{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","results":{"codes":[]},"settings":"","params":[]},"next":{"description":"","pages":[]},"title":"Foundation Medicine data","type":"basic","slug":"fm-data","excerpt":"","body":"[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"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](https://gdc.cancer.gov/) (GDC). In keeping with this commitment, the CGC transitioned from hosting the CGHub version of this dataset to the [GDC Legacy Archive](https://portal.gdc.cancer.gov/legacy-archive/search/f) Data Release 11.0 version on July 10, 2018.\\n\\nAs 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](https://gdc.cancer.gov/support). 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.\"\n}\n[/block]\nFoundation Medicine ([FM](https://gdc.cancer.gov/about-gdc/contributed-genomic-data-cancer-research/foundation-medicine/foundation-medicine)) contains genomic profiling data from approximately 18,000 adult patients with a diverse array of cancers that underwent genomic profiling.\n\nFoundations Medicine Inc. ([FMI](https://www.foundationmedicine.com/)) 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.\n\nThe 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).\n\nTo start analyzing the data available in the Foundation Medicine dataset, access the CGC [Data Browser](doc:about-the-data-browser).\n\n###Cancer types\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Disease Type\",\n    \"h-1\": \"Primary Site\",\n    \"0-0\": \"Acinar Cell Neoplasms\",\n    \"0-1\": \"Other and unspecified major salivary glands, Pancreas, Prostate gland\",\n    \"1-0\": \"Adenomas and Adenocarcinomas\",\n    \"1-1\": \"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\",\n    \"2-0\": \"Adnexal and Skin Appendage Neoplasms\",\n    \"2-1\": \"Skin\",\n    \"3-0\": \"Basal Cell Neoplasms\",\n    \"3-1\": \"Skin\",\n    \"4-0\": \"Complex Epithelial Neoplasms\",\n    \"4-1\": \"Breast, Bronchus and lung\",\n    \"5-0\": \"Complex Mixed and Stromal Neoplasms\",\n    \"5-1\": \"Bronchus and lung, Not Reported, Other and ill-defined digestive organs, Other and unspecified major salivary glands, Ovary, Uterus, NOS\",\n    \"6-0\": \"Cystic, Mucinous and Serous Neoplasms\",\n    \"6-1\": \"Colon, Other and unspecified female genital organs, Ovary, Pancreas, Retroperitoneum and peritoneum, Uterus, NOS\",\n    \"7-0\": \"Ductal and Lobular Neoplasms\",\n    \"7-1\": \"Breast, Kidney, Other and unspecified major salivary glands, Pancreas, Prostate gland, Thyroid gland\",\n    \"8-0\": \"Epithelial Neoplasms, NOS\",\n    \"8-1\": \"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\",\n    \"9-0\": \"Germ Cell Neoplasms\",\n    \"9-1\": \"Heart, mediastinum, and pleura, Ovary, Testis\",\n    \"10-0\": \"Gliomas\",\n    \"10-1\": \"Spinal cord, cranial nerves, and other parts of central nervous system\",\n    \"11-0\": \"Meningiomas\",\n    \"11-1\": \"Spinal cord, cranial nerves, and other parts of central nervous system\",\n    \"12-0\": \"Mesothelial Neoplasms\",\n    \"12-1\": \"Heart, mediastinum, and pleura\",\n    \"13-0\": \"Miscellaneous Tumors\",\n    \"13-1\": \"Not Reported\",\n    \"14-0\": \"Mucoepidermoid Neoplasms\",\n    \"14-1\": \"Other and ill-defined sites, Other and unspecified major salivary glands\",\n    \"15-0\": \"Neuroepitheliomatous Neoplasms\",\n    \"15-1\": \"Peripheral nerves and autonomic nervous system\",\n    \"16-0\": \"Nevi and Melanomas\",\n    \"16-1\": \"Anus and anal canal, Eye and adnexa, Other and ill-defined sites, Skin, Unknown\",\n    \"17-0\": \"Not Reported\",\n    \"17-1\": \"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\",\n    \"18-0\": \"Paragangliomas and Glomus Tumors\",\n    \"18-1\": \"Adrenal gland, Not Reported\",\n    \"19-0\": \"Specialized Gonadal Neoplasms\",\n    \"19-1\": \"Ovary\",\n    \"20-0\": \"Squamous Cell Neoplasms\",\n    \"20-1\": \"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\",\n    \"21-0\": \"Thymic Epithelial Neoplasms\",\n    \"21-1\": \"Thymus\",\n    \"22-0\": \"Transitional Cell Papillomas and Carcinomas\",\n    \"22-1\": \"Anus and anal canal, Bladder, Kidney, Other and unspecified urinary organs, Unknown, Ureter\"\n  },\n  \"cols\": 2,\n  \"rows\": 23\n}\n[/block]\n###Data types and access levels\n\nThere are two types of data in the dataset and those are open and controlled. Access to controlled data must be obtained through [dbGaP](https://www.ncbi.nlm.nih.gov/gap/).  \n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Data Type\",\n    \"h-1\": \"Data Format\",\n    \"h-2\": \"Number of cases\",\n    \"h-3\": \"NUmber of files\",\n    \"h-4\": \"Estimated File Size\",\n    \"0-0\": \"Clinical and Biospecimen\",\n    \"0-1\": \"XML (original),\\nTSV (GDC Generated)\",\n    \"0-2\": \"18004\",\n    \"0-3\": \"84\",\n    \"0-4\": \"15 MB\",\n    \"1-0\": \"Short Variants (substitutions and indels)\",\n    \"1-1\": \"XML (original),\\nMAF and VCF Files (GDC Generated)\",\n    \"1-2\": \"18004\",\n    \"h-5\": \"Data Access Level\",\n    \"0-5\": \"Open\",\n    \"1-3\": \"36050\",\n    \"1-4\": \"173 MB\",\n    \"1-5\": \"Controlled\",\n    \"2-5\": \"Controlled\",\n    \"3-5\": \"Controlled\",\n    \"2-4\": \"Harmonized Results Coming Soon\",\n    \"3-4\": \"Harmonized Results Coming Soon\",\n    \"2-0\": \"Copy Number\\nAlteration\",\n    \"2-1\": \"XML (original)\",\n    \"3-1\": \"XML (original)\",\n    \"3-0\": \"Structural\\nRearrangements\",\n    \"2-2\": \"Harmonized Results Coming Soon\",\n    \"2-3\": \"Harmonized Results Coming Soon\",\n    \"3-2\": \"Harmonized Results Coming Soon\",\n    \"3-3\": \"Harmonized Results Coming Soon\"\n  },\n  \"cols\": 6,\n  \"rows\": 4\n}\n[/block]","updates":[],"order":6,"isReference":false,"hidden":false,"sync_unique":"","link_url":"","link_external":false,"_id":"6040d1ac999d27004e99bbd5","createdAt":"2021-03-04T12:25:16.199Z","user":"566590c83889610d0008a253","category":{"sync":{"isSync":false,"url":""},"pages":[],"title":"DATASETS HUB","slug":"datasets-hub","order":7,"from_sync":false,"reference":false,"_id":"58458b4fba4f1c0f009692bb","createdAt":"2016-12-05T15:44:15.650Z","project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","__v":0},"version":{"version":"1.0","version_clean":"1.0.0","codename":"","is_stable":true,"is_beta":true,"is_hidden":false,"is_deprecated":false,"categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f","5c222bed4bc358002f21459a","5c22412594a2a5005cc9e919","5c41ae1c33592700190a291e","5c8a525e2ba7b2003f9b153c","5cbf14d58c79c700ef2b502e","5db6f03a6e187c006f667fa4","5f894c7d3b0894006477ca01","6176d5bf8f59c6001038c2f7"],"_id":"55faf11ba62ba1170021a9aa","releaseDate":"2015-09-17T16:58:03.490Z","createdAt":"2015-09-17T16:58:03.490Z","project":"55faf11ba62ba1170021a9a7","__v":48},"project":"55faf11ba62ba1170021a9a7","__v":0,"parentDoc":null}

Foundation Medicine data


[block:callout] { "type": "info", "body": "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](https://gdc.cancer.gov/) (GDC). In keeping with this commitment, the CGC transitioned from hosting the CGHub version of this dataset to the [GDC Legacy Archive](https://portal.gdc.cancer.gov/legacy-archive/search/f) Data Release 11.0 version on July 10, 2018.\n\nAs 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](https://gdc.cancer.gov/support). 