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Identification of novel gastric cancer‐associated CNVs by integrated analysis of microarray
Author(s) -
Park ChanHee,
Rha SunYoung,
Jeung HeiCheul,
Kang SeungHui,
Ki DongHyuk,
Lee WonSuk,
Noh SungHoon,
Chung HyunCheol
Publication year - 2010
Publication title -
journal of surgical oncology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.201
H-Index - 111
eISSN - 1096-9098
pISSN - 0022-4790
DOI - 10.1002/jso.21585
Subject(s) - copy number variation , copy number analysis , comparative genomic hybridization , cancer , cdkn2a , microarray , microarray analysis techniques , biology , oncogene , gene dosage , genetics , medicine , cancer research , genome , gene , gene expression , cell cycle
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. J. Surg. Oncol. 2010;102:454–461. © 2010 Wiley‐Liss, Inc.