{"id":5655,"date":"2023-09-04T03:15:40","date_gmt":"2023-09-04T03:15:40","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-collection\/ptrc-hgsoc\/"},"modified":"2023-09-13T12:01:44","modified_gmt":"2023-09-13T12:01:44","slug":"ptrc-hgsoc","status":"publish","type":"tcia_collection","link":"https:\/\/cm.vastapps.dev\/tcia-collection\/ptrc-hgsoc\/","title":{"rendered":"PTRC-HGSOC"},"featured_media":0,"template":"","citation-tax":[],"cancer_types":["High grade serous ovarian cancer"],"citations":[4581,4582,2925],"collection_doi":"10.7937\/6RDA-P940","collection_download_info":"Click the Versions tab for more info about data releases.\n<h4><u><strong>Clinical Data notes:<\/strong><\/u><\/h4>\nA note about the values in CSV spreadsheet \"PTRC-HGSOC_List_clinical_data\" Patient Age column, there are some ages that were anonymized in accordance with TCIA policy, that is, to bin any age over 89 into a common age group \"90+\". Please be aware that some of these are not actual ages of patients.","collection_downloads":[5194,5195],"full_export":"<h1 id=\"Proteogenomicanalysisofchemorefractoryhighgradeserousovariancancer(PTRCHGSOC)-Summary\">Summary<\/h1><p style=\"text-align: left;\"><span style=\"color: rgb(32,33,36);\">In our study, we have generated proteomic and genomic (RNA sequencing and whole genome sequencing) profiles from high grade serous ovarian cancer (HGSOC) tumor biopsies. All biospecimens are formalin-fixed, parrafin-embedded (FFPE) tissues and annotated for patient sensitivity to platinum chemotherapy (refractory or sensitive). For all 174 tumors that were analyzed, we have H&amp;E-stained and imaged the first and last sections (\u201cbookend\u201d) cut from each FFPE block to allow study of tumor pathology. These H&amp;E pathology images are uploaded in this dataset. The bookend FFPE slides were cut at 4 \u03bcm thickness using a microtome and mounted on glass slides (Leica Biosystems Cat# 3800040) for H&amp;E staining. Digital images of the H&amp;E slides were recorded using a ScanScope AT Slide Scanner (Leica Aperio Technologies, Vista, CA, USA) under 20X objective magnification (0.5 \u03bcm resolution). Images were analyzed by HALO Image Analysis Platform software (Indicta Labs, Albuquerque, New Mexico, USA).<\/span><\/p><p style=\"text-align: left;\">The following clinical data are also provided for these subjects:\u00a0<\/p><ul style=\"text-align: left;\"><li>Chemotherapy response status: (sensitive\/refractory; refractory is defined in our study as clinical ovarian cancer that progresses while on platinum-based therapy or within 4 weeks)<\/li><li>neo-adjuvant treatment (yes\/no)<\/li><li>Tumor location<\/li><li>Tumor grade, stage, substage<\/li><li>Patient age<\/li><li>Patient ethnicity<\/li><li>Patient race<\/li><li>Age of sample<\/li><\/ul><p style=\"text-align: left;\"><span style=\"color: rgb(32,33,36);\">The goals of the study were to understand mechanisms of platinum resistance in epithelial ovarian cancers (EOCs) in order to: i) predict EOCs that will respond to DNA-damaging platinum therapy, and ii) identify potential new drug targets in resistant disease to point to desperately needed new therapeutic approaches. The ability to predict platinum-resistant\/refractory disease would be clinically impactful by enabling the immediate triage of patients with refractory disease to clinical trials of experimental therapies, avoiding use of ineffective standard of care chemotherapy and helping to identify novel treatments. In this study, we generated proteomic and genomic (RNA sequencing and whole genome sequencing) profiling datasets and H&amp;E images from high grade serous ovarian cancer (HGSOC) tumor biopsies representing platinum-sensitive and platinum-refractory disease.