAGaa/tcaa 0 0.678 GGGTCCTGTCAGAAGTGGACTT +NKX2-2 4821 broad.mit.edu;hgsc.bcm.edu GRCh37 20 21492574 21492574 + frameshift_variant Frame_Shift_Del DEL T T - TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 36 34 ENST00000377142.4:c.809delA p.Gln270ArgfsTer47 p.Q270Rfs*47 ENST00000377142 NM_002509.3 270 cAg/cg 0 0.706 CCAAGTCCACTGCTGGGCCTG +BCOR 54880 broad.mit.edu;hgsc.bcm.edu GRCh37 X 39932365 39932366 + frameshift_variant Frame_Shift_Del DEL CT CT - TCGA-DU-7302-01 TCGA-DU-7302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 53 ENST00000378444.4:c.2233_2234delAG p.Arg745GlufsTer6 p.R745Efs*6 ENST00000378444 NM_001123385.1 745 AGg/g 0 0.515 CCGGGATCTCCTCTCTGGTTTC +FERMT3 83706 hgsc.bcm.edu;broad.mit.edu GRCh37 11 63988497 63988497 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 128 8 ENST00000279227.5:c.1567C>T p.Arg523Trp p.R523W ENST00000279227 NM_178443.2 523 Cgg/Tgg 0 0.652 GCTCACCCCACGGATCCTGGA +EXPH5 23086 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 108381318 108381318 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 56 ENST00000265843.4:c.4916G>A p.Cys1639Tyr p.C1639Y ENST00000265843 NM_015065.2 1639 tGc/tAc 0 0.483 CAGTGGGTTGCACTCCACTGT +LRIG3 121227 hgsc.bcm.edu;broad.mit.edu GRCh37 12 59276787 59276787 + synonymous_variant Silent SNP G G A TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 4 ENST00000320743.3:c.1344C>T p.Cys448= p.C448= ENST00000320743 NM_153377.4 448 tgC/tgT 0 0.403 GCTGGCAATCGCACAAAAGGC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7574012 7574012 + stop_gained Nonsense_Mutation SNP C C A rs17882252 TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 12 ENST00000269305.4:c.1015G>T p.Glu339Ter p.E339* ENST00000269305 NM_001126112.2 339 Gag/Tag 0 0.537 CGGAACATCTCGAAGCGCTCA +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7579311 7579311 + splice_donor_variant Splice_Site SNP C C T rs68140816 TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 56 ENST00000269305.4:c.375+1G>A p.X125_splice ENST00000269305 NM_001126112.2 0 0.532 GGGCAACTGACCGTGCAAGTC +CWC25 54883 hgsc.bcm.edu;broad.mit.edu GRCh37 17 36958970 36958970 + synonymous_variant Silent SNP C C T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 114 9 ENST00000225428.5:c.1146G>A p.Arg382= p.R382= ENST00000225428 NM_017748.4 382 cgG/cgA 0 0.547 ACTTCCCATCCCGGGAGTCCA +ERCC1 2067 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 45916941 45916941 + synonymous_variant Silent SNP A A T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 13 ENST00000013807.5:c.837T>A p.Pro279= p.P279= ENST00000013807 NM_202001.2 279 ccT/ccA 0 0.522 TTACTTTCTGAGGGCCCAGGC +DNAJC6 9829 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 65858364 65858364 + synonymous_variant Silent SNP T T G TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 7 ENST00000371069.4:c.1719T>G p.Ala573= p.A573= ENST00000371069 NM_001256864.1 573 gcT/gcG 0 0.582 CGCCAGCGGCTCCTCCCACCA +C20orf26 26074 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 20123549 20123549 + missense_variant Missense_Mutation SNP A A T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 6 ENST00000245957.5:c.908A>T p.Glu303Val p.E303V ENST00000245957 NM_015585.3 303 gAg/gTg 0 0.488 ATAGTCGAGGAGTTGCAGGAA +ADSL 158 hgsc.bcm.edu;broad.mit.edu GRCh37 22 40762494 40762494 + missense_variant Missense_Mutation SNP G G A TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 5 ENST00000216194.7:c.1423G>A p.Val475Met p.V475M ENST00000216194 NM_000026.2 475 Gtg/Atg 0 0.358 ATATGAAAGCGTGATGAAGGT +MYO3B 140469 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 171509614 171509614 + missense_variant Missense_Mutation SNP T T C TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 8 ENST00000408978.4:c.4009T>C p.Ser1337Pro p.S1337P ENST00000408978 NM_138995.4 1337 Tct/Cct 0 0.418 AAAAGGAGACTCTTTTGCTCA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 34 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +RPL37A 6168 hgsc.bcm.edu;broad.mit.edu GRCh37 2 217364056 217364056 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 8 ENST00000491306.1:c.67C>T p.Arg23Trp p.R23W ENST00000491306 NM_000998.4 23 Cgg/Tgg 0 0.502 GGCCTCCCTCCGGAAAATGGT +COL6A3 1293 hgsc.bcm.edu;broad.mit.edu GRCh37 2 238277572 238277572 + missense_variant Missense_Mutation SNP A A G TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 5 ENST00000295550.4:c.4534T>C p.Ser1512Pro p.S1512P ENST00000295550 NM_004369.3 1512 Tcc/Ccc 0 0.562 TTCAGTGGGGACCCCCCTCTG +BRD8 10902 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 137501597 137501597 + missense_variant Missense_Mutation SNP T T C TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 60 9 ENST00000254900.5:c.1198A>G p.Met400Val p.M400V ENST00000254900 NM_139199.1 400 Atg/Gtg 0 0.458 GCAATATCCATCTTCTCAGCC +CD109 135228 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 74491008 74491008 + synonymous_variant Silent SNP T T C TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 6 ENST00000287097.5:c.1929T>C p.Asp643= p.D643= ENST00000287097 643 gaT/gaC 0 0.323 TATTGACAGATGCAAACCTCA +MDN1 23195 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 90397120 90397120 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 13 ENST00000369393.3:c.11393G>A p.Arg3798Gln p.R3798Q ENST00000369393 3798 cGg/cAg 0 0.403 AAGATGTTTCCGCAAAGACAA +FBXL18 80028 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 5540405 5540405 + missense_variant Missense_Mutation SNP T T C TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 19 ENST00000382368.3:c.1495A>G p.Met499Val p.M499V ENST00000382368 NM_024963.4 499 Atg/Gtg 0 0.672 TTGCGGGGCATGGCGGAGGAG +CNTLN 54875 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 17236520 17236520 + synonymous_variant Silent SNP G G A TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 11 ENST00000380647.3:c.783G>A p.Leu261= p.L261= ENST00000380647 261 ctG/ctA 0 0.368 TAAATGACCTGGAGAAATTGA +VSIG4 11326 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 65253475 65253475 + missense_variant Missense_Mutation SNP G G A TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 19 ENST00000374737.4:c.253C>T p.Arg85Cys p.R85C ENST00000374737 NM_001257403.1 85 Cgc/Tgc 0 0.547 ACATGCAGGCGGCCCTGGTAC +UNC93A 54346 broad.mit.edu;ucsc.edu GRCh37 6 167728856 167728856 + synonymous_variant Silent SNP C C T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 360 30 ENST00000230256.3:c.1290C>T p.Cys430= p.C430= ENST00000230256 NM_018974.3 430 tgC/tgT 0 0.542 TTGTGGAGTGCGTGGAGTCCA +IGFBP2 3485 broad.mit.edu;ucsc.edu GRCh37 2 217525369 217525369 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 63 11 ENST00000233809.4:c.532C>T p.Arg178Trp p.R178W ENST00000233809 NM_000597.2 178 Cgg/Tgg 0 0.612 CAGTGCTGGCCGGAAGCCCCT +HIVEP2 3097 broad.mit.edu;ucsc.edu GRCh37 6 143095693 143095693 + synonymous_variant Silent SNP T T C TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 207 29 ENST00000367603.2:c.183A>G p.Ala61= p.A61= ENST00000367603 NM_006734.3 61 gcA/gcG 0 0.498 CAAACAGTTGTGCTGATGCTG +FLRT2 23768 broad.mit.edu;ucsc.edu GRCh37 14 86089274 86089274 + synonymous_variant Silent SNP C C T rs146568257 byFrequency TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 96 45 ENST00000330753.4:c.1416C>T p.Ser472= p.S472= ENST00000330753 NM_013231.4 472 agC/agT 0 0.517 GCATAGTCAGCGGTGAGAAGC +MUC16 94025 broad.mit.edu;ucsc.edu GRCh37 19 8987333 8987333 + splice_region_variant,synonymous_variant Splice_Region SNP G G A TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 112 14 ENST00000397910.4:c.41754C>T p.Thr13918= p.T13918= ENST00000397910 NM_024690.2 13918 acC/acT 0 0.597 TGACCACCCCGGCTAGGGCAG +TNFRSF9 3604 broad.mit.edu;ucsc.edu GRCh37 1 7998823 7998823 + missense_variant Missense_Mutation SNP C C T rs9657963 byFrequency TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 157 17 ENST00000377507.3:c.166G>A p.Ala56Thr p.A56T ENST00000377507 NM_001561.5 56 Gca/Aca 0 0.408 TGTCCACCTGCGCTGGAGAAA +ADAMTS9 56999 broad.mit.edu;ucsc.edu GRCh37 3 64526873 64526873 + missense_variant Missense_Mutation SNP C C T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 120 23 ENST00000498707.1:c.5419G>A p.Gly1807Arg p.G1807R ENST00000498707 NM_182920.1 1807 Ggg/Agg 0 0.473 CGCCGGCTCCCGTTATAGGGA +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76890105 76890106 + frameshift_variant Frame_Shift_Ins INS - - CATA TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 61 16 ENST00000373344.5:c.4785_4788dupTATG p.Gly1597TyrfsTer5 p.G1597Yfs*5 ENST00000373344 NM_000489.3 1596 -/TATG 0 0.371 TTACCAAGGCCCATACAGTGGG +TCF12 6938 broad.mit.edu GRCh37 15 57565437 57565438 + stop_gained,frameshift_variant Nonsense_Mutation INS - - TTGAC TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 9 ENST00000438423.2:c.1956_1957insTGACT p.Ser653Ter p.S653* ENST00000438423 NM_207037.1 652 ctt/ctTTGACt 0 0.441 GCAGTCATCCTTAGTCTAGAAC +ATRX 546 broad.mit.edu GRCh37 X 76938654 76938655 + frameshift_variant Frame_Shift_Ins INS - - T TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 9 ENST00000373344.5:c.2093dupA p.Asp699GlyfsTer2 p.D699Gfs*2 ENST00000373344 NM_000489.3 698 aag/aaAg 0 0.356 TACGCTTATCCTTTTTTCTCAC +ATRX 546 broad.mit.edu GRCh37 X 76845302 76845302 + splice_donor_variant Splice_Site SNP A A G TCGA-FG-8182-01 TCGA-FG-8182-10 Untested Somatic Phase_I WXS none Illumina GAIIx 8 3 ENST00000373344.5:c.6217+2T>C p.X2073_splice ENST00000373344 NM_000489.3 0 0.328 TTTGTAGCTCACCTTTATAAA +SLIT1 6585 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 98797514 98797514 + synonymous_variant Silent SNP G G A rs141130521 byFrequency TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 23 ENST00000266058.4:c.2307C>T p.Asp769= p.D769= ENST00000266058 NM_003061.2 769 gaC/gaT 0 0.597 ACTGGTTCCCGTCCAAATAGC +MS4A12 54860 hgsc.bcm.edu;broad.mit.edu GRCh37 11 60268575 60268575 + missense_variant Missense_Mutation SNP A A G TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 181 11 ENST00000016913.4:c.334A>G p.Ile112Val p.I112V ENST00000016913 NM_017716.2 112 Ata/Gta 0 0.373 TTTGTGTTTAATATCCTTCTC +C11orf82 220042 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 82643883 82643883 + synonymous_variant Silent SNP A A T TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 17 ENST00000533655.1:c.1503A>T p.Gly501= p.G501= ENST00000533655 NM_145018.3 501 ggA/ggT 0 0.368 ACTGTAAAGGAAATCTAAGTC +KDM4E 390245 hgsc.bcm.edu;broad.mit.edu GRCh37 11 94759050 94759050 