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Series GSE21057 Query DataSets for GSE21057
Status Public on Jul 01, 2010
Title Copy number alterations in pleural mesothelioma
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Integrated profiling of somatic molecular alterations present in tumors is necessary to further our understanding of the tumorigenic process. We investigated the potential relationships between gene copy number alterations and DNA methylation profiles in a case series of pleural mesotheliomas (n=23). Gene copy number (CN) alterations profiled with 500K SNP arrays and DNA methylation measured at over 750 cancer-related genes with methylation bead-arrays were examined concomitantly. Considering each probed locus, there were no instances of significantly correlated CN alteration and methylation (no loci with Q < 0.05) and averaging loci over their associated genes revealed only two genes with significantly correlated CN and methylation alterations (Q < 0.04). In contrast to the lack of discrete correlations, the overall extent of tumor CN alteration was significantly associated with DNA methylation profile when comparing CN alteration extent among methylation profile classes (P < 0.02), and there was evidence that this association was partially attributable to prevalent allele loss observed at the maintenance DNA methyltransferase DNMT1. Taken together, this work indicates a strong association between global genetic and global epigenetic dysregulation in mesothelioma rather than a discrete, local coordination of gene inactivation, and further highlights the utility and necessity of integrative genomics approaches in cancer biology.
 
Overall design From the total study population, 23 tumors from the incident case series were chosen for copy number alteration profiling by hybridizing 5ml containing ≥ 50ng/ml of tumor or matched peripheral blood DNA to each of the two GeneChips® that comprise the Human Mapping 500K single-nucleotide polymorphism array set (Affymetrix, Santa Clara, CA), following manufacturer protocols and standard operating procedures at the Harvard Partners Microarray Core servicing facility. Probe intensities at each locus were determined in the GCOS software and genotypes calls were generated using the Genotyping Analysis Software (Affymetrix). Probe signals were normalized to their matched referent peripheral blood sample data using the Copy Number Analysis Tool v4.0.1 software (CNAT) (Affymetrix) with median scaling and default tuning parameters, and copy number states were inferred by Hidden Markov Model analysis.

The supplementary file 'GSE21057_tumor_copy_number.txt' contains the (blood-normalized) copy number calls for each tumor sample.
 
Contributor(s) Christensen BC, Kelsey KT, Nelson HH
Citation(s) 20587528
Submission date Mar 24, 2010
Last update date May 17, 2017
Contact name Brock Clarke Christensen
E-mail(s) brock.clarke.christensen@dartmouth.edu
Organization name Dartmouth Medical School
Street address 7650 Remsen
City Hanover
State/province NH
ZIP/Postal code 03755
Country USA
 
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (92)
GSM526327 Matched blood, B_023, Nsp
GSM526328 Matched blood, B_023, Sty
GSM526329 Matched blood, B_159, Nsp
This SubSeries is part of SuperSeries:
GSE21058 Integrated profiling reveals a global correlation between epigenetic and genetic alterations in mesothelioma
Relations
BioProject PRJNA129693

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
GSE21057_RAW.tar 2.4 Gb (http)(custom) TAR (of CEL, CHP)
GSE21057_tumor_copy_number.txt.gz 2.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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