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." } [/block] Foundation Medicine ([FM](https://gdc.cancer.gov/about-gdc/contributed-genomic-data-cancer-research/foundation-medicine/foundation-medicine)) contains genomic profiling data from approximately 18,000 adult patients with a diverse array of cancers that underwent genomic profiling. Foundations Medicine Inc. ([FMI](https://www.foundationmedicine.com/)) 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](doc:about-the-data-browser). ###Cancer types [block:parameters] { "data": { "h-0": "Disease Type", "h-1": "Primary Site", "0-0": "Acinar Cell Neoplasms", "0-1": "Other and unspecified major salivary glands, Pancreas, Prostate gland", "1-0": "Adenomas and Adenocarcinomas", "1-1": "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", "2-0": "Adnexal and Skin Appendage Neoplasms", "2-1": "Skin", "3-0": "Basal Cell Neoplasms", "3-1": "Skin", "4-0": "Complex Epithelial Neoplasms", "4-1": "Breast, Bronchus and lung", "5-0": "Complex Mixed and Stromal Neoplasms", "5-1": "Bronchus and lung, Not Reported, Other and ill-defined digestive organs, Other and unspecified major salivary glands, Ovary, Uterus, NOS", "6-0": "Cystic, Mucinous and Serous Neoplasms", "6-1": "Colon, Other and unspecified female genital organs, Ovary, Pancreas, Retroperitoneum and peritoneum, Uterus, NOS", "7-0": "Ductal and Lobular Neoplasms", "7-1": "Breast, Kidney, Other and unspecified major salivary glands, Pancreas, Prostate gland, Thyroid gland", "8-0": "Epithelial Neoplasms, NOS", "8-1": "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", "9-0": "Germ Cell Neoplasms", "9-1": "Heart, mediastinum, and pleura, Ovary, Testis", "10-0": "Gliomas", "10-1": "Spinal cord, cranial nerves, and other parts of central nervous system", "11-0": "Meningiomas", "11-1": "Spinal cord, cranial nerves, and other parts of central nervous system", "12-0": "Mesothelial Neoplasms", "12-1": "Heart, mediastinum, and pleura", "13-0": "Miscellaneous Tumors", "13-1": "Not Reported", "14-0": "Mucoepidermoid Neoplasms", "14-1": "Other and ill-defined sites, Other and unspecified major salivary glands", "15-0": "Neuroepitheliomatous Neoplasms", "15-1": "Peripheral nerves and autonomic nervous system", "16-0": "Nevi and Melanomas", "16-1": "Anus and anal canal, Eye and adnexa, Other and ill-defined sites, Skin, Unknown", "17-0": "Not Reported", "17-1": "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", "18-0": "Paragangliomas and Glomus Tumors", "18-1": "Adrenal gland, Not Reported", "19-0": "Specialized Gonadal Neoplasms", "19-1": "Ovary", "20-0": "Squamous Cell Neoplasms", "20-1": "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", "21-0": "Thymic Epithelial Neoplasms", "21-1": "Thymus", "22-0": "Transitional Cell Papillomas and Carcinomas", "22-1": "Anus and anal canal, Bladder, Kidney, Other and unspecified urinary organs, Unknown, Ureter" }, "cols": 2, "rows": 23 } [/block] ###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](https://www.ncbi.nlm.nih.gov/gap/). [block:parameters] { "data": { "h-0": "Data Type", "h-1": "Data Format", "h-2": "Number of cases", "h-3": "NUmber of files", "h-4": "Estimated File Size", "0-0": "Clinical and Biospecimen", "0-1": "XML (original),\nTSV (GDC Generated)", "0-2": "18004", "0-3": "84", "0-4": "15 MB", "1-0": "Short Variants (substitutions and indels)", "1-1": "XML (original),\nMAF and VCF Files (GDC Generated)", "1-2": "18004", "h-5": "Data Access Level", "0-5": "Open", "1-3": "36050", "1-4": "173 MB", "1-5": "Controlled", "2-5": "Controlled", "3-5": "Controlled", "2-4": "Harmonized Results Coming Soon", "3-4": "Harmonized Results Coming Soon", "2-0": "Copy Number\nAlteration", "2-1": "XML (original)", "3-1": "XML (original)", "3-0": "Structural\nRearrangements", "2-2": "Harmonized Results Coming Soon", "2-3": "Harmonized Results Coming Soon", "3-2": "Harmonized Results Coming Soon", "3-3": "Harmonized Results Coming Soon" }, "cols": 6, "rows": 4 } [/block]