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Series GSE76730 Query DataSets for GSE76730
Status Public on Aug 31, 2016
Title Affymetrix SNP array data for NSCLC samples
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Non-small cell lung cancer (NSCLC) presents a notoriously genomically unstable cancer type, with numerous large scale and focal genomic aberrations resulting in gene copy number variations across the whole genome. The relations of these gene copy number changes to subsequent mRNA levels are only fragmentarily understood. The aim of this study was an integrated analysis of gene copy number changes and corresponding gene expression in a large clinically annotated NSCLC patient cohort. Fresh frozen tumor sample from 190 resected NSCLC patients were subjected to SNP arrays and gene expression array analysis resulting 39788 tested copy number/ RNA expression pairs. Correlation analysis using an externally centered correlation coefficient (ECCC) revealed that gene expression of 19058 genes was significantly influenced by gene copy number changes (FDR < 0.05). However, only 440 probe sets demonstrated high correlations (ECCC > 0.7) that were mostly due to few cases with high gene copy number gains. These gene copy number dependent genes were clustered in only few chromosomal hot spot regions and classical oncogenes (e.g. EGFR, MDM2, KRAS) are overrepresented among these genes. In a meta-analysis, including 1585 NSCLC patients, gene expression levels from 70 of 440 (16%) gene-copy-number-dependent genes were associated with survival.
In conclusion, the genome-wide analysis indicates that gene copy number aberrations influence directly gene expression levels in a distinct subset of genes. The concrete illustration of these molecular relations help to interpret the impact of gene copy number changes and may serve as starting points to identify new cancer drivers in NSCLC.
Overall design Affymetrix Gene Chip Human Mapping 250K Nsp I arrays wer performed according to the manufacturer's directions with genomic DNA extracted from fresh frozen lung cancer tissue.
Copy number analysis of Affymetrix 250 K arrays was performed on DNA from 190 NSCLC patients. These data sets belongs to the previous described cohort of 100 cases (Micke et al. 2011, GSE28582). Thus altogether the cohort used in the comprehensive gene copy number analysis comprised 190 patients.
Contributor(s) Micke P, Botling J, Jabs V, König H, Edlund K, Hellwig B, Grinberg M, Madjar K, Rahnenführer J, Ekman S, Bergkvist M, Ickstadt K, Hengstler JG
Citation(s) 22011649, 29112949
Submission date Jan 11, 2016
Last update date Jun 19, 2019
Contact name Patrick Micke
Organization name Uppsala University
Street address Rudbeck laboratory
City Uppsala
ZIP/Postal code 75185
Country Sweden
Platforms (1)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
Samples (190)
GSM2036728 NSCLC_sample_10B
GSM2036729 NSCLC_sample_101 A
GSM2036730 NSCLC_sample_105A
BioProject PRJNA308490

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
GSE76730_RAW.tar 4.9 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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