<\/span><\/p><p><br\/><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=\"#1457551529ba0f6d7166845d88ea4d96f32f0c097\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#14575515298a69c5e18ad4bc6830e870bde7ad1e6\"><strong>Detailed Description<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#145755152fe28d6f997f64317a780ac52342f7cd0\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#14575515274ca2fa474884476a4946bc25b29b0ed\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"1457551529ba0f6d7166845d88ea4d96f32f0c097\" active=\"true\" name=\"Data Access\" ><h3 id=\"Proteogenomicanalysisofchemorefractoryhighgradeserousovariancancer(PTRCHGSOC)-DataAccess\">Data Access<\/h3><div class=\"table-wrap\"><table class=\"wrapped relative-table confluenceTable\" style=\"width: 84.0354%;\"><colgroup><col style=\"width: 47.9418%;\"\/><col style=\"width: 30.2821%;\"\/><col style=\"width: 21.7209%;\"\/><\/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\"><span style=\"color: rgb(33,37,41);\">Tissue Slide Images (SVS, 120.5 GB)<\/span><\/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:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/365?passcode=98493b0851c5e85b3100058110bb6aff73ae6280\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/pathdb.cancerimagingarchive.net\/imagesearch?f[0]=collection:ptrc_hgsoc\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><\/p><span style=\"color: rgb(33,37,41);text-decoration: none;\">(Download requires Aspera plugin<\/span>)<\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 4.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">Clinical data (CSV)<\/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\/145755152\/PTRC-HGSOC_List_clincal_data.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\/4.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 4.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p>Click the Versions tab for more info about data releases.<\/p><h4 class=\"auto-cursor-target\" id=\"Proteogenomicanalysisofchemorefractoryhighgradeserousovariancancer(PTRCHGSOC)-ClinicalDatanotes:\"><u><strong>Clinical Data notes:<\/strong><\/u><\/h4><p class=\"auto-cursor-target\"><span style=\"color: rgb(23,43,77);\">A note about the values in CSV spreadsheet &quot;PTRC-HGSOC_List_clinical_data&quot; Patient Age column, there are some ages that were anonymized in accordance with TCIA policy, that is, to bin any age over 89 into a common age group &quot;90+&quot;. Please be aware that some of these are not actual ages of patients.<\/span><\/p><\/div><div class=\"tabs-pane \" id=\"14575515298a69c5e18ad4bc6830e870bde7ad1e6\" name=\"Detailed Description\" ><h3 id=\"Proteogenomicanalysisofchemorefractoryhighgradeserousovariancancer(PTRCHGSOC)-DetailedDescription\">Detailed Description<\/h3><div class=\"table-wrap\"><table class=\"wrapped confluenceTable\"><colgroup><col\/><col\/><\/colgroup><tbody><tr><th class=\"confluenceTh\"><p>Image Statistics<\/p><\/th><th class=\"confluenceTh\">Pathology Image Statistics<\/th><\/tr><tr><td class=\"confluenceTd\"><p>Modalities<\/p><\/td><td class=\"confluenceTd\"><p>Pathology<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Patients<\/p><\/td><td class=\"confluenceTd\"><p>174<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Images<\/p><\/td><td class=\"confluenceTd\"><p>348<\/p><\/td><\/tr><tr><td class=\"confluenceTd\">Images Size (GB)<\/td><td class=\"confluenceTd\">120.5<\/td><\/tr><\/tbody><\/table><\/div><h4 class=\"auto-cursor-target\" id=\"Proteogenomicanalysisofchemorefractoryhighgradeserousovariancancer(PTRCHGSOC)-ClinicalDatanotes:.1\"><u><strong>Clinical Data notes:<\/strong><\/u><\/h4><p class=\"auto-cursor-target\"><span style=\"color: rgb(23,43,77);\">A note about the values in CSV spreadsheet &quot;PTRC-HGSOC_List_clinical_data&quot; Patient Age column, there are some ages that were anonymized in accordance with TCIA policy, that is, to bin any age over 89 into a common age group &quot;90+&quot;. Please be aware that some of these are not actual ages of patients.