Identification of genes with a correlation between copy number and expression in gastric cancer.

BMC Medical Genomics
Lei ChengQing Hua Zhang

Abstract

To elucidate gene expression associated with copy number changes, we performed a genome-wide copy number and expression microarray analysis of 25 pairs of gastric tissues. We applied laser capture microdissection (LCM) to obtain samples for microarray experiments and profiled DNA copy number and gene expression using 244K CGH Microarray and Human Exon 1.0 ST Microarray. Obviously, gain at 8q was detected at the highest frequency (70%) and 20q at the second (63%). We also identified molecular genetic divergences for different TNM-stages or histological subtypes of gastric cancers. Interestingly, the C20orf11 amplification and gain at 20q13.33 almost separated moderately differentiated (MD) gastric cancers from poorly differentiated (PD) type. A set of 163 genes showing the correlations between gene copy number and expression was selected and the identified genes were able to discriminate matched adjacent noncancerous samples from gastric cancer samples in an unsupervised two-way hierarchical clustering. Quantitative RT-PCR analysis for 4 genes (C20orf11, XPO5, PUF60, and PLOD3) of the 163 genes validated the microarray results. Notably, some candidate genes (MCM4 and YWHAZ) and its adjacent genes such as PRKDC, UBE2V2, ANKRD46, ...Continue Reading

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Datasets Mentioned

BETA
GSE33428

Methods Mentioned

BETA
laser capture microdissection
chromosomal aberrations
surgical resection
Feature Extraction
Assay
dissection

Software Mentioned

GeneChip Operating Software
Affymetrix
Agilent CGH Analytics
Expression Consol
DAVID
Primer Express
Treeview
SPSS
Feature Extraction

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