{"id":3024,"date":"2023-08-31T18:53:27","date_gmt":"2023-08-31T18:53:27","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-analysis-result\/tcga-breast-radiogenomics\/"},"modified":"2023-09-13T12:08:36","modified_gmt":"2023-09-13T12:08:36","slug":"tcga-breast-radiogenomics","status":"publish","type":"tcia_analysis_result","link":"https:\/\/cm.vastapps.dev\/tcia-analysis-result\/tcga-breast-radiogenomics\/","title":{"rendered":"TCGA-BREAST-RADIOGENOMICS"},"featured_media":0,"template":"","cancer_types":["Breast"],"citations":[2955,2956,2957,2958,2959,2960,2925],"full_export":"<h2 id=\"TCGABreastPhenotypeResearchGroupDatasets(TCGABreastRadiogenomics)-Description\">Description<\/h2><p>At the time of our study, 108 cases with breast MRI data were available in the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=3539225\">The Cancer Genome Atlas Breast Invasive Carcinoma Collection (TCGA-BRCA)<\/a>\u00a0collection. In order to minimize variations in image quality across the multi-institutional cases we included only breast MRI studies acquired on GE 1.5 Tesla magnet strength scanners (GE Medical Systems, Milwaukee, Wisconsin, USA) scanners, yielding a total of 93 cases. We then excluded cases that had missing images in the dynamic sequence (1 patient), or at the time did not have gene expression analysis available in the\u00a0<a href=\"http:\/\/tcga-data.nci.nih.gov\/\" class=\"external-link\" rel=\"nofollow\">TCGA Data Portal<\/a>\u00a0(8 patients). After these criteria, a dataset of 84 breast cancer patients resulted, with MRIs from four institutions: Memorial Sloan Kettering Cancer Center, the Mayo Clinic, the University of Pittsburgh Medical Center, and the Roswell Park Cancer Institute. The resulting cases contributed by each institution were 9 (date range 1999-2002), 5 (1999-2003), 46 (1999-2004), and 24 (1999-2002), respectively. The dataset of biopsy proven invasive breast cancers included 74 (88%) ductal, 8 (10%) lobular, and 2 (2%) mixed. Of these, 73 (87%) were ER+, 67 (80%) were PR+, and 19 (23%) were HER2+.\u00a0 Various types of analyses were conducted using the combined imaging, genomic, and clinical data.\u00a0 Those analyses are described within several manuscripts created by the group (cited below).<\/p><p><br\/><\/p><div class=\"tab-style-builtin\"><div class=\"localtabs-macro\"><div class=\"aui-tabs horizontal-tabs\" role=\"application\" data-aui-responsive=\"true\"><ul class=\"tabs-menu\"><li class=\"menu-item bv-localtab  active-tab \"><a href=\"#190391123fdac6fd16e0458b82c83e760920206f\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#1903911254b0f62037804f6789498f05d6cb472a\"><strong>Detailed Description<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#19039112643c18405f174aa3b6d2c874b379770b\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#19039112c044a281a0e3495db066f2ffb8c34369\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"190391123fdac6fd16e0458b82c83e760920206f\" active=\"true\" name=\"Data Access\" ><h3 id=\"TCGABreastPhenotypeResearchGroupDatasets(TCGABreastRadiogenomics)-DataAccess\"><span style=\"color: rgb(23,43,77);\">Data Access<\/span><\/h3><p><br\/><\/p><div class=\"table-wrap\"><table class=\"wrapped fixed-width confluenceTable\" style=\"width: 33.1174%;\"><colgroup><col style=\"width: 34.6721%;\"\/><col style=\"width: 38.2152%;\"\/><col style=\"width: 27.2164%;\"\/><\/colgroup><tbody><tr><th class=\"confluenceTh\">Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><th class=\"confluenceTh\">License<\/th><\/tr><tr><td class=\"confluenceTd\">Radiologist Annotations (XLS)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/tcga%20breast%20radiologist%20reads.xls?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Segmentations (ZIP, XLS)<\/p><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/TCGA_Segmented_Lesions_UofC.zip?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">Quantitative Radiomic Features<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/TCGA%20Run%202014_91cases_features_UChicago%20V2010%20MRI%20Workstation.xls?