Identification of functional genomic regions with copy number alteration in liver cancer

Copy number alterations (CNAs) happen frequently in solid tumors. Several oncogenes and tumor suppressor genes have been identified with CNAs. However, the systematic survey of CNA regulated functions is still lack. By employing systems biology approaches, instead of examining individual genes, we directly identified the spatial functional hotspots in human genome. Total 249 genomic regions, or segments, with 410 enriched biological functions were identified. An aCGH data set of hepatocellular carcinoma (HCC) tumors was employed in this study and several putative affected functions of CNAs were identified. Our results indicate that 4 immune related segments were lost in most of patients. In addition, our data implied these immune related segments might be involved in HCC oncogenesis. The result further demonstrated that our method enables researchers to survey biological functions of CNAs and to construct regulation hypothesis at pathway and functional levels.