Foundation Medicine

Foundation Medicine Inc.

Foundation Medicine Inc. (FMI) is a molecular information company that specializes in precision medicine. FMI has generated genomic profiles for thousands of cancer patients, which are designed to match each patient to a personalized treatment plan.

Program Description

FMI has provided the Genomic Data Commons (GDC) with genomic profiling data from approximately 18,000 adult patients with a diverse array of cancers that underwent genomic profiling using FoundationOne®, FMI's commercially available, comprehensive genomic profiling assay. FMI routinely analyzes cancer specimens using the advanced sequencing technology of FoundationOne. The GDC modified FMI’s patient data with a LiftOver pipeline to harmonize genomic profiles with the GRCh38 reference genome.

The dataset is described in the accompanying publication: Hartmaier R.J. et al, “High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis”, Cancer Res. 2017 May 1;77(9):2464-2475 http://cancerres.aacrjournals.org/content/77/9/2464.long

Data Overview

The FMI data can be found on the GDC Data Portal. To request access to protected Foundation Medicine data please apply to dbGaP for access to the Foundation Medicine Adult Cancer Clinical Dataset (FM-AD) (study accession phs001179).

Cancer Types

Data Types and Access Levels

Data Type Data Format # of Cases and Files Estimated File Size Data Access Level
Clinical and Biospecimen XML (original),
TSV (GDC Generated)
18004 cases
84 files
15 MB Open
Short Variants (substitutions and indels) XML (original),
MAF and VCF Files (GDC Generated)
18004 cases
36050 files
173 MB Controlled
Copy Number
Alterations
XML (original) Harmonized Results Coming Soon Harmonized Results Coming Soon Controlled
Structural
Rearrangements
XML (original) Harmonized Results Coming Soon Harmonized Results Coming Soon Controlled

 

Raw Data

The raw data that was imported into the GDC is available as a controlled-access, XML-format file. The file can be downloaded by passing the following command to the GDC Data Transfer Tool with the proper authentication token:
gdc-client download 592ba789-6869-4fc2-8e47-8429a4ee36b0 -t gdc_token_file.txt