<\/span><\/p><\/div><div class=\"tabs-pane \" id=\"145755152fe28d6f997f64317a780ac52342f7cd0\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"Proteogenomicanalysisofchemorefractoryhighgradeserousovariancancer(PTRCHGSOC)-Citations&amp;DataUsagePolicy\">Citations &amp; Data Usage Policy<\/h3><p>\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\"><span style=\"color: rgb(0,0,0);\">Chowdhury, S., Kennedy, J. J., Ivey, R. G., Murillo, O., Hosseini, N., Song, X., Petralia, F., Calinawan, A., Voytovich, U. J., Savage, S. R., Berry, A., Reva, B., Ozbek, U., Krek, A., Ma, W., da Veiga Leprevost, F., Ji, J., Yoo, S., Lin, C., \u2026 Paulovich, A. G. (2023). Proteogenomic analysis of chemo-refractory high grade serous ovarian cancer (PTRC-HGSOC) (Version 1) [dataset]. The Cancer Imaging Archive. <a href=\"https:\/\/doi.org\/10.7937\/6RDA-P940\" style=\"color: rgb(0,0,0);\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.7937\/6RDA-P940<\/a><\/span><\/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><span style=\"color: rgb(0,0,0);\">Chowdhury, S., Kennedy, J. J., Ivey, R. G., Murillo, O. D., Hosseini, N., Song, X., Petralia, F., Calinawan, A., Savage, S. R., Berry, A. B., Reva, B., Ozbek, U., Krek, A., Ma, W., da Veiga Leprevost, F., Ji, J., Yoo, S., Lin, C., Voytovich, U. J., \u2026 Paulovich, A. G. (2023). Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. In Cell (Vol. 186, Issue 16, pp. 3476-3498.e35). Elsevier BV. <a style=\"color: rgb(0,0,0);\" href=\"https:\/\/doi.org\/10.1016\/j.cell.2023.07.004\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1016\/j.cell.2023.07.004<\/a><\/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(0,0,0);text-decoration: none;\">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). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045\u20131057). Springer Science and Business Media LLC.<\/span><span style=\"color: rgb(102,102,102);text-decoration: none;\"> <\/span><span style=\"color: rgb(102,102,102);text-decoration: none;\"><a title=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" href=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" class=\"external-link\" rel=\"nofollow\"><span>https:\/\/doi.org\/10.1007\/s10278-013-9622-7<\/span><\/a><\/span><\/p><\/div><\/div><h3 id=\"Proteogenomicanalysisofchemorefractoryhighgradeserousovariancancer(PTRCHGSOC)-OtherPublicationsUsingThisData\">Other Publications Using This Data<\/h3><p><span>TCIA maintains\u00a0<\/span><a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\" class=\"external-link\" rel=\"nofollow\">a list of publications<\/a><span> which leverage TCIA data. <\/span> If you have a manuscript you'd like to add please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" class=\"external-link\" rel=\"nofollow\"> contact the TCIA Helpdesk<\/a>.<\/p><\/div><div class=\"tabs-pane \" id=\"14575515274ca2fa474884476a4946bc25b29b0ed\" name=\"Versions\" ><h3 id=\"Proteogenomicanalysisofchemorefractoryhighgradeserousovariancancer(PTRCHGSOC)-Version1(Current):Updated2023\/08\/03\">Version 1 (Current): Updated 2023\/08\/03<\/h3><div class=\"table-wrap\"><table class=\"wrapped confluenceTable\"><colgroup><col\/><col\/><col\/><\/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\"><span style=\"color: rgb(33,37,41);\">Tissue Slide Images (SVS, 120.5 GB)<\/span><\/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:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/365?passcode=98493b0851c5e85b3100058110bb6aff73ae6280\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/pathdb.cancerimagingarchive.net\/imagesearch?f[0]=collection:ptrc_hgsoc\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 4.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">Clinical data (CSV)<\/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\/145755152\/PTRC-HGSOC_List_clincal_data.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\/4.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 4.