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\"><span style=\"color: rgb(33,37,41);\">MammaPrint, Oncotype DX, and PAM50\u00a0<\/span>Multi-gene Assays (XLS)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/Perou%20TCGA%20BRCA%20MRIs%2BPAM50%2BGHI21%2BNKI70%20MAILED.xlsx?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">Clinical Data (XLS)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/brca-clinicalforwiki.xls?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p><span style=\"color: rgb(23,43,77);\"><span style=\"color: rgb(33,37,41);\">Click the Versions tab for more info about data releases.<\/span><\/span><\/p><p><br\/><\/p><p style=\"text-align: left;\"><strong><span style=\"color: rgb(29,28,29);text-decoration: none;\">Collections Used in this Third Party Analysis<\/span><\/strong><br style=\"text-decoration: none;text-align: left;\"\/><span style=\"color: rgb(29,28,29);text-decoration: none;\">Below is a list of the Collections used in these analyses:<\/span><\/p><div class=\"table-wrap\"><table class=\"relative-table wrapped confluenceTable\" style=\"width: 32.0288%;\"><colgroup><col style=\"width: 35.1987%;\"\/><col style=\"width: 37.2983%;\"\/><col style=\"width: 27.483%;\"\/><\/colgroup><tbody><tr><th class=\"confluenceTh\">Source Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><th class=\"confluenceTh\">License<\/th><\/tr><tr><td class=\"confluenceTd\"><p><span style=\"color: rgb(33,37,41);\">Corresponding Original\u00a0 Images from <\/span><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a style=\"text-decoration: none;text-align: left;\" rel=\"nofollow\" class=\"external-link\" href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.AB2NAZRP\">TCGA-BRCA<\/a> <span style=\"color: rgb(33,37,41);\">(DICOM, 52G)<\/span><\/span><\/span><\/p><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/doiJNLP-I50pw3Gc.tcia?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><br\/><\/p><p>(Open with the<span style=\"color: rgb(23,43,77);\">\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\" style=\"text-decoration: underline;\">NBIA Data Retriever<\/a>\u00a0)<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p><br\/><\/p><p><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><span style=\"color: rgb(23,43,77);\">Please contact <a class=\"external-link\" rel=\"nofollow\" href=\"mailto:help@cancerimagingarchive.net\">help@cancerimagingarchive.net<\/a>\u00a0 with any questions regarding usage.<\/span><\/span><\/span><\/p><\/div><div class=\"tabs-pane \" id=\"1903911254b0f62037804f6789498f05d6cb472a\" name=\"Detailed Description\" ><h3 id=\"TCGABreastPhenotypeResearchGroupDatasets(TCGABreastRadiogenomics)-DetailedDescription\">Detailed Description<\/h3><p><u><strong>How to use the Segmentations<\/strong><\/u><\/p><p>With regards to the naming structure, *S2-1.les: S2 means DCE-MRI sequence 2, lesion #1. Sometimes, there are multiple DCE-MRI sequences on TCIA data, and so\u00a0the team used the sequence that corresponded to\u00a0the one on which the radiologists annotated the truth.\u00a0 Each of our tumor segmentation files is a binary file, consisting of the following format:<\/p><p>1. six uint16 values for the inclusive coordinates of the lesion\u2019s cuboid , relative to the image:<br\/>y_start y_end<br\/>x_start x_end<br\/>z_start z_end<\/p><p>2. the N int8 on\/off voxels (0 or 1) for the above specified cube, where N = (y_end y_start +1) * (x_end - x_start + 1) * (z_end - z_start + 1).<\/p><p>A voxel value of 1 denotes that it is part of the lesion, while a value of zero denotes it is not.<\/p><p><span style=\"letter-spacing: 0.0px;\">Please reference these data\u00a0<\/span> <span style=\"letter-spacing: 0.0px;\">extracted using version\u00a0<\/span> <span style=\"letter-spacing: 0.0px;\"> <strong> <u>V2010<\/u> <\/strong> <\/span> <span style=\"letter-spacing: 0.0px;\">\u00a0of the UChicago MRI Quantitative Radiomics workstation.