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

Li, Weiyang, Zeng, Xi, Lee, Nikki P., Liu, Xiao, Chen, Shengpei, Guo, Bing, Yi, Shang, Zhuang, Xuehan, Chen, Fang, Wang, Guan, Poon, Ronnie T., Fan, Sheung Tat, Mao, Mao, Li, Yingrui, Li, Songgang, Wang, Jun, Wang, Jian, Xu, Xun, Jiang, Hui and Zhang, Xiuqing (2013) HIVID: an efficient method to detect HBV integration using low coverage sequencing. Genomics, 102 4: 338-344. doi:10.1016/j.ygeno.2013.07.002

Author Li, Weiyang
Zeng, Xi
Lee, Nikki P.
Liu, Xiao
Chen, Shengpei
Guo, Bing
Yi, Shang
Zhuang, Xuehan
Chen, Fang
Wang, Guan
Poon, Ronnie T.
Fan, Sheung Tat
Mao, Mao
Li, Yingrui
Li, Songgang
Wang, Jun
Wang, Jian
Xu, Xun
Jiang, Hui
Zhang, Xiuqing
Title HIVID: an efficient method to detect HBV integration using low coverage sequencing
Journal name Genomics   Check publisher's open access policy
ISSN 0888-7543
Publication date 2013-10
Year available 2013
Sub-type Article (original research)
DOI 10.1016/j.ygeno.2013.07.002
Open Access Status Not yet assessed
Volume 102
Issue 4
Start page 338
End page 344
Total pages 7
Place of publication Waltham, MA, United States
Publisher Academic Press
Language eng
Abstract 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 400. bp 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.
Keyword Capture
Hepatocellular carcinoma
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
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Citation counts: TR Web of Science Citation Count  Cited 14 times in Thomson Reuters Web of Science Article | Citations
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