Foundation Medicine data

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Seven Bridges is committed to providing CGC users with the most up-to-date version of this dataset that is available from the NCI Genomic Data Commons (GDC). In keeping with this commitment, the CGC transitioned from hosting the CGHub version of this dataset to the GDC Legacy Archive Data Release 11.0 version on July 10, 2018.
As of this date, all files accessible via the Data Browser and the API correspond to files in the GDC Legacy Archive. Files that were added to individual projects before this date and are no longer represented in the new dataset version will no longer be accessible via those projects but may be obtainable from the GDC archive by contacting the GDC Help Desk. We look forward to continuing to collaborate with the GDC in the months ahead to ensure the timely availability through the CGC of new data releases for this dataset.

Foundation Medicine (FM) contains genomic profiling data from approximately 18,000 adult patients with a diverse array of cancers that underwent genomic profiling.

Foundations Medicine Inc. (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(link is external).

To start analyzing the data available in the Foundation Medicine dataset, access the CGC Data Browser.

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

There are two types of data in the dataset and those are open and controlled. Access to controlled data must be obtained through dbGaP.

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