GEO DataSets

Analysis of primary tumors from glioblastoma patients: long-term survivors with >36 months overall survival (OS), short-term survivors with <12 months OS, and patients with intermediate OS. Results provide insight into the molecular characterization of long-term survivors of glioblastoma.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 disease state sets

Platform:

GPL570

Series:

GSE53733

70 Samples

Download data: CEL

(Submitter supplied) Gene expression profiling revealed over-representation of a distinct (proneural-like) expression signature in long-term survivors that was linked to IDH1/2 mutation. However, among the IDH1/2-wildtype patients, tumors from long-term survivors did not show distinct gene expression profiles and included proneural, classical and mesenchymal glioblastoma subtypes. We performed genome- and/or transcriptome-wide molecular profiling of primary tumor samples from 70 glioblastoma patients of the German Glioma Network, including 23 longterm survivors with >36 months overall survival (OS), 16 short-term survivors with <12 months OS, and 31 patients with intermediate OS

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5205

Platform:

GPL570

70 Samples

Download data: CEL

(Submitter supplied) Glioblastoma (GBM) is a highly aggressive type of glioma with poor prognosis. However, a small number of patients live much longer than the median survival. A better understanding of these long-term survivors (LTS) may provide important insight into the biology of GBM. We identified 7 patients with GBM treated at Memorial Sloan-Kettering Cancer Center (MSKCC) with survival greater than 48 months. We characterized the transcriptome of each patient and determined rates of MGMT promoter methylation and IDH1 and IDH2 mutational status. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5669

Platform:

GPL571

7 Samples

Download data: CEL

Analysis of 7 patients with glioblastoma (GBM) treated at Memorial Sloan-Kettering Cancer Center, with survival > 48 months. These long-term survivors (LTSs) represent proneural, neural, classical, and mesenchymal subtypes of GBM. Results provide insight into molecular characteristics of GBM LTSs.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 4 disease state, 7 individual, 7 time sets

Platform:

GPL571

Series:

GSE54077

7 Samples

Download data: CEL

(Submitter supplied) Molecular profiling of cerebral gliomas distinguishes biologically distinct tumor groups and provides prognostically relevant information beyond histological classification and IDH1/2 mutation status. We performed microarray-based genome- and transcriptome-wide molecular profiling of primary tumor samples from 137 patients with cerebral gliomas, 61 WHO grade II and 76 WHO grade III tumors.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

137 Samples

Download data: CEL

(Submitter supplied) In this study, we aimed to characterize the global DNA methylation pattern of mainly IDH1 wild type survival outliers of glioblastoma.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

44 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL28542 GPL28485

1079 Samples

Download data: RCC

(Submitter supplied) Background. We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations. Results. NanoString data were available from 512 patients in the discovery ATE dataset. Elastic net identified a prognostic signature of nine genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL28542

154 Samples

Download data: RCC

(Submitter supplied) Background. We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations. Results. NanoString data were available from 512 patients in the discovery ATE dataset. Elastic net identified a prognostic signature of nine genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL28542

123 Samples

Download data: RCC

(Submitter supplied) Background. We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations. Results. NanoString data were available from 512 patients in the discovery ATE dataset. Elastic net identified a prognostic signature of nine genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL28485

339 Samples

Download data: RCC

(Submitter supplied) Background. We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations. Results. NanoString data were available from 512 patients in the discovery ATE dataset. Elastic net identified a prognostic signature of nine genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL28485

463 Samples

Download data: RCC, TSV

(Submitter supplied) Genome-wide DNA methylation profiling of 7 de novo replication repair deficient glioblastoma, IDH-wildtype in adult patients. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of the 7 glioblastomas.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

7 Samples

Download data: IDAT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL570 GPL13534 GPL571

192 Samples

Download data: CEL

(Submitter supplied) Glioma CIMP (G-CIMP) is a powerful determinant of tumor pathogenicity but the molecular cause of G-CIMP is a fundamental question that is unresolved. Here, we show that mutation of a single gene, isocitrate dehydrogenase 1 (IDH1), directly causes the G-CIMP in gliomas by remodeling the methylome.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

134 Samples

Download data: TXT

(Submitter supplied) Glioma CIMP (G-CIMP) is a powerful determinant of tumor pathogenicity but the molecular cause of G-CIMP is a fundamental question that is unresolved. Here, we show that mutation of a single gene, isocitrate dehydrogenase 1 (IDH1), directly causes the G-CIMP in gliomas by remodeling the methylome.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL571 GPL570

58 Samples

Download data: CEL

(Submitter supplied) Background: Less than 5% of glioblastoma multiforme (GBM) patients survive more than 5-years (long-term survivors, LTS). Nevertheless, the molecular fingerprint of LTS remains uncharted. We aimed to characterize LTS by clinicopathological assessment, DNA methylation (DNAm)/Copy Number Variation (CNV) and mutation profiling. Methods: This multicentric project proposed by Alliance Against Cancer was coordinated by Fondazione IRCCS Istituto Neurologico Carlo Besta. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

51 Samples

Download data: IDAT

(Submitter supplied) The Illumina HumanMethylation 450 BeadChip was used on 20 matched pairs of early and late secondary gliomas to assess the changes in DNA methylation during progression.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

40 Samples

Download data: TXT

(Submitter supplied) Through parallel processing of genomic DNA with bisulfite and oxidative bisulfite treatments on Illumina 450K arrays we resolved both 5mC and 5hmC in glioblastoma tissues. We developed and applied a novel technique for estimating 5mC, 5hmC, and unmethylated proportions from array data to glioblastoma tissues and compare with normal brain tissue. Genomic distribution of 5hmC was associated with features of transcription despite the glioblastoma genome being relatively depleted of 5hmC. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

60 Samples

Download data: IDAT

(Submitter supplied) Macrophages are the most common infiltrating immune cells in glioblastoma (GBM), and play a wide variety of pro-tumor and anti-tumor roles. However, the different subpopulations of macrophages and their effects on the tumor microenvironment remain poorly understood. Here, we combine new and previously-published single-cell RNA-seq data from 86,279 single cells from a total of 63 gliomas to profile 17,774 individual macrophages. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: TXT

(Submitter supplied) Some aspects of the gene expression-based classification method were robust because the gliomasphere cultures retained their classification over many passages, and IDH1 mutant gliomaspheres were all proneural. While gene expression of a subset of gliomasphere cultures was more like the parent tumor than any other tumor, gliomaspheres did not always harbor the same classification as their parent tumor. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

71 Samples

Download data: CEL