HIVID: An efficient method to detect HBV integration using low coverage sequencing

We reported HIVID (high-throughput Viral Integration Detection), a novel experimental and computational method to detect the location of Hepatitis B Virus (HBV) integration breakpoints in Hepatocellular Carcinoma (HCC) genome. In this method, the fragments with HBV sequence were enriched by a set of HBV probes and then processed to high-throughput sequencing. In order to evaluate the performance of HIVID, we compared the results of HIVID with that of whole genome sequencing method (WGS) in 28 HCC tumors. We detected a total of 246 HBV integration breakpoints in HCC genome, 113 out of which were within 400bp upstream or downstream of 125 breakpoints identified by WGS method, covering 89.3% (125/140) of total breakpoints. The integration was located in the gene TERT, MLL4, and CCNE1. In addition, we discovered 133 novel breakpoints missed by WGS method, with 66.7% (10/15) of validation rate. Our study shows HIVID is a cost-effective methodology with high specificity and sensitivity to identify viral integration in human genome. •HIVID can detect 89.3% integration breakpoints which had been identified by WGS method.•HIVID discovered 133 novel breakpoints missed by WGS method, with 66.7% (10/15) of validation rate.•The integration hotspots of human genome were located in the gene TERT, MLL4 and CCNE1.•HIVID is a cost-effective methodology with high specificity and sensitivity to identify viral integration in human genome.