TCGA GRCh38 data
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The Cancer Genome Atlas (TCGA) is one of the richest and most complete genomics datasets and was compiled to understand the molecular basis of cancers. Data collection for TCGA began in 2006 as a joint effort by the National Cancer Institute (NCI), National Human Genome Research Institute (NHGRI), the National Institutes of Health (NIH), and the U.S. Department of Health and Human Services.
Over the past decade, TCGA has grown to contain data on 33 different tumor types and over 11,000 cases (patients). Between 50 and 1500 cases have been sampled for each tumor type. For each case, multiple samples were analyzed, using microarray technology for genome characterization, and next-generation technology for sequencing. TCGA data currently represents more than 2.5 petabytes of information and is expected to grow as new samples are processed.
This page details data within TCGA GRCh38. Nomenclature for TCGA GRCh38 is in accordance with GDC. For instance, the category Data type for legacy TCGA data is renamed Data Category for harmonized TCGA GRCh38 data. Similarly, Data subtype in legacy TCGA data is Data type in harmonized GRCh38 data. For a full list of TCGA GRCh38 data available on the CGC, see the table below. The table details data categories and types, the data format of data subtypes, and the access level of each data type.
|Data category||Data type||Data format||Data access tier|
|Biospecimen||Biospecimen supplement||BCR XML||Open data|
|Clinical||Clinical supplement||BCR XML||Open data|
|Copy Number Variation||Copy Number Segment||TXT||Open data|
|Copy Number Variation||Masked Copy Number Segment||TXT||Open data|
|DNA Methylation||Methylation Beta Value||TXT||Open data|
|Raw Sequencing Data||Aligned reads||BAM||Controlled data|
|Simple Nucleotide Variation||Aggregated Somatic Mutation||MAF||Controlled data|
|Simple Nucleotide Variation||Annotated Somatic Mutation||VCF||Controlled data|
|Simple Nucleotide Variation||Masked Somatic Mutation||MAF||Controlled data|
|Simple Nucleotide Variation||Raw Simple Somatic Mutation||VCF||Controlled data|
|Transcriptome profiling||Gene Expression Quantification||TXT||Open data|
|Transcriptome profiling||Isoform Expression Quantification||TSV||Open data|
|Transcriptome profiling||miRNA Expression Quantification||TSV||Open data|
|Biospecimen||Slide Image||SVS||Open data|
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