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Series GSE26576 Query DataSets for GSE26576
Status Public on Sep 21, 2011
Title Genome-wide Analyses of Diffuse Intrinsic Pontine Gliomas
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by SNP array
Summary Purpose: More than 90% of children with diffuse intrinsic pontine glioma (DIPG) die within 2 years of diagnosis. There is a dire need to identify therapeutic targets, however lack of patient material for research has limited progress. We evaluated a large cohort of diffuse intrinsic pontine gliomas (DIPGs) to identify recurrent genomic abnormalities and gene expression signatures underlying DIPG.
Patients and Methods: We used single nucleotide polymorphism arrays to evaluate genomic copy number imbalances in 43 DIPGs from 40 patients and in 8 low-grade exophytic brainstem gliomas. Gene expression arrays were used to evaluate expression signatures from 27 DIPGs, 6 low-grade exophytic brainstem gliomas and 66 low-grade gliomas arising outside the brainstem.
Results: Frequencies of specific large-scale and focal imbalances varied significantly between DIPGs and pediatric glioblastomas outside the brainstem. Focal amplifications of genes within the receptor tyrosine kinase-Ras-PI3-kinase signaling pathway were found in 47% of DIPG, with PDGFRA and MET showing the highest frequency. 30% of DIPG contained focal amplifications of cell-cycle regulatory genes controlling RB phosphorylation, and 21% had concurrent amplification of genes from both pathways. Some tumors showed heterogeneity in amplification patterns. DIPGs showed distinct gene expression signatures relating to developmental processes compared to pediatric glioblastomas arising outside the brainstem, while expression signatures of low-grade exophytic brainstem gliomas were similar to low-grade gliomas outside the brainstem.
 
Overall design Copy number analaysis: 43 DIPG samples, 8 Low Grade Gliomas using SNP6.0. Available matched normals are also profiled with SNP6.0.
Expression analysis: 29 DIPG samples, 6 Low grade samples

Please contact Suzanne Baker at Suzanne.Baker@stjude.org for CEL files and genotype calls.
 
Contributor(s) Paugh BS, Broniscer A, Qu C, Miller C, Zhang J, Olson JM, Geyer R, Chi S, da Silva NS, Onar-Thomas A, Baker J, Gajjar A, Ellison DW, Baker SJ
Citation(s) 21931021
Submission date Jan 12, 2011
Last update date Mar 25, 2019
Contact name Chunxu Qu
E-mail(s) chunxu.qu@stjude.org
Phone 9015952433
Organization name St Jude Children's Research Institute
Department Pathology
Lab Mullighan
Street address 262 Danny Thomas Pl
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platforms (2)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (126)
GSM488003 mRNA of GBM-HGG047, Glioblastoma, 7.3 years, Diffuse pontine glioma
GSM488008 mRNA of GBM-HGG077, Glioblastoma, 4 years, Diffuse pontine glioma
GSM648500 mRNA of BSG002T, brainstem low-grade gloma
Relations
BioProject PRJNA136251

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE26576_RAW.tar 169.4 Mb (http)(custom) TAR (of CEL)

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