<\/span><\/p><\/div><div class=\"tabs-pane \" id=\"19039112643c18405f174aa3b6d2c874b379770b\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"TCGABreastPhenotypeResearchGroupDatasets(TCGABreastRadiogenomics)-Citations&amp;DataUsagePolicy\">Citations &amp; Data Usage Policy\u00a0<\/h3><p class=\"auto-cursor-target\">\n<p>\nUsers must abide by the <a href=\"https:\/\/wiki.cancerimagingarchive.net\/x\/c4hF\" class=\"external-link\" rel=\"nofollow\">TCIA Data Usage Policy and Restrictions<\/a>. Attribution should include references to the following citations:\n<\/p><\/p><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Data Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p><span style=\"color: rgb(102,102,102);\"><span class=\"nolink\" style=\"color: rgb(0,0,0);\">Morris, E., Burnside, E., Whitman, G., Zuley, M., Bonaccio, E., Ganott, M., Sutton, E., Net, J., Brandt, K., Li, H., Drukker, K., Perou, C., &amp; Giger, M. L. (2014). <strong>Using Computer-extracted Image Phenotypes from Tumors on Breast MRI to Predict Stage [Data set]<\/strong>. The Cancer Imaging Archive. <a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2014.8SIPIY6G\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.7937\/K9\/TCIA.2014.8SIPIY6G<\/a><\/span><\/span><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">TCIA Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p><span style=\"color: rgb(102,102,102);\">Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., &amp; Prior, F. (2013). <strong>The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository<\/strong>. Journal of Digital Imaging, 26(6), 1045\u20131057. <a href=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1007\/s10278-013-9622-7<\/a><\/span><\/p><\/div><\/div><p><span style=\"color: rgb(23,43,77);\"> <strong>In addition to the dataset citation above, please be sure to cite the following if you utilize these data in your research:<\/strong> <\/span><\/p><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Publication Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p><span style=\"color: rgb(102,102,102);\">Guo, W., Li, H., Zhu, Y., Lan, L., Yang, S., Drukker, K., Morris, E., Burnside, E., Whitman, G., Giger, M. L., Ji, Y., &amp; TCGA Breast Phenotype Research Group. (2015). <strong>Prediction of clinical phenotypes in invasive breast carcinomas from the integration of radiomics and genomics data<\/strong>. Journal of Medical Imaging, 2(4), 041007. <a href=\"https:\/\/doi.org\/10.1117\/1.jmi.2.4.041007\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1117\/1.jmi.2.4.041007<\/a><\/span><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Publication Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Burnside E, Drukker K, Li H, Bonaccio E, Zuley M, Ganott M, Net JM, Sutton E, Brandt K, Whitman G, Conzen S, Lan L, Ji Y, Zhu Y, Jaffe C, Huang E, Freymann J, Kirby J, Morris EA, Giger ML. (2016)\u00a0 <strong>Using computer-extracted image phenotypes from tumors on breast MRI to predict breast cancer pathologic stage.<\/strong> Cancer 122(5): 748-757 . DOI: <a href=\"https:\/\/doi.org\/10.1002\/cncr.29791\" class=\"external-link\" rel=\"nofollow\">10.1002\/cncr.29791<\/a><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Publication Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Zhu Y, Li H, Guo W, Drukker K, Lan L, Giger ML*, Ji Y*:\u00a0 <strong>Deciphering genomic underpinnings of quantitative MRI-based radiomic phenotypes of invasive breast carcinoma<\/strong>.\u00a0 Nature \u2013 Scientific Reports 5:17787. doi: <a href=\"https:\/\/doi.org\/10.1038\/srep17787\" class=\"external-link\" rel=\"nofollow\">10.1038\/srep17787<\/a>, 2015.<\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Publication Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Li H, Zhu Y, Burnside ES, Drukker K, Hoadley KA, Fan C, Conzen SD, Whitman GJ, Sutton EJ, Net JM, Ganott M, Huang E, Morris EA, Perou CM, Ji Y, Giger ML. (2016) <strong>MR Imaging radiomics signatures for predicting the risk of breast cancer recurrence as given by research versions of gene assays of MammaPrint, Oncotype DX, and PAM50.