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 11 ENST00000450979.2:c.329C>T p.Pro110Leu p.P110L ENST00000450979 NM_001161630.1 110 cCg/cTg 0 0.468 TATCAGACTCCGCCACACCAG +RASSF9 9182 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 86199470 86199470 + synonymous_variant Silent SNP C C T TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 141 14 ENST00000361228.3:c.318G>A p.Glu106= p.E106= ENST00000361228 NM_005447.3 106 gaG/gaA 0 0.448 TATTGGGCTGCTCATCTCCCC +UHRF1BP1L 23074 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 100478361 100478361 + missense_variant Missense_Mutation SNP T T C TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 29 ENST00000279907.7:c.1181A>G p.His394Arg p.H394R ENST00000279907 NM_015054.1 394 cAt/cGt 0 0.393 CTCAAATTCATGCAATAACTC +BAHD1 22893 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 40751367 40751367 + missense_variant Missense_Mutation SNP G G A rs150307966 TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 29 ENST00000416165.1:c.704G>A p.Arg235His p.R235H ENST00000416165 NM_014952.3 235 cGc/cAc 0 0.627 GTAGATGGGCGCTCCACTGAG +CA5A 763 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 87938397 87938397 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 114 44 ENST00000309893.2:c.454G>A p.Ala152Thr p.A152T ENST00000309893 NM_001739.1 152 Gca/Aca 0 0.577 CAAACCTCTGCGGGGTACGCG +KSR1 8844 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 25932772 25932772 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 26 19 ENST00000398988.3:c.1582C>T p.Arg528Trp p.R528W ENST00000398988 NM_014238.1 528 Cgg/Tgg 0 0.597 CCGGCAGACGCGGCATGAGAA +UNC13A 23025 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 17752258 17752258 + missense_variant Missense_Mutation SNP C C A TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 31 ENST00000519716.2:c.2580G>T p.Glu860Asp p.E860D ENST00000519716 NM_001080421.2 860 gaG/gaT 0 0.567 CGTCCACAATCTCCTGGGCTG +ZNF614 80110 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 52519785 52519785 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 11 ENST00000270649.6:c.1066C>T p.Arg356Cys p.R356C ENST00000270649 NM_025040.3 356 Cgc/Tgc 0 0.428 ACAAGATAGCGCTTCATGGTG +LRRC8B 23507 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 90049110 90049110 + missense_variant Missense_Mutation SNP C C T TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 52 ENST00000330947.2:c.901C>T p.Arg301Cys p.R301C ENST00000330947 NM_001134476.1 301 Cgc/Tgc 0 0.383 AGGATATAAGCGCTACCAGTG +MAVS 57506 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 3841977 3841977 + splice_acceptor_variant Splice_Site SNP A A G TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 93 51 ENST00000428216.2:c.293-2A>G p.X98_splice ENST00000428216 NM_020746.4 0 0.602 TTTGTCCTCTAGGGACCTCGG +ADAMTS1 9510 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 28210518 28210518 + missense_variant Missense_Mutation SNP T T A TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 27 ENST00000284984.3:c.2284A>T p.Arg762Trp p.R762W ENST00000284984 NM_006988.3 762 Agg/Tgg 0 0.448 CCATTGTTCCTGGATCCCCTC +ERG 2078 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 39774503 39774503 + missense_variant Missense_Mutation SNP G G A TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 15 ENST00000288319.7:c.649C>T p.Arg217Trp p.R217W ENST00000288319 NM_182918.3 217 Cgg/Tgg 0 0.438 TGCATTAACCGTGGAGAGTTT +ZNF280A 129025 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 22869694 22869694 + synonymous_variant Silent SNP C C T rs150360634 TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 114 67 ENST00000302097.3:c.261G>A p.Ser87= p.S87= ENST00000302097 NM_080740.3 87 tcG/tcA 0 0.468 TTGCAGGCTGCGACACGTGAG +SCN2A 6326 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 166245292 166245292 + missense_variant Missense_Mutation SNP C C A TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 98 53 ENST00000357398.3:c.4976C>A p.Ala1659Glu p.A1659E ENST00000357398 1659 gCg/gAg 0 0.493 TCCCTTCCTGCGTTGTTTAAC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 52 41 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +SLC36A1 206358 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 150867793 150867793 + missense_variant Missense_Mutation SNP A A G rs140057648 TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 29 ENST00000243389.3:c.1409A>G p.Asn470Ser p.N470S ENST00000243389 NM_078483.2 470 aAt/aGt 0 0.567 ATCTTCATCAATTCCACCTGT +SLIT3 6586 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 168093480 168093480 + synonymous_variant Silent SNP G G A TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 12 ENST00000519560.1:c.4551C>T p.Cys1517= p.C1517= ENST00000519560 NM_003062.3 1517 tgC/tgT 0 0.627 CGAGGCAGCCGCACTCTAAGT +KLHDC10 23008 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 129761996 129761996 + missense_variant Missense_Mutation SNP A A G TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 66 ENST00000335420.5:c.733A>G p.Thr245Ala p.T245A ENST00000335420 NM_014997.3 245 Aca/Gca 0 0.423 CAGAGAGTGGACACAACTGAA +CDCA2 157313 hgsc.bcm.edu;ucsc.edu GRCh37 8 25337481 25337481 + synonymous_variant Silent SNP G G A rs112148375 byFrequency TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 69 32 ENST00000330560.3:c.873G>A p.Ser291= p.S291= ENST00000330560 NM_152562.2 291 tcG/tcA 0 0.507 ATGCCGTTTCGCCTGACACGT +CCDC88B 283234 broad.mit.edu;ucsc.edu GRCh37 11 64111866 64111866 + missense_variant Missense_Mutation SNP A A C rs142814776 TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 19 ENST00000356786.5:c.1853A>C p.Gln618Pro p.Q618P ENST00000356786 NM_032251.5 618 cAg/cCg 0 0.647 CAGGCCCCGCAGTTGCTGGGA +SZT2 23334 broad.mit.edu;hgsc.bcm.edu GRCh37 1 43912030 43912033 + frameshift_variant Frame_Shift_Del DEL CAAA CAAA - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 36 ENST00000562955.1:c.8846_8849delAACA p.Lys2949SerfsTer33 p.K2949Sfs*33 ENST00000562955 NM_015284.3 2948 gtCAAA/gt 0 0.559 ACTTCTGTGTCAAACAGTTTGCCC +PI4KB 5298 broad.mit.edu;hgsc.bcm.edu GRCh37 1 151265460 151265461 + frameshift_variant Frame_Shift_Del DEL TT TT - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 46 ENST00000368875.2:c.2354_2355delAA p.Lys785ArgfsTer9 p.K785Rfs*9 ENST00000368875 NM_002651.2 785 aAA/a 0 0.564 GGAACCTCTCTTTGAGGTTTCG +OR14A16 284532 broad.mit.edu;hgsc.bcm.edu GRCh37 1 247978839 247978840 + frameshift_variant Frame_Shift_Del DEL AT AT - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 29 ENST00000357627.1:c.192_193delAT p.Ser65PhefsTer54 p.S65Ffs*54 ENST00000357627 NM_001001966.1 64 ctATct/ctct 0 0.421 TCCAAGAAAGATAGATTCTTCA +BRE 9577 broad.mit.edu;hgsc.bcm.edu GRCh37 2 28550157 28550158 + frameshift_variant Frame_Shift_Del DEL AG AG - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 135 57 ENST00000344773.2:c.1108_1109delGA p.Asp370CysfsTer152 p.D370Cfs*152 ENST00000344773 NM_004899.4 369 AGa/a 0 0.609 CCAAGGGAGCAGAGATGCCTGC +RAB3GAP1 22930 broad.mit.edu;hgsc.bcm.edu GRCh37 2 135920344 135920346 + inframe_deletion In_Frame_Del DEL AAG AAG - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 75 29 ENST00000442034.1:c.2417_2419delAGA p.Lys806del p.K806del ENST00000442034 NM_001172435.1 805 AAG/- 0 0.315 TTCTTCAGTTAAGAAGATCATAA +SP3 6670 broad.mit.edu;hgsc.bcm.edu GRCh37 2 174774916 174774917 + frameshift_variant Frame_Shift_Del DEL AT AT - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 42 ENST00000310015.6:c.2098_2099delAT p.Ile700Ter p.I700* ENST00000310015 NM_001172712.1 700 ATt/t 0 0.376 GTGTGTTTTAATATGTTTGGCA +ZBTB20 26137 broad.mit.edu;hgsc.bcm.edu GRCh37 3 114058229 114058231 + inframe_deletion In_Frame_Del DEL AGG AGG - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 26 ENST00000474710.1:c.1847_1849delCCT p.Ser616del p.S616del ENST00000474710 NM_001164342.1 616 tCCTta/tta 0 0.507 TAATCCTTTAAGGAGAAGGAGCG +GALNTL6 442117 broad.mit.edu;hgsc.bcm.edu GRCh37 4 173961139 173961141 + inframe_deletion In_Frame_Del DEL AGA AGA - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 60 25 ENST00000506823.1:c.1700_1702delAGA p.Lys567del p.K567del ENST00000506823 NM_001034845.2 565 gAGAag/gag 0 0.424 AACCCCGCAGAGAAGAAGATTTT +FNDC9 408263 broad.mit.edu;hgsc.bcm.edu GRCh37 5 156770389 156770391 + inframe_deletion In_Frame_Del DEL CTC CTC - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 89 47 ENST00000312349.4:c.154_156delGAG p.Glu52del p.E52del ENST00000312349 NM_001001343.3 52 GAG/- 0 0.537 GAGGCACCTTCTCCTCGTGGTGG +EPB41L2 2037 broad.mit.edu;hgsc.bcm.edu GRCh37 6 131277495 131277497 + inframe_deletion In_Frame_Del DEL TCC TCC - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 36 ENST00000337057.3:c.129_131delGGA p.Glu44del p.E44del ENST00000337057 NM_001431.3 43 gaGGAa/gaa 0 0.483 GGAACCTTTTTCCTCCTCTGGAT +KMT2E 55904 broad.mit.edu;hgsc.bcm.edu GRCh37 7 104717788 104717789 + frameshift_variant Frame_Shift_Del DEL AA AA - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 41 ENST00000311117.3:c.1040_1041delAA p.Lys347ArgfsTer5 p.K347Rfs*5 ENST00000311117 NM_182931.2 346 gcAAaa/gcaa 0 0.292 TTAAATCTGCAAAAGATTTGCC +FAM91A1 157769 broad.mit.edu;hgsc.bcm.edu GRCh37 8 124789562 124789563 + splice_donor_variant,coding_sequence_variant Splice_Site DEL TG TG - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 17 ENST00000334705.7:c.367+1_367+2delGT p.X123_splice ENST00000334705 NM_144963.2 123 0 0.302 TGCTGCTGACTGTAAGTATTTA +RUSC2 9853 broad.mit.edu;hgsc.bcm.edu GRCh37 9 35560631 35560633 + inframe_deletion In_Frame_Del DEL GAG GAG - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 15 10 ENST00000455600.1:c.3998_4000delAGG p.Glu1333del p.E1333del ENST00000455600 NM_001135999.1 1332 GAG/- 0 0.7 CCCTGCCTCTGAGGAGGCCCTGG +ARHGEF39 84904 broad.mit.edu;hgsc.bcm.edu GRCh37 9 35663036 35663037 + frameshift_variant Frame_Shift_Del DEL CT CT - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 51 ENST00000378387.3:c.579_580delAG p.Arg193SerfsTer11 p.R193Sfs*11 ENST00000378387 NM_032818.2 193 agAGtc/agtc 0 0.53 ATAGTATGGACTCTCTGGGCAG +NOTCH1 4851 broad.mit.edu;hgsc.bcm.edu GRCh37 9 139397632 139397635 + splice_donor_variant,coding_sequence_variant Splice_Site DEL ACTC ACTC - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 71 19 ENST00000277541.6:c.5166_5167+2delGAGT p.X1722_splice ENST00000277541 NM_017617.3 1722 0 0.662 GGCCACACTTACTCTGCACGGCCT +NOTCH1 4851 broad.mit.edu;hgsc.bcm.edu GRCh37 9 139413073 139413075 + inframe_deletion In_Frame_Del DEL AGG AGG - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 24 ENST00000277541.6:c.1067_1069delCCT p.Ser356del p.S356del ENST00000277541 NM_017617.3 356 tCCTtc/ttc 0 0.65 TCGCAGTAGAAGGAGGCCACACG +KAT6B 23522 broad.mit.edu;hgsc.bcm.edu GRCh37 10 76784946 76784949 + frameshift_variant Frame_Shift_Del DEL ACAA ACAA - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 23 ENST00000287239.4:c.3606_3609delAACA p.Thr1203ArgfsTer21 p.T1203Rfs*21 ENST00000287239 NM_001256468.1 1201 agACAA/ag 0 0.451 GGAAGAAAAGACAAACAGAGGAAG +CLEC9A 283420 broad.mit.edu;hgsc.bcm.edu GRCh37 12 10205309 10205321 + frameshift_variant Frame_Shift_Del DEL CCTCTCTTCAGTG CCTCTCTTCAGTG - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 11 ENST00000355819.1:c.23_35delCCTCTCTTCAGTG p.Thr8ArgfsTer25 p.T8Rfs*25 ENST00000355819 NM_207345.2 8 aCCTCTCTTCAGTGg/ag 0 0.441 GAAATATACACCTCTCTTCAGTGGGATAGCCCA +ALDH1L2 160428 broad.mit.edu;hgsc.bcm.edu GRCh37 12 105464505 105464507 + inframe_deletion In_Frame_Del DEL CTT CTT - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 20 ENST00000258494.9:c.269_271delAAG p.Glu90del p.E90del ENST00000258494 NM_001034173.3 90 gAAGtg/gtg 0 0.463 GCTTCTGCCACTTCTTTGATGGT +BRMS1L 84312 broad.mit.edu;hgsc.bcm.edu GRCh37 14 36295747 36295749 + inframe_deletion In_Frame_Del DEL AAG AAG - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 11 ENST00000216807.7:c.28_30delAAG p.Lys10del p.K10del ENST00000216807 NM_032352.3 9 AAG/- 0 0.631 CCGAGGGGATAAGAAGGAGACCA +PIGW 284098 broad.mit.edu;hgsc.bcm.edu GRCh37 17 34893506 34893508 + inframe_deletion In_Frame_Del DEL AGG AGG - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 141 50 ENST00000592983.1:c.561_563delGAG p.Arg188del p.R188del ENST00000592983 186 AGG/- 0 0.424 TCTAGAGGTCAGGAGGAGAAAAT +SPECC1L 23384 broad.mit.edu;hgsc.bcm.edu GRCh37 22 24718811 24718812 + frameshift_variant Frame_Shift_Del DEL TT TT - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 50 ENST00000314328.9:c.1864_1865delTT p.Leu622GlyfsTer2 p.L622Gfs*2 ENST00000314328 NM_015330.4 621 acTTtg/actg 0 0.416 AAGCAGAGACTTTGGCTAGTAG +BCOR 54880 broad.mit.edu GRCh37 X 39934072 39934075 + frameshift_variant Frame_Shift_Del DEL TGTT TGTT - TCGA-HW-A5KJ-01 TCGA-HW-A5KJ-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 7 ENST00000378444.4:c.524_527delAACA p.Lys175ArgfsTer40 p.K175Rfs*40 ENST00000378444 NM_001123385.1 175 aAACAg/ag 0 0.539 GAGAGGGCTCTGTTTGTCGCTGGC +OR4A15 81328 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 55136122 55136122 + missense_variant Missense_Mutation SNP A A T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 78 64 ENST00000314706.3:c.763A>T p.Thr255Ser p.T255S ENST00000314706 NM_001005275.1 255 Act/Tct 0 0.438 CTCTCTTAAGACTCAGAGTTT +OR5D16 390144 hgsc.bcm.edu;broad.mit.edu GRCh37 11 55606760 55606760 + missense_variant Missense_Mutation SNP A A G TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 5 ENST00000378396.1:c.533A>G p.His178Arg p.H178R ENST00000378396 NM_001005496.1 178 cAt/cGt 0 0.423 ACAATCAATCATTTCTTCTGT +NPAS4 266743 hgsc.bcm.edu;broad.mit.edu GRCh37 11 66192121 66192121 + missense_variant Missense_Mutation SNP C C T rs142965018 byFrequency TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 183 17 ENST00000311034.2:c.1760C>T p.Thr587Met p.T587M ENST00000311034 NM_178864.3 587 aCg/aTg 0 0.607 GGGGACTGCACGCTCTTGGCC +MMP1 4312 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 102666337 102666337 + splice_region_variant,synonymous_variant Splice_Region SNP C C T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 11 ENST00000315274.6:c.627G>A p.Glu209= p.E209= ENST00000315274 NM_002421.3 209 gaG/gaA 0 0.368 GTAAGTTGTACTCTAAAAAGG +GRIN2B 2904 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 13716801 13716801 + missense_variant Missense_Mutation SNP C C T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 20 ENST00000609686.1:c.3371G>A p.Arg1124Lys p.R1124K ENST00000609686 NM_000834.3 1124 aGg/aAg 0 0.617 TTCCTTGTCCCTGAAGTAGCG +KRT84 3890 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 52777394 52777394 + synonymous_variant Silent SNP G G A TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 18 18 ENST00000257951.3:c.735C>T p.Val245= p.V245= ENST00000257951 NM_033045.3 245 gtC/gtT 0 0.577 AGCCCTCTAGGACATCCTGCA +ACAD10 80724 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 112193513 112193513 + synonymous_variant Silent SNP G G A TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 130 19 ENST00000455480.2:c.3096G>A p.Pro1032= p.P1032= ENST00000455480 NM_001136538.1 1032 ccG/ccA 0 0.517 TGGTCGCCCCGTCCATGGCCT +RAB27A 5873 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 55497820 55497820 + missense_variant Missense_Mutation SNP C C T rs141362723 by1000genomes TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 65 ENST00000396307.2:c.551G>A p.Arg184Gln p.R184Q ENST00000396307 NM_004580.4 184 cGa/cAa 0 0.463 CCGTTCCATTCGCTTCATTAT +HSDL1 83693 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 84163854 84163854 + missense_variant Missense_Mutation SNP G G A TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 165 16 ENST00000219439.4:c.403C>T p.Pro135Ser p.P135S ENST00000219439 NM_001146051.1 135 Cca/Tca 0 0.473 TCTCGAATTGGAAGGTAGATC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 by1000genomes TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 3 29 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 0 0.542 GGCACAAACACGCACCTCAAA +ARHGEF10L 55160 hgsc.bcm.edu;broad.mit.edu GRCh37 1 17961457 17961457 + missense_variant Missense_Mutation SNP G G C TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 3 ENST00000361221.3:c.1873G>C p.Val625Leu p.V625L ENST00000361221 NM_018125.3 625 Gtg/Ctg 0 0.642 CAAGGACAATGTGCTCATCCA +ELMOD3 84173 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 85617291 85617291 + synonymous_variant Silent SNP C C T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 23 ENST00000315658.7:c.846C>T p.Pro282= p.P282= ENST00000315658 NM_032213.4 282 ccC/ccT 0 0.567 AGGTCATCCCCGTGGTGAACA +GPR39 2863 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 133175296 133175296 + synonymous_variant Silent SNP C C T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 30 ENST00000329321.3:c.681C>T p.Ala227= p.A227= ENST00000329321 NM_001508.2 227 gcC/gcT 0 0.612 TCTTCGGCGCCTTCGTGGTCT +TANK 10010 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 162087893 162087893 + missense_variant Missense_Mutation SNP C C T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 126 10 ENST00000392749.2:c.932C>T p.Pro311Leu p.P311L ENST00000392749 NM_001199135.1 311 cCc/cTc 0 0.383 AAAACAAAGCCCTCAAATCTC +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 24 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +SLC6A11 6538 hgsc.bcm.edu;broad.mit.edu GRCh37 3 10885932 10885932 + missense_variant Missense_Mutation SNP G G C TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 44 3 ENST00000254488.2:c.657G>C p.Glu219Asp p.E219D ENST00000254488 NM_014229.1 219 gaG/gaC 0 0.587 ACGGGATCGAGCACATCGGGA +MAN2B2 23324 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 6612960 6612960 + synonymous_variant Silent SNP C C T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 15 ENST00000285599.3:c.2518C>T p.Leu840= p.L840= ENST00000285599 NM_015274.1 840 Ctg/Ttg 0 0.627 GAGGAGCGCACTGGCGCTGCA +COL25A1 84570 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 109805344 109805344 + missense_variant Missense_Mutation SNP G G A TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 25 ENST00000399132.1:c.1010C>T p.Pro337Leu p.P337L ENST00000399132 NM_198721.2 337 cCg/cTg 0 0.413 CTTTATCCCCGGAAGTCCAGG +SCAND3 114821 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 28540794 28540794 + missense_variant Missense_Mutation SNP A A G TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 9 ENST00000452236.2:c.2872T>C p.Cys958Arg p.C958R ENST00000452236 NM_052923.1 958 Tgt/Cgt 0 0.353 tccaaaccacatttgttaaca +PTCHD4 442213 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 47976601 47976601 + missense_variant Missense_Mutation SNP A A T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 18 ENST00000339488.4:c.676T>A p.Phe226Ile p.F226I ENST00000339488 NM_001013732.3 226 Ttt/Att 0 0.527 GTCTTATGAAAGTCCCTCCAG +CDK14 5218 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 90613505 90613505 + synonymous_variant Silent SNP T T A TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 115 42 ENST00000265741.3:c.936T>A p.Ala312= p.A312= ENST00000265741 NM_012395.2 312 gcT/gcA 0 0.348 AAGGAGTTGCTGCTTTTCCAG +XKR9 389668 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 71646066 71646066 + missense_variant Missense_Mutation SNP T T C TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 6 ENST00000408926.3:c.529T>C p.Trp177Arg p.W177R ENST00000408926 NM_001011720.1 177 Tgg/Cgg 0 0.299 TGCTATTTCTTGGTCAACTGT +CDH17 1015 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 95182644 95182644 + synonymous_variant Silent SNP G G A TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 101 64 ENST00000027335.3:c.1047C>T p.Val349= p.V349= ENST00000027335 NM_004063.3 349 gtC/gtT 0 0.438 CATTCTCCTGGACCTCAAATA +FAM78A 286336 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 134136482 134136482 + synonymous_variant Silent SNP C C T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 28 ENST00000372271.3:c.579G>A p.Leu193= p.L193= ENST00000372271 NM_033387.3 193 ctG/ctA 0 0.617 TGGTGGCCACCAGCCAGGTGG +FRMD7 90167 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 131214037 131214037 + synonymous_variant Silent SNP T T C TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 85 ENST00000298542.4:c.1047A>G p.Lys349= p.K349= ENST00000298542 NM_194277.2 349 aaA/aaG 0 0.398 ACCTTACTTGTTTTGACACAT +RPS4Y2 140032 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 Y 22930744 22930744 + missense_variant Missense_Mutation SNP C C A TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 22 ENST00000288666.5:c.414C>A p.His138Gln p.H138Q ENST00000288666 NM_001039567.2 138 caC/caA 0 0.438 GAATTCCACACCTGGTGACTC +PALD1 27143 broad.mit.edu;ucsc.edu GRCh37 10 72307126 72307126 + missense_variant Missense_Mutation SNP C C T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 29 ENST00000263563.6:c.2186C>T p.Ala729Val p.A729V ENST00000263563 NM_014431.2 729 gCg/gTg 0 0.617 GTGGACGCAGCGCTGGACACT +GPX2 2877 broad.mit.edu;ucsc.edu GRCh37 14 65406296 65406296 + synonymous_variant