Programs and Data Sets

The National Cancer Institute (NCI) Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies (known as Programs) in support of precision medicine. For more information about the GDC, see the GDC Overview.

Between ISB-CGC and the NCI GDC, there are many cancer data sets available on the Google Cloud Platform. ISB-CGC hosts some carefully curated, high-level clinical, biospecimen and molecular data sets and tables in Google BigQuery as well as radiology and pathology images in Google Cloud Storage. The GDC hosts several more data sets that include low-level sequencing data.

The ISB-CGC started with The Cancer Genome Atlas (TCGA) data sets but has expanded to include other data sets from programs such as Therapeutically Applicable Research To Generate Effective Treatments (TARGET). Along with the NCI GDC data sets, ISB-CGC hosts data sets from programs such as Catalogue Of Somatic Mutations In Cancer (COSMIC) from the Wellcome Trust Sanger Institute. We are always interested in adding new data sets, so if you have any suggestions or requests for additional data, please let us know (feedback@isb-cgc.org).

Clinical, Biospecimen and Processed -Omics Data Sets

From Genomic Data Commons

../_images/omicsData.png

Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are available in the GDC Cloud Storage buckets, in ISB-CGC BigQuery tables and through ISB-CGC web tools. The table below lists each Program and where (through ISB-CGC) that you can find its data.

  • Within the detailed documentation on each Program (click on the Program name), there is an example of how to use the metadata stored in ISB-CGC BigQuery tables to locate the Program’s files on the GDC Google Cloud Storage buckets.
  • To learn more about using this data with ISB-CGC web tools, go to the ISB-CGC Web Interface section of this document.
  • To locate these tables in the ISB-CGC BigQuery project, use the ISB-CGC BigQuery Table Search.
Program GDC Google Cloud Storage ISB-CGC BigQuery Tables ISB-CGC Cohort Builder
BEATAML checkmark checkmark *  
CCLE checkmark checkmark checkmark
CGCI checkmark    
CPTAC checkmark    
CTSP checkmark    
FM checkmark    
GENIE checkmark    
HCMI checkmark checkmark *  
MMRF checkmark    
NCICCR checkmark    
OHSU checkmark    
ORGANOID checkmark checkmark *  
TARGET checkmark checkmark checkmark
TCGA checkmark checkmark checkmark
TCGA Pathology and Radiology images checkmark checkmark checkmark
VAREPOP checkmark    
WCDT checkmark    

*RNA-seq data available

From Other Sources

Program GDC Google Cloud Storage ISB-CGC BigQuery Tables ISB-CGC Cohort Builder
COSMIC No, the COSMIC database is maintained by the Wellcome Sanger Institute, UK Yes, COSMIC data is in BigQuery for registered users. Learn more about how to gain access to the COSMIC data here  
Pan-Cancer Atlas   checkmark  

Reference Data Sets

ISB-CGC hosts reference tables in BigQuery with information that describes or annotates human or other genomes, or is necessary to work with data generated by specific platforms.

File Metadata Data Sets

ISB-CGC hosts metadata tables in BigQuery with information that points to the raw and processed cancer data in the NCI GDC Google Cloud Storage buckets.


Have feedback or corrections? Please email us at feedback@isb-cgc.org.