\u00a0<\/strong> Radiology 281(2):382-391. doi: <a href=\"http:\/\/dx.doi.org\/10.1148\/radiol.2016152110\" class=\"external-link\" rel=\"nofollow\">10.1148\/radiol.2016152110<\/a><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Publication Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Li H, Zhu Y, Burnside ES, \u2026. Perou CM, Ji Y, Giger ML:\u00a0 <strong>Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA\/TCIA Dataset<\/strong>. npj Breast Cancer (2016) 2, 16012; doi:<a href=\"https:\/\/doi.org\/10.1038\/npjbcancer.2016.12\" class=\"external-link\" rel=\"nofollow\">10.1038\/npjbcancer.2016.12<\/a>; published online 11 May 2016.<\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Acknowledgment<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Please also include the following acknowledgement:<\/p><p>\u201cThe authors would like to thank the TCGA Breast Phenotype Research Group for providing the computer-extracted tumor segmentation data used in this study. The tumor segmentation data comes from the University of Chicago lab of Maryellen Giger,<br\/>whose lab members participated in the TCGA Breast Phenotype Research Group. In any presentation, poster, paper, etc, the segmentations should be identified as \u201cChicago Dynamic MRI Explorer 2005 Version\u201d. We would also like to acknowledge The Cancer Imaging Archive and The Cancer Genome Atlas initiatives for making the imaging and the clinical data used in this study publicly available.\u201d<\/p><\/div><\/div><h3 id=\"TCGABreastPhenotypeResearchGroupDatasets(TCGABreastRadiogenomics)-OtherPublicationsUsingThisData\">Other Publications Using This Data<\/h3><p><span>TCIA maintains<\/span> <a rel=\"nofollow\" href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\" class=\"external-link\"> a list of publications<\/a> <span> that leverage TCIA data. <\/span> If you have a manuscript you'd like to add please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" rel=\"nofollow\" class=\"external-link\"> contact the TCIA Helpdesk<\/a>.<\/p><\/div><div class=\"tabs-pane \" id=\"19039112c044a281a0e3495db066f2ffb8c34369\" name=\"Versions\" ><h3 id=\"TCGABreastPhenotypeResearchGroupDatasets(TCGABreastRadiogenomics)-Version1(Current):2018\/09\/04\">Version 1 (Current): 2018\/09\/04<\/h3><div class=\"table-wrap\"><table class=\"wrapped fixed-table confluenceTable\"><colgroup><col style=\"width: 188.0px;\"\/><col style=\"width: 239.0px;\"\/><\/colgroup><tbody><tr><th class=\"confluenceTh\">Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><\/tr><tr><td class=\"confluenceTd\">Images (DICOM)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/doiJNLP-I50pw3Gc.tcia?version=1&amp;modificationDate=1585591880465&amp;api=v2\" data-linked-resource-id=\"70222900\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"doiJNLP-I50pw3Gc.tcia\" data-linked-resource-content-type=\"application\/x-nbia-manifest-file\" data-linked-resource-container-id=\"19039112\" data-linked-resource-container-version=\"36\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image\" draggable=\"false\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/TCGA%20Breast%20Phenotype%20Research%20Group%20Data%20sets%20(TCGA-Breast-Radiogenomics)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">Annotations (XLS)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/tcga%20breast%20radiologist%20reads.xls?version=1&amp;modificationDate=1536079750689&amp;api=v2\" data-linked-resource-id=\"41517785\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"tcga breast radiologist reads.xls\" data-nice-type=\"Excel Spreadsheet\" data-linked-resource-content-type=\"application\/vnd.ms-excel\" data-linked-resource-container-id=\"19039112\" data-linked-resource-container-version=\"36\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image