{"id":5619,"date":"2023-09-04T03:13:06","date_gmt":"2023-09-04T03:13:06","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-collection\/ivygap\/"},"modified":"2023-09-13T12:00:07","modified_gmt":"2023-09-13T12:00:07","slug":"ivygap","status":"publish","type":"tcia_collection","link":"https:\/\/cm.vastapps.dev\/tcia-collection\/ivygap\/","title":{"rendered":"IVYGAP"},"featured_media":0,"template":"","citation-tax":[],"cancer_types":["Glioblastoma"],"citations":[4513,4514,2925],"collection_doi":"10.7937\/K9\/TCIA.2016.XLwaN6nL","collection_download_info":"Some data in this collection contains images that could potentially be used to reconstruct a human face.  To safeguard the privacy of participants, users must sign and submit a <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\">TCIA Restricted License Agreement<\/a> to <a href=\"mailto:help@cancerimagingarchive.net\">help@cancerimagingarchive.net<\/a> before accessing the data.\n\nClick the Versions tab for more info about data releases.","collection_downloads":[5101],"full_export":"<h1 id=\"IvyGlioblastomaAtlasProject(IvyGAP)-Summary\">Summary<\/h1>This data collection consists of MRI\/CT scan data for brain tumor patients that form the cohort for the resource Ivy Glioblastoma Atlas Project (Ivy GAP). There are 390 studies for 39 patients that include pre-surgery, post-surgery and follow up scans. The Ivy GAP is a collaborative partnership between the <a href=\"http:\/\/ivyfoundation.org\/\" class=\"external-link\" rel=\"nofollow\">Ben and Catherine Ivy Foundation<\/a>, which generously provided the financial support, the <a href=\"https:\/\/www.alleninstitute.org\/\" class=\"external-link\" rel=\"nofollow\">Allen Institute for Brain Science<\/a>, and the <a href=\"http:\/\/www.swedish.org\/services\/neuroscience-institute\/our-services\/ivy-center\" class=\"external-link\" rel=\"nofollow\">Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment<\/a>. The goal of the project is to provide online resources to scientists and physicians dedicated to the development of innovative treatments and diagnostics that will enhance the quality of life and survival of patients with brain cancer.<p>These resources represent an unprecedented platform for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels. In addition to the DICOM images in TCIA there are two interactive databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities:<\/p><ol><li><a href=\"http:\/\/glioblastoma.alleninstitute.org\/\" class=\"external-link\" rel=\"nofollow\"> <span>Ivy Glioblastoma Atlas Project<\/span> <\/a> - An open\/public database providing in situ hybridization (ISH) and RNA sequencing (RNA-Seq) data, which map gene expression across the anatomic structures and putative cancer stem cell clusters in glioblastoma. The associated histological dataset is annotated and is suitable for neuropathological examination.<\/li><li><a href=\"https:\/\/ivygap.org\/home\" class=\"external-link\" rel=\"nofollow\">Ivy GAP Clinical and Genomic Database<\/a> -\u00a0 A database offering detailed clinical, genomic, and expression array data sets that are designed to elucidate the pathways involved in glioblastoma development and progression. This database requires registration for access.<\/li><\/ol><p><span style=\"color: rgb(31,73,125);\">The Ivy GAP is described in the resource paper (70 authors not all listed here) :\u00a0<\/span><span style=\"color: rgb(31,73,125);\">Puchalski, R. B., Shah, N., \u2026, Foltz, G. D. (2018). <strong>An anatomic transcriptional atlas of human glioblastoma.<\/strong> In Science (Vol. 360, Issue 6389, pp. 660\u2013663).\u00a0 <a href=\"https:\/\/doi.org\/10.1126\/science.aaf2666\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1126\/science.aaf2666<\/a><\/span><\/p><p><span style=\"color: rgb(31,73,125);\">For scientific or other inquiries about this dataset, please\u00a0<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" class=\"external-link\" rel=\"nofollow\" style=\"text-decoration: underline;text-align: left;\">contact the TCIA Helpdesk<\/a><span style=\"color: rgb(33,37,41);\">.