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.
Park
Chan-Hee
CH
Cancer Metastasis Research Center, Yonsei University College of Medicine, Seoul, South Korea.
Rha
Sun-Young
SY
Jeung
Hei-Cheul
HC
Kang
Seung-Hui
SH
Ki
Dong-Hyuk
DH
Lee
Won-Suk
WS
Noh
Sung-Hoon
SH
Chung
Hyun-Cheol
HC
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
D012333:RNA, Messenger