confluence-thumbnail\" draggable=\"false\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/TCGA%20Breast%20Phenotype%20Research%20Group%20Data%20sets%20(TCGA-Breast-Radiogenomics)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a><\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Segmentations (ZIP, XLS)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/TCGA_Segmented_Lesions_UofC.zip?version=1&amp;modificationDate=1531858341082&amp;api=v2\" data-linked-resource-id=\"39878997\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"TCGA_Segmented_Lesions_UofC.zip\" data-nice-type=\"Zip Archive\" data-linked-resource-content-type=\"application\/zip\" data-linked-resource-container-id=\"19039112\" data-linked-resource-container-version=\"36\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image confluence-thumbnail\" draggable=\"false\" alt=\"3D Segmentations\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/TCGA%20Breast%20Phenotype%20Research%20Group%20Data%20sets%20(TCGA-Breast-Radiogenomics)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a> <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/TCGA%20Run%202014_91cases_features_UChicago%20V2010%20MRI%20Workstation.xls?version=1&amp;modificationDate=1537206521480&amp;api=v2\" data-linked-resource-id=\"41517952\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"TCGA Run 2014_91cases_features_UChicago V2010 MRI Workstation.xls\" data-nice-type=\"Excel Spreadsheet\" data-linked-resource-content-type=\"application\/vnd.ms-excel\" data-linked-resource-container-id=\"19039112\" data-linked-resource-container-version=\"36\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image confluence-thumbnail\" draggable=\"false\" alt=\"Quantitative Radiomics\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/TCGA%20Breast%20Phenotype%20Research%20Group%20Data%20sets%20(TCGA-Breast-Radiogenomics)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a><\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Multi-gene Assays (XLS)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/Perou%20TCGA%20BRCA%20MRIs%2BPAM50%2BGHI21%2BNKI70%20MAILED.xlsx?version=1&amp;modificationDate=1531858646967&amp;api=v2\" data-linked-resource-id=\"39878998\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"Perou TCGA BRCA MRIs+PAM50+GHI21+NKI70 MAILED.xlsx\" data-nice-type=\"Excel Spreadsheet\" data-linked-resource-content-type=\"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet\" data-linked-resource-container-id=\"19039112\" data-linked-resource-container-version=\"36\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image confluence-thumbnail\" draggable=\"false\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/TCGA%20Breast%20Phenotype%20Research%20Group%20Data%20sets%20(TCGA-Breast-Radiogenomics)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a><\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Clinical Data (XLS)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/19039112\/brca-clinicalforwiki.xls?version=1&amp;modificationDate=1531858676301&amp;api=v2\" data-linked-resource-id=\"39878999\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"brca-clinicalforwiki.xls\" data-nice-type=\"Excel Spreadsheet\" data-linked-resource-content-type=\"application\/vnd.ms-excel\" data-linked-resource-container-id=\"19039112\" data-linked-resource-container-version=\"36\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image confluence-thumbnail\" draggable=\"false\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/TCGA%20Breast%20Phenotype%20Research%20Group%20Data%20sets%20(TCGA-Breast-Radiogenomics)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><\/div><\/div><\/div><\/div><p><br\/><\/p>","make_new_version_button":"","related_collections":["TCGA-BRCA"],"result_doi":"10.7937\/K9\/TCIA.2014.8SIPIY6G","versions":false,"cancer_locations":["Breast"],"publications_related":"","result_download_info":"<br\/>\n\nClick the Versions tab for more info about data releases.