Schema for TCGA Pan-Cancer - TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)
  Database: hg38    Primary Table: CESC Data last updated: 2019-05-03
Big Bed File Download: /gbdb/hg38/gdcCancer/CESC.bb
Item Count: 102,712
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.)
chromStart166070532Start position in chromosome
chromEnd166070533End position in chromosome
nameC>GName of item
score1Score from 0-1000
strand.+ or -
thickStart166070532Start of where display should be thick (start codon)
thickEnd166070533End 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
freq0.00346020761246Variant frequency
Hugo_SymbolFAM78BHugo symbol
Entrez_Gene_Id149297Entrez Gene Id
Variant_ClassificationMissense_MutationClass of variant
Variant_TypeSNPType of variant
Reference_AlleleCReference allele
Tumor_Seq_Allele1CTumor allele 1
Tumor_Seq_Allele2GTumor allele 2
dbSNP_RSnoveldbSNP RS number
dbSNP_Val_StatusdbSNP validation status
days_to_death--Number of days till death
cigarettes_per_day0.712328767123Number of cigarettes per day
weight78.0Weight
alcohol_history--Any alcohol consumption?
alcohol_intensity--Frequency of alcohol consumption
bmi26.0616793077Body mass index
years_smoked--Number of years smoked
height173.0Height
genderfemaleGender
project_idTCGA-CESCTCGA Project id
ethnicitynot hispanic or latinoEthnicity
Tumor_Sample_BarcodeTCGA-ZJ-AB0I-01A-11D-A42O-09Tumor sample barcode
Matched_Norm_Sample_BarcodeTCGA-ZJ-AB0I-10A-01D-A42R-09Matcheds normal sample barcode
case_ida4f13656-a941-498a-9ac9-f020ed559b35Case 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
chr1166070532166070533C>G1.1660705321660705330,0,011010.00346020761246FAM78B149297Missense_MutationSNPCCGnovel--0.71232876712378.0----26.0616793077--173.0femaleTCGA-CESCnot hispanic or latinoTCGA-ZJ-AB0I-01A-11D-A42O-09TCGA-ZJ-AB0I-10A-01D-A42R-09a4f13656-a941-498a-9ac9-f020ed559b35
chr1166070601166070602A>C1.1660706011660706020,0,011010.00346020761246FAM78B149297Missense_MutationSNPAACnovel--0.10958904109667.0----25.5296448712--162.0femaleTCGA-CESCnot reportedTCGA-VS-A9UU-01A-11D-A42O-09TCGA-VS-A9UU-10B-01D-A42R-094770ec81-9174-4d2a-af54-70c00696fb0b
chr1166070738166070739C>G1.1660707381660707390,0,011010.00346020761246FAM78B149297Missense_MutationSNPCCG----------------femaleTCGA-CESCnot reportedTCGA-DG-A2KH-01A-21D-A22X-09TCGA-DG-A2KH-10A-01D-A22X-096248f2a3-0da9-419f-ab77-c3f6f4353eb5
chr1166612564166612565G>C1.1666125641666125650,0,011010.00346020761246FMO9P116123RNASNPGGCnovel----68.0----25.9106843469--162.0femaleTCGA-CESCnot hispanic or latinoTCGA-EA-A3HU-01A-11D-A20U-09TCGA-EA-A3HU-10B-01D-A20U-099912432e-74bc-4846-93b4-fa2bf8070bd1
chr1166840991166840992G>A1.1668409911668409920,0,011010.00346020761246POGK57645SilentSNPGGA----83.0----31.2394143551--163.0femaleTCGA-CESCnot hispanic or latinoTCGA-EA-A3HT-01A-61D-A21Q-09TCGA-EA-A3HT-10A-01D-A21Q-093c5b2452-014b-495f-b86a-f522ed84bc3b
chr1166848953166848954C>T1.1668489531668489540,0,011010.00346020761246POGK57645SilentSNPCCTrs147708165byCluster----42.0----16.40625--160.0femaleTCGA-CESCnot hispanic or latinoTCGA-2W-A8YY-01A-11D-A37N-09TCGA-2W-A8YY-10A-01D-A37N-095aeac31a-176a-4f93-a376-a93a670821bb
chr1166849563166849564C>A1.1668495631668495640,0,011010.00346020761246POGK57645Missense_MutationSNPCCA----------------femaleTCGA-CESCnot reportedTCGA-DG-A2KH-01A-21D-A22X-09TCGA-DG-A2KH-10A-01D-A22X-096248f2a3-0da9-419f-ab77-c3f6f4353eb5
chr1166849665166849667insTTCATTTC1.1668496651668496670,0,012010.00346020761246POGK57645Frame_Shift_InsINS--TTCATTTCnovel----78.0----39.7959183673--140.0femaleTCGA-CESChispanic or latinoTCGA-DS-A1OC-01A-11D-A14W-08TCGA-DS-A1OC-10A-01D-A14W-08e711b88e-fa0e-4781-8549-7a53ed3a13a1
chr1166849954166849955G>C1.1668499541668499550,0,011010.00346020761246POGK57645Missense_MutationSNPGGCnovel----114.0----44.53125--160.0femaleTCGA-CESCnot hispanic or latinoTCGA-C5-A8XJ-01A-11D-A37N-09TCGA-C5-A8XJ-10A-01D-A37N-09e89d0cb1-6ec2-43ee-a6d9-b922b680af34
chr1166850267166850268C>T1.1668502671668502680,0,011010.00346020761246POGK57645SilentSNPCCTrs752062847----42.0----16.40625--160.0femaleTCGA-CESCnot hispanic or latinoTCGA-2W-A8YY-01A-11D-A37N-09TCGA-2W-A8YY-10A-01D-A37N-095aeac31a-176a-4f93-a376-a93a670821bb

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.