Identification of novel gastric cancer-associated cnvs by integrated analysis of microarray

Background: Microarray-CGH facilitates analysis of cancer-associated genomic differences between normal and tumor tissues and provides a genome-wide assessment of copy number variations (CNVs). Methods: To identify CNVs and their clinical significance in gastric cancer, Microarray-CGH was performed to identify CNVs with genomic DNA (gDNA) from normal placenta tissue, peripheral blood mononuclear cells (PBMCs), and normal gastric tissue. Results: A total of 20 CNVs, including 8 novel CNVs, were identified by Microarray-CGH. Among the 20 CNVs, 5 showed an aberration frequency of over 50%. In addition, mRNA expression of W72437 (TFIIH), AI968311 (GAGE10), AI352361, and AA169807 (PTCH1) in normal tissues and AA485362 (GPX1), AI201652, and AI968311 (GAGE10) in cancer tissues was associated with DNA change. As a whole, incidences of oncogene-like, suppressor-like, and innocent CNVs were 13.8%, 13.2%, and 73.0%, respectively (gain 11.4%, loss 11.8%). AA936795 (C19orf61) appeared as an oncogene-like CNV (9/30, 30%), A1352361 (13/30, 43%), and AA281797 (LOC728340, 10/30, 33%) appeared as tumor suppressor-related CNVs. Conclusions: This study identified gastric cancer-associated and innocent CNVs in gDNA isolated from placenta tissue and PBMC, which are generally used as reference samples in Microarray-CGH. These novel CNVs may be used for gastric cancer-specific gene selection in comparative analysis of genomics.