EURASIP Journal on Bioinformatics and Systems Biology: Identification of genomic functional hotspots with copy number alteration in liver cancer

Tzu-Hung HsiaoHung-I Harry ChenStephanie RoesslerXin Wei Wang & Yidong Chen

Abstract

Copy number alterations (CNAs) can be observed in most cancer patients. Several oncogenes and tumor suppressor genes with CNAs have been identified in different kinds of tumors. However, the systematic survey of CNA-affected functions is still lack. By employing systems biology approaches, instead of examining individual genes, we directly identified the functional hotspots on the human genome. A total of 838 hotspots on the human genome with 540 enriched Gene Ontology functions were identified. Seventy-six aCGH array data of hepatocellular carcinoma (HCC) tumors were employed in this study. A total of 150 regions which putatively affected by CNAs and the encoded functions were identified. Our results indicate that two immune-related hotspots had copy number alterations in most of the patients. In addition, our data implied that these immune-related regions might be involved in HCC oncogenesis. Also, we identified 39 hotspots of which copy number status was associated with patient survival. Our data implied that copy number alterations of the regions may contribute to the dysregulation of the encoded functions. These results further demonstrated that our method enables researchers to survey biological functions of CNAs and to construct regulation hypothesis at the pathway and functional levels.

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