<\/span><\/span><\/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=\"#22515597d212867019114558b1c5e052c23c5434\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#22515597b7feb4d1e1a14964b1ae9b703332245f\"><strong>Detailed Description<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#2251559774598bde57704e04ba1ba1173b4e9abe\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#22515597423771f2d50e4167913545d4a8f0270c\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"22515597d212867019114558b1c5e052c23c5434\" active=\"true\" name=\"Data Access\" ><h3 id=\"IvyGlioblastomaAtlasProject(IvyGAP)-DataAccess\">Data Access<\/h3><p>\nSome data in this collection contains images that could potentially be used to reconstruct a human face.  To safeguard the privacy of participants, users must sign and submit a <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\" class=\"external-link\" rel=\"nofollow\">TCIA Restricted License Agreement<\/a> to <a href=\"mailto:help@cancerimagingarchive.net\" class=\"external-link\" rel=\"nofollow\">help@cancerimagingarchive.net<\/a> before accessing the data.<\/p><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\">Images (DICOM, 130.4GB)<\/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\/22515597\/doiJNLP-IvyGAP.tcia?version=1&amp;modificationDate=1534787022177&amp;api=v2\" 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:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=IvyGAP\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><\/p><br\/><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\" class=\"external-link\" rel=\"nofollow\">TCIA Restricted<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p>Click the Versions tab for more info about data releases.<\/p><h3 style=\"text-align: left;\" id=\"IvyGlioblastomaAtlasProject(IvyGAP)-AdditionalResourcesforthisDataset\">Additional Resources for this Dataset<\/h3><p class=\"xmsonormal\" style=\"text-align: left;\"><span style=\"color: black;\">IvyGap provides access to additional resources for this data.<\/span><\/p><ul><li class=\"xmsonormal\" style=\"text-align: left;\"><span style=\"color: black;\"><a href=\"http:\/\/glioblastoma.alleninstitute.org\/\" class=\"external-link\" rel=\"nofollow\">Summary ISH, RNA, gene expression and clinical data<\/a><\/span><\/li><li class=\"xmsonormal\" style=\"text-align: left;\"><span style=\"color: black;\"><a href=\"https:\/\/ivygap.org\/home\" class=\"external-link\" rel=\"nofollow\">Detailed clinical, genomic, and expression array data<\/a><\/span><\/li><li class=\"xmsonormal\" style=\"text-align: left;\"><span style=\"color: black;\"><a href=\"https:\/\/registry.opendata.aws\/allen-ivy-glioblastoma-atlas\/\" class=\"external-link\" rel=\"nofollow\">Pathology images<\/a><\/span><\/li><\/ul><h3 id=\"IvyGlioblastomaAtlasProject(IvyGAP)-ThirdPartyAnalysesofthisDataset\">Third Party Analyses of this Dataset<\/h3><p>TCIA encourages the community to <a href=\"http:\/\/www.cancerimagingarchive.net\/analysis-results\/\" class=\"external-link\" rel=\"nofollow\">publish your analyses of our datasets<\/a>. Below is a list of such third party analyses published using this Collection:<\/p><ul><li><a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=52763018\">SDTM datasets of clinical data and measurements for selected cancer collections to TCIA (DI-Cubed-Reports)<\/a><\/li><li><a href=\"https:\/\/doi.org\/10.7937\/9j41-7d44\" class=\"external-link\" rel=\"nofollow\">Multi-Institutional Paired Expert Segmentations and Radiomic Features of the Ivy GAP Dataset<\/a><\/li><\/ul><\/div><div class=\"tabs-pane \" id=\"22515597b7feb4d1e1a14964b1ae9b703332245f\" name=\"Detailed Description\" ><h3 