TCGA Pan-Cancer Track Settings
 
TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)   (All Phenotype and Literature tracks)

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 KICH  Kidney Chromophobe   Data format 
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 All Cancers  All TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)   Data format 
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 ACC  Adrenocortical carcinoma   Data format 
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 BLCA  Bladder Urothelial Carcinoma   Data format 
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 BRCA  Breast invasive carcinoma   Data format 
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 CESC  Cervical squamous cell carcinoma and endocervical adenocarcinoma   Data format 
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 CHOL  Cholangiocarcinoma   Data format 
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 COAD  Colon adenocarcinoma   Data format 
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 DLBC  Lymphoid Neoplasm Diffuse Large B-cell Lymphoma   Data format 
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 ESCA  Esophageal carcinoma   Data format 
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 GBM  Glioblastoma multiforme   Data format 
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 HNSC  Head and Neck squamous cell carcinoma   Data format 
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 KIRC  Kidney renal clear cell carcinoma   Data format 
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 KIRP  Kidney renal papillary cell carcinoma   Data format 
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 LAML  Acute Myeloid Leukemia   Data format 
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 LGG  Brain Lower Grade Glioma   Data format 
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 LIHC  Liver hepatocellular carcinoma   Data format 
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 LUAD  Lung adenocarcinoma   Data format 
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 LUSC  Lung squamous cell carcinoma   Data format 
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 MESO  Mesothelioma   Data format 
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 OV  Ovarian serous cystadenocarcinoma   Data format 
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 PAAD  Pancreatic adenocarcinoma   Data format 
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 PCPG  Pheochromocytoma and Paraganglioma   Data format 
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 PRAD  Prostate adenocarcinoma   Data format 
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 READ  Rectum adenocarcinoma   Data format 
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 SARC  Sarcoma   Data format 
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 SKCM  Skin Cutaneous Melanoma   Data format 
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 STAD  Stomach adenocarcinoma   Data format 
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 TGCT  Testicular Germ Cell Tumors   Data format 
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 THCA  Thyroid carcinoma   Data format 
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 THYM  Thymoma   Data format 
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 UCEC  Uterine Corpus Endometrial Carcinoma   Data format 
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 UCS  Uterine Carcinosarcoma   Data format 
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 UVM  Uveal Melanoma   Data format 
    
Assembly: Human Dec. 2013 (GRCh38/hg38)

Description

This track shows the genomic positions of somatic variants found through whole genome sequencing of tumors as part of The Cancer Genome Atlas (TCGA) by the National Cancer Institute, made available through the Genomic Data Commons Portal. The data shown here is sometimes called the "Pan-Cancer dataset", a collection of thirty-three TCGA projects processed in a uniform way.

Display Conventions and Configuration

Variants can be filtered by project ID and gender from the track details page. Pressing the "All" button allows the user to specify whether the checked values all have to be true of a particular variant, or if only one of them need be present to satisfy the filter.

The vertical viewing range in full mode can also be used to filter what variants are shown. Variants that have a sampleCount more or less than the min and max values specificed in the viewing range are not displayed.

Data access

The raw data can be explored interactively with the Table Browser or the Data Integrator.

For automated download and analysis, the genome annotation for all the thirty-three projects is stored in a bigBed file that can be downloaded from our download server. There are also bigBed files for each of the thirty-three projects in that directory. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g.,

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/gdcCancer/gdcCancer.bb -chrom=chr21 -start=0 -end=100000000 stdout

Methods

All MuTect Variant calls were downloaded from the GDC portal in January 2019 and reformatted at UCSC to the bigBed format with a short script, cancerMafToBigBed.

Credits

Thanks to GDC for making the TCGA data available on their web site.