Identification of genes with correlated patterns of variations in DNA copy number and gene expression level in gastric cancer

Sanghwa Yang, Hei Cheul Jeung, Ha Jin Jeong, Yeon Ho Choi, Ji Eun Kim, Jae Joon Jung, Sun Young Rha, Woo Ick Yang, Hyun Cheol Chung

Research output: Contribution to journalArticlepeer-review

45 Citations (Scopus)

Abstract

To identify DNA copy number changes that had a direct influence on mRNA expression in gastric cancer, cDNA microarray-based comparative genomic hybridization (aCGH) and gene expression profiling were performed using 17 K cDNA microarrays. A set of 158 genes showing Pearson correlation coefficients over 0.6 between DNA copy number changes and mRNA expression level variations was selected. In an independent gene expression profiling of 60 tissue samples, the 158 genes were able to distinguish most of the normal and tumor tissues in an unsupervised hierarchical clustering, suggesting that the differential expression patterns displayed by this specific group of genes are most likely based on the gene copy number changes. Furthermore, 43 statistically significant (P < 0.01) genes were selected that correctly distinguished all of the tissue samples. The copy number changes detected by aCGH can be verified by fluorescence in situ hybridization and real-time polymerase chain reaction. The selected genes include those that were previously identified as being tumor suppressors or deleted in various tumors, including GATA binding protein 4 (GATA4), monoamine oxidase A (MAOA), cyclin C (CCNC), and oncogenes including malignant fibrous histiocytoma amplified sequence 1 (MFHAS1/MASL1), high mobility group AT-hook 2 (HMGA2), PPAR binding protein (PPARBP), growth factor receptor-bound protein 7 (GRB7), and TBC1 (tre-2, BUB2, cdc16) domain family, member 1 (TBC1D1).

Original languageEnglish
Pages (from-to)451-459
Number of pages9
JournalGenomics
Volume89
Issue number4
DOIs
Publication statusPublished - 2007 Apr

Bibliographical note

Funding Information:
This work was funded by the Korea Science and Engineering Fund (KOSEF) through the Cancer Metastasis Research Center (CMRC) at Yonsei University College of Medicine and by R01-2004-000-10057-0 from the Basic Research Program by MOST (KOSEF) (S.H. Yang).

All Science Journal Classification (ASJC) codes

  • Genetics

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