AbstractCancer is a genetic disease with frequent somatic alterations in DNA. Study of recurrent copy number aberrations (CNAs) in human cancers would enable the elucidation of disease mechanisms and the identification of key oncogenic drivers with causal roles in oncogenesis. We have comprehensively and systematically characterized CNAs and accompanied gene expression changes in the tumors and their matched non-tumor liver tissues from 286 hepatocellular carcinoma (HCC) patients. Our analysis identified 29 recurrently amplified regions and 22 deleted regions with a high level of copy number changes, harboring established oncogenes and tumor suppressors, including CCND1, MET, CDKN2A and CDKN2B, as well as many other genes not previously reported to be involved in liver carcinogenesis. Pathway analysis of cis-acting genes in the amplification and deletion peaks suggests the alterations of core cancer pathways, including cell cycle, p53, PI3K, MAPK, Wnt and TGFβ signaling, in large proportions of HCC patients. We further credentialed two candidate driver genes, BCL9 and MTDH, from the recurrent focal amplification peaks and showed that they play a significant role in HCC growth and survival. In summary, we have demonstrated that characterizing the CNA landscape in HCC will facilitate the understanding of disease mechanisms and the identification of oncogenic drivers that may serve as potential therapeutic targets for the treatment of this devastating disease.Citation Format: Kai Wang, Ho Yeong Lim, Stephanie Shi, Jeeyun Lee, Shibing Deng, Tao Xie, Zhou Zhu, Yuli Wang, David Pocalyko, Wei J. Yang, Paul A. Rejto, Mao Mao, Cheol-Keun Park, Jiangchun Xu. Genomic landscape of copy number aberrations enables the identification of oncogenic drivers in hepatocellular carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2002. doi:10.1158/1538-7445.AM2013-2002