Silent SNP C C T rs17885748 TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 20 ENST00000389614.5:c.483G>A p.Pro161= p.P161= ENST00000389614 NM_002083.3 161 ccG/ccA 0 0.537 GCTCTCCCTCCGGCCCTATGA +FRY 10129 broad.mit.edu;ucsc.edu GRCh37 13 32852686 32852686 + splice_donor_variant Splice_Site SNP G G C TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 100 16 ENST00000380250.3:c.8469+1G>C p.X2823_splice ENST00000380250 NM_023037.2 0 0.443 CGAAGAAAAGGTAATAAAAGC +OR2M7 391196 broad.mit.edu;ucsc.edu GRCh37 1 248487368 248487368 + missense_variant Missense_Mutation SNP T T C TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 182 108 ENST00000317965.2:c.503A>G p.Tyr168Cys p.Y168C ENST00000317965 NM_001004691.1 168 tAc/tGc 0 0.448 AGACCCACAGTAGGAGAAGGA +MYO18A 399687 broad.mit.edu;ucsc.edu GRCh37 17 27430667 27430667 + missense_variant Missense_Mutation SNP G G C TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 47 3 ENST00000527372.1:c.3457C>G p.Leu1153Val p.L1153V ENST00000527372 NM_078471.3 1153 Ctg/Gtg 0 0.667 AAGCACTCCAGCAGCTCCTCC +APRT 353 broad.mit.edu;ucsc.edu GRCh37 16 88876924 88876924 + synonymous_variant Silent SNP G G A TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 2 ENST00000378364.3:c.228C>T p.Ala76= p.A76= ENST00000378364 NM_000485.2 76 gcC/gcT 0 0.637 CAAGCTCCTGGGCCAGGGAGG +SDAD1P1 404668 broad.mit.edu;ucsc.edu GRCh37 8 26237249 26237249 + non_coding_transcript_exon_variant RNA SNP G G A TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 6 ENST00000519902.1:n.2700C>T *900* ENST00000519902 0 0.458 GGGATTTCCCGGGGACAGCGT +PHF23 79142 broad.mit.edu;ucsc.edu GRCh37 17 7139547 7139547 + synonymous_variant Silent SNP T T C TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 81 41 ENST00000320316.3:c.699A>G p.Pro233= p.P233= ENST00000320316 NM_024297.2 233 ccA/ccG 0 0.552 GCCCAGGAGGTGGGAGTCTAT +RUNX1T1 862 broad.mit.edu;ucsc.edu GRCh37 8 93026829 93026829 + missense_variant Missense_Mutation SNP C C T TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 88 12 ENST00000436581.2:c.479G>A p.Arg160His p.R160H ENST00000436581 160 cGc/cAc 0 0.507 AACGAGGGTGCGAACTCTTTC +ASPM 259266 broad.mit.edu;hgsc.bcm.edu GRCh37 1 197070598 197070599 + frameshift_variant Frame_Shift_Del DEL TC TC - rs144088344 by1000genomes TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 12 ENST00000367409.4:c.7782_7783delGA p.Lys2595SerfsTer6 p.K2595Sfs*6 ENST00000367409 NM_018136.4 2594 caGAaa/caaa 0 0.356 TGAAATACTTTCTGTTTCTTTT +AMOTL2 51421 broad.mit.edu;hgsc.bcm.edu GRCh37 3 134078153 134078155 + inframe_deletion In_Frame_Del DEL TGT TGT - TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 21 ENST00000249883.5:c.2074_2076delACA p.Thr692del p.T692del ENST00000249883 NM_016201.3 692 ACA/- 0 0.596 GGGCGTCTGCTGTTTGTCGCTCA +CYP3A7 1551 broad.mit.edu;hgsc.bcm.edu GRCh37 7 99312223 99312224 + frameshift_variant Frame_Shift_Del DEL TT TT - TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 89 19 ENST00000336374.2:c.752_753delAA p.Lys251IlefsTer26 p.K251Ifs*26 ENST00000336374 NM_000765.3 251 aAA/a 0 0.312 GTTTTACAGATTTTGTTAGAAA +RANBP6 26953 broad.mit.edu;hgsc.bcm.edu GRCh37 9 6013101 6013102 + frameshift_variant Frame_Shift_Del DEL AG AG - TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 97 24 ENST00000259569.5:c.2506_2507delCT p.Leu836AlafsTer3 p.L836Afs*3 ENST00000259569 NM_012416.3 836 CTg/g 0 0.337 CTCATCTTGCAGAGACATCTCA +UHRF2 115426 broad.mit.edu;hgsc.bcm.edu GRCh37 9 6497275 6497278 + frameshift_variant Frame_Shift_Del DEL CAGT CAGT - TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 40 16 ENST00000276893.5:c.1685_1688delTCAG p.Val562GlufsTer2 p.V562Efs*2 ENST00000276893 NM_152896.2 561 cCAGTc/cc 0 0.426 GCTGGTAAGCCAGTCAGAGTGATA +AKAP8 10270 broad.mit.edu;hgsc.bcm.edu GRCh37 19 15471767 15471769 + inframe_deletion In_Frame_Del DEL GAA GAA - TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 21 10 ENST00000269701.2:c.1417_1419delTTC p.Phe473del p.F473del ENST00000269701 NM_005858.3 473 TTC/- 0 0.571 CGATCTTCTTGAAGAAGTGCTCC +LENG9 94059 broad.mit.edu;hgsc.bcm.edu GRCh37 19 54973460 54973461 + frameshift_variant Frame_Shift_Del DEL TG TG - TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 53 44 ENST00000333834.4:c.1315_1316delCA p.Gln439ValfsTer58 p.Q439Vfs*58 ENST00000333834 NM_198988.1 439 CAg/g 0 0.644 CCCTGGAGACTGTAGTGTACTC +USP9X 8239 broad.mit.edu;hgsc.bcm.edu GRCh37 X 41088882 41088884 + inframe_deletion In_Frame_Del DEL AAG AAG - TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 15 ENST00000324545.8:c.7285_7287delAGA p.Arg2429del p.R2429del ENST00000324545 NM_001039590.2 2427 gaAAGa/gaa 0 0.404 ATGAACTTGAAAGAAGACCATAT +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76918976 76918977 + frameshift_variant Frame_Shift_Del DEL TA TA - TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 5 21 ENST00000373344.5:c.4014_4015delTA p.His1338GlnfsTer11 p.H1338Qfs*11 ENST00000373344 NM_000489.3 1338 caTAgg/cagg 0 0.356 CGCAAAAGCCTATGTCTGTATC +ARID1A 8289 broad.mit.edu GRCh37 1 27057848 27057848 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-HW-7490-01 TCGA-HW-7490-10 Untested Somatic Phase_I WXS none Illumina GAIIx 245 25 ENST00000324856.7:c.1558delC p.Gln520SerfsTer99 p.Q520Sfs*99 ENST00000324856 NM_006015.4 519 tCc/tc 0 0.632 CCTCCATACTCCCAGCAGCCA +OR6Q1 219952 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 57799000 57799000 + synonymous_variant Silent SNP G G A TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 70 ENST00000302622.3:c.576G>A p.Ser192= p.S192= ENST00000302622 NM_001005186.2 192 tcG/tcA 0 0.498 TAGCCTTGTCGTGCTCAGATG +CMKLR1 1240 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 108685742 108685742 + missense_variant Missense_Mutation SNP C C T TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 55 29 ENST00000312143.7:c.998G>A p.Arg333His p.R333H ENST00000312143 NM_001142344.1 333 cGc/cAc 0 0.483 ATTGACCAGGCGAGAGAAGAG +SLITRK6 84189 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 13 86370348 86370348 + missense_variant Missense_Mutation SNP T T C TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 22 80 ENST00000400286.2:c.296A>G p.Asn99Ser p.N99S ENST00000400286 NM_032229.2 99 aAt/aGt 0 0.353 ATCTGCAATATTGTTAAATCC +TRIM9 114088 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 51448645 51448645 + missense_variant Missense_Mutation SNP G G C TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 58 43 ENST00000298355.3:c.1780C>G p.Pro594Ala p.P594A ENST00000298355 NM_015163.5 594 Cct/Gct 0 0.517 CCAAAGGCAGGATCAGGGTGG +IDH2 3418 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 90631838 90631838 + missense_variant Missense_Mutation SNP C C T rs121913503 TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 36 ENST00000330062.3:c.515G>A p.Arg172Lys p.R172K ENST00000330062 NM_002168.2 172 aGg/aAg 0 0.632 ATGGGCGTGCCTGCCAATGGT +DVL2 1856 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7132713 7132713 + synonymous_variant Silent SNP T T C TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 41 ENST00000005340.5:c.801A>G p.Thr267= p.T267= ENST00000005340 NM_004422.2 267 acA/acG 0 0.567 TTAGCGTGACTGTGATGATAT +CIC 23152 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 42791757 42791757 + missense_variant Missense_Mutation SNP C C T TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 10 37 ENST00000575354.2:c.643C>T p.Arg215Trp p.R215W ENST00000575354 NM_015125.3 215 Cgg/Tgg 0 0.612 CAAGCGGCACCGGGCCCTGGT +TTC7A 57217 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 47220609 47220609 + missense_variant Missense_Mutation SNP G G A TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 57 50 ENST00000319190.5:c.785G>A p.Arg262Lys p.R262K ENST00000319190 NM_020458.2 262 aGa/aAa 0 0.547 AAGGGCATGAGAGAGCTCCGG +AGPS 8540 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 178386040 178386040 + missense_variant Missense_Mutation SNP T T G TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 81 38 ENST00000264167.4:c.1741T>G p.Phe581Val p.F581V ENST00000264167 NM_003659.3 581 Ttt/Gtt 0 0.383 CTACTTCTATTTTGCCTTTAA +SCN10A 6336 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 38739794 38739794 + synonymous_variant Silent SNP G G A rs142804903 TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 78 ENST00000449082.2:c.4917C>T p.Asp1639= p.D1639= ENST00000449082 NM_006514.2 1639 gaC/gaT 0 0.547 TGAACATGTCGTCGATGCCAG +TINAG 27283 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 54191662 54191662 + missense_variant Missense_Mutation SNP G G A TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 65 32 ENST00000259782.4:c.572G>A p.Arg191His p.R191H ENST00000259782 NM_014464.3 191 cGc/cAc 0 0.373 TTTAAATTTCGCCTTGGCACT +LAMB4 22798 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 107748127 107748127 + missense_variant Missense_Mutation SNP G G T TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 31 ENST00000388781.3:c.540C>A p.Asp180Glu p.D180E ENST00000388781 NM_007356.2 180 gaC/gaA 0 0.398 CACAAACAATGTCTCCCACTC +SLC37A3 84255 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 140058508 140058508 + synonymous_variant Silent SNP G G A rs142313913 byFrequency TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 99 63 ENST00000326232.9:c.453C>T p.Asn151= p.N151= ENST00000326232 NM_207113.1 151 aaC/aaT 0 0.512 GCAGCAGGCCGTTCACAATCC +VPS13A 23230 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 79936584 79936584 + missense_variant Missense_Mutation SNP G G A TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 37 25 ENST00000360280.3:c.5752G>A p.Asp1918Asn p.D1918N ENST00000360280 NM_033305.2 1918 Gat/Aat 0 0.338 TTTAAGTATGGATTATATCCG +PIK3CA 5290 broad.mit.edu;hgsc.bcm.edu GRCh37 3 178916938 178916940 + inframe_deletion In_Frame_Del DEL GAA GAA - TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 44 ENST00000263967.3:c.328_330delGAA p.Glu110del p.E110del ENST00000263967 NM_006218.2 109 GAA/- 0 0.34 AGGCAACCGTGAAGAAAAGATCC +FUT5 2527 broad.mit.edu;hgsc.bcm.edu GRCh37 19 5867346 5867347 + frameshift_variant Frame_Shift_Ins INS - - GG rs111394159 TCGA-HW-7491-01 TCGA-HW-7491-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 25 ENST00000252675.5:c.389_390dupCC p.Ser131ProfsTer118 p.S131Pfs*118 ENST00000252675 130 -/CC 0 0.663 AGGTTGGCACTGGGGTTGTACA +LDB1 8861 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 103871263 103871263 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 66 43 ENST00000425280.1:c.56C>T