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

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 and gender from the track details page. Pressing the "Advanced" 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.