id=\"IvyGlioblastomaAtlasProject(IvyGAP)-DetailedDescription\">Detailed Description<\/h3><div class=\"table-wrap\"><table class=\"wrapped confluenceTable\"><colgroup><col\/><col\/><\/colgroup><tbody><tr><th class=\"confluenceTh\"><div class=\"tablesorter-header-inner\"><p>Collection Statistics<\/p><\/div><\/th><th class=\"confluenceTh\"><div class=\"tablesorter-header-inner\"><p><br\/><\/p><\/div><\/th><\/tr><tr><td class=\"confluenceTd\"><p>Modalities<\/p><\/td><td class=\"confluenceTd\"><p>MR<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Participants<\/p><\/td><td class=\"confluenceTd\"><p>39<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Studies<\/p><\/td><td class=\"confluenceTd\"><p>390<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Series<\/p><\/td><td class=\"confluenceTd\"><p>5223<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Images<\/p><\/td><td class=\"confluenceTd\"><p>846743<\/p><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Image Size (GB)<\/td><td colspan=\"1\" class=\"confluenceTd\">130.4<\/td><\/tr><\/tbody><\/table><\/div><h4 id=\"IvyGlioblastomaAtlasProject(IvyGAP)-SupportingDocumentation\">Supporting Documentation<\/h4><p>In addition to the DICOM images in TCIA there are two additional databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities:<\/p><ol><li>The <a href=\"http:\/\/glioblastoma.alleninstitute.org\/\" class=\"external-link\" rel=\"nofollow\">Ivy Glioblastoma Atlas Project web site<\/a> includes the following data:<ol><li><a class=\"external-link\" href=\"http:\/\/glioblastoma.alleninstitute.org\/ish\" rel=\"nofollow\">ISH:<\/a> Image data at cellular resolution of <em>in situ<\/em> hybridization (ISH) tissue sections and adjacent hematoxylin and eosin (H&amp;E)-stained sections annotated for anatomic structures<ol><li><strong>Anatomic Structures ISH Survey<\/strong>: Primary screen of 8 tumors with probes for 343 genes enriched in glioblastoma.<\/li><li><strong>Anatomic Structures ISH for Enriched Genes<\/strong>: Subsequent screen of 29 tumors with probes for 37 genes enriched in glioblastoma structures identified in Anatomic Structures RNA-Seq Study (see below).<\/li><li><strong>Cancer Stem Cells ISH Survey<\/strong>: Primary screen of 16 tumors with probes for 55 genes enriched in putative cancer stem cells, resulting in a 20 probe reference set, which was then used in an extensive screen of 42 tumors.<\/li><li><strong>Cancer Stem Cells ISH for Enriched Genes<\/strong>: Subsequent screen of 37 tumors with probes for 76 genes enriched in clusters of putative cancer stem cells identified in the Cancer Stem Cells RNA-Seq Study (see below).<\/li><\/ol><\/li><li><a class=\"external-link\" href=\"http:\/\/glioblastoma.alleninstitute.org\/rnaseq\/search\/index.html\" rel=\"nofollow\">RNA-Seq:<\/a> RNA sequencing data for anatomic structures identified in the Anatomic Structures ISH Survey and putative cancer stem cell clusters isolated by laser microdissection<ol><li><strong>Anatomic Structures RNA-Seq<\/strong>: Screen of 5 structures (Leading Edge, Infiltrating Tumor, Cellular Tumor, Microvascular Proliferation, and Pseudopalisading Cells Around Necrosis) identified by H&amp;E staining. A total of 122 RNA samples were generated from 10 tumors.<\/li><li><strong>Cancer Stem Cells RNA-Seq<\/strong>: Screen of 35 clusters of putative cancer stem cells identified by ISH with a 17 reference probe subset (validated in the Cancer Stem Cells ISH Survey). A total of 148 RNA samples were generated from 34 tumors.<\/li><\/ol><\/li><li><a class=\"external-link\" href=\"http:\/\/glioblastoma.alleninstitute.org\/ish\" rel=\"nofollow\">Specimen Metadata:<\/a> De-identified clinical data for each patient and tumor.<\/li><\/ol><\/li><li>The <a href=\"https:\/\/ivygap.org\/home\" class=\"external-link\" rel=\"nofollow\">Ivy GAP Clinical and Genomic Database<\/a> contains detailed clinical information including pathology images, genomic data, and prospectively collected outcomes data. This site requires separate registration.