p.Ser19Leu p.S19L ENST00000425280 NM_001113407.1 19 tCg/tTg 0 0.547 CTCCTTCGGCGAGTACAGCTT +OOSP2 219990 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 59812148 59812148 + missense_variant Missense_Mutation SNP T T C TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 139 28 ENST00000278855.2:c.248T>C p.Val83Ala p.V83A ENST00000278855 NM_173801.3 83 gTt/gCt 0 0.398 TCCTAGGTAGTTTCTGAGGAA +TMEM109 79073 hgsc.bcm.edu;broad.mit.edu GRCh37 11 60687346 60687346 + missense_variant Missense_Mutation SNP G G C TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 266 15 ENST00000227525.3:c.181G>C p.Val61Leu p.V61L ENST00000227525 NM_024092.2 61 Gtg/Ctg 0 0.542 AGGTCGATCTGTGCGAGGGAC +ZW10 9183 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 113628513 113628513 + missense_variant Missense_Mutation SNP T T C TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 148 16 ENST00000200135.3:c.796A>G p.Ile266Val p.I266V ENST00000200135 NM_004724.3 266 Ata/Gta 0 0.378 TGGCTTTCTATCACAGCATGA +STAB2 55576 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 104049284 104049284 + synonymous_variant Silent SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 56 60 ENST00000388887.2:c.1659C>T p.Tyr553= p.Y553= ENST00000388887 NM_017564.9 553 taC/taT 0 0.423 GTGGACCATACACCATTTTTG +TDG 6996 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 104374683 104374683 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 246 28 ENST00000392872.3:c.421C>T p.Pro141Ser p.P141S ENST00000392872 NM_003211.4 141 Ccg/Tcg 0 0.363 TGGCATAAACCCGGGACTAAT +HS3ST4 9951 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 26147367 26147367 + missense_variant Missense_Mutation SNP A A T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 86 21 ENST00000331351.5:c.1169A>T p.Lys390Ile p.K390I ENST00000331351 NM_006040.2 390 aAa/aTa 0 0.517 TATTTCAACAAAACCAAGGGG +APOBR 55911 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 28507468 28507468 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 13 16 ENST00000564831.1:c.1106G>A p.Gly369Glu p.G369E ENST00000564831 NM_018690.3 369 gGg/gAg 0 0.657 GCCTCAGGAGGGGACGAGGCC +CDH19 28513 hgsc.bcm.edu;broad.mit.edu GRCh37 18 64172539 64172539 + missense_variant,splice_region_variant Missense_Mutation SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 173 10 ENST00000262150.2:c.1829G>A p.Gly610Glu p.G610E ENST00000262150 NM_021153.3 610 gGg/gAg 0 0.303 AAAAATAAACCCTGATGAAGA +DOHH 83475 hgsc.bcm.edu;broad.mit.edu GRCh37 19 3492382 3492382 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 3 3 ENST00000427575.1:c.467G>A p.Arg156His p.R156H ENST00000427575 NM_001145165.1 156 cGt/cAt 0 0.746 CCCCACGTCACGCTCCTCAGC +C3 718 hgsc.bcm.edu;broad.mit.edu GRCh37 19 6697496 6697496 + synonymous_variant Silent SNP G G A rs140780068 TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 128 9 ENST00000245907.6:c.2655C>T p.Thr885= p.T885= ENST00000245907 NM_000064.2 885 acC/acT 0 0.587 GGATGGTTACGGTCTGCTGGT +PLD3 23646 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 40883897 40883897 + synonymous_variant Silent SNP C C G TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 147 23 ENST00000409587.1:c.1290C>G p.Thr430= p.T430= ENST00000409587 430 acC/acG 0 0.647 CTCTAGGAACCTCCAACTGGT +HCN3 57657 hgsc.bcm.edu;broad.mit.edu GRCh37 1 155257756 155257756 + synonymous_variant Silent SNP G G A TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 114 9 ENST00000368358.3:c.1827G>A p.Ala609= p.A609= ENST00000368358 NM_020897.2 609 gcG/gcA 0 0.627 TGGTACATGCGCCCCTTCAGG +OR1C1 26188 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 247920937 247920937 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 45 54 ENST00000408896.2:c.772G>A p.Val258Ile p.V258I ENST00000408896 NM_012353.2 258 Gtc/Atc 0 0.512 CTGAAATAGACGGCGATGGCT +MICALL1 85377 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 38323471 38323471 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 44 ENST00000215957.6:c.1519C>T p.Pro507Ser p.P507S ENST00000215957 NM_033386.3 507 Cca/Tca 0 0.677 CACACCATCGCCAGCGCTCAG +CLIP4 79745 hgsc.bcm.edu;broad.mit.edu GRCh37 2 29356592 29356592 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 127 8 ENST00000320081.5:c.439C>T p.Arg147Cys p.R147C ENST00000320081 NM_024692.4 147 Cgc/Tgc 0 0.368 TTTGCGGAGTCGCTGGACAAA +CAPN13 92291 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 30966407 30966407 + synonymous_variant Silent SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 138 104 ENST00000295055.8:c.1287G>A p.Ser429= p.S429= ENST00000295055 NM_144575.2 429 tcG/tcA 0 0.473 TGTTTCTGAACGAGGAAAAAA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 103 50 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +GRM7 2917 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 7188209 7188209 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 191 39 ENST00000357716.4:c.590G>A p.Arg197His p.R197H ENST00000357716 NM_000844.3 197 cGc/cAc 0 0.522 TTCTTCTCTCGCGTGGTGCCA +KLHL18 23276 hgsc.bcm.edu;broad.mit.edu GRCh37 3 47361235 47361235 + synonymous_variant Silent SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 296 16 ENST00000232766.5:c.222C>T p.Cys74= p.C74= ENST00000232766 NM_025010.4 74 tgC/tgT 0 0.493 TGATGGAGTGCAAGCAGGATG +GPR116 221395 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 46826878 46826878 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 215 49 ENST00000283296.7:c.2762G>A p.Ser921Asn p.S921N ENST00000283296 NM_001098518.1 921 aGc/aAc 0 0.448 CATCACTAAGCTCTCTGCAAA +MCM9 254394 hgsc.bcm.edu;broad.mit.edu GRCh37 6 119245149 119245149 + missense_variant Missense_Mutation SNP A A G TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 369 27 ENST00000316316.6:c.448T>C p.Cys150Arg p.C150R ENST00000316316 NM_017696.2 150 Tgc/Cgc 0 0.458 ACATGCTTGCATTTGTTACAC +SCRN1 9805 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 29963705 29963705 + synonymous_variant Silent SNP G G A TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 158 18 ENST00000434476.2:c.1173C>T p.Thr391= p.T391= ENST00000434476 NM_001145514.1 391 acC/acT 0 0.557 GCTCCAGCATGGTGCTCCTCA +RNF133 168433 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 122338205 122338205 + synonymous_variant Silent SNP G G A TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 393 138 ENST00000340112.2:c.768C>T p.Cys256= p.C256= ENST00000340112 NM_139175.1 256 tgC/tgT 0 0.398 AGCAAATTACGCAGCTATCCC +CEP41 95681 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 130038826 130038826 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 490 46 ENST00000223208.5:c.1028G>A p.Arg343Gln p.R343Q ENST00000223208 NM_018718.2 343 cGa/cAa 0 0.577 CTGAGCGCTTCGGGCACCAGG +FAM154A 158297 hgsc.bcm.edu;broad.mit.edu GRCh37 9 18928507 18928507 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 154 10 ENST00000380534.4:c.968G>A p.Arg323Gln p.R323Q ENST00000380534 NM_153707.2 323 cGa/cAa 0 0.562 AAGTGCAGGTCGGCAGGACTG +SPATA31E1 286234 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 90501762 90501762 + missense_variant Missense_Mutation SNP G G A TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 203 27 ENST00000325643.5:c.2360G>A p.Arg787His p.R787H ENST00000325643 NM_178828.4 787 cGc/cAc 0 0.577 CCTGTGCGTCGCTCCTGGCTC +ABCA2 20 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 139912486 139912486 + missense_variant Missense_Mutation SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 50 11 ENST00000341511.6:c.2035G>A p.Asp679Asn p.D679N ENST00000341511 NM_212533.2 679 Gat/Aat 0 0.662 TCCACCACATCGTGCCCCACA +NDOR1 27158 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 140110623 140110623 + synonymous_variant Silent SNP A A G TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 141 20 ENST00000371521.4:c.1659A>G p.Ala553= p.A553= ENST00000371521 NM_001144026.1 553 gcA/gcG 0 0.642 GCCAGGGTGCATACTTCTACC +LCLAT1 253558 broad.mit.edu;ucsc.edu GRCh37 2 30863465 30863465 + missense_variant Missense_Mutation SNP A A G TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 157 19 ENST00000309052.4:c.1225A>G p.Asn409Asp p.N409D ENST00000309052 NM_182551.3 409 Aat/Gat 0 0.343 GCCACATTTAAATTCAAAGAA +PDE1A 5136 broad.mit.edu;ucsc.edu GRCh37 2 183095781 183095781 + stop_gained Nonsense_Mutation SNP A A C TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 255 39 ENST00000435564.1:c.543T>G p.Tyr181Ter p.Y181* ENST00000435564 NM_001258312.1 181 taT/taG 0 0.323 TAAACAGTTCATAAATCATAA +MIB2 142678 broad.mit.edu;ucsc.edu GRCh37 1 1563188 1563188 + synonymous_variant Silent SNP C C T TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 12 8 ENST00000505820.2:c.2004C>T p.Arg668= p.R668= ENST00000505820 668 cgC/cgT 0 0.692 TGTGTGAGCGCGGCTGTGACG +CELSR1 9620 broad.mit.edu;ucsc.edu GRCh37 22 46929761 46929761 + missense_variant Missense_Mutation SNP C C T rs145654024 TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 359 35 ENST00000262738.3:c.3307G>A p.Asp1103Asn p.D1103N ENST00000262738 NM_014246.1 1103 Gac/Aac 0 0.607 ATCTGGAAGTCGGGCAGCACA +TP53 7157 broad.mit.edu;hgsc.bcm.edu GRCh37 17 7577101 7577101 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 90 ENST00000269305.4:c.837delG p.Arg280GlufsTer65 p.R280Efs*65 ENST00000269305 NM_001126112.2 279 ggG/gg 0 0.547 GCCGGTCTCTCCCAGGACAGG +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76907649 76907650 + frameshift_variant Frame_Shift_Del DEL TC TC - TCGA-E1-5302-01 TCGA-E1-5302-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 180 ENST00000373344.5:c.4511_4512delGA p.Arg1504GlnfsTer5 p.R1504Qfs*5 ENST00000373344 NM_000489.3 1504 cGA/c 0 0.386 CAATACGTTTTCGTCTCTCTTC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578406 7578406 + missense_variant Missense_Mutation SNP C C T rs28934578 TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 62 28 ENST00000269305.4:c.524G>A p.Arg175His p.R175H ENST00000269305 NM_001126112.2 175 cGc/cAc 0 0.652 GTGGGGGCAGCGCCTCACAAC +TP53 7157 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 7578467 7578467 + missense_variant Missense_Mutation SNP T T G TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 48 45 ENST00000269305.4:c.463A>C p.Thr155Pro p.T155P ENST00000269305 NM_001126112.2 155 Acc/Ccc 0 0.612 CGGACGCGGGTGCCGGGCGGG +KRT33A 3883 hgsc.bcm.edu;broad.mit.edu GRCh37 17 39502881 39502881 + missense_variant Missense_Mutation SNP G G A rs148488457 TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 89 6 ENST00000007735.3:c.916C>T p.Arg306Cys