{"id":43753,"date":"2023-11-20T03:50:00","date_gmt":"2023-11-20T09:50:00","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/collection\/tcga-brca\/"},"modified":"2024-08-23T19:05:02","modified_gmt":"2024-08-24T00:05:02","slug":"tcga-brca","status":"publish","type":"tcia_collection","link":"https:\/\/stage.cancerimagingarchive.net\/collection\/tcga-brca\/","title":{"rendered":"TCGA-BRCA"},"featured_media":0,"template":"","class_list":["post-43753","tcia_collection","type-tcia_collection","status-publish"],"cancer_types":["Breast Cancer"],"citations":[43731,43733,9225],"collection_doi":"10.7937\/K9\/TCIA.2016.AB2NAZRP","collection_download_info":"","collection_downloads":[43735],"versions":[43749,43751],"additional_resources":"The NCI Cancer Research Data Commons (CRDC) provides access to additional data and a cloud-based data science infrastructure that connects data sets with analytics tools to allow users to share, integrate, analyze, and visualize cancer research data.\r\n<ul>\r\n \t<li><a href=\"https:\/\/portal.imaging.datacommons.cancer.gov\/explore\/filters\/?collection_id=tcga_brca\">Imaging Data Commons (IDC)<\/a>\u00a0(Imaging Data)<\/li>\r\n \t<li><a href=\"https:\/\/portal.gdc.cancer.gov\/projects\/TCGA-BRCA\">Genomic Data Commons (GDC)<\/a>\u00a0(Genomic, Digitized Histopathology &amp; Clinical Data)<\/li>\r\n<\/ul>","cancer_locations":["Breast"],"collection_page_accessibility":"Public","publications_related":"","version_change_log_archived":"<h3>Version 3 (Current): Updated 2020\/05\/29<\/h3><table><colgroup><col \/><col \/><\/colgroup><tbody><tr><th colspan=\"1\">Data Type<\/th><th colspan=\"1\">Download all or Query\/Filter<\/th><\/tr><tr><td colspan=\"1\">Images (DICOM, 88.1GB)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/TCIA_TCGA-BRCA_09-16-2015.tcia\" download=\"TCIA_TCGA-BRCA_09-16-2015.tcia\"><button><i><\/i> Download<\/button><\/a>\u00a0 <a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=TCGA-BRCA\"><button><i><\/i> Search<\/button><\/a>\u00a0<\/p><p>(Download requires the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Tissue Slide Images (web)<\/td><td colspan=\"1\"><div><p><a href=\"https:\/\/portal.gdc.cancer.gov\/image-viewer?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22content%22%3A%7B%22field%22%3A%22cases.case_id%22%2C%22value%22%3A%5B%22set_id%3AYEEmK4gB-Ny-1EyOwW07%22%5D%7D%2C%22op%22%3A%22IN%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-BRCA%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_type%22%2C%22value%22%3A%5B%22Slide%20Image%22%5D%7D%7D%5D%7D\"><button><i><\/i> Search<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Clinical Data (TXT)<\/td><td colspan=\"1\"><div><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/3539225\/gdc_download_clinical_brca.tar.gz?version=1&amp;modificationDate=1590767151599&amp;api=v2\" download=\"\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Biomedical Data (TXT)<\/td><td colspan=\"1\"><div><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/3539225\/gdc_download_biomedical_brca.tar.gz?version=1&amp;modificationDate=1590767187116&amp;api=v2\" download=\"\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Genomics (web)<\/td><td colspan=\"1\"><div><p><a href=\"https:\/\/portal.gdc.cancer.gov\/projects\/TCGA-BRCA\"><button><i><\/i> Search<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><\/tbody><\/table><p>Updated clinical data link with latest spreadsheets from GDC. Added new biomedical spreadsheets from GDC.<\/p><h3>Version 2: Updated 2016\/09\/08<\/h3><p>Downloads require\u00a0the <a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>.