<\/li><li><span style=\"letter-spacing: 0.0px;\">\u00a0Additionally, the pathology images from this study are also available externally from <a href=\"https:\/\/registry.opendata.aws\/allen-ivy-glioblastoma-atlas\/\" class=\"external-link\" rel=\"nofollow\">here<\/a> on Amazon Web Services (AWS).\u00a0<\/span><\/li><\/ol><\/div><div class=\"tabs-pane \" id=\"2251559774598bde57704e04ba1ba1173b4e9abe\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"IvyGlioblastomaAtlasProject(IvyGAP)-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>Shah, N., Feng, X., Lankerovich, M., Puchalski, R. B., &amp; Keogh, B. (2016). <strong>Data from Ivy Glioblastoma Atlas Project (IvyGAP) [Data set].<\/strong> The Cancer Imaging Archive. <a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.XLwaN6nL\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.XLwaN6nL<\/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\">Puchalski RB, Shah N, Miller J, Dalley R, Nomura SR, Yoon J-G, Smith KA, Lankerovich M, Bertagnolli D, Bickley K, Boe AF, Brouner K, Butler S, Caldejon S, Chapin M, Datta S, Dee N, Desta T, Dolbeare T, Dotson N, Ebbert A, Feng D, Feng X, Fisher M, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Hejazinia N, Hohmann J, Hothi P, Howard R, Joines K, Kriedberg A, Kuan L, Lau C, Lee F, Lee H, Lemon T, Long F, Mastan N, Mott E, Murthy C, Ngo K, Olson E, Reding M, Riley Z, Rosen D, Sandman D, Shapovalova N, Slaughterbeck CR, Sodt A, Stockdale G, Szafer A, Wakeman W, Wohnoutka PE, White SJ, Marsh D, Rostomily RC, Ng L, Dang C, Jones A, Keogh B, Gittleman HR, Barnholtz-Sloan JS, Cimino PJ, Uppin MS, Keene CD, Farrokhi FR, Lathia JD, Berens ME, Iavarone A, Bernard A, Lein E, Phillips JW, Rostad SW, Cobbs C, Hawrylycz MJ, Foltz GD.\u00a0(2018). <strong>An anatomic transcriptional atlas of human glioblastoma.<\/strong> Science, 360(6389), 660\u2013663. <a href=\"https:\/\/doi.org\/10.1126\/science.aaf2666\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1126\/science.aaf2666<\/a><\/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>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><\/p><\/div><\/div><h3 id=\"IvyGlioblastomaAtlasProject(IvyGAP)-OtherPublicationsUsingThisData\">Other Publications Using This Data<\/h3><p><span>TCIA maintains<a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\" class=\"external-link\" rel=\"nofollow\"> a list of publications<\/a> that leverage our data. <\/span>If you have a publication you'd like to add, please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" class=\"external-link\" rel=\"nofollow\"> contact TCIA's Helpdesk<\/a>.<\/p><ol><li>Beig, N., Bera, K., Prasanna, P., Antunes, J., Correa, R., Singh, S., . . . Tiwari, P. (2020). Radiogenomic-Based Survival Risk Stratification of Tumor Habitat on Gd-T1w MRI Is Associated with Biological Processes in Glioblastoma. Clin Cancer Res. doi:10.1158\/1078-0432.CCR-19-2556<\/li><li>Gevaert, O., Nabian, M., Bakr, S., Everaert, C., Shinde, J., Manukyan, A., . . . Pochet, N. (2020). Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes. JCO Clin Cancer Inform, 4, 421-435. doi:10.1200\/CCI.19.00125<\/li><li>Le, N. Q. K., Hung, T. N. K., Do, D. T., Lam, L. H. T., Dang, L. H., &amp; Huynh, T.-T. (2021). Radiomics-based machine learning model for efficiently classifying transcriptome subtypes in glioblastoma patients from MRI. Comput Biol Med, 132, 104320. doi:10.1016\/j.compbiomed.2021.104320<\/li><li>Mi, E., Mauricaite, R., Pakzad-Shahabi, L., Chen, J., Ho, A., &amp; Williams, M. (2022). Deep learning-based quantification of temporalis muscle has prognostic value in patients with glioblastoma. Br J Cancer, 126(2), 196-203. doi:10.1038\/s41416-021-01590-9\u00a0<\/li><li>Miller, T. E., Liau, B. B., Wallace, L. C., Morton, A. R., Xie, Q., Dixit, D., . . . Rich, J. N. (2017). Transcription elongation factors represent in vivo cancer dependencies in glioblastoma. Nature, 547(7663), 355. doi:10.1038\/nature23000<\/li><li>Puchalski, R. B., Shah, N., Miller, J., Dalley, R., Nomura, S. R., Yoon, J.