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
Data Access
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
| Data Type | Data Format | Data Access Level |
|---|---|---|
| Clinical and Biospecimen | XML (original), TSV (GDC Generated) | Open |
| Short Variants (substitutions and indels) | XML (original), MAF and VCF Files (GDC Generated) | 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