<\/p><table><colgroup><col \/><col \/><\/colgroup><tbody><tr><th colspan=\"1\">Data Type<\/th><th colspan=\"1\">Download all or Query\/Filter<\/th><\/tr><tr><td colspan=\"1\">Images (DICOM, 88.1GB)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/TCIA_TCGA-BRCA_09-16-2015.tcia\" download=\"TCIA_TCGA-BRCA_09-16-2015.tcia\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><p>(Download requires the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Clinical Data (TXT)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/TCGA-BRCA-Clinical-Data-090616.zip\" download=\"TCGA-BRCA-Clinical-Data-090616.zip\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Genomics (web)<\/td><td colspan=\"1\"><div><p><a href=\"https:\/\/portal.gdc.cancer.gov\/projects\/TCGA-BRCA\"><button><i><\/i> Search<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><\/tbody><\/table><p>Extracted latest release of clinical data (TXT) from the GDC Data Portal.<\/p><h3>Version 1: Updated 2014\/12\/30<\/h3><table><colgroup><col \/><col \/><\/colgroup><tbody><tr><th colspan=\"1\">Data Type<\/th><th colspan=\"1\">Download all or Query\/Filter<\/th><\/tr><tr><td colspan=\"1\">Images (DICOM, 88.1GB)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/TCIA_TCGA-BRCA_09-16-2015.tcia\" download=\"TCIA_TCGA-BRCA_09-16-2015.tcia\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><p>(Download requires the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Clinical Data (TXT)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/TCGA-BRCA-Clinical-Data.zip\" download=\"TCGA-BRCA-Clinical-Data.zip\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Genomics (web)<\/td><td colspan=\"1\"><div><p><a href=\"https:\/\/portal.gdc.cancer.gov\/projects\/TCGA-BRCA\"><button><i><\/i> Search<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><\/tbody><\/table>","collection_status":"Complete","publications_using":"TCIA maintains\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\">a list of publications<\/a> which leverage our data. If you have a manuscript you'd like to add please <a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\">contact TCIA's Helpdesk<\/a>.","related_analysis_results":[45551,45635,45713,45915,45937,45965,45803],"species":["Human"],"version_number":"3","collection_title":"The Cancer Genome Atlas Breast Invasive Carcinoma Collection","date_updated":"2020-05-29","related_collection":false,"subjects":"139","analysis_results":"","collection_short_title":"TCGA-BRCA","data_types":["MR","MG"],"version_change_log":"Updated clinical data link with latest spreadsheets from GDC. Added new biomedical spreadsheets from GDC.","collection_browse_title":"TCGA-BRCA","detailed_description":"<h3>GDC Data Portal - Clinical and Genomic Data<\/h3>\r\nThe\u00a0<a href=\"https:\/\/portal.gdc.cancer.gov\/exploration?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22TCGA%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-BRCA%22%5D%7D%7D%5D%7D\">GDC Data Portal<\/a>\u00a0has extensive clinical and genomic data, which can be matched to the patient identifiers on the images here in TCIA. \u00a0Below is a snapshot of clinical data extracted on 9\/8\/2016.\r\n<ul>\r\n \t<li><a href=\"\/wp-content\/uploads\/TCGA-BRCA-Clinical-Data-090616.zip\" download=\"TCGA-BRCA-Clinical-Data-090616.zip\" data-linked-resource-container-id=\"3539225\" data-linked-resource-container-version=\"114\" data-linked-resource-content-type=\"application\/zip\" data-linked-resource-default-alias=\"TCGA-BRCA Clinical Data 090616.zip\" data-linked-resource-id=\"22643551\" data-linked-resource-type=\"attachment\" data-linked-resource-version=\"1\" data-nice-type=\"Zip Archive\">TCGA-BRCA Clinical Data.zip<\/a><\/li>\r\n<\/ul>\r\nExplanations of the clinical data can be found on the Biospecimen Core Resource Clinical Data Forms linked below:\r\n<ul>\r\n \t<li><a href=\"\/wp-content\/uploads\/Breast-Case-Quality-Control-Form-1.pdf\" download=\"Breast-Case-Quality-Control-Form-1.pdf\" data-linked-resource-container-id=\"3539225\" data-linked-resource-container-version=\"114\" data-linked-resource-content-type=\"application\/pdf\" data-linked-resource-default-alias=\"Breast