-G., . . . Foltz, G. D. (2018). An anatomic transcriptional atlas of human glioblastoma. Science, 360(6389), 660-663. doi:10.1126\/science.aaf2666<\/li><li>Soike, M. H., McTyre, E. R., Shah, N., Puchalski, R. B., Holmes, J. A., Paulsson, A. K., . . . Strowd, R. E. (2018). Glioblastoma radiomics: can genomic and molecular characteristics correlate with imaging response patterns? Neuroradiology, 1-9. doi:10.1007\/s00234-018-2060-y<\/li><li>van der Voort, S. R., Incekara, F., Wijnenga, M. M. J., Kapsas, G., Gahrmann, R., Schouten, J. W., . . . Klein, S. (2022). Combined molecular subtyping, grading, and segmentation of glioma using multi-task deep learning. Neuro Oncol. doi:10.1093\/neuonc\/noac166<\/li><li>Verma, R., Hill, V. B., Statsevych, V., Bera, K., Correa, R., Leo, P., . . . Tiwari, P. (2022). Stable and Discriminatory Radiomic Features from the Tumor and Its Habitat Associated with Progression-Free Survival in Glioblastoma: A Multi-Institutional Study. American Journal of Neuroradiology, 43(8), 1115-1123. doi:10.3174\/ajnr.A7591<\/li><li>Vo, V. T. A., Kim, S., Hua, T. N. M., Oh, J., &amp; Jeong, Y. (2022). Iron commensalism of mesenchymal glioblastoma promotes ferroptosis susceptibility upon dopamine treatment. Communications Biology, 5(1). doi:10.1038\/s42003-022-03538-y<\/li><li>Zander, E., Ardeleanu, A., Singleton, R., Bede, B., Wu, Y., &amp; Zheng, S. (2022). A functional artificial neural network for noninvasive pretreatment evaluation of glioblastoma patients. Neurooncol Adv, 4(1), vdab167. doi:10.1093\/noajnl\/vdab167<\/li><li>Zheng, S., &amp; Tao, W. (2021). Identification of Novel Transcriptome Signature as a Potential Prognostic Biomarker for Anti-Angiogenic Therapy in Glioblastoma Multiforme. Cancers (Basel), 13(5). doi:10.3390\/cancers13051013<\/li><\/ol><h3 id=\"IvyGlioblastomaAtlasProject(IvyGAP)-Altmetrics\">Altmetrics<\/h3><p><script type='text\/javascript' src='https:\/\/d1bxh8uas1mnw7.cloudfront.net\/assets\/embed.js'><\/script>\n<div data-badge-popover=\"right\" data-badge-type='donut' data-doi=\"10.7937\/K9\/TCIA.2016.XLwaN6nL\" class=\"altmetric-embed\"><\/div>\n<meta name=\"DC.Identifier\" content=\"10.7937\/K9\/TCIA.2016.XLwaN6nL\" \/>\n<meta name=\"citation_doi\" content=\"10.7937\/K9\/TCIA.2016.XLwaN6nL\" \/>\n<meta name=\"citation_title\" content=\" Data from Ivy GAP.\" \/><\/p><\/div><div class=\"tabs-pane \" id=\"22515597423771f2d50e4167913545d4a8f0270c\" name=\"Versions\" ><h3 id=\"IvyGlioblastomaAtlasProject(IvyGAP)-Version1(Current):Updated2016\/12\/30\">Version 1 (Current): Updated 2016\/12\/30<\/h3><div class=\"table-wrap\"><table class=\"wrapped confluenceTable\"><colgroup> <col\/> <col\/> <\/colgroup><tbody><tr><th colspan=\"1\" class=\"confluenceTh\">Data Type<\/th><th colspan=\"1\" class=\"confluenceTh\">Download all or Query\/Filter<\/th><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Images (DICOM, 130.4GB)<\/td><td colspan=\"1\" 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\/22515597\/doiJNLP-IvyGAP.tcia?version=1&amp;modificationDate=1534787022177&amp;api=v2\" 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:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=IvyGAP\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><\/p>\u00a0<p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Summary ISH, RNA, gene expression and clinical data (external)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"http:\/\/glioblastoma.alleninstitute.org\/\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><\/p><a href=\"http:\/\/glioblastoma.alleninstitute.org\/\" class=\"external-link\" rel=\"nofollow\"><\/a><p><br\/><\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\"><p>Detailed