Identification of genes with a correlation between copy number and expression in gastric cancer
<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Methods</p> <p>We applied lase...
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| Main Authors: | , , , , , , , , |
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| Format: | Book |
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BMC,
2012-05-01T00:00:00Z.
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| Summary: | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Methods</p> <p>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.</p> <p>Results</p> <p>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 <it>C20orf11</it> 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 (<it>C20orf11</it>, <it>XPO5</it>, <it>PUF60</it>, and <it>PLOD3</it>) of the 163 genes validated the microarray results. Notably, some candidate genes (<it>MCM4</it> and <it>YWHAZ</it>) and its adjacent genes such as <it>PRKDC</it>, <it>UBE2V2</it>, <it>ANKRD46</it>, <it>ZNF706</it>, and <it>GRHL2</it>, were concordantly deregulated by genomic aberrations.</p> <p>Conclusions</p> <p>Taken together, our results reveal diverse chromosomal region alterations for different TNM-stages or histological subtypes of gastric cancers, which is helpful in researching clinicopathological classification, and highlight several interesting genes as potential biomarkers for gastric cancer.</p> |
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| Item Description: | 10.1186/1755-8794-5-14 1755-8794 |