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><\/div><\/div><\/div><\/div><p><br\/><\/p><p><br\/><\/p>","versions":false,"additional_resources":"","cancer_locations":["Ovary"],"collection_page_accessibility":"Public","publications_related":"","version_change_log":"","version_change_log_archived":"","analysis_results":"","collection_status":"Complete","publications_using":"TCIA maintains\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\">a list of publications<\/a> which 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>.","species":["Human"],"collection_title":"Proteogenomic analysis of chemo-refractory high grade serous ovarian cancer","detailed_description":"<h4><u><strong>Clinical Data notes:<\/strong><\/u><\/h4>\nA note about the values in CSV spreadsheet \"PTRC-HGSOC_List_clinical_data\" Patient Age column, there are some ages that were anonymized in accordance with TCIA policy, that is, to bin any age over 89 into a common age group \"90+\". Please be aware that some of these are not actual ages of patients.","related_analysis_results":false,"subjects":"174","collection_short_title":"PTRC-HGSOC","data_types":["Pathology"],"date_updated":"2023-09-13","collection_browse_title":"","supporting_data":["Clinical"],"collection_featured_image":false,"collection_summary":"In our study, we have generated proteomic and genomic (RNA sequencing and whole genome sequencing) profiles from high grade serous ovarian cancer (HGSOC) tumor biopsies. All biospecimens are formalin-fixed, parrafin-embedded (FFPE) tissues and annotated for patient sensitivity to platinum chemotherapy (refractory or sensitive). For all 174 tumors that were analyzed, we have H&amp;E-stained and imaged the first and last sections (\u201cbookend\u201d) cut from each FFPE block to allow study of tumor pathology. These H&amp;E pathology images are uploaded in this dataset. The bookend FFPE slides were cut at 4 \u03bcm thickness using a microtome and mounted on glass slides (Leica Biosystems Cat# 3800040) for H&amp;E staining. Digital images of the H&amp;E slides were recorded using a ScanScope AT Slide Scanner (Leica Aperio Technologies, Vista, CA, USA) under 20X objective magnification (0.5 \u03bcm resolution). Images were analyzed by HALO Image Analysis Platform software (Indicta Labs, Albuquerque, New Mexico, USA).<p>The following clinical data are also provided for these subjects:\u00a0<\/p><ul><li>Chemotherapy response status: (sensitive\/refractory; refractory is defined in our study as clinical ovarian cancer that progresses while on platinum-based therapy or within 4 weeks)<\/li><li>neo-adjuvant treatment (yes\/no)<\/li><li>Tumor location<\/li><li>Tumor grade, stage, substage<\/li><li>Patient age<\/li><li>Patient ethnicity<\/li><li>Patient race<\/li><li>Age of sample<\/li><\/ul><p>The goals of the study were to understand mechanisms of platinum resistance in epithelial ovarian cancers (EOCs) in order to: i) predict EOCs that will respond to DNA-damaging platinum therapy, and ii) identify potential new drug targets in resistant disease to point to desperately needed new therapeutic approaches. The ability to predict platinum-resistant\/refractory disease would be clinically impactful by enabling the immediate triage of patients with refractory disease to clinical trials of experimental therapies, avoiding use of ineffective standard of care chemotherapy and helping to identify novel treatments. In this study, we generated proteomic and genomic (RNA sequencing and whole genome sequencing) profiling datasets and H&amp;E images from high grade serous ovarian cancer (HGSOC) tumor biopsies representing platinum-sensitive and platinum-refractory disease.<\/p>\n<br\/><br\/>","collection_acknowledgements":"","collection_funding":"","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections\/5655"}],"collection":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections"}],"about":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/types\/tcia_collection"}],"wp:attachment":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media?parent=5655"}],"wp:term":[{"taxonomy":"tcia_citation_tax","embeddable":true,"href":"https:\/\/cm.vastapps.dev\/api\/v1\/citation-tax?post=5655"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}