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Article: Viral integration detection strategies and a technical update on Virus-Clip

TitleViral integration detection strategies and a technical update on Virus-Clip
Authors
KeywordsOncovirus
Viral genomic integration
In silico detection
Tumorigenesis
Human malignancies
Issue Date2021
PublisherTech Science Press. The Journal's web site is located at http://www.techscience.com/journal/biocell
Citation
BIOCELL, 2021, v. 45 n. 6, p. 1495-1500 How to Cite?
AbstractOncovirus infection is crucial in human malignancies. Certain oncoviruses can lead to structural variations in the human genome known as viral genomic integration, which can contribute to tumorigenesis. Existing viral integration detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration phenomenon. We discuss about major procedures in performing viral integration detection. More importantly, we provide a technical update on Virus-Clip to facilitate its usage on the latest human genome builds (hg19 and hg38) and the adoption of multi-thread mode for faster initial read alignment. By comparing the execution of Virus-Clip using single-thread and multi-thread modes of read alignment on targeted-panel sequencing data of HBV-associated hepatocellular carcinoma patients, we demonstrate the marked improvement of multi-thread mode in terms of significantly reduced execution time, while there is negligible difference in memory usage. Taken together, with the current update of Virus-Clip, it will continue supporting the in silico detection of oncoviral integration for better understanding of various human malignancies.
Persistent Identifierhttp://hdl.handle.net/10722/304051
ISSN
2023 Impact Factor: 0.8
2023 SCImago Journal Rankings: 0.231
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorHo, DWH-
dc.contributor.authorLyu, X-
dc.contributor.authorNg, IOL-
dc.date.accessioned2021-09-23T08:54:34Z-
dc.date.available2021-09-23T08:54:34Z-
dc.date.issued2021-
dc.identifier.citationBIOCELL, 2021, v. 45 n. 6, p. 1495-1500-
dc.identifier.issn0327-9545-
dc.identifier.urihttp://hdl.handle.net/10722/304051-
dc.description.abstractOncovirus infection is crucial in human malignancies. Certain oncoviruses can lead to structural variations in the human genome known as viral genomic integration, which can contribute to tumorigenesis. Existing viral integration detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration phenomenon. We discuss about major procedures in performing viral integration detection. More importantly, we provide a technical update on Virus-Clip to facilitate its usage on the latest human genome builds (hg19 and hg38) and the adoption of multi-thread mode for faster initial read alignment. By comparing the execution of Virus-Clip using single-thread and multi-thread modes of read alignment on targeted-panel sequencing data of HBV-associated hepatocellular carcinoma patients, we demonstrate the marked improvement of multi-thread mode in terms of significantly reduced execution time, while there is negligible difference in memory usage. Taken together, with the current update of Virus-Clip, it will continue supporting the in silico detection of oncoviral integration for better understanding of various human malignancies.-
dc.languageeng-
dc.publisherTech Science Press. The Journal's web site is located at http://www.techscience.com/journal/biocell-
dc.relation.ispartofBIOCELL-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectOncovirus-
dc.subjectViral genomic integration-
dc.subjectIn silico detection-
dc.subjectTumorigenesis-
dc.subjectHuman malignancies-
dc.titleViral integration detection strategies and a technical update on Virus-Clip-
dc.typeArticle-
dc.identifier.emailHo, DWH: dwhho@hku.hk-
dc.identifier.emailLyu, X: lyuxy@HKUCC-COM.hku.hk-
dc.identifier.emailNg, IOL: iolng@hku.hk-
dc.identifier.authorityHo, DWH=rp02285-
dc.identifier.authorityNg, IOL=rp00335-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.32604/biocell.2021.017227-
dc.identifier.scopuseid_2-s2.0-85115189799-
dc.identifier.hkuros325558-
dc.identifier.volume45-
dc.identifier.issue6-
dc.identifier.spage1495-
dc.identifier.epage1500-
dc.identifier.isiWOS:000692530400008-
dc.publisher.placeUnited States-

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