Data Types Collected by TCGA

The Cancer Genome Atlas (TCGA) collected many types of data for each of over 20,000 tumor and normal samples. Each step in the Genome Characterization Pipeline generated numerous data points, such as:

clinical information (e.g., smoking status)
molecular analyte metadata (e.g., sample portion weight)
molecular characterization data (e.g., gene expression values)

Below is supporting information and documentation for the different steps of molecular characterization.

Case Enrollment Documentation

Documents on case enrollment, followup, and other forms related to the intake of samples and clinical data are available from the Biospecimen Core Resource.

Sample Processing Documentation

TCGA used a compendium of standard operating procedures for processing tissues and other biological samples into molecular analytes for molecular characterization. These protocols are available from NCI's Biospecimen Research Database.

Summary of Data Types Collected

The data collected for a specific case in TCGA may have differed according to sample quality and quantity, cancer type, or technology available at the time of analysis. Below is a general summary of the types of clinical, molecular characterization, and other types of data that may have been generated for the different cancer types studied.

Raw data (e.g. BAMs), germline and non-validated mutations, and genotypes are under controlled access (indicated in red). Derived data is available open access (exceptions are noted in table below).

All data collected and processed by the program is available at the Genomic Data Commons (GDC), including TCGA publication supplemental and associated data files. Questions about locating or accessing data should be directed to the GDC support team. Resources for TCGA users and TCGA FAQs are available.

Experimental protocols for each platform can be found in individual publications.

Summary of Data Types Collected
Type	Subtype	Cancer Types Applicable	Description	Format	Notes
Clinical	Clinical data	All	Available clinical information (may include demographic information, treatment information, survival data, etc)	XML (per patient), tab-delimited TXT (grouped "biotab" per cancer type)	Clinical data forms used by the TSS Additional information in the Clinical Data Elements (CDE) Browser
	Biospecimen data	All	Information on how samples were processed by the Biospecimen Core Resource Center	XML (per patient), tab-delimited TXT (grouped "biotab" per cancer type)	Protocols used by the BCR for processing of samples Additional information in the CDE Browser
	Pathology Reports	All	Pathology reports (for select cases)	PDF
Copy Number	SNP microarray	All		CEL, IDAT, tab-delimited TXT (raw values per SNP, copy number, and loss of heterozygosity), tab-delimited TXT ( normalized values and purity/ploidy)	Probe information contained in array design files for each platform
	Copy number microarray	GBM, OV, LUSC		tab-delimited TXT (raw signals per probe), tab-delimited TSV (normalized values per aggregated region), MAT,	Probe information contained in array design files for each platform
	Low-Pass DNA Sequencing	Some tumor types	Low pass, whole genome sequencing of tumor and normal matched samples and analysis of differences in read counts between tumor and normal	BAM, VCF, tab-delimited TSV (normal v tumor calls)
DNA	Whole exome	All	Whole exome sequencing of tumor and normal matched samples	BAM, VCF, MAF (mutation calls)	Germline mutation calls and unvalidated non-coding somatic variants are controlled-access
	Whole genome	All	Whole genome sequencing for tumor and normal matched samples (for select cases)	BAM, VCF, MAF (mutation calls)	Germline mutation calls and unvalidated non-coding somatic variants are controlled-access
	SNP microarray	All		CEL, IDAT, tab-delimited TXT (raw values per SNP), tab-delimited TXT (genotypes per SNP)	Germline mutation calls and unvalidated non-coding somatic variants are controlled-access
	Sequence traces	GBM, OV	Raw output from capillary sequencing technology	SCF, TR	May be available at NCBI Trace Archive
Imaging	Diagnostic image	All	Whole slide images of tissue used to diagnose participant	SVS	Available at the GDC, open access
	Tissue image	All	Whole slide images of tissue samples from each participant that were used for TCGA analyses	SVS	Available at the GDC, open access
	Radiological image	Some	Pre-surgical radiological imaging (e.g. MRI, CT, PET, etc) (for select cases)	DCM	Available at The Cancer Imaging Archive, open access
Methylation	Bisulfite sequencing	Some tumor types	Whole genome sequencing performed after bisulfite treatment of tumor samples	BAM, VCF (methylation and mutation calls), BED (methylation calls per CpG site)
Methylation	Bead array	All		tab-delimited TXT (raw signal values, beta values, beta values mapped to genome), IDAT	Probe information contained in array design files for each platform
Microsatellite Instability		COAD, READ, UCEC	Markers indicating presence or absence of a MSI shift, allele homozygosity/heterozygosity, and loss of heterozygosity observed in tumor samples	FSA, TXT (summary of trace file)	MSI classifications within clinical biotab files
miRNA	miRNA Sequencing	All except GBM	miRNA sequencing of tumor samples	BAM, tab-delimited TXT (normalized expression values per miRNA or isoform)
miRNA	Array-based	GBM, OV		TXT (raw signals per probe, normalized expression values per probe, gene, or exons)	Probe information contained in array design files for each platform
mRNA Expression	mRNA sequencing	All	mRNA sequencing of tumor sampls using a poly(A) enrichment RNA preparation	BAM, TXT (normalized expression values per gene, isoform, exon, or splice junction)	May be labeled as RNASeqV1 and RNASeqv2
	Total RNA Sequencing	Some tumor types	mRNA sequencing of tumor samples using ribosomal depletion RNA preparation	BAM, TXT (normalized expression values per gene, isoform, exon, or splice junction)	May be labeled as TotalRNASeqV2
	Microarray	BRCA, COAD, GBM, KIRC, KIRP, LAML, LGG, LUAD, LUSC, OV, READ, UCEC		CEL (raw signals per probe), TXT (raw signals per probe, normalized expression values per probe, gene, or exons)	Probe information contained in array design files for each platform
Protein Expression	Reverse-Phase Protein Array	All	High resolution images of protein array slides (up to 1000 participant tumor samples per slide) and raw signals per slide	TIFF, tab-delimited TXT (signal values, dilution curves, normalized expression values)