p.R306C ENST00000007735 NM_004138.3 306 Cgc/Tgc 0 0.587 GAGCTGTAGCGGGCCTCGCTC +DCC 1630 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 51025871 51025871 + missense_variant Missense_Mutation SNP T T C TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 124 85 ENST00000442544.2:c.4102T>C p.Ser1368Pro p.S1368P ENST00000442544 NM_005215.3 1368 Tct/Cct 0 0.443 ACCACTTTTGTCTCAGCCAGG +PTPN14 5784 hgsc.bcm.edu;broad.mit.edu GRCh37 1 214625279 214625279 + missense_variant Missense_Mutation SNP C C G TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 134 9 ENST00000366956.5:c.213G>C p.Gln71His p.Q71H ENST00000366956 NM_005401.4 71 caG/caC 0 0.458 ATCGTGCTTGCTGGCTCTTGC +KIF16B 55614 hgsc.bcm.edu;broad.mit.edu GRCh37 20 16360692 16360692 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 199 12 ENST00000408042.1:c.1955G>A p.Arg652His p.R652H ENST00000408042 NM_001199866.1 652 cGc/cAc 0 0.522 CTCCTGCTTGCGAATCTGGAG +PPP1R16B 26051 hgsc.bcm.edu;broad.mit.edu GRCh37 20 37547124 37547124 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 5 ENST00000299824.1:c.1519G>A p.Ala507Thr p.A507T ENST00000299824 NM_015568.2 507 Gcc/Acc 0 0.612 CAGCAGCATGGCCAGGACGGG +DSCAM 1826 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 41496241 41496241 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 66 ENST00000400454.1:c.3577G>A p.Ala1193Thr p.A1193T ENST00000400454 NM_001271534.1 1193 Gcg/Acg 0 0.597 TTCACACCCGCGGGAGGACCT +TMPRSS2 7113 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 21 42845269 42845269 + synonymous_variant Silent SNP G G A TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 9 7 ENST00000398585.3:c.993C>T p.Ala331= p.A331= ENST00000398585 NM_001135099.1 331 gcC/gcT 0 0.692 CGCAGTGGGCGGCTGTCACGA +REL 5966 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 61149057 61149057 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 10 ENST00000295025.8:c.1247C>T p.Ala416Val p.A416V ENST00000295025 NM_002908.2 416 gCc/gTc 0 0.502 TCATCAGTGGCCCACCCCACC +DYNC1I2 1781 hgsc.bcm.edu;broad.mit.edu GRCh37 2 172586272 172586272 + missense_variant Missense_Mutation SNP T T C TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 141 10 ENST00000397119.3:c.1445T>C p.Ile482Thr p.I482T ENST00000397119 NM_001378.2 482 aTc/aCc 0 0.398 ATCACTGGCATCCATTGTCAT +NBEAL1 65065 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 204003429 204003429 + missense_variant Missense_Mutation SNP G G C TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 246 24 ENST00000449802.1:c.4719G>C p.Gln1573His p.Q1573H ENST00000449802 NM_001114132.1 1573 caG/caC 0 0.373 CTCAAATTCAGATCCAGTTGC +NDUFS1 4719 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 206991481 206991481 + missense_variant Missense_Mutation SNP C C G TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 181 18 ENST00000455934.2:c.2014G>C p.Asp672His p.D672H ENST00000455934 NM_001199984.1 672 Gat/Cat 0 0.393 CCTTCAATATCATCATATCGA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113113 209113113 + missense_variant Missense_Mutation SNP G G A rs121913499 TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 76 53 ENST00000345146.2:c.394C>T p.Arg132Cys p.R132C ENST00000345146 NM_005896.2 132 Cgt/Tgt 0 0.398 TAAGCATGACGACCTATGATG +VIL1 7429 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 219299321 219299321 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 81 68 ENST00000248444.5:c.1573G>A p.Ala525Thr p.A525T ENST00000248444 NM_007127.2 525 Gcc/Acc 0 0.572 GGGAACTGGCGCCAACAACAC +MAB21L2 10586 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 151505024 151505024 + missense_variant Missense_Mutation SNP G G C TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 73 8 ENST00000317605.4:c.843G>C p.Glu281Asp p.E281D ENST00000317605 NM_006439.4 281 gaG/gaC 0 0.627 TGCTGTACGAGTGCGAGAAAC +CTSO 1519 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 156847189 156847189 + stop_lost Nonstop_Mutation SNP C C G TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 9 ENST00000433477.3:c.965G>C p.Ter322SerextTer12 p.*322Sext*12 ENST00000433477 NM_001334.2 322 tGa/tCa 0 0.308 CCCAACATGTCACACAAATAT +DNAH5 1767 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 13769245 13769245 + missense_variant,splice_region_variant Missense_Mutation SNP C C G TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 235 68 ENST00000265104.4:c.9721G>C p.Val3241Leu p.V3241L ENST00000265104 NM_001369.2 3241 Gtc/Ctc 0 0.413 TCTTTTAAGACCTAATTCAAT +KIAA0825 285600 hgsc.bcm.edu;broad.mit.edu GRCh37 5 93856210 93856210 + missense_variant Missense_Mutation SNP T T G TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 6 ENST00000329378.7:c.713A>C p.Asp238Ala p.D238A ENST00000329378 NM_173665.2 238 gAt/gCt 0 0.308 AGCTATTACATCTAAATTTGA +LRRC16A 55604 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 25606448 25606448 + missense_variant Missense_Mutation SNP G G C TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 23 8 ENST00000329474.6:c.3794G>C p.Ser1265Thr p.S1265T ENST00000329474 NM_001173977.1 1265 aGt/aCt 0 0.592 CCCAAACCCAGTCTGGCAGCA +CLIC1 1192 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 31698750 31698750 + missense_variant Missense_Mutation SNP T T C TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 20 ENST00000375780.2:c.595A>G p.Ile199Val p.I199V ENST00000375780 NM_001287593.1 199 Atc/Gtc 0 0.582 GCCTCGGGGATGGTGAATCCC +BTNL2 56244 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 32370727 32370727 + missense_variant Missense_Mutation SNP C C T rs79379254 TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 24 24 ENST00000454136.3:c.694G>A p.Val232Ile p.V232I ENST00000454136 232 Gtc/Atc 0 0.582 AGGCTGATGACCGACCCCTTC +ABCB1 5243 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 7 87183089 87183089 + synonymous_variant Silent SNP T T C TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 67 49 ENST00000265724.3:c.987A>G p.Gly329= p.G329= ENST00000265724 NM_000927.4 329 ggA/ggG 0 0.378 TGAGTACTTGTCCAATAGAAT +TAS2R4 50832 hgsc.bcm.edu;broad.mit.edu GRCh37 7 141478489 141478489 + missense_variant Missense_Mutation SNP C C G TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 258 20 ENST00000247881.2:c.201C>G p.Ile67Met p.I67M ENST00000247881 NM_016944.1 67 atC/atG 0 0.443 TGAACACCATCTACTTCGTCT +PLAA 9373 hgsc.bcm.edu;broad.mit.edu GRCh37 9 26905915 26905915 + missense_variant Missense_Mutation SNP C C T TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 64 6 ENST00000397292.3:c.1982G>A p.Arg661Lys p.R661K ENST00000397292 NM_001031689.2 661 aGg/aAg 0 0.458 GCAAAAAGTCCTGAGAGCAAG +AGPAT3 56894 broad.mit.edu;ucsc.edu GRCh37 21 45379705 45379705 + missense_variant Missense_Mutation SNP G G A TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 5 ENST00000398063.2:c.143G>A p.Arg48His p.R48H ENST00000398063 NM_001037553.1 48 cGc/cAc 0 0.667 CTCTACCGCCGCCTCAACTGC +PURG 29942 broad.mit.edu;ucsc.edu GRCh37 8 30889490 30889490 + missense_variant Missense_Mutation SNP T T C TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 58 ENST00000475541.1:c.809A>G p.Asp270Gly p.D270G ENST00000475541 NM_013357.2 270 gAc/gGc 0 0.438 CCTTTTATTGTCCACTCTGAA +ATRX 546 broad.mit.edu;hgsc.bcm.edu GRCh37 X 76919037 76919038 + frameshift_variant Frame_Shift_Ins INS - - T TCGA-CS-6666-01 TCGA-CS-6666-10 Untested Somatic Phase_I WXS none Illumina GAIIx 3 21 ENST00000373344.5:c.3953dupA p.Asn1318LysfsTer6 p.N1318Kfs*6 ENST00000373344 NM_000489.3 1318 aat/aaAt 0 0.351 AATTGACTTGATTTTTTGCTTC +DDX24 57062 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 14 94528925 94528925 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 77 23 ENST00000330836.5:c.761C>T p.Ala254Val p.A254V ENST00000330836 NM_020414.3 254 gCg/gTg 0 0.458 CTGCAACACCGCATGAATCAT +NF1 4763 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 29663350 29663350 + splice_acceptor_variant Splice_Site SNP G G C TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 72 6 ENST00000358273.4:c.6007-1G>C p.X2003_splice ENST00000358273 NM_001042492.2 0 0.328 TCTTCAACTAGATTACAGATC +CACNA1G 8913 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 48703623 48703623 + synonymous_variant Silent SNP A A G TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 32 13 ENST00000359106.5:c.6645A>G p.Leu2215= p.L2215= ENST00000359106 NM_018896.4 2215 ttA/ttG 0 0.642 GAAGCAGCTTAGAGTTGGACA +SSTR2 6752 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 71166516 71166516 + missense_variant Missense_Mutation SNP C C G TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 54 11 ENST00000357585.2:c.1058C>G p.Thr353Ser p.T353S ENST00000357585 NM_001050.2 353 aCc/aGc 0 0.547 CTGAATGAGACCACGGAGACC +VAV1 7409 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 19 6833209 6833209 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 16 ENST00000602142.1:c.1523C>T p.Pro508Leu p.P508L ENST00000602142 NM_005428.3 508 cCg/cTg 0 0.438 AACATCTATCCGGAGAATGCC +OR7A5 26659 hgsc.bcm.edu;ucsc.edu GRCh37 19 14938560 14938560 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 30 13 ENST00000322301.3:c.494G>A p.Arg165Gln p.R165Q ENST00000322301 165 cGg/cAg 0 0.443 GAAGGACAGCCGTACTACCAT +FLG 2312 hgsc.bcm.edu;broad.mit.edu GRCh37 1 152282972 152282972 + missense_variant Missense_Mutation SNP C C G TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 211 17 ENST00000368799.1:c.4390G>C p.Gly1464Arg p.G1464R ENST00000368799 NM_002016.1 1464 Gga/Cga 0 0.572 CCTTGTCTTCCTCCAGTGCTG +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 59 38 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +OR5AC2 81050 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 97806608 97806608 + missense_variant Missense_Mutation SNP G G A TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 31 24 ENST00000358642.2:c.592G>A p.Ala198Thr p.A198T ENST00000358642 NM_054106.1 198 Gca/Aca 0 0.289 ATCTATTAACGCACTAATGAT +RETNLB 84666 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 108475916 108475916 + synonymous_variant Silent SNP G G T TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 19 4 ENST00000295755.6:c.117C>A p.Leu39= p.L39= ENST00000295755 NM_032579.2 39 ctC/ctA 0 0.498 CTAGACTGTTGAGAACATCCT +MRPL3 11222 hgsc.bcm.edu;broad.mit.edu GRCh37 3 131190117 131190117 + synonymous_variant Silent SNP A A C TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 83 4 ENST00000264995.3:c.636T>G p.Gly212= p.G212= ENST00000264995 NM_007208.3 212 ggT/ggG 0 0.403 GAAAACCTTTACCAATACTGA +ALPK1 80216 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 113352721 113352721 + missense_variant Missense_Mutation SNP C C A TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 46 18 ENST00000458497.1:c.2018C>A p.Pro673His p.P673H ENST00000458497 NM_001102406.1 673 cCc/cAc 0 0.493 CCCTTGACACCCTTCTCGCCT +FSTL5 56884 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 162577517 162577517 + missense_variant Missense_Mutation SNP T T C TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 25 14 ENST00000306100.5:c.857A>G p.Asn286Ser p.N286S ENST00000306100 NM_001128427.2 286 aAt/aGt 0 0.353 TAGAATAATATTGTTCCTTTT +FSTL5 56884 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 4 162577525 162577525 + missense_variant Missense_Mutation SNP T T A rs61746784 TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 29 15 ENST00000306100.5:c.849A>T p.Lys283Asn p.K283N ENST00000306100 NM_001128427.2 283 aaA/aaT 0 0.353 TATTGTTCCTTTTCCAGATAA +MCC 4163 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 112439958 112439958 + synonymous_variant Silent SNP G G T rs142794653 byFrequency TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 117 31 ENST00000408903.3:c.1122C>A p.Ser374= p.S374= ENST00000408903 NM_001085377.1 374 tcC/tcA 0 0.572 CCTCGGCCACGGAGAGGCTGC +UBLCP1 134510 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 158697549 158697549 + missense_variant Missense_Mutation SNP C C A TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 85 9 ENST00000296786.6:c.346C>A p.Leu116Met p.L116M ENST00000296786 NM_145049.3 116 Ctg/Atg 0 0.333 AGAAAACCTACTGAAAATTTC +RREB1 6239 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 7229828 7229828 + missense_variant Missense_Mutation SNP C C T TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 264 47 ENST00000379938.2:c.1496C>T p.Ala499Val p.A499V ENST00000379938 NM_001003700.1 499 gCg/gTg 0 0.642 CCACTGCAGGCGATCTTCAAG +GPR115 221393 hgsc.bcm.edu;broad.mit.edu GRCh37 6 47682356 47682356 + missense_variant Missense_Mutation SNP A A G TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 337 22 ENST00000283303.2:c.1375A>G p.Ile459Val p.I459V ENST00000283303 NM_153838.3 459 Ata/Gta 0 0.458 GTGGTTTATCATAGGCTCTCA +KIT 3815 broad.mit.edu;ucsc.edu GRCh37 4 55573431 55573431 + missense_variant Missense_Mutation SNP T T A TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 20 ENST00000288135.5:c.1093T>A p.Ser365Thr p.S365T ENST00000288135 NM_000222.2 365 Tct/Act 0 0.403 TTATCCCAAGTCTGAGAATGA +OR4M1 441670 broad.mit.edu;ucsc.edu GRCh37 14 20248557 20248557 + missense_variant Missense_Mutation SNP G G T TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 288 30 ENST00000315957.4:c.76G>T p.Val26Phe p.V26F ENST00000315957 NM_001005500.1 26 Gtc/Ttc 0 0.388 GGTCCAACTAGTCCTATTTGT +RUFY2 55680 broad.mit.edu;ucsc.edu GRCh37 10 70141155 70141155 + missense_variant,splice_region_variant Missense_Mutation SNP T T C TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 122 77 ENST00000388768.2:c.1046A>G p.Asp349Gly p.D349G ENST00000388768 NM_017987.4 349 gAt/gGt 0 0.358 ATTCTCTACATCCTGCAATTT +FRMD4B 23150 broad.mit.edu;hgsc.bcm.edu GRCh37 3 69230517 69230518 + frameshift_variant Frame_Shift_Del DEL TT TT - TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 11 ENST00000398540.3:c.2383_2384delAA p.Lys795GlufsTer21 p.K795Efs*21 ENST00000398540 NM_015123.1 795 AAg/g 0 0.446 CTCCTGACTCTTTGAGTAAACA +C8orf47 203111 broad.mit.edu;hgsc.bcm.edu GRCh37 8 99101783 99101784 + frameshift_variant Frame_Shift_Ins INS - - A TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 28 10 ENST00000318528.3:c.541dupA p.Thr181AsnfsTer12 p.T181Nfs*12 ENST00000318528 NM_173549.2 180 caa/cAaa 0 0.52 TGAGAATCCACAAACTGCTGCA +SS18 6760 broad.mit.edu;hgsc.bcm.edu GRCh37 18 23632625 23632626 + frameshift_variant Frame_Shift_Del DEL AT AT - TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 125 32 ENST00000415083.2:c.569_570delAT p.Tyr190TrpfsTer49 p.Y190Wfs*49 ENST00000415083 NM_001007559.1 190 tAT/t 0 0.426 GTCTGGGACCATAGTTTCCCAT +FUBP1 8880 broad.mit.edu GRCh37 1 78444677 78444678 + frameshift_variant Frame_Shift_Del DEL AT AT - TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 7 10 ENST00000370768.2:c.11_12delAT p.Tyr4PhefsTer24 p.Y4Ffs*24 ENST00000370768 NM_003902.3 4 tAT/t 0 0.559 GCACTGTTGAATAGTCTGCCAT +CIC 23152 ucsc.edu GRCh37 19 42791721 42791721 + missense_variant Missense_Mutation SNP C C G TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 3 ENST00000575354.2:c.607C>G p.Pro203Ala p.P203A ENST00000575354 NM_015125.3 203 Ccc/Gcc 0 0.627 CATCCGGCGGCCCATGAATGC +CIC 23152 ucsc.edu GRCh37 19 42791790 42791790 + missense_variant Missense_Mutation SNP G G T TCGA-DU-6397-01 TCGA-DU-6397-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 3 ENST00000575354.2:c.676G>T p.Asp226Tyr p.D226Y ENST00000575354 NM_015125.3 226 Gac/Tac 0 0.612 TCCCAACCAGGACAACCGGAC +ANKRD30A 91074 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 10 37419199 37419199 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 43 10 ENST00000361713.1:c.235G>A p.Val79Ile p.V79I ENST00000361713 NM_052997.2 79 Gta/Ata 0 0.423 TATAAATCTCGTAGATGTGTA +FOXM1 2305 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 2968215 2968215 + synonymous_variant Silent SNP C C T TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 105 22 ENST00000342628.2:c.1995G>A p.Thr665= p.T665= ENST00000342628 NM_202002.2 665 acG/acA 0 0.592 TGGCTGGGGGCGTGAGCCTCC +USP30 84749 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 109519737 109519737 + splice_acceptor_variant Splice_Site SNP G G A TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 128 31 ENST00000257548.5:c.781-1G>A p.X261_splice ENST00000257548 NM_032663.3 0 0.428 TCATGCTGTAGGGTCACCCAT +CYP1A2 1544 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 75042314 75042314 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 39 15 ENST00000343932.4:c.235C>T p.Arg79Cys p.R79C ENST00000343932 NM_000761.3 79 Cgc/Tgc 0 0.672 CCTGCAGATCCGCATTGGCTC +USP31 57478 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 23080559 23080559 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 150 16 ENST00000219689.7:c.2867G>A p.Arg956His p.R956H ENST00000219689 NM_020718.3 956 cGc/cAc 0 0.552 GTTCAATCTGCGGGTGTCCGA +PRSS54 221191 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 16 58324928 58324928 + missense_variant Missense_Mutation SNP G G T TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 76 18 ENST00000219301.4:c.198C>A p.His66Gln p.H66Q ENST00000219301 NM_001080492.1 66 caC/caA 0 0.607 CGAAAGCCAGGTGTGTGTACT +FUBP1 8880 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 78429792 78429792 + stop_gained Nonsense_Mutation SNP A A T TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 99 29 ENST00000370768.2:c.996T>A p.Cys332Ter p.C332* ENST00000370768 NM_003902.3 332 tgT/tgA 0 0.328 CAGCATGTTGACATCGGTCTG +CFH 3075 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 196648911 196648911 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 34 6 ENST00000367429.4:c.778C>T p.Pro260Ser p.P260S ENST00000367429 NM_000186.3 260 Cct/Tct 0 0.294 GCGTCCGTTGCCTTCATGTGA +CNST 163882 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 246810446 246810446 + missense_variant Missense_Mutation SNP A A G TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 42 14 ENST00000366513.4:c.943A>G p.Lys315Glu p.K315E ENST00000366513 NM_152609.2 315 Aaa/Gaa 0 0.388 TTTAGAGAGTAAAACTTGTCT +CCT7 10574 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 73478419 73478419 + stop_gained Nonsense_Mutation SNP C C G TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 95 30 ENST00000258091.5:c.1269C>G p.Tyr423Ter p.Y423* ENST00000258091 NM_006429.3 423 taC/taG 0 0.517 TGCGGGATTACTCAAGGACTA +IDH1 3417 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 2 209113112 209113112 + missense_variant Missense_Mutation SNP C C T rs121913500 TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 16 ENST00000345146.2:c.395G>A p.Arg132His p.R132H ENST00000345146 NM_005896.2 132 cGt/cAt 0 0.393 ATAAGCATGACGACCTATGAT +SRD5A1 6715 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 6663021 6663021 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 84 25 ENST00000274192.5:c.655G>A p.Ala219Thr p.A219T ENST00000274192 NM_001047.2 219 Gcg/Acg 0 0.408 TGTCCAAGGCGCGGCTTTTGC +GRIA1 2890 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 153175109 153175109 + intron_variant Intron SNP T T C TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 51 10 ENST00000518783.1:c.2415+814T>C *805* ENST00000518783 NM_001258021.1 0 0.473 CAAATGGTGGTACGATAAAGG +SLC34A1 6569 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 176825109 176825109 + missense_variant Missense_Mutation SNP G G A TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 21 ENST00000324417.5:c.1742G>A p.Arg581His p.R581H ENST00000324417 NM_003052.4 581 cGc/cAc 0 0.667 TTCCTGCCTCGCTGGATGCAC +SCAND3 114821 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 28540669 28540669 + synonymous_variant Silent SNP G G A TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 87 19 ENST00000452236.2:c.2997C>T p.Cys999= p.C999= ENST00000452236 NM_052923.1 999 tgC/tgT 0 0.328 gatgaatgaagcaatgtgttg +TFAP2B 7021 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 50807962 50807962 + missense_variant Missense_Mutation SNP C C A TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 87 12 ENST00000393655.3:c.1034C>A p.Thr345Lys p.T345K ENST00000393655 NM_003221.3 345 aCa/aAa 0 0.517 CGGCAGCACACAGACCCGAGT +LAMA2 3908 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 6 129823889 129823889 + missense_variant Missense_Mutation SNP C C T TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 9 ENST00000421865.2:c.8330C>T p.Ala2777Val p.A2777V ENST00000421865 NM_001079823.1 2777 gCa/gTa 0 0.408 ATTGCAATTGCATTTGATGAC +CLIC2 1193 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 X 154508571 154508571 + stop_gained Nonsense_Mutation SNP A A C TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 16 20 ENST00000369449.2:c.449T>G p.Leu150Ter p.L150* ENST00000369449 NM_001289.4 150 tTa/tGa 0 0.408 TGGGGTGTTTAAGTAGTCATC +CAMK2D 817 broad.mit.edu;ucsc.edu GRCh37 4 114436309 114436309 + synonymous_variant Silent SNP G G A TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 70 16 ENST00000342666.5:c.735C>T p.Ala245= p.A245= ENST00000342666 245 gcC/gcT 0 0.398 TGAGGTCTTTGGCTTCAGGAG +DHX35 60625 broad.mit.edu;ucsc.edu GRCh37 20 37634881 37634881 + synonymous_variant Silent SNP C C T TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 263 65 ENST00000252011.3:c.1104C>T p.Tyr368= p.Y368= ENST00000252011 NM_021931.3 368 taC/taT 0 0.522 TCCGAGCCTACAATCCCAGGA +PIK3CA 5290 broad.mit.edu GRCh37 3 178916938 178916940 + inframe_deletion In_Frame_Del DEL GAA GAA - TCGA-HT-7620-01 TCGA-HT-7620-10 Untested Somatic Phase_I WXS none Illumina GAIIx 38 9 ENST00000263967.3:c.328_330delGAA p.Glu110del p.E110del ENST00000263967 NM_006218.2 109 GAA/- 0 0.34 AGGCAACCGTGAAGAAAAGATCC +NLRP14 338323 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 11 7064302 7064302 + missense_variant Missense_Mutation SNP G G A TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 209 27 ENST00000299481.4:c.1045G>A p.Ala349Thr p.A349T ENST00000299481 NM_176822.3 349 Gcc/Acc 0 0.428 TAAGAGGTGGGCCATGAAAGT +NCKAP1L 3071 hgsc.bcm.edu;ucsc.edu GRCh37 12 54914539 54914539 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 495 231 ENST00000293373.6:c.1687C>T p.Arg563Cys p.R563C ENST00000293373 NM_005337.4 563 Cgt/Tgt 0 0.463 TGCCATGTTGCGTTATGCCAT +LGR5 8549 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 12 71978453 71978453 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 187 95 ENST00000266674.5:c.2663C>T p.Pro888Leu p.P888L ENST00000266674 NM_001277226.1 888 cCa/cTa 0 0.458 GTGCCATCACCAGCTTATCCA +IDH2 3418 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 15 90631838 90631838 + missense_variant Missense_Mutation SNP C C T rs121913503 TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 82 51 ENST00000330062.3:c.515G>A p.Arg172Lys p.R172K ENST00000330062 NM_002168.2 172 aGg/aAg 0 0.632 ATGGGCGTGCCTGCCAATGGT +KRT36 8689 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 17 39642800 39642800 + missense_variant Missense_Mutation SNP G G A TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 27 5 ENST00000328119.6:c.1232C>T p.Thr411Met p.T411M ENST00000328119 NM_003771.4 411 aCg/aTg 0 0.577 CTTGCATGCCGTGGCACAAGG +CDH20 28316 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 59174700 59174700 + synonymous_variant Silent SNP G G A TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 144 15 ENST00000262717.4:c.924G>A p.Glu308= p.E308= ENST00000262717 308 gaG/gaA 0 0.433 TCAATGCAGAGATGAAATATA +SERPINB3 6317 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 18 61323264 61323264 + missense_variant Missense_Mutation SNP A A C TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 131 29 ENST00000283752.5:c.800T>G p.Met267Arg p.M267R ENST00000283752 NM_006919.2 267 aTg/aGg 0 0.378 TGTCCATTCCATCAATTTCTC +GBP5 115362 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 89728016 89728016 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 80 66 ENST00000343435.5:c.1534G>A p.Glu512Lys p.E512K ENST00000343435 NM_001134486.2 512 Gag/Aag 0 0.463 ATCATTTGCTCGTTCTGCCTT +PCNXL2 80003 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 1 233344354 233344354 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 93 14 ENST00000258229.9:c.2773G>A p.Ala925Thr p.A925T ENST00000258229 NM_014801.3 925 Gcc/Acc 0 0.423 CTGGCTTTGGCCCCTGTATCA +PCSK2 5126 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 20 17434533 17434533 + synonymous_variant Silent SNP C C T TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 152 26 ENST00000262545.2:c.1032C>T p.Asp344= p.D344= ENST00000262545 NM_002594.3 344 gaC/gaT 0 0.597 CCCTGTACGACGAGAGCTGCT +PI4KA 5297 hgsc.bcm.edu;broad.mit.edu GRCh37 22 21115635 21115635 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 127 11 ENST00000255882.6:c.2748G>A p.Met916Ile p.M916I ENST00000255882 NM_058004.3 916 atG/atA 0 0.368 AGTAGCAGAACATTACCTGGA +SPECC1L 23384 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 22 24717648 24717648 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 187 86 ENST00000314328.9:c.700C>T p.His234Tyr p.H234Y ENST00000314328 NM_015330.4 234 Cac/Tac 0 0.438 TATTATGGCTCACCAGCCGAC +C2orf71 388939 hgsc.bcm.edu;broad.mit.edu GRCh37 2 29294007 29294007 + missense_variant Missense_Mutation SNP G G A TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 91 41 ENST00000331664.5:c.3121C>T p.Pro1041Ser p.P1041S ENST00000331664 NM_001029883.2 1041 Cca/Tca 0 0.687 GTGGTGGGTGGGCTTAGCACC +RIF1 55183 hgsc.bcm.edu;broad.mit.edu GRCh37 2 152293371 152293371 + missense_variant Missense_Mutation SNP C C A TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 120 11 ENST00000243326.5:c.1226C>A p.Thr409Asn p.T409N ENST00000243326 409 aCt/aAt 0 0.418 GCCCCGGGAACTCCCCGAATG +CHRNA1 1134 hgsc.bcm.edu;broad.mit.edu GRCh37 2 175614763 175614763 + missense_variant Missense_Mutation SNP C C T rs137852804 TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 148 9 ENST00000261007.5:c.988G>A p.Val330Ile p.V330I ENST00000261007 NM_001039523.2 330 Gtc/Atc 0 0.537 GAGGCAATGACGAACACCATG +PLXNB1 5364 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 3 48461210 48461210 + missense_variant Missense_Mutation SNP G G C TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 14 7 ENST00000358536.4:c.2485C>G p.Pro829Ala p.P829A ENST00000358536 NM_002673.4 829 Cca/Gca 0 0.701 ATGGCCCCTGGGAAAGTGGTG +NIPBL 25836 hgsc.bcm.edu;broad.mit.edu GRCh37 5 37008732 37008732 + stop_gained Nonsense_Mutation SNP C C G TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 224 12 ENST00000282516.8:c.4328C>G p.Ser1443Ter p.S1443* ENST00000282516 NM_133433.3 1443 tCa/tGa 0 0.274 CAGGTATTCTCAAGATATGAA +C5orf34 375444 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 5 43506030 43506030 + stop_gained Nonsense_Mutation SNP C C T TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 269 22 ENST00000306862.2:c.752G>A p.Trp251Ter p.W251* ENST00000306862 NM_198566.2 251 tGg/tAg 0 0.408 AGGATATTTCCATTCCTCTGG +ADRB2 154 hgsc.bcm.edu;broad.mit.edu GRCh37 5 148206922 148206922 + synonymous_variant Silent SNP C C T TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 288 20 ENST00000305988.4:c.528C>T p.Ala176= p.A176= ENST00000305988 NM_000024.5 176 gcC/gcT 0 0.537 GGTACCGGGCCACCCACCAGG +GRM1 2911 hgsc.bcm.edu;broad.mit.edu GRCh37 6 146720659 146720659 + synonymous_variant Silent SNP G G C TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 128 9 ENST00000361719.2:c.2484G>C p.Gly828= p.G828= ENST00000361719 828 ggG/ggC 0 0.488 TGGCTCTGGGGTGCATGTTCA +RALYL 138046 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 8 85774590 85774590 + missense_variant Missense_Mutation SNP G G A TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 49 7 ENST00000517638.1:c.512G>A p.Arg171His p.R171H ENST00000517638 NM_001100391.1 171 cGt/cAt 0 0.507 CCGCTGAAGCGTCCCAGAGTG +KLF4 9314 hgsc.bcm.edu;broad.mit.edu;ucsc.edu GRCh37 9 110249405 110249405 + missense_variant Missense_Mutation SNP G G A TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 177 88 ENST00000374672.4:c.1168C>T p.Arg390Trp p.R390W ENST00000374672 NM_004235.4 390 Cgg/Tgg 0 0.587 GTCCTTTTCCGGGGCCACGAT +CHMP1A 5119 broad.mit.edu;ucsc.edu GRCh37 16 89715806 89715806 + missense_variant Missense_Mutation SNP C C T TCGA-DH-5141-01 TCGA-DH-5141-10 Untested Somatic Phase_I WXS none Illumina GAIIx 151 70 ENST00000397901.3:c.205G>A p.Val69Ile p.V69I ENST00000397901 NM_002768.4 69 Gta/Ata 0 0.597 ACTGCGTCTACGCGGGACGCC
--- a/test-data/test/clin Wed May 14 06:46:42 2025 +0000 +++ b/test-data/test/clin Tue Jun 24 05:55:40 2025 +0000 @@ -1,931 +1,931 @@ -sample,Crizotinib,Erlotinib,Irinotecan,Lapatinib,Nilotinib,Paclitaxel,Palbociclib,PD-0325901,PLX4720,Selumetinib,Sorafenib,Topotecan -target_dataset:SNU-503,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -target_dataset:MOLP-2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -target_dataset:Hs 695T,0.0137798414144127,0.00279596883187221,0.321048617899494,0.0123784672647789,0.00727865041898364,0.425845588447356,0.0648429496552876,0.344708384078938,0.0802339062256618,0.16073821868368,0,0.258897062513722 -target_dataset:SNU-C1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -target_dataset:COV434,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -target_dataset:Becker,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -target_dataset:TO 175.T,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA 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-target_dataset:DMS 79,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -target_dataset:HEL 92.1.7,0,0.0177813221317003,NA,0.00334915945898784,0.018735464800044,0.633499797060302,0,0.0495097744571229,0.0114121971711227,0.0226248375526365,0.0281875000000003,0.343565318062566 -target_dataset:BT-20,0.00538540755712196,0.135831213554948,0.329299675326338,0.0577058433906533,0.0528750000000003,0.62499968838294,0,NA,0.00728214637996323,0.017985394405743,0.0823599999999969,0.252513220832068 -target_dataset:RPMI-7951,0.0663138489949516,0.0109625104648995,NA,0.0101707509831928,NA,0.890655493157463,NA,0.197593848525163,0.0418312338126707,0.122791705494357,0,0.412802134288002 -target_dataset:HEK TE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -target_dataset:GI-1,0.0554844949909191,0.0218896481720671,NA,0.0263227432457074,NA,0.715916289235424,NA,0.101254762209423,0.0358484185754373,0.0446274842637695,0.0494678240079706,0.268284182547972 -target_dataset:TE 159.T,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -target_dataset:NCI-H1355,0.0397847556892167,0.170404319767082,NA,0.162261593072831,0.00955820110095166,0.604401253355353,0.114961394506362,0.412695825443437,0.050931889329994,0.299147129365416,NA,0.0916456708468782 -target_dataset:OC 316,0.0132017395355424,0.0341578512748455,0.393795090700988,0.0467524125114623,0.0208361362367381,0.826627284142302,0.00930811103759723,0.069047441593875,0.0240980175560026,0.0239579507029604,0,0.392025882240121 -target_dataset:HuH-28,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -target_dataset:SNU-878,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -target_dataset:H4,0.111348578072488,0.0303917922741951,NA,0,0.025775362541623,0.654294925658615,0.096600786325714,0.00108137329107788,0.0357219845034107,0,0.00708750000000025,0.306452218614489 -target_dataset:Daudi,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 24 05:55:40 2025 +0000 @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tables> + <table name="cbioportal" comment_char="#"> + <columns>value, name, version</columns> + <file path="tool-data/flexynesis.loc" /> + </table> +</tables>