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World J Gastroenterol. Dec 21, 2013; 19(47): 8873-8879
Published online Dec 21, 2013. doi: 10.3748/wjg.v19.i47.8873
Target genes discovery through copy number alteration analysis in human hepatocellular carcinoma
De-Leung Gu, Yen-Hsieh Chen, Jou-Ho Shih, Chi-Hung Lin, Yuh-Shan Jou, Chian-Feng Chen
De-Leung Gu, Yen-Hsieh Chen, Jou-Ho Shih, Yuh-Shan Jou, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
Yen-Hsieh Chen, Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
De-Leung Gu, Chi-Hung Lin, Institute of Microbiology and Immunology, School of Life Science, National Yang-Ming University, Taipei 11221, Taiwan
Jou-Ho Shih, Genome and Systems Biology Degree Program, National Taiwan University, Taipei 10617, Taiwan
Chi-Hung Lin, Chian-Feng Chen, VYM Genome Research Center, National Yang-Ming University, Taipei 11221, Taiwan
Author contributions: Gu DL, Chen YH and Shih JH performed the research and contributed equally to this work; Lin CH, Jou YS and Chen CF supervised and wrote the manuscript.
Supported by The National Research Program for Biopharmaceuticals and by the National Science Council, Taiwan with grant numbers No. 101-2320-B-010-066-MY3, No. 101-2325-B-001-011 and No. 101-2320-B-001 -029-MY3
Correspondence to: Chian-Feng Chen PhD, VYM Genome Research Center, National Yang-Ming University, 155 Linong Street, Sec.2, Taipei 11221, Taiwan. cfchen@ym.edu.tw
Telephone: +886-2-28267000  Fax: +886-2-28261444
Received: September 29, 2013
Revised: November 20, 2013
Accepted: December 5, 2013
Published online: December 21, 2013
Core Tip

Core tip: In addition to detecting somatic mutations in cancer genomes with high-throughput short-read sequencing technologies, analysis of copy number alteration in hepatocellular carcinoma (HCC) cancer genomes genotyped by high density single nucleotide polymorphism arrays is a cost-effective approach to reveal genome-wide somatic alterations accumulated during tumorigenesis. Integration with other genomic data from HCC tissues derived from high-throughput short-read sequencing, proteomics, epigenomics and transcriptomics could provide lines of evidence to identify common and novel HCC genes for potential clinical applications.