Please use this identifier to cite or link to this item: https://doi.org/10.1093/nar/gkaa1237
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dc.titleSurVirus: a repeat-aware virus integration caller
dc.contributor.authorRajaby, Ramesh
dc.contributor.authorZhou, Yi
dc.contributor.authorMeng, Yifan
dc.contributor.authorZeng, Xi
dc.contributor.authorLi, Guoliang
dc.contributor.authorWu, Peng
dc.contributor.authorSung, Wing-Kin
dc.date.accessioned2022-06-07T08:28:22Z
dc.date.available2022-06-07T08:28:22Z
dc.date.issued2021-01-14
dc.identifier.citationRajaby, Ramesh, Zhou, Yi, Meng, Yifan, Zeng, Xi, Li, Guoliang, Wu, Peng, Sung, Wing-Kin (2021-01-14). SurVirus: a repeat-aware virus integration caller. NUCLEIC ACIDS RESEARCH 49 (6). ScholarBank@NUS Repository. https://doi.org/10.1093/nar/gkaa1237
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.urihttps://scholarbank.nus.edu.sg/handle/10635/226646
dc.description.abstractA significant portion of human cancers are due to viruses integrating into human genomes. Therefore, accurately predicting virus integrations can help uncover the mechanisms that lead to many devastating diseases. Virus integrations can be called by analysing second generation high-throughput sequencing datasets. Unfortunately, existing methods fail to report a significant portion of integrations, while predicting a large number of false positives. We observe that the inaccuracy is caused by incorrect alignment of reads in repetitive regions. False alignments create false positives, while missing alignments create false negatives. This paper proposes SurVirus, an improved virus integration caller that corrects the alignment of reads which are crucial for the discovery of integrations. We use publicly available datasets to show that existing methods predict hundreds of thousands of false positives; SurVirus, on the other hand, is significantly more precise while it also detects many novel integrations previously missed by other tools, most of which are in repetitive regions. We validate a subset of these novel integrations, and find that the majority are correct. Using SurVirus, we find that HPV and HBV integrations are enriched in LINE and Satellite regions which had been overlooked, as well as discover recurrent HBV and HPV breakpoints in human genome-virus fusion transcripts.
dc.language.isoen
dc.publisherOXFORD UNIV PRESS
dc.sourceElements
dc.subjectScience & Technology
dc.subjectLife Sciences & Biomedicine
dc.subjectBiochemistry & Molecular Biology
dc.subjectHEPATITIS-B-VIRUS
dc.subjectHUMAN-PAPILLOMAVIRUS
dc.subjectHBV INTEGRATION
dc.subjectPATTERNS
dc.subjectDNA
dc.typeArticle
dc.date.updated2022-06-07T01:16:03Z
dc.contributor.departmentDEPT OF COMPUTER SCIENCE
dc.contributor.departmentDEPARTMENT OF COMPUTER SCIENCE
dc.description.doi10.1093/nar/gkaa1237
dc.description.sourcetitleNUCLEIC ACIDS RESEARCH
dc.description.volume49
dc.description.issue6
dc.published.statePublished
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