clinical, genomic, and expression array data (external)<\/p><\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/ivygap.org\/home\" 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><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Pathology images (external)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/registry.opendata.aws\/allen-ivy-glioblastoma-atlas\/\" 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><\/tr><\/tbody><\/table><\/div><\/div><\/div><\/div><\/div>","versions":false,"additional_resources":"IvyGap provides access to additional resources for this data.\n<ul><li><a href=\"http:\/\/glioblastoma.alleninstitute.org\/\">Summary ISH, RNA, gene expression and clinical data<\/a><\/li><li><a href=\"https:\/\/ivygap.org\/home\">Detailed clinical, genomic, and expression array data<\/a><\/li><li><a href=\"https:\/\/registry.opendata.aws\/allen-ivy-glioblastoma-atlas\/\">Pathology images<\/a><\/li><\/ul>","cancer_locations":["Brain"],"collection_page_accessibility":"Public","publications_related":"","version_change_log":"","version_change_log_archived":"","analysis_results":"TCIA encourages the community to <a href=\"http:\/\/www.cancerimagingarchive.net\/analysis-results\/\">publish your analyses of our datasets<\/a>. Below is a list of such third party analyses published using this Collection:\n<ul><li><a href=\"\/pages\/viewpage.action?pageId=52763018\">SDTM datasets of clinical data and measurements for selected cancer collections to TCIA (DI-Cubed-Reports)<\/a><\/li><li><a href=\"https:\/\/doi.org\/10.7937\/9j41-7d44\">Multi-Institutional Paired Expert Segmentations and Radiomic Features of the Ivy GAP Dataset<\/a><\/li><\/ul>","collection_status":"Complete","publications_using":"TCIA maintains<a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\"> a list of publications<\/a> that leverage our data. If you have a publication you'd like to add, please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\"> contact TCIA's Helpdesk<\/a>.\n<ol><li>Beig, N., Bera, K., Prasanna, P., Antunes, J., Correa, R., Singh, S., . . . Tiwari, P. (2020). Radiogenomic-Based Survival Risk Stratification of Tumor Habitat on Gd-T1w MRI Is Associated with Biological Processes in Glioblastoma. Clin Cancer Res. doi:10.1158\/1078-0432.CCR-19-2556<\/li><li>Gevaert, O., Nabian, M., Bakr, S., Everaert, C., Shinde, J., Manukyan, A., . . . Pochet, N. (2020). Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes. JCO Clin Cancer Inform, 4, 421-435. doi:10.1200\/CCI.19.00125<\/li><li>Le, N. Q. K., Hung, T. N. K., Do, D. T., Lam, L. H. T., Dang, L. H., &amp; Huynh, T.-T. (2021). Radiomics-based machine learning model for efficiently classifying transcriptome subtypes in glioblastoma patients from MRI. Comput Biol Med, 132, 104320. doi:10.1016\/j.compbiomed.2021.104320<\/li><li>Mi, E., Mauricaite, R., Pakzad-Shahabi, L., Chen, J., Ho, A., &amp; Williams, M. (2022). Deep learning-based quantification of temporalis muscle has prognostic value in patients with glioblastoma. Br J Cancer, 126(2), 196-203. doi:10.1038\/s41416-021-01590-9\u00a0<\/li><li>Miller, T. E., Liau, B. B., Wallace, L. C., Morton, A. R., Xie, Q., Dixit, D., . . . Rich, J. N. (2017). Transcription elongation factors represent in vivo cancer dependencies in glioblastoma. Nature, 547(7663), 355. doi:10.1038\/nature23000<\/li><li>Puchalski, R. B., Shah, N., Miller, J., Dalley, R., Nomura, S. R., Yoon, J.