Schema for TCGA Pan-Cancer - TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)
  Database: hg38    Primary Table: DLBC Data last updated: 2019-05-03
Big Bed File Download: /gbdb/hg38/gdcCancer/DLBC.bb
Item Count: 6,387
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.)
chromStart166849244Start position in chromosome
chromEnd166849245End position in chromosome
nameG>AName of item
score1Score from 0-1000
strand.+ or -
thickStart166849244Start of where display should be thick (start codon)
thickEnd166849245End 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
freq0.027027027027Variant frequency
Hugo_SymbolPOGKHugo symbol
Entrez_Gene_Id57645Entrez Gene Id
Variant_ClassificationSilentClass of variant
Variant_TypeSNPType of variant
Reference_AlleleGReference allele
Tumor_Seq_Allele1GTumor 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
weight80.0Weight
alcohol_history--Any alcohol consumption?
alcohol_intensity--Frequency of alcohol consumption
bmi32.4556777151Body mass index
years_smoked--Number of years smoked
height157.0Height
genderfemaleGender
project_idTCGA-DLBCTCGA Project id
ethnicityhispanic or latinoEthnicity
Tumor_Sample_BarcodeTCGA-GS-A9U3-01A-11D-A38X-10Tumor sample barcode
Matched_Norm_Sample_BarcodeTCGA-GS-A9U3-10A-01D-A38X-10Matcheds normal sample barcode
case_idfdecb74f-ac4e-46b1-b23a-5f7fde96ef9fCase 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
chr1166849244166849245G>A1.1668492441668492450,0,011010.027027027027POGK57645SilentSNPGGAnovel----80.0----32.4556777151--157.0femaleTCGA-DLBChispanic or latinoTCGA-GS-A9U3-01A-11D-A38X-10TCGA-GS-A9U3-10A-01D-A38X-10fdecb74f-ac4e-46b1-b23a-5f7fde96ef9f
chr1166850165166850166G>A1.1668501651668501660,0,011010.027027027027POGK57645SilentSNPGGAnovel----68.0----28.3038501561--155.0femaleTCGA-DLBChispanic or latinoTCGA-GS-A9TQ-01A-11D-A382-10TCGA-GS-A9TQ-10A-01D-A385-1045b0cf9f-a879-417f-8f39-7770552252c0
chr1167126627167126628delC1.1671266271671266280,0,011010.027027027027DUSP2792235Frame_Shift_DelDELCC-novel----41.5----19.4689435166--146.0femaleTCGA-DLBCnot hispanic or latinoTCGA-FF-8043-01A-11D-2210-10TCGA-FF-8043-10A-01D-2210-10a8e2df1e-4042-42af-9231-3a00e83489f0
chr1167127557167127558G>A1.1671275571671275580,0,011010.027027027027DUSP2792235SilentSNPGGArs142434634by1000G;byCluster;byFrequency----75.0----23.1481481481--180.0maleTCGA-DLBCnot hispanic or latinoTCGA-VB-A8QN-01A-11D-A382-10TCGA-VB-A8QN-10A-01D-A385-10a6923479-4e68-4ea8-87ed-e9642b9d43d5
chr1167128239167128240C>T1.1671282391671282400,0,011010.027027027027DUSP2792235Missense_MutationSNPCCTnovel----89.9----30.744502582--171.0femaleTCGA-DLBCnot hispanic or latinoTCGA-FF-8042-01A-11D-2210-10TCGA-FF-8042-10A-01D-2210-10f0a326d2-1f3e-4a5d-bca8-32aaccc52338
chr1167630259167630260C>T1.1676302591676302600,0,011010.027027027027RCSD1922415'UTRSNPCCTnovel----68.0----24.0929705215--168.0maleTCGA-DLBChispanic or latinoTCGA-GS-A9TZ-01A-11D-A38X-10TCGA-GS-A9TZ-10A-01D-A38X-10eda9496e-be80-4a13-bf06-89f0cc9e937f
chr1167772482167772483A>G1.1677724821677724830,0,011010.027027027027MPZL19019Missense_MutationSNPAAGrs750771385----82.0----28.710479325--169.0maleTCGA-DLBCnot hispanic or latinoTCGA-FA-8693-01A-11D-2397-10TCGA-FA-8693-10A-01D-2397-10a43e5f0e-a21f-48d8-97e0-084d413680b7
chr1168044908168044909A>G1.1680449081680449090,0,011010.027027027027DCAF655827Missense_MutationSNPAAGnovel248.0--65.0----26.3702381435--157.0femaleTCGA-DLBCnot hispanic or latinoTCGA-FA-A7Q1-01A-11D-A382-10TCGA-FA-A7Q1-10A-01D-A385-100030a28c-81aa-44b0-8be0-b35e1dcbf98c
chr1169106734169106735C>A1.1691067341691067350,0,011010.027027027027ATP1B14815'UTRSNPCCAnovel313.0--73.0----25.2595155709--170.0maleTCGA-DLBCnot hispanic or latinoTCGA-FF-A7CR-01A-11D-A382-10TCGA-FF-A7CR-10A-01D-A385-10f784bc3a-751b-4025-aab2-0af2f6f24266
chr1169132212169132213C>A1.1691322121691322130,0,011010.027027027027ATP1B14813'FlankSNPCCAnovel----75.0----23.1481481481--180.0maleTCGA-DLBCnot hispanic or latinoTCGA-VB-A8QN-01A-11D-A382-10TCGA-VB-A8QN-10A-01D-A385-10a6923479-4e68-4ea8-87ed-e9642b9d43d5

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.