Case Quality Control Form (1).pdf\" data-linked-resource-id=\"70225472\" data-linked-resource-type=\"attachment\" data-linked-resource-version=\"1\" data-nice-type=\"PDF Document\">Breast Case Quality Control Form<\/a><\/li>\r\n \t<li><a href=\"\/wp-content\/uploads\/Breast-Enrollment-Form.pdf\" download=\"Breast-Enrollment-Form.pdf\" data-linked-resource-container-id=\"3539225\" data-linked-resource-container-version=\"114\" data-linked-resource-content-type=\"application\/pdf\" data-linked-resource-default-alias=\"Breast Enrollment Form.pdf\" data-linked-resource-id=\"70225473\" data-linked-resource-type=\"attachment\" data-linked-resource-version=\"1\" data-nice-type=\"PDF Document\">Breast Enrollment Form<\/a><\/li>\r\n \t<li><a href=\"\/wp-content\/uploads\/Breast-FollowUp-Form.pdf\" download=\"Breast-FollowUp-Form.pdf\" data-linked-resource-container-id=\"3539225\" data-linked-resource-container-version=\"114\" data-linked-resource-content-type=\"application\/pdf\" data-linked-resource-default-alias=\"Breast FollowUp Form.pdf\" data-linked-resource-id=\"70225474\" data-linked-resource-type=\"attachment\" data-linked-resource-version=\"1\" data-nice-type=\"PDF Document\">Breast Follow-Up Form<\/a><\/li>\r\n<\/ul>\r\n<h3>A Note about TCIA and TCGA Subject Identifiers and Dates<\/h3>\r\n<strong>Subject Identifiers:<\/strong>\u00a0a subject with radiology images stored in TCIA is identified with a Patient ID that is identical to the Patient ID of the same subject with demographic, clinical, pathological, and\/or genomic data stored in TCGA. For each TCGA case, the baseline TCGA imaging studies found on TCIA are pre-surgical.\r\n\r\n<strong>Dates:<\/strong>\u00a0TCIA and TCGA handle dates differently, and there are no immediate plans to reconcile:\r\n<ul>\r\n \t<li><u>TCIA Dates:<\/u>\u00a0dates (be they birth dates, imaging study dates, etc.) in the Digital Imaging and Communications in Medicine (DICOM) headers of TCIA radiology images have been offset by a random number of days. The offset is a number of days between 3 and 10 years prior to the real date that is consistent for each TCIA image-submitting site and collection, but that varies among sites and among collections from the same site. Thus, the number of days between a subject\u2019s longitudinal imaging studies are accurately preserved when more than one study has been archived while still meeting HIPAA requirements.<\/li>\r\n \t<li><u>TCGA Dates:<\/u>\u00a0the patient demographic and clinical event dates are all the number of days from the index date, which is the actual date of pathologic diagnosis. So all the dates in the data are relative negative or positive integers, except for the \u201cdays_to_pathologic_diagnosis\u201d value, which is 0 \u2013 the index date. The years of birth and diagnosis are maintained in the distributed clinical data file. The NCI retains a copy of the data with complete dates, but those data are not made available.With regard to other TCGA dates, if a date comes from a HIPAA \u201ccovered entity\u2019s\u201d medical record, it is turned into the relative day count from the index date. Dates like the date TCGA received the specimen or when the TCGA case report form was filled out are not such covered dates, and they will appear as\u00a0real dates (month, day, and year).<\/li>\r\n<\/ul>","supporting_data":["Clinical","Genomics","Image Analyses","Histopathology"],"collection_featured_image":false,"collection_summary":"<p>The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) data collection is part of a larger effort to\u00a0build a research community focused on connecting cancer phenotypes to genotypes by providing clinical images matched to subjects from\u00a0<a href=\"http:\/\/cancergenome.nih.gov\/\">The Cancer Genome Atlas (TCGA)<\/a>. Clinical, genetic, and pathological data resides in the\u00a0<a href=\"https:\/\/portal.gdc.cancer.gov\/exploration?