-G., . . . Foltz, G. D. (2018). An anatomic transcriptional atlas of human glioblastoma. Science, 360(6389), 660-663. doi:10.1126\/science.aaf2666<\/li><li>Soike, M. H., McTyre, E. R., Shah, N., Puchalski, R. B., Holmes, J. A., Paulsson, A. K., . . . Strowd, R. E. (2018). Glioblastoma radiomics: can genomic and molecular characteristics correlate with imaging response patterns? Neuroradiology, 1-9. doi:10.1007\/s00234-018-2060-y<\/li><li>van der Voort, S. R., Incekara, F., Wijnenga, M. M. J., Kapsas, G., Gahrmann, R., Schouten, J. W., . . . Klein, S. (2022). Combined molecular subtyping, grading, and segmentation of glioma using multi-task deep learning. Neuro Oncol. doi:10.1093\/neuonc\/noac166<\/li><li>Verma, R., Hill, V. B., Statsevych, V., Bera, K., Correa, R., Leo, P., . . . Tiwari, P. (2022). Stable and Discriminatory Radiomic Features from the Tumor and Its Habitat Associated with Progression-Free Survival in Glioblastoma: A Multi-Institutional Study. American Journal of Neuroradiology, 43(8), 1115-1123. doi:10.3174\/ajnr.A7591<\/li><li>Vo, V. T. A., Kim, S., Hua, T. N. M., Oh, J., &amp; Jeong, Y. (2022). Iron commensalism of mesenchymal glioblastoma promotes ferroptosis susceptibility upon dopamine treatment. Communications Biology, 5(1). doi:10.1038\/s42003-022-03538-y<\/li><li>Zander, E., Ardeleanu, A., Singleton, R., Bede, B., Wu, Y., &amp; Zheng, S. (2022). A functional artificial neural network for noninvasive pretreatment evaluation of glioblastoma patients. Neurooncol Adv, 4(1), vdab167. doi:10.1093\/noajnl\/vdab167<\/li><li>Zheng, S., &amp; Tao, W. (2021). Identification of Novel Transcriptome Signature as a Potential Prognostic Biomarker for Anti-Angiogenic Therapy in Glioblastoma Multiforme. Cancers (Basel), 13(5). doi:10.3390\/cancers13051013<\/li><\/ol>\n<h3>Altmetrics<\/h3>\n<script src=\"https:\/\/d1bxh8uas1mnw7.cloudfront.net\/assets\/embed.js\" type=\"text\/javascript\">\/\/<![CDATA[\n \n\/\/]]>\n<\/script>\n<meta content=\"10.7937\/K9\/TCIA.2016.XLwaN6nL\"\/>\n<meta content=\"10.7937\/K9\/TCIA.2016.XLwaN6nL\"\/>\n<meta content=\" Data from Ivy GAP.\"\/>","species":["Human"],"collection_title":"Ivy Glioblastoma Atlas Project","detailed_description":"<h4>Supporting Documentation<\/h4>\nIn addition to the DICOM images in TCIA there are two additional databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities:\n<ol><li>The <a href=\"http:\/\/glioblastoma.alleninstitute.org\/\">Ivy Glioblastoma Atlas Project web site<\/a> includes the following data:<ol><li><a href=\"http:\/\/glioblastoma.alleninstitute.org\/ish\">ISH:<\/a> Image data at cellular resolution of <em>in situ<\/em> hybridization (ISH) tissue sections and adjacent hematoxylin and eosin (H&amp;E)-stained sections annotated for anatomic structures<ol><li><strong>Anatomic Structures ISH Survey<\/strong>: Primary screen of 8 tumors with probes for 343 genes enriched in glioblastoma.<\/li><li><strong>Anatomic Structures ISH for Enriched Genes<\/strong>: Subsequent screen of 29 tumors with probes for 37 genes enriched in glioblastoma structures identified in Anatomic Structures RNA-Seq Study (see below).<\/li><li><strong>Cancer Stem Cells ISH Survey<\/strong>: Primary screen of 16 tumors with probes for 55 genes enriched in putative cancer stem cells, resulting in a 20 probe reference set, which was then used in an extensive screen of 42 tumors.<\/li><li><strong>Cancer Stem Cells ISH for Enriched Genes<\/strong>: Subsequent screen of 37 tumors with probes for 76 genes enriched in clusters of putative cancer stem cells identified in the Cancer Stem Cells RNA-Seq Study (see below).<\/li><\/ol><\/li><li><a href=\"http:\/\/glioblastoma.alleninstitute.org\/rnaseq\/search\/index.html\">RNA-Seq:<\/a> RNA sequencing data for anatomic structures identified in the Anatomic Structures ISH Survey and putative cancer stem cell clusters isolated by laser microdissection<ol><li><strong>Anatomic Structures RNA-Seq<\/strong>: Screen of 5 structures (Leading Edge, Infiltrating Tumor, Cellular Tumor, Microvascular Proliferation, and Pseudopalisading Cells Around Necrosis) identified by H&amp;E staining. A total of 122 RNA samples were generated from 10 tumors.<\/li><li><strong>Cancer Stem Cells RNA-Seq<\/strong>: Screen of 35 clusters of putative cancer stem cells identified by ISH with a 17 reference probe subset (validated in the Cancer Stem Cells ISH Survey). A total of 148 RNA samples were generated from 34 tumors.