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Series GSE42631 Query DataSets for GSE42631
Status Public on Nov 30, 2012
Title GeneChip Mapping 500K set and Genome-Wide Human SNP 6.0 Array for glioblastomas
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary High-density single nucleotide polymorphism (SNP) arrays were used to investigate genome-wide copy number (CN) alterations and loss of heterozygosity (LOH) in glioblastomas (GBM) patients; our aim focused on the identification and detailed characterization of the genetic alterations of the chromosomes altered in these tumors and the identification of subgroups of GBM with distinct cytogenetic patterns of alteration for the affected chromosomes potentially associated with the behavior of the disease. Overall, gains of chromosome 7, losses of chromosomes 9p and 10 were the most frequent chromosomal alterations. The 7p11.2 region was amplified in several cases. Based on CN alterations for chromosomes 7, 9 and 10, five different cytogenetic patterns with a significant impact on patient survival were identified; noteworthy, cases with EGFR amplification showed a better survival, specifically among patients older than 60 years. In addition, our results provide further evidence about the relevance of the EGFR, CDKN2A/B, MTAP genes, and other genes coded in chromosome 10 in the pathogenesis of GBM. Altogether, our results confirm the cytogenetic heterogeneity of GBM and suggest that stratification of these tumors into genetic subsets based on the combined assessment of cytogenetic alterations involving chromosomes 7, 9 and 10, may contribute to the prognostic evaluation of GBM.
 
Overall design GeneChip Mapping 500K set and Genome Wide Human SNP 6.0 Array were used to profile GBM with matched blood DNA samples. Loss of heterozygosity (LOH) and copy number abnormality (CNA) profiles were derived from each tumour-blood pair.
 
Contributor(s) Tabernero MD, Orfao JA
Citation(s) 21884817, 23029397
Submission date Nov 29, 2012
Last update date Nov 27, 2018
Contact name MariaDolores Tabernero
E-mail(s) taberner@usal.es
Fax 0034-923-264795
Organization name Hospital Universitario de Salamanca y Centro del C√°ncer
Lab Unidad de Investigación
Street address Paseo San Vicente 58-182
City Salamanca
ZIP/Postal code 37007
Country Spain
 
Platforms (3)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (192)
GSM1046326 Sample#G6Blood DNA_NSP
GSM1046327 Sample#G6Blood DNA_STY
GSM1046328 Sample#G6Tumor DNA _NSP
Relations
BioProject PRJNA182381

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
GSE42631_52SNP_6_CN_GBM.txt.gz 41.9 Mb (ftp)(http) TXT
GSE42631_52SNP_6probesCN_GBM.txt.gz 42.0 Mb (ftp)(http) TXT
GSE42631_70nsp_CNdata_blood_and_tumorGBM.txt.gz 16.4 Mb (ftp)(http) TXT
GSE42631_70sty_CNdata_blood_and_tumorGBM.txt.gz 15.3 Mb (ftp)(http) TXT
GSE42631_RAW.tar 6.4 Gb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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