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- Publisher Website: 10.1016/j.ygeno.2013.07.002
- Scopus: eid_2-s2.0-84886258354
- PMID: 23867110
- WOS: WOS:000326425300021
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Article: HIVID: An efficient method to detect HBV integration using low coverage sequencing
Title | HIVID: An efficient method to detect HBV integration using low coverage sequencing |
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Authors | |
Keywords | Capture Cost-effective Hepatocellular carcinoma High-throughput Integration |
Issue Date | 2013 |
Publisher | Academic Press. The Journal's web site is located at http://www.elsevier.com/locate/ygeno |
Citation | Genomics, 2013, v. 102 n. 4, p. 338-344 How to Cite? |
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 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. |
Persistent Identifier | http://hdl.handle.net/10722/186347 |
ISSN | 2023 Impact Factor: 3.4 2023 SCImago Journal Rankings: 0.850 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Li, W | - |
dc.contributor.author | Zeng, X | - |
dc.contributor.author | Lee, NPY | - |
dc.contributor.author | Poon, RTP | - |
dc.contributor.author | Fan, ST | - |
dc.date.accessioned | 2013-08-20T12:03:46Z | - |
dc.date.available | 2013-08-20T12:03:46Z | - |
dc.date.issued | 2013 | - |
dc.identifier.citation | Genomics, 2013, v. 102 n. 4, p. 338-344 | - |
dc.identifier.issn | 0888-7543 | - |
dc.identifier.uri | http://hdl.handle.net/10722/186347 | - |
dc.description.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 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. | - |
dc.language | eng | - |
dc.publisher | Academic Press. The Journal's web site is located at http://www.elsevier.com/locate/ygeno | - |
dc.relation.ispartof | Genomics | - |
dc.subject | Capture | - |
dc.subject | Cost-effective | - |
dc.subject | Hepatocellular carcinoma | - |
dc.subject | High-throughput | - |
dc.subject | Integration | - |
dc.title | HIVID: An efficient method to detect HBV integration using low coverage sequencing | - |
dc.type | Article | - |
dc.identifier.email | Lee, NPY: nikkilee@hku.hk | - |
dc.identifier.email | Poon, RTP: poontp@hku.hk | - |
dc.identifier.email | Fan, ST: stfan@hku.hk | - |
dc.identifier.authority | Lee, NPY=rp00263 | - |
dc.identifier.authority | Poon, RTP=rp00446 | - |
dc.identifier.authority | Fan, ST=rp00355 | - |
dc.description.nature | link_to_subscribed_fulltext | - |
dc.identifier.doi | 10.1016/j.ygeno.2013.07.002 | - |
dc.identifier.pmid | 23867110 | - |
dc.identifier.scopus | eid_2-s2.0-84886258354 | - |
dc.identifier.hkuros | 220020 | - |
dc.identifier.volume | 102 | - |
dc.identifier.issue | 4 | - |
dc.identifier.spage | 338 | - |
dc.identifier.epage | 344 | - |
dc.identifier.isi | WOS:000326425300021 | - |
dc.publisher.place | United States | - |
dc.identifier.issnl | 0888-7543 | - |