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Series GSE50024 Query DataSets for GSE50024
Status Public on Mar 31, 2014
Title Affymetrix SNP 6.0 array data for Diffuse Intrinsic Pontine Glioma
Organism Homo sapiens
Experiment type SNP genotyping by SNP array
Genome variation profiling by SNP array
Summary Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment and near 100% fatality. The failure of most therapies can be attributed to the delicate location of these tumors and choosing therapies based on assumptions that DIPGs are molecularly similar to adult disease. Recent studies have unraveled the unique genetic make-up of this brain cancer with nearly 80% harboring a K27M-H3.3 or K27M-H3.1 mutation. However, DIPGs are still thought of as one disease with limited understanding of the genetic drivers of these tumors. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling, discovering that DIPGs are three molecularly distinct subgroups (H3-K27M, Silent, MYCN) and uncovering a novel recurrent activating mutation in the activin receptor ACVR1, in 20% of DIPGs. Mutations in ACVR1 were constitutively activating, leading to SMAD phosphorylation and increased expression of downstream activin signaling targets ID1 and ID2. Our results highlight distinct molecular subgroups and novel therapeutic targets for this incurable pediatric cancer.
 
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from snap frozen biopsy and autopsy brain tissue from DIPG patients.
Copy number analysis on Affymetrix 6.0 SNP arrays was performed for 45 paediatric DIPG samples, 27 matched normal brain samples, and HapMap samples.
 
Contributor(s) Buczkowicz P, Hoeman C, Rakopoulos P, Pajovic S, Letourneau L, Dzamba M, Morrison A, Lewis P, Bouffet E, Bartels U, Zuccaro J, Agnihotri S, Ryall S, Barszczyk M, Chornenkyy Y, Bourgey M, Bourque G, Montpetit A, Cordero F, Castelo-Branco P, Mangerel J, Tabori U, Ho PC, Huang A, Taylor K, Mackay A, Bendel AE, Nazarian J, Fangusaro JR, Karajannis M, Zagzag D, Foreman NK, Donson A, Hegert JV, Smith A, Chan J, Lafay-Cousin L, Dunn S, Hukin J, Dunham C, Scheinemann K, Michaud J, Zelcer S, Ramsay D, Cain J, Brennan C, Souweidane MM, Jones C, Allis CD
Citation(s) 24705254
Submission date Aug 20, 2013
Last update date Nov 27, 2018
Contact name Pawel Buczkowicz
E-mail(s) pawel.buczkowicz@sickkids.ca
Organization name Hospital for Sick Children
Department Paediatric Laboratory Medicine
Lab BTRC
Street address 686 Bay Street
City Toronto
State/province Ontario
ZIP/Postal code M5G 0A4
Country Canada
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (72)
GSM1212584 Diffuse Intrinsic Pontine Glioma 1 - Tumour-6.0
GSM1212585 Diffuse Intrinsic Pontine Glioma 3 - Tumour-6.0
GSM1212586 Diffuse Intrinsic Pontine Glioma 4 - Tumour-6.0
This SubSeries is part of SuperSeries:
GSE50025 Diffuse Intrinsic Pontine Glioma
Relations
BioProject PRJNA215836

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
GSE50024_RAW.tar 2.9 Gb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file
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