FM Data Set

About the Foundation Medicine

The Foundation Medicine Adult Cancer Clinical Data Set (FM) was a study conducted by Foundation Medicine Inc. (FMI), which is a molecular information company that specializes in precision medicine. FMI has generated genomic profiles for thousands of cancer patients, which they designed to match each patient with a personalized treatment plan.

About the Foundation Medicine Data

FM data set consists of more than 18,000 unique solid tumor samples that underwent genomic profiling on a single uniform platform as part of standard clinical care. The data set is derived from the FoundationOne® genomic profiling assay version 2 that interrogates exonic regions of 287 cancer-related genes and selected introns from 19 genes known to undergo rearrangements in human cancer. The Genomic Data Commons (GDC) currently has VCF, TSV, and MAF data available. There are more than 36,008 VCF files, 84 TSV files, and 42 MAF files available with, 36,050 of them that are Controlled Access and 84 files, which are Open Access. The project identification in the GDC Data Portal is FM-AD.

For more information on the FM data, please refer to these sites:

Accessing the Foundation Medicine Data on the Cloud

Besides accessing the files on the GDC Data Portal, you can also access them from the GDC Google Cloud Storage Bucket, which means that you don’t need to download them to perform analysis. ISB-CGC stores the cloud file locations in tables in the isb-cgc-bq.GDC_case_file_metadata data set in BigQuery.

  • To access these metadata files, go to the Google BigQuery console.
  • Perform SQL queries to find the FM files. Here is an example:
SELECT active.*, file_gdc_url
FROM `isb-cgc-bq.GDC_case_file_metadata.fileData_active_current` as active, `isb-cgc-bq.GDC_case_file_metadata.GDCfileID_to_GCSurl_current` as GCSurl
WHERE program_name = 'FM'
AND active.file_gdc_id = GCSurl.file_gdc_id

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