The Cancer Genome Atlas

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, and WXS Masked Somatic Mutation 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

How to Cite

The Cancer Genome Atlas was accessed on DATE from https://registry.opendata.aws/tcga.

Usage Examples

Tools & Applications

• Broad Institute FireCloud by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• ISB Cancer Genomics Cloud by Institute for Systems Biology
  
• TCGA Cancers Selected for Study by National Cancer Institute
  
• Using TCGA Data, Resources, and Materials by National Cancer Institute
  

Publications

• "Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons" by Galen F. Gao, Joel S. Parker, et al.
  
• A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples by Han Chen, Chunyan Li, et al.
  
• An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics by Jianfang Liu, Tara Lichtenberg, et al.
  
• Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer by Katherine A. Hoadley, Christina Yau, et al.
  
• Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas by Yang Liu, Nilay S. Sethi, et al.
  
• Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients by André Kahles, Kjong-Van Lehmann, et al.
  
• Comprehensive Characterization of Cancer Driver Genes and Mutations by Matthew H. Bailey, Collin Tokheim, et al.
  
• Genomic and Functional Approaches to Understanding Cancer Aneuploidy by Alison M. Taylor, Juliann Shih, et al.
  
• Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas by Theo A. Knijnenburg, Linghua Wang, et al.
  
• Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas by Joshua D. Campbell, Christina Yau, et al.
  
• Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types by Zhongqi Ge, Jake S. Leighton, et al.
  
• Machine Learning Detects Pan-Cancer Ras Pathway Activation in The Cancer Genome Atlas by Gregory P. Way, Francisco Sanchez-Vega, et al.
  
• Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation by Tathiane M. Malta, Artem Sokolov, et al.
  
• Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers by Xinxin Peng, Zhongyuan Chen, et al.
  
• Oncogenic Signaling Pathways in The Cancer Genome Atlas by Francisco Sanchez-Vega, Marco Mina, et al.
  
• Pan-Cancer Alterations of the MYC Oncogene and its Proximal Network Across The Cancer Genome Atlas by Franz X. Schaub, Varsha Dhankani, et al.
  
• Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context by Hua-Sheng Chiu, Sonal Somvanshi, et al.
  
• Pathogenic Germline Variants in 10,389 Adult Cancers by Kuan-lin Huang, R. Jay Mashl, et al.
  
• Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines by Kyle Ellrott, Matthew H. Bailey, et al.
  
• Spatial Organization And Molecular Correlation Of Tumor-Infiltrating Lymphocytes Using Deep Learning On Pathology Images by Joel Saltz, Rajarsi Gupta, et al.
  
• The chromatin accessibility landscape of primary human cancers by M. Ryan Corces, Jeffrey M. Granja, et al.
  
• The Immune Landscape of Cancer by Vésteinn Thorsson, David L. Gibbs, et al.