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22TCGA%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-BRCA%22%5D%7D%7D%5D%7D\">Genomic Data Commons (GDC) Data Portal<\/a> while the radiological data is stored on The Cancer Imaging Archive (TCIA).\u00a0<\/p><p>Matched TCGA patient identifiers allow researchers to explore the TCGA\/TCIA databases for correlations between tissue genotype, radiological phenotype and patient outcomes. \u00a0Tissues for TCGA were collected from many sites all over the world in order to reach their accrual targets, usually around 500 specimens per cancer type. \u00a0For this reason the image data sets are also extremely heterogeneous in terms of scanner modalities, manufacturers and acquisition protocols. \u00a0In most cases the images were acquired as part of routine care and not as part of a controlled research study or clinical trial.\u00a0<\/p><h3>CIP TCGA Radiology Initiative<\/h3><p>Imaging Source Site (ISS) Groups are being populated and governed by participants from institutions that have provided imaging data to the archive for a given cancer type. Modeled after TCGA analysis groups, ISS groups are given the opportunity to publish a marker paper for a given cancer type\u00a0per\u00a0the guidelines in the table above. This opportunity will generate increased participation in building these multi-institutional data sets as they become an open community resource. \u00a0Learn more about the\u00a0<u><strong><a href=\"\/display\/Public\/TCGA+Breast+Phenotype+Research+Group\">TCGA Breast Phenotype Research Group<\/a><\/strong><\/u>.<\/p>","collection_acknowledgements":"<p>We would like to acknowledge the individuals and institutions that have provided data for this collection:<\/p><ul><li>Mayo Clinic, Rochester, MN - Special thanks to\u00a0<strong>Wilma Lingle, MD and\u00a0<strong>Bradley J. Erickson, MD, Ph.D.<\/strong><\/strong>\u00a0from the Department of Radiology, Mayo Medical School.<\/li><li>University of Pittsburgh\/UPMC, Pittsburgh, PA - Special thanks to\u00a0\u00a0<strong>Margarita L Zuley, MD and\u00a0<strong>Rose Jarosz<\/strong>.<br \/><\/strong><\/li><li><p>Roswell Park, Buffalo, NY - Special thanks to\u00a0<strong>Ermelinda Bonaccio, MD<\/strong>\u00a0and\u00a0<strong>Joe Filippin<\/strong>i from the Department of Diagnostic Radiology.<\/p><\/li><li><p>University of Miami, Miller School of Medicine, Miami, FL - Special thanks to\u00a0<strong>Jose M. Net<\/strong>,\u00a0<strong>MD<\/strong>\u00a0and\u00a0<strong>Len Levi<\/strong>.<\/p><\/li><li><p>Memorial Sloan-Kettering Cancer Center\/MSKCC, New York, NY - Special thanks to\u00a0<strong>Elizabeth A Morris MD<\/strong>,\u00a0<strong>Gloria Guman Figler, and Pierre Elnajjar<\/strong>.<\/p><\/li><li>University of North Carolina, Chapel Hill, NC - Special thanks to\u00a0<strong>J. Keith Smith<\/strong>,\u00a0<strong>MD, Ph.D.<\/strong>\u00a0and\u00a0<strong>Shanah Kirk<\/strong>\u00a0from the Department of Radiology.<\/li><li>University of Chicago, Chicago, IL\u00a0\u2013 Special thanks to\u00a0<strong>Maryellen Giger, MD<\/strong>, and\u00a0<strong>Nick Gruszauskas, PhD<\/strong>, from the Department of Radiology.<\/li><\/ul>","collection_funding":"","hide_from_browse_table":"0","program":["TCGA"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/43753","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections"}],"about":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/types\/tcia_collection"}],"version-history":[{"count":1,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/43753\/revisions"}],"predecessor-version":[{"id":47403,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/43753\/revisions\/47403"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=43753"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}