title: Identification of novel gastric cancer-associated CNVs by integrated analysis of microarray.
abstract: 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.
authors.affiliation: Cancer Metastasis Research Center, Yonsei University College of Medicine, Seoul, South Korea.
authors.forename: Chan-Hee
authors.initials: CH
authors.lastname: Park
authors.forename: Sun-Young
authors.initials: SY
authors.lastname: Rha
authors.forename: Hei-Cheul
authors.initials: HC
authors.lastname: Jeung
authors.forename: Seung-Hui
authors.initials: SH
authors.lastname: Kang
authors.forename: Dong-Hyuk
authors.initials: DH
authors.lastname: Ki
authors.forename: Won-Suk
authors.initials: WS
authors.lastname: Lee
authors.forename: Sung-Hoon
authors.initials: SH
authors.lastname: Noh
authors.forename: Hyun-Cheol
authors.initials: HC
authors.lastname: Chung
mesh_terms: D005260:Female; D018628:Gene Dosage; D016147:Genes, Tumor Suppressor; D016678:Genome; D006801:Humans; D007963:Leukocytes, Mononuclear; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010920:Placenta; D011247:Pregnancy; D012333:RNA, Messenger / Q000032:analysis; D013274:Stomach Neoplasms / Q000235:genetics* / Q000378:metabolism
chemical_list: D012333:RNA, Messenger