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

Disease Type Primary Site
Acinar Cell Neoplasms Other and unspecified major salivary glands, Pancreas, Prostate gland
Adenomas and Adenocarcinomas Adrenal gland, Bladder, Breast, Bronchus and lung, Cervix uteri, Colon, Esophagus, Gallbladder, Kidney, Liver and intrahepatic bile ducts, Nasopharynx, Other and ill-defined digestive organs, Other and ill-defined sites, Other and unspecified female genital organs, Other and unspecified major salivary glands, Other and unspecified parts of biliary tract, Other endocrine glands and related structures, Ovary, Pancreas, Prostate gland, Rectum, Retroperitoneum and peritoneum, Skin, Small intestine, Stomach, Thyroid gland, Trachea, Unknown, Uterus, NOS
Adnexal and Skin Appendage Neoplasms Skin
Basal Cell Neoplasms Skin
Complex Epithelial Neoplasms Breast, Bronchus and lung
Complex Mixed and Stromal Neoplasms Bronchus and lung, Not Reported, Other and ill-defined digestive organs, Other and unspecified major salivary glands, Ovary, Uterus, NOS
Cystic, Mucinous and Serous Neoplasms Colon, Other and unspecified female genital organs, Ovary, Pancreas, Retroperitoneum and peritoneum, Uterus, NOS
Ductal and Lobular Neoplasms Breast, Kidney, Other and unspecified major salivary glands, Pancreas, Prostate gland, Thyroid gland
Epithelial Neoplasms, NOS Bladder, Breast, Bronchus and lung, Esophagus, Kidney, Nasopharynx, Not Reported, Other and ill-defined sites, Other and unspecified major salivary glands, Ovary, Pancreas, Prostate gland, Thymus, Thyroid gland, Unknown
Germ Cell Neoplasms Heart, mediastinum, and pleura, Ovary, Testis
Gliomas Spinal cord, cranial nerves, and other parts of central nervous system
Meningiomas Spinal cord, cranial nerves, and other parts of central nervous system
Mesothelial Neoplasms Heart, mediastinum, and pleura
Miscellaneous Tumors Not Reported
Mucoepidermoid Neoplasms Other and ill-defined sites, Other and unspecified major salivary glands
Neuroepitheliomatous Neoplasms Peripheral nerves and autonomic nervous system
Nevi and Melanomas Anus and anal canal, Eye and adnexa, Other and ill-defined sites, Skin, Unknown
Not Reported Breast, Bronchus and lung, Not Reported, Other and unspecified female genital organs, Other and unspecified parts of biliary tract, Other and unspecified urinary organs, Spinal cord, cranial nerves, and other parts of central nervous system
Paragangliomas and Glomus Tumors Adrenal gland, Not Reported
Specialized Gonadal Neoplasms Ovary
Squamous Cell Neoplasms Anus and anal canal, Bladder, Bronchus and lung, Cervix uteri, Esophagus, Nasopharynx, Not Reported, Other and ill-defined sites, Penis, Rectum, Skin, Thyroid gland, Unknown, Vagina, Vulva
Thymic Epithelial Neoplasms Thymus
Transitional Cell Papillomas and Carcinomas Anus and anal canal, Bladder, Kidney, Other and unspecified urinary organs, Unknown, Ureter

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