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


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