<\/li><\/ol><\/li><li><a href=\"http:\/\/glioblastoma.alleninstitute.org\/ish\">Specimen Metadata:<\/a> De-identified clinical data for each patient and tumor.<\/li><\/ol><\/li><li>The <a href=\"https:\/\/ivygap.org\/home\">Ivy GAP Clinical and Genomic Database<\/a> contains detailed clinical information including pathology images, genomic data, and prospectively collected outcomes data. This site requires separate registration.<\/li><li>\u00a0Additionally, the pathology images from this study are also available externally from <a href=\"https:\/\/registry.opendata.aws\/allen-ivy-glioblastoma-atlas\/\">here<\/a> on Amazon Web Services (AWS).\u00a0<\/li><\/ol>","related_analysis_results":["DI-CUBED-REPORTS","IVYGAP-RADIOMICS","RSNA-ASNR-MICCAI-BRATS-2021"],"subjects":"39","collection_short_title":"IvyGAP","data_types":["MR","Pathology"],"date_updated":"2023-09-13","collection_browse_title":"","supporting_data":["Clinical","Genomics"],"collection_featured_image":false,"collection_summary":"This data collection consists of MRI\/CT scan data for brain tumor patients that form the cohort for the resource Ivy Glioblastoma Atlas Project (Ivy GAP). There are 390 studies for 39 patients that include pre-surgery, post-surgery and follow up scans. The Ivy GAP is a collaborative partnership between the <a href=\"http:\/\/ivyfoundation.org\/\">Ben and Catherine Ivy Foundation<\/a>, which generously provided the financial support, the <a href=\"https:\/\/www.alleninstitute.org\/\">Allen Institute for Brain Science<\/a>, and the <a href=\"http:\/\/www.swedish.org\/services\/neuroscience-institute\/our-services\/ivy-center\">Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment<\/a>. The goal of the project is to provide online resources to scientists and physicians dedicated to the development of innovative treatments and diagnostics that will enhance the quality of life and survival of patients with brain cancer.\nThese resources represent an unprecedented platform for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels. In addition to the DICOM images in TCIA there are two interactive databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities:\n<ol><li><a href=\"http:\/\/glioblastoma.alleninstitute.org\/\"> Ivy Glioblastoma Atlas Project <\/a> - An open\/public database providing in situ hybridization (ISH) and RNA sequencing (RNA-Seq) data, which map gene expression across the anatomic structures and putative cancer stem cell clusters in glioblastoma. The associated histological dataset is annotated and is suitable for neuropathological examination.<\/li><li><a href=\"https:\/\/ivygap.org\/home\">Ivy GAP Clinical and Genomic Database<\/a> -\u00a0 A database offering detailed clinical, genomic, and expression array data sets that are designed to elucidate the pathways involved in glioblastoma development and progression. This database requires registration for access.<\/li><\/ol>\nThe Ivy GAP is described in the resource paper (70 authors not all listed here) :\u00a0Puchalski, R. B., Shah, N., \u2026, Foltz, G. D. (2018). <strong>An anatomic transcriptional atlas of human glioblastoma.<\/strong> In Science (Vol. 360, Issue 6389, pp. 660\u2013663).\u00a0 <a href=\"https:\/\/doi.org\/10.1126\/science.aaf2666\">https:\/\/doi.org\/10.1126\/science.aaf2666<\/a>\nFor scientific or other inquiries about this dataset, please\u00a0<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\">contact the TCIA Helpdesk<\/a>.\n<br\/>","collection_acknowledgements":"","collection_funding":"","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections\/5619"}],"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=5619"}],"wp:term":[{"taxonomy":"tcia_citation_tax","embeddable":true,"href":"https:\/\/cm.vastapps.dev\/api\/v1\/citation-tax?post=5619"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}