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Ivy Glioblastoma Atlas project

This is the online help for the Ivy Glioblastoma Atlas Project web application.

The Ivy Glioblastoma Atlas Project is a foundational resource for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels. . The project is organized into six studies that were designed to identify genes enriched in glioblastoma, three of those studies were based on the anatomic structures or features of glioblastoma and three were focused on putative cancer stem cells.

IVY Studies

Color Key

Study

Description

Anatomic Structures ISH Survey

Primary screen of 8 tumors with probes for 343 genes enriched in glioblastoma

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.

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

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

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

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

KEY FEATURES:

In Situ Hybridization (ISH): Cellular resolution gene expression image data with adjacent hematoxylin and eosin (H&E)-stained sections that have been manually annotated for anatomic structures.

  • Anatomic Structures ISH Survey: Initial screen of 8 tumors with 341 probes to glioblastoma-enriched genes.
  • Anatomic Structures ISH for Enriched Genes: Screen of 29 tumors with 50 probes to genes that were demonstrated to be enriched in particular anatomic structures as identified in the Anatomic Structures RNA-Seq study.
  • Cancer Stem Cells ISH Survey: Screen of 16 tumors with 63 probes to identify a reference set of probes corresponding to genes enriched in putative Cancer Stem Cells.
  • Cancer Stem Cells ISH Study for Enriched Genes: Screen of 37 tumors with 79 probes to genes enriched in putative cancer stem cell clusters as identified by RNASeq in the Cancer Stem Cells RNA-Seq study.

RNA-Seq: RNA sequencing data from anatomic structures and putative cancer stem cell clusters

  • Anatomic Structures RNA-Seq: Screen of 5 glioblastoma anatomic structures (Leading Edge, Infiltrating Tumor, Cellular Tumor, Microvascular Proliferation, and Pseudopalisading Cells Around Necrosis).
  • Cancer Stem Cells RNA-Seq: Screen of 75 putative cancer stem cell clusters identified by ISH with the probe reference set identified in the Cancer Stem Cells ISH Survey.

Specimen Datalink to IVY GAP: Partner database with de-identified clinical data for each patient and tumor, and search portal for each tumor block’s ISH and annotated H&E image data. User registration is required for access to detailed clinical and sequence data.

Related Resources

Ivy GAP Clinical and Genomic Database: Partner database with additional clinical, genomic, and transcriptomic data for Ivy GAP.
The Cancer Genome Atlas (TCGA): NIH-funded initiative for genomic mapping of cancers, including glioblastoma.

Moved from Documentation

DATA SETS

The 6 studies generated several data modalities, which are listed below.

Clinical
• De-identified clinical data for 41 patients including age, gender, initial KPS, neurosurgery (resection number), hemisphere, chemotherapy, radiation therapy, recurrence by 6 months, and multifocality
Image
• MRI anonymized scans (42)
• Resected tumor images (42) with tissue block subdivisions and orientation of tumor in brain
• ISH (22,000) acquired with 20x objective for 0.50μm/pixel resolution of 15K x 18K pixel images
• H&E (11,500) acquired with 20x objective for 0.50μm/pixel resolution of 15K x 18K pixel images
• Annotated anatomic structures in H&E images (11,500)
• Nuclear counts for anatomic structures in H&E images (11,500 data sets)

Transcriptome
• RNA-Seq (270 laser microdissection samples) with depth of 15 million mapped reads
• RNA-Seq (27 bulk tumor samples) with 100-150 million mapped reads

Genomic
• Affymetrix SNP array 6.0
• Fusion genes
• Mutations: EGFR amplification, EGFRvIII deletion, PTEN deletion, IDH1 point mutation

Epigenetic
• MGMT methylation status

Tumor derived cell lines and xenografts

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