Schema for TCGA Pan-Cancer - TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)
  Database: hg38    Primary Table: LUAD Data last updated: 2019-05-03
Big Bed File Download: /gbdb/hg38/gdcCancer/LUAD.bb
Item Count: 206,783
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.)
chromStart166070206Start position in chromosome
chromEnd166070207End position in chromosome
nameC>TName of item
score1Score from 0-1000
strand.+ or -
thickStart166070206Start of where display should be thick (start codon)
thickEnd166070207End 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
freq0.00176366843034Variant 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_Allele2TTumor allele 2
dbSNP_RSrs185998444dbSNP RS number
dbSNP_Val_Statusby1000G;byClusterdbSNP validation status
days_to_death--Number of days till death
cigarettes_per_day4.38356164384Number 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
gendermaleGender
project_idTCGA-LUADTCGA Project id
ethnicitynot hispanic or latinoEthnicity
Tumor_Sample_BarcodeTCGA-69-7978-01A-11D-2184-08Tumor sample barcode
Matched_Norm_Sample_BarcodeTCGA-69-7978-10A-01D-2184-08Matcheds normal sample barcode
case_idf462cfef-f60a-4d3e-b92d-b8d8f50b6bb3Case 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
chr1166070206166070207C>T1.1660702061660702070,0,011010.00176366843034FAM78B1492973'UTRSNPCCTrs185998444by1000G;byCluster--4.38356164384------------maleTCGA-LUADnot hispanic or latinoTCGA-69-7978-01A-11D-2184-08TCGA-69-7978-10A-01D-2184-08f462cfef-f60a-4d3e-b92d-b8d8f50b6bb3
chr1166070217166070218C>G1.1660702171660702180,0,011010.00176366843034FAM78B1492973'UTRSNPCCGnovel----------------maleTCGA-LUADnot hispanic or latinoTCGA-50-5049-01A-01D-1625-08TCGA-50-5049-10A-01D-1625-089944f46f-9fa8-4e2c-a806-776bec7f8803
chr1166070317166070318G>C1.1660703171660703180,0,011010.00176366843034FAM78B149297Missense_MutationSNPGGC1293.0--------------maleTCGA-LUADnot hispanic or latinoTCGA-55-6968-01A-11D-1945-08TCGA-55-6968-11A-01D-1945-0883a6ed20-b3cf-48b9-8ed3-a080cd4951fa
chr1166070348166070349C>G1.1660703481660703490,0,011010.00176366843034FAM78B149297Missense_MutationSNPCCG--1.3698630137--------25.0--femaleTCGA-LUADnot hispanic or latinoTCGA-64-5781-01A-01D-1625-08TCGA-64-5781-10A-01D-1625-0841c4c704-825e-49f5-9d54-dbd7d30725e0
chr1166070378166070379C>A1.1660703781660703790,0,011010.00176366843034FAM78B149297Missense_MutationSNPCCA370.0--------------femaleTCGA-LUADnot hispanic or latinoTCGA-50-6594-01A-11D-1753-08TCGA-50-6594-11A-01D-1753-088504fd86-a70a-4cba-9ec8-25c9e60ca549
chr1166070650166070651C>A1.1660706501660706510,0,011010.00176366843034FAM78B149297Missense_MutationSNPCCA--2.19178082192------------femaleTCGA-LUADnot hispanic or latinoTCGA-86-8074-01A-11D-2238-08TCGA-86-8074-10A-01D-2238-08482eb2a7-6fed-4e4c-b1b6-14d6d869f855
chr1166070698166070699C>G1.1660706981660706990,0,011010.00176366843034FAM78B149297Missense_MutationSNPCCGnovel------------------TCGA-LUAD--TCGA-17-Z031-01A-01W-0746-08TCGA-17-Z031-11A-01W-0746-08c43c8eea-7014-4abe-b805-397a9062d3e0
chr1166070704166070705C>A1.1660707041660707050,0,011010.00176366843034FAM78B149297Missense_MutationSNPCCAnovel--1.64383561644------------maleTCGA-LUADnot hispanic or latinoTCGA-44-8120-01A-11D-2238-08TCGA-44-8120-10A-01D-2238-0883e38dbd-edab-47f2-b19f-6ea38fc6bece
chr1166154756166154757C>A1.1661547561661547570,0,011010.00176366843034FAM78B149297IntronSNPCCA666.02.02739726027--------37.0--maleTCGA-LUADnot reportedTCGA-78-7150-01A-21D-2036-08TCGA-78-7150-10A-01D-2036-08a0e57b39-960e-4e46-8aa0-d0ee2fd9a7cc
chr1166166153166166154G>T1.1661661531661661540,0,011010.00176366843034FAM78B149297Missense_MutationSNPGGT--2.19178082192------------maleTCGA-LUADnot hispanic or latinoTCGA-55-7903-01A-11D-2167-08TCGA-55-7903-10A-01D-2167-0877c4dbb2-eceb-4e0d-bcde-63dc817d5f35

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.