Schema for TCGA Pan-Cancer - TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)
  Database: hg38    Primary Table: COAD Data last updated: 2019-05-03
Big Bed File Download: /gbdb/hg38/gdcCancer/COAD.bb
Item Count: 253,759
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.)
chromStart166070116Start position in chromosome
chromEnd166070117End position in chromosome
nameC>AName of item
score1Score from 0-1000
strand.+ or -
thickStart166070116Start of where display should be thick (start codon)
thickEnd166070117End 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
freq0.00250626566416Variant frequency
Hugo_SymbolFAM78BHugo symbol
Entrez_Gene_Id149297Entrez Gene Id
Variant_Classification3'UTRClass of variant
Variant_TypeSNPType of variant
Reference_AlleleCReference allele
Tumor_Seq_Allele1CTumor allele 1
Tumor_Seq_Allele2ATumor allele 2
dbSNP_RSnoveldbSNP RS number
dbSNP_Val_StatusdbSNP validation status
days_to_death--Number of days till death
cigarettes_per_day--Number of cigarettes per day
weight68.0Weight
alcohol_history--Any alcohol consumption?
alcohol_intensity--Frequency of alcohol consumption
bmi31.0445580716Body mass index
years_smoked--Number of years smoked
height148.0Height
genderfemaleGender
project_idTCGA-COADTCGA Project id
ethnicitynot hispanic or latinoEthnicity
Tumor_Sample_BarcodeTCGA-AM-5821-01A-01D-1650-10Tumor sample barcode
Matched_Norm_Sample_BarcodeTCGA-AM-5821-10A-01D-1650-10Matcheds normal sample barcode
case_id605baa86-79e3-484d-82d2-4de27d405ba1Case 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
chr1166070116166070117C>A1.1660701161660701170,0,011010.00250626566416FAM78B1492973'UTRSNPCCAnovel----68.0----31.0445580716--148.0femaleTCGA-COADnot hispanic or latinoTCGA-AM-5821-01A-01D-1650-10TCGA-AM-5821-10A-01D-1650-10605baa86-79e3-484d-82d2-4de27d405ba1
chr1166070250166070251G>T1.1660702501660702510,0,011010.00250626566416FAM78B149297Missense_MutationSNPGGTnovel----58.0----20.5498866213--168.0maleTCGA-COADnot hispanic or latinoTCGA-CA-6717-01A-11D-1835-10TCGA-CA-6717-10A-01D-1835-10268c01b3-d2ce-44c0-a2fe-ea846a1253cc
chr1166070335166070336G>A1.1660703351660703360,0,011010.00250626566416FAM78B149297Missense_MutationSNPGGA----59.0----23.9360623149--157.0femaleTCGA-COADnot hispanic or latinoTCGA-CM-6678-01A-11D-1835-10TCGA-CM-6678-10A-01D-1835-10d7048098-09b3-4763-ad54-9c5c6fe14bc0
chr1166070352166070353C>T1.1660703521660703530,0,011010.00250626566416FAM78B149297Missense_MutationSNPCCTrs754839641byFrequency----61.0----20.6192536506--172.0maleTCGA-COADnot hispanic or latinoTCGA-CA-6719-01A-11D-1835-10TCGA-CA-6719-10A-01D-1835-109cdca5d8-ea77-4df9-b2ba-0d5e8ec37bcd
chr1166070403166070404C>T1.1660704031660704040,0,011010.00250626566416FAM78B149297Missense_MutationSNPCCTrs775991053byFrequency2134.0--------------femaleTCGA-COADnot hispanic or latinoTCGA-CK-4951-01A-01D-1408-10TCGA-CK-4951-10A-01D-2188-102db3c23d-c591-4ea0-b0a8-ed9c4343c80e
chr1166070404166070405G>A1.1660704041660704050,0,011010.00250626566416FAM78B149297Missense_MutationSNPGGArs747327778----------------maleTCGA-COADnot reportedTCGA-AA-3862-01A-01W-0995-10TCGA-AA-3862-10A-01W-0995-1005ff79c5-1127-4cac-8f4c-84089a3f2cde
chr1166070410166070411C>A1.1660704101660704110,0,011010.00250626566416FAM78B149297Missense_MutationSNPCCA----------------femaleTCGA-COADnot hispanic or latinoTCGA-CK-5913-01A-11D-1650-10TCGA-CK-5913-10A-01D-1650-103758f4f7-ac2f-4f9d-bee2-526196f8129a
chr1166070687166070688A>T1.1660706871660706880,0,011010.00250626566416FAM78B149297SilentSNPAAT----99.6----33.6668469443--172.0maleTCGA-COADnot hispanic or latinoTCGA-A6-5657-01A-01D-1650-10TCGA-A6-5657-10A-01D-1650-10dbbee8f5-d83d-4195-85cf-f89d327da0a9
chr1166165997166165998C>A1.1661659971661659980,0,011010.00250626566416FAM78B149297Missense_MutationSNPCCA----71.0----26.7228725206--163.0femaleTCGA-COADnot hispanic or latinoTCGA-AD-A5EJ-01A-11D-A28G-10TCGA-AD-A5EJ-10A-01D-A28G-10613aa3e8-a70b-45a9-9c08-0c2346c8bf00
chr1166166058166166059C>T2.1661660581661660590,0,011020.00501253132832FAM78B149297Missense_MutationSNPCCT--,2047.0--,--71.2,57.0--,----,--27.1300106691,24.5095404461--,--162.0,152.5female,femaleTCGA-COAD,TCGA-COADnot hispanic or latino,not hispanic or latinoTCGA-CM-6171-01A-11D-1650-10,TCGA-G4-6302-01A-11D-1719-10TCGA-CM-6171-10A-01D-1650-10,TCGA-G4-6302-10A-01D-1719-10eed7405f-f8f3-41a4-a0e7-242f23087f59,7144a65f-a63f-4b79-8fe2-cfe48696de03

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.