HIVID: An efficient method to detect HBV integration using low coverage sequencing
HIVID: An efficient method to detect HBV integration using low coverage sequencing
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DOI：
10.1016/j.ygeno.2013.07.002
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发表时间：
2013-10-01
期刊：
影响因子：
4.4
通讯作者：
Zhang, Xiuqing
中科院分区：
文献类型：
--
作者：
Li, Weiyang;Zeng, Xi;Zhang, Xiuqing
我们报道了高通量病毒整合检测(HIVID)，这是一种新的实验和计算方法，用于检测肝细胞癌(HCC)基因组中乙肝病毒(HBV)整合断裂点的位置。在该方法中，含有HBVDNA序列的片段被一组HBVDNA探针富集，然后进行高通量测序。为了评价HIVID的检测效果，我们比较了28例肝癌组织的HIVID检测结果和全基因组测序方法(WGS)的检测结果。共检测到246个HBVDNA整合断裂点，其中113个位于WGS法确定的125个断裂点上下游400bp以内，占总断裂点的89.3%(125/140)。整合基因定位于TERT、MLL4和CCNE1基因。此外，我们还发现了WGS方法遗漏的133个新断点，准确率为66.7%(10/15)。我们的研究表明，HIVID是一种识别人类基因组中病毒整合的高成本、高特异性和高灵敏度的方法。(C)Elsevier Inc.出版的2013年。
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. (C) 2013 Published by Elsevier Inc.