\n<br\/>\n<strong>Collections Used in this Third Party Analysis<\/strong><br\/>Below is a list of the Collections used in these analyses:\n\n<br\/>\nPlease contact <a href=\"mailto:help@cancerimagingarchive.net\">help@cancerimagingarchive.net<\/a>\u00a0 with any questions regarding usage.","result_downloads":[3155,3156,3157,3158,3159,3160],"result_page_accessibility":"Public","version_change_log_archived":"","additional_resources":"","date_updated":"2018-09-04","publications_using":"TCIA maintains <a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\"> a list of publications<\/a>  that leverage TCIA data.  If you have a manuscript you'd like to add please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\"> contact the TCIA Helpdesk<\/a>.","result_title":"TCGA Breast Phenotype Research Group Data sets","subjects":"84","detailed_description":"<u><strong>How to use the Segmentations<\/strong><\/u>\nWith regards to the naming structure, *S2-1.les: S2 means DCE-MRI sequence 2, lesion #1. Sometimes, there are multiple DCE-MRI sequences on TCIA data, and so\u00a0the team used the sequence that corresponded to\u00a0the one on which the radiologists annotated the truth.\u00a0 Each of our tumor segmentation files is a binary file, consisting of the following format:\n1. six uint16 values for the inclusive coordinates of the lesion\u2019s cuboid , relative to the image:<br\/>y_start y_end<br\/>x_start x_end<br\/>z_start z_end\n2. the N int8 on\/off voxels (0 or 1) for the above specified cube, where N = (y_end y_start +1) * (x_end - x_start + 1) * (z_end - z_start + 1).\nA voxel value of 1 denotes that it is part of the lesion, while a value of zero denotes it is not.\nPlease reference these data\u00a0 extracted using version\u00a0  <strong> <u>V2010<\/u> <\/strong>  \u00a0of the UChicago MRI Quantitative Radiomics workstation.","result_short_title":"TCGA-Breast-Radiogenomics","supporting_data":["Radiologist assessments of image features","Tumor segmentations","radiomic features","multi-gene assays"],"version_change_log":"","collections":"","result_browse_title":"","version_number":[],"collection_downloads":false,"result_summary":"At the time of our study, 108 cases with breast MRI data were available in the\u00a0<a href=\"\/pages\/viewpage.action?pageId=3539225\">The Cancer Genome Atlas Breast Invasive Carcinoma Collection (TCGA-BRCA)<\/a>\u00a0collection. In order to minimize variations in image quality across the multi-institutional cases we included only breast MRI studies acquired on GE 1.5 Tesla magnet strength scanners (GE Medical Systems, Milwaukee, Wisconsin, USA) scanners, yielding a total of 93 cases. We then excluded cases that had missing images in the dynamic sequence (1 patient), or at the time did not have gene expression analysis available in the\u00a0<a href=\"http:\/\/tcga-data.nci.nih.gov\/\">TCGA Data Portal<\/a>\u00a0(8 patients). After these criteria, a dataset of 84 breast cancer patients resulted, with MRIs from four institutions: Memorial Sloan Kettering Cancer Center, the Mayo Clinic, the University of Pittsburgh Medical Center, and the Roswell Park Cancer Institute. The resulting cases contributed by each institution were 9 (date range 1999-2002), 5 (1999-2003), 46 (1999-2004), and 24 (1999-2002), respectively. The dataset of biopsy proven invasive breast cancers included 74 (88%) ductal, 8 (10%) lobular, and 2 (2%) mixed. Of these, 73 (87%) were ER+, 67 (80%) were PR+, and 19 (23%) were HER2+.\u00a0 Various types of analyses were conducted using the combined imaging, genomic, and clinical data.\u00a0 Those analyses are described within several manuscripts created by the group (cited below).\n<br\/>","result_featured_image":false,"result_acknowledgements":"","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/analysis-results\/3024"}],"collection":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/analysis-results"}],"about":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/types\/tcia_analysis_result"}],"wp:attachment":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media?parent=3024"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}