Title: Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues

Authors: Kellie J. Archer, Zhongming Zhao, Tobias Guennel, Daniel G. Maluf, Robert A. Fisher, Valeria R. Mas

Addresses: Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia 23298-0032, USA. ' Vanderbilt University Medical Center, Departments of Biomedical Informatics, Psychiatry, and Cancer Biology, Memphis, Tennessee 37232, USA. ' Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia 23298-0032, USA. ' Department of Surgery, Virginia Commonwealth University, Richmond, Virginia 23298, USA. ' Department of Surgery, Virginia Commonwealth University, Richmond, Virginia 23298, USA. ' Departments of Surgery and Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, USA

Abstract: High-throughput genomic technologies are increasingly being used to identify therapeutic targets and risk factors for specific diseases. Using 116 independent liver samples, we identified 793 probe sets that demonstrated a significant association in the frequency of absent calls as tissues progressed from normal to pre-neoplastic to neoplastic, followed by a bioinformatic approach which identified that 78.9% of the significant probe sets contained at least one CpG island in the gene promoter region compared with 58.9% of the remaining genes examined. Our results indicate that further high-throughput methylation studies to more fully characterize molecular events involved in hepatocarcinogenesis are warranted.

Keywords: HCC; hepatocellular carcinoma; HCV; hepatitis C virus; methylation; microarray; hepatocarcinogenesis; liver tissues; bioinformatics; gene silencing; malignant hepatoma; liver cancer.

DOI: 10.1504/IJCBDD.2010.034499

International Journal of Computational Biology and Drug Design, 2010 Vol.3 No.1, pp.52 - 67

Published online: 05 Aug 2010 *

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