Schema for TCGA Pan-Cancer - TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)
  Database: hg38    Primary Table: GBM Data last updated: 2019-05-03
Big Bed File Download: /gbdb/hg38/gdcCancer/GBM.bb
Item Count: 82,174
The data is stored in the binary BigBed format.

Format description: somatic variants converted from MAF files obtained through the NCI GDC
fieldexampledescription
chromchr1Chromosome (or contig, scaffold, etc.)
chromStart166070275Start position in chromosome
chromEnd166070276End position in chromosome
nameG>AName of item
score1Score from 0-1000
strand.+ or -
thickStart166070275Start of where display should be thick (start codon)
thickEnd166070276End of where display should be thick (stop codon)
reserved0,0,0Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes1Comma separated list of block sizes
chromStarts0Start positions relative to chromStart
sampleCount1Number of samples with this variant
freq0.00254452926209Variant frequency
Hugo_SymbolFAM78BHugo symbol
Entrez_Gene_Id149297Entrez Gene Id
Variant_ClassificationMissense_MutationClass of variant
Variant_TypeSNPType of variant
Reference_AlleleGReference allele
Tumor_Seq_Allele1GTumor allele 1
Tumor_Seq_Allele2ATumor allele 2
dbSNP_RSrs746434862dbSNP RS number
dbSNP_Val_StatusdbSNP validation status
days_to_death--Number of days till death
cigarettes_per_day--Number of cigarettes per day
weight--Weight
alcohol_history--Any alcohol consumption?
alcohol_intensity--Frequency of alcohol consumption
bmi--Body mass index
years_smoked--Number of years smoked
height--Height
genderfemaleGender
project_idTCGA-GBMTCGA Project id
ethnicitynot hispanic or latinoEthnicity
Tumor_Sample_BarcodeTCGA-06-5416-01A-01D-1486-08Tumor sample barcode
Matched_Norm_Sample_BarcodeTCGA-06-5416-10A-01D-1486-08Matcheds normal sample barcode
case_id3a3fc890-1985-4353-861b-dc3abfb364b1Case ID number

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartssampleCountfreqHugo_SymbolEntrez_Gene_IdVariant_ClassificationVariant_TypeReference_AlleleTumor_Seq_Allele1Tumor_Seq_Allele2dbSNP_RSdbSNP_Val_Statusdays_to_deathcigarettes_per_dayweightalcohol_historyalcohol_intensitybmiyears_smokedheightgenderproject_idethnicityTumor_Sample_BarcodeMatched_Norm_Sample_Barcodecase_id
chr1166070275166070276G>A1.1660702751660702760,0,011010.00254452926209FAM78B149297Missense_MutationSNPGGArs746434862----------------femaleTCGA-GBMnot hispanic or latinoTCGA-06-5416-01A-01D-1486-08TCGA-06-5416-10A-01D-1486-083a3fc890-1985-4353-861b-dc3abfb364b1
chr1166070448166070449A>T1.1660704481660704490,0,011010.00254452926209FAM78B149297Missense_MutationSNPAATnovel3881.0--------------femaleTCGA-GBMnot hispanic or latinoTCGA-12-1088-01A-01W-0611-08TCGA-12-1088-10C-01W-0611-08ac72738c-8b33-4f03-917c-86b114a2b9bd
chr1166070463166070464G>A1.1660704631660704640,0,011010.00254452926209FAM78B149297Missense_MutationSNPGGA----------------maleTCGA-GBMnot reportedTCGA-74-6578-01A-11D-1845-08TCGA-74-6578-10A-01D-1845-084dee170b-175c-4e08-83f4-af1317b07209
chr1166070562166070563C>G1.1660705621660705630,0,011010.00254452926209FAM78B149297Missense_MutationSNPCCGnovel----------------maleTCGA-GBMnot reportedTCGA-15-1446-01A-01W-0611-08TCGA-15-1446-10A-01W-0612-0805d5da50-52fe-4342-9c15-9ee4c1d6662e
chr1166849181166849182C>T1.1668491811668491820,0,011010.00254452926209POGK57645SilentSNPCCTrs201306097by1000G;byCluster684.0--------------femaleTCGA-GBMnot hispanic or latinoTCGA-19-5956-01A-11D-1696-08TCGA-19-5956-10A-01D-1696-087e70a318-3acc-42f3-8287-158a2199f0bc
chr1166849272166849273C>T1.1668492721668492730,0,011010.00254452926209POGK57645Nonsense_MutationSNPCCT----------------femaleTCGA-GBMnot hispanic or latinoTCGA-06-5416-01A-01D-1486-08TCGA-06-5416-10A-01D-1486-083a3fc890-1985-4353-861b-dc3abfb364b1
chr1166849314166849315G>A1.1668493141668493150,0,011010.00254452926209POGK57645Missense_MutationSNPGGArs770055510byFrequency1818.0--------------femaleTCGA-GBMnot hispanic or latinoTCGA-12-3644-01A-01W-0922-08TCGA-12-3644-10A-01W-0922-08f6c6e2c9-a3d6-4b81-a421-04ffef6b8744
chr1166849843166849845insC1.1668498431668498450,0,012010.00254452926209POGK57645Frame_Shift_InsINS--Cnovel754.0--------------femaleTCGA-GBMnot hispanic or latinoTCGA-12-0819-01A-01W-0424-08TCGA-12-0819-10A-01W-0424-08025a7401-a65d-4ea0-8b4e-0ba775b0322a
chr1166850490166850491C>T1.1668504901668504910,0,011010.00254452926209POGK576453'UTRSNPCCTnovel----------------femaleTCGA-GBMnot hispanic or latinoTCGA-06-5416-01A-01D-1486-08TCGA-06-5416-10A-01D-1486-083a3fc890-1985-4353-861b-dc3abfb364b1
chr1166922799166922800G>A1.1669227991669228000,0,011010.00254452926209ILDR2387597Missense_MutationSNPGGAnovel30.0--------------maleTCGA-GBMnot reportedTCGA-14-1794-01A-01W-0643-08TCGA-14-1794-10A-01W-0643-08eb9c8e66-6710-4141-ae28-1e5c88eaee47

TCGA Pan-Cancer (gdcCancer) Track Description
 

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.