The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients
- Zhaoshi Jiang1,
- Suchit Jhunjhunwala1,
- Jinfeng Liu1,
- Peter M. Haverty2,
- Michael I. Kennemer3,
- Yinghui Guan4,
- William Lee5,
- Paolo Carnevali3,
- Jeremy Stinson6,
- Stephanie Johnson7,
- Jingyu Diao8,
- Stacy Yeung6,
- Adrian Jubb7,
- Weilan Ye6,
- Thomas D. Wu5,
- Sharookh B. Kapadia8,
- Frederic J. de Sauvage6,
- Robert C. Gentleman5,
- Howard M. Stern7,
- Somasekar Seshagiri6,
- Krishna P. Pant3,
- Zora Modrusan6,
- Dennis G Ballinger3 and
- Zemin Zhang5,9
- 1 Department of Bioinformatics and Computational Biology, Genentech Inc;
- 2 .Department of Bioinformatics and Computational Biology, Genentech Inc.;
- 3 Complete Genomics Inc.;
- 4 Department of Molecular Biology, Genentech Inc.,;
- 5 Department of Bioinformatics and Computational Biology, Genentech Inc.;
- 6 Department of Molecular Biology, Genentech Inc.;
- 7 Department of Pathology, Genentech Inc.;
- 8 Department of Microbial Pathogenesis, Genentech Inc.
- ↵* Corresponding author; email: zhang.zemin{at}gene.com
Abstract
Hepatitis B virus (HBV) infection is a leading risk factor for hepatocellular carcinoma (HCC). HBV integration into the host genome has been reported but its scale, impact and contribution to HCC development is not clear. Here, we sequenced the tumor and non-tumor genomes (>80X coverage) and transcriptomes of four HCC patients and identified 255 HBV integration sites. Increased sequencing to 240X coverage revealed a proportionally higher number of integration sites. Clonal expansion of HBV-integrated hepatocytes was found specifically in tumor samples. We observe a diverse collection of genomic perturbations near viral integration sites, including direct gene disruption, viral promoter-driven human transcription, viral-human transcript fusion and DNA copy number alteration. Thus, we report the most comprehensive characterization of HBV integration in hepatocellular carcinoma patients. Such widespread random viral integration will likely increase carcinogenic opportunities in HBV-infected individuals.
- Received October 25, 2011.
- Accepted January 19, 2012.
- Copyright © 2012, Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
