The HBV Integration Study In Hepatocellular Carcinoma Genome

During Hepatitis B virus infection, the viral integration to the host genome is a very interesting phenomenon. Regarding the mechanism of HBV integration, the current view is that the process is related to DNA double-strand break repair and integration location on the host genome is rather random. The viral fragments integrated into the host genome also show some degree of randomness with slight bias towards X Protein. Although the impact of HBV integration on host cells is still unsettled, it is generally believed that this process is associated with cancer. Previous studies of HBV integration use primarily PCR based methods. Due to its limited power, information that can be extracted is quite limited.In the Cancer Genome Project at Beijing Institute of Genomics, we analyzed all the HBV integration sites in a single case of HCC based on the whole-genome sequence data. By mapping the reads from pair-end or mate-pair sequencing, we identified1177HBV-integration-related pair-end or mate-pair reads in tumor and normal tissues. For integration sites with a large number of supporting reads, molecular biology methods are employed to explore them in greater detail. In this process, we applied single primer PCR to the study of HBV integration sites.We totally found264hbv integration sites,19of them are tumor cell specific, which4located in intron and others in intergenic region. For fragments integrated into the host genome, most of them from X gene or C gene. They can be permutations of several ORFs, not just simply one part of HBV genome.In this case study, we also found out7HBV integration sites which closely linked to copy number variation, for all of them appear in boundaries of copy number change. Through the Sanger sequencing of heterozygous loci around the integration sites, we found the form of copy number variation linked with HBV integration is free from2original chromosomes. For oncogenes such as CCND1located in CNV region, this finding established a bridge for the HBV integration-copy number variation-cancer initiation. Comparing differences of HBV integration between tumor and normal tissues, we found that HBV integration in the normal tissue is much more scattered than tumor, indicating that normal tissues are made up of more but smaller clone groups.