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Series GSE207762 Query DataSets for GSE207762
Status Public on Jul 10, 2022
Title Integrative Genomic Analysis of Medulloblastoma Identiļ¬es a Molecular Subgroup That Drives Poor Clinical Outcome [DNA copy number]
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Medulloblastomas are heterogeneous tumors that collectively represent the most common malignant brain tumor in children. To understand the molecular characteristics underlying their heterogeneity and to identify whether such characteristics represent risk factors for patients with this disease, we performed an integrated genomic analysis of a large series of primary tumors.
Identified are six molecular subgroups of medulloblastoma, each with a unique combination of numerical and structural chromosomal aberrations that globally influence mRNA and miRNA expression. We reveal the relative contribution of each subgroup to clinical outcome as a whole and show that a previously unidentified molecular subgroup, characterized genetically by c-MYC copy number gains and transcriptionally by enrichment of photoreceptor pathways and increased miR-183-96-182 expression, is associated with significantly lower rates of event-free and overall survivals. Our results detail the complex genomic heterogeneity of medulloblastomas and identify a previously unrecognized molecular subgroup with poor clinical outcome for which more effective therapeutic strategies should be developed.
Overall design We profiled the mRNA transcriptome of 194 medulloblastomas and performed high-density single nucleotide polymorphism array and miRNA analysis on 115 and 98 of these, respectively. Non-negative matrix factorization-based clustering of mRNA expression data was used to identify molecular subgroups of medulloblastoma; DNA copy number, miRNA profiles, and clinical outcomes were analyzed for each. We additionally validated our findings in three previously published independent medulloblastoma data sets. DNA copy number data was generated by using Affymetrix 250K Sty arrays or Affymetrix 6.0 arrays to obtain signal intensities and genotype calls.
The submitter-provided processed data (that forms the basis of the study's conclusion) is included in the
Contributor(s) Cho Y, Tsherniak A, Tamayo P, Santagata S, Ligon A, Creulich H, Berhoukim R, Amani V, Goumnerova L, Eberhart CG, Lau CC, Olson JM, Gilbertson RJ, Gajjar A, Delattre O, Kool M, Ligon K, Meyerson M, Mesirov JP, Pomeroy SL
Citation(s) 21098324
Submission date Jul 08, 2022
Last update date Aug 12, 2022
Contact name Jill P Mesirov
Organization name University of California, San Diego
Department Medicine
Street address 9500 Gilman Drive
City San Diego
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (2)
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (121)
GSM6315022 Medulloblastoma cell line A08_95018
GSM6315023 Medulloblastoma cell line A11_95066
GSM6315024 Medulloblastoma cell line B04_94956
BioProject PRJNA857031

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 1.1 Mb (ftp)(http) TXT
GSE207762_RAW.tar 3.4 Gb (http)(custom) TAR (of CEL)
Processed data are available on Series record

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