The Cancer Genome Atlas

cancer genomic life sciences STRIDES whole genome sequencing

Description

The Cancer Genome Atlas (TCGA), a collaboration between the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI), aims to generate comprehensive, multi-dimensional maps of the key genomic changes in major types and subtypes of cancer. TCGA has analyzed matched tumor and normal tissues from 11,000 patients, allowing for the comprehensive characterization of 33 cancer types and subtypes, including 10 rare cancers. The dataset contains open Clinical Supplement, Biospecimen Supplement, RNA-Seq Gene Expression Quantification, miRNA-Seq Isoform Expression Quantification, miRNA Expression Quantification, Genotyping Array Copy Number Segment, Genotyping Array Masked Copy Number Segment, Genotyping Array Gene Level Copy Number Scores, WXS Masked Somatic Mutation, Methylation Array Methylation Beta Value Tissue Slide Image, and Diagnostic Slide Image data from Genomic Data Commons (GDC). This dataset also contains controlled Whole Exome Sequencing (WXS), RNA-Seq, miRNA-Seq, ATAC-Seq Aligned Reads, WXS Annotated Somatic Mutation, WXS Raw Somatic Mutation, and WXS Aggregated Somatic Mutation data from GDC. TCGA is made available on AWS via the NIH STRIDES Initiative.

Update Frequency

Genomic Data Commons (GDC) is source of truth for this dataset; GDC offers monthly data releases, although this dataset may not be updated at every release.

License

NIH Genomic Data Sharing Policy: https://gdc.cancer.gov/access-data/data-access-policies

Documentation

https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga

Managed By

See all datasets managed by Center for Translational Data Science at The University of Chicago.

Contact

dcf-support@datacommons.io

Usage Examples

Tools & Applications
Publications

Resources on AWS

  • Description
    Clinical Supplement, Biospecimen Supplement, RNA-Seq Gene Expression Quantification, miRNA-Seq Isoform Expression Quantification, miRNA Expression Quantification, Genotyping Array Copy Number Segment, Genotyping Array Masked Copy Number Segment, Genotyping Array Gene Level Copy Number Scores, WXS Masked Somatic Mutation, Methylation Array Methylation Beta Value Tissue Slide Image, Diagnostic Slide Image
    Resource type
    S3 Bucket
    Amazon Resource Name (ARN)
    arn:aws:s3:::tcga-2-open
    AWS Region
    us-east-1
    AWS CLI Access (No AWS account required)
    aws s3 ls s3://tcga-2-open/ --no-sign-request
  • Description
    WXS/RNA-Seq/miRNA-Seq/ATAC-Seq Aligned Reads, WXS Annotated Somatic Mutation, WXS Raw Somatic Mutation, WXS Aggregated Somatic Mutation
    Resource type
    S3 Bucket Controlled Access
    Amazon Resource Name (ARN)
    arn:aws:s3:::tcga-2-controlled
    AWS Region
    us-east-1

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