This data collection consists of MRI/CT scan data for brain tumor patients that form the cohort for the resource Ivy Glioblastoma Atlast Project (Ivy GAP) as summarized below. There are 399 scans 390 studies for 41 39 patients that include pre-surgery, post-surgery and follow up scans. The Ivy

GAP

is a collaborative partnership between the Ben and Catherine Ivy Foundation, which generously provided the financial support, the Allen Institute for Brain Science, and the Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment. 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.

Localtab
active true title Data Access
Data Access  Choosing the Download option will provide you with a file to launch the TCIA Download Manager to download the entire collection. If you want to browse or filter the data to select only specific scans/studies please use the Search optionC lick the  Download button to save a ".tcia" manifest file to your computer, which you must open with the NBIA Data Retriever . Click the Search button to open our Data Portal, where you can browse the data collection and/or download a subset of its contents. Data Type Download all or Query/Filter Images (DICOM, 183GB 130.4GB) Image Modified   Image Added Summary ISH, RNA, gene expression and clinical data Image Added Detailed clinical, genomic, and expression array data Image Modified Click the Versions tab for more info about data releases. Third Party Analyses of this Dataset TCIA encourages the community to publish your analyses of our datasets. Below is a list of such third party analyses published using this Collection: SDTM datasets of clinical data and measurements for selected cancer collections to TCIA (DI-Cubed-Reports) Multi-Institutional Paired Expert Segmentations and Radiomic Features of the Ivy GAP Dataset

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:

1. The Ivy Glioblastoma Atlas Project web site includes the following data:
   1. ISH: Image data at cellular resolution of in situ hybridization (ISH) tissue sections and adjacent hematoxylin and eosin (H&E)-stained sections annotated for anatomic structures
      1. Anatomic Structures ISH Survey: Primary screen of 8 tumors with probes for 343 genes enriched in glioblastoma.
      2. Anatomic Structures ISH for Enriched Genes: Subsequent screen of 29 tumors with probes for 37 genes enriched in glioblastoma structures identified in Anatomic Structures RNA-Seq Study (see below).
      3. Cancer Stem Cells ISH Survey: 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.
      4. Cancer Stem Cells ISH for Enriched Genes: 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).
   2. RNA-Seq: RNA sequencing data for anatomic structures identified in the Anatomic Structures ISH Survey and putative cancer stem cell clusters isolated by laser microdissection
      1. Anatomic Structures RNA-Seq: Screen of 5 structures (Leading Edge, Infiltrating Tumor, Cellular Tumor, Microvascular Proliferation, and Pseudopalisading Cells Around Necrosis) identified by H&E staining. A total of 122 RNA samples were generated from 10 tumors.
      2. Cancer Stem Cells RNA-Seq: 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.
   3. Specimen Metadata: De-identified clinical data for each patient and tumor.
2. The Ivy GAP Clinical and Genomic Database contains detailed clinical information including pathology images, genomic data, and prospectively collected outcomes data. This site requires separate registration.

 

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Localtab
title Versions
Version 1 (Current): Updated 2015 2016/ 09 12/ 14 30 Data Type Download all or Query/Filter Images (DICOM, xxxGB 130.4GB) Image Modified   Image Removed

Image Added Summary ISH, RNA, gene expression and clinical data Image Added Detailed clinical, genomic, and expression array data Image Added