{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T05:39:39Z","timestamp":1773812379325,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2021,5,11]],"date-time":"2021-05-11T00:00:00Z","timestamp":1620691200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Senior Research Fellowship","award":["1116955"],"award-info":[{"award-number":["1116955"]}]},{"DOI":"10.13039\/501100023250","name":"Lorenzo and Pamela Galli Charitable Trust","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100023250","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["1188098"],"award-info":[{"award-number":["1188098"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Victorian State Government Operational Infrastructure Support"},{"name":"Australian Government NHMRC Independent Research Institute Infrastructure Support"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Integration of viruses into infected host cell DNA can cause DNA damage and disrupt genes. Recent cost reductions and growth of whole genome sequencing has produced a wealth of data in which viral presence and integration detection is possible. While key research and clinically relevant insights can be uncovered, existing software has not achieved widespread adoption, limited in part due to high computational costs, the inability to detect a wide range of viruses, as well as precision and sensitivity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we describe VIRUSBreakend, a high-speed tool that identifies viral DNA presence and genomic integration. It utilizes single breakends, breakpoints in which only one side can be unambiguously placed, in a novel virus-centric variant calling and assembly approach to identify viral integrations with high sensitivity and a near-zero false discovery rate. VIRUSBreakend detects viral integrations anywhere in the host genome including regions such as centromeres and telomeres unable to be called by existing tools. Applying VIRUSBreakend to a large metastatic cancer cohort, we demonstrate that it can reliably detect clinically relevant viral presence and integration including HPV, HBV, MCPyV, EBV and HHV-8.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>VIRUSBreakend is part of the Genomic Rearrangement IDentification Software Suite (GRIDSS). It is available under a GPLv3 license from https:\/\/github.com\/PapenfussLab\/VIRUSBreakend.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab343","type":"journal-article","created":{"date-parts":[[2021,5,3]],"date-time":"2021-05-03T07:25:31Z","timestamp":1620026731000},"page":"3115-3119","source":"Crossref","is-referenced-by-count":22,"title":["VIRUSBreakend: Viral Integration Recognition Using Single Breakends"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0951-7116","authenticated-orcid":false,"given":"Daniel L","family":"Cameron","sequence":"first","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia"},{"name":"Department of Medical Biology, University of Melbourne , Melbourne, VIC 3010, Australia"},{"name":"Hartwig Medical Foundation Australia , Sydney, NSW 2060, Australia"}]},{"given":"Nina","family":"Jacobs","sequence":"additional","affiliation":[{"name":"Hartwig Medical Foundation , Amsterdam 1098, The Netherlands"}]},{"given":"Paul","family":"Roepman","sequence":"additional","affiliation":[{"name":"Hartwig Medical Foundation , Amsterdam 1098, The Netherlands"}]},{"given":"Peter","family":"Priestley","sequence":"additional","affiliation":[{"name":"Hartwig Medical Foundation Australia , Sydney, NSW 2060, Australia"}]},{"given":"Edwin","family":"Cuppen","sequence":"additional","affiliation":[{"name":"Hartwig Medical Foundation , Amsterdam 1098, The Netherlands"},{"name":"Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht , Utrecht 3584, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1102-8506","authenticated-orcid":false,"given":"Anthony T","family":"Papenfuss","sequence":"additional","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia"},{"name":"Department of Medical Biology, University of Melbourne , Melbourne, VIC 3010, Australia"},{"name":"Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia"},{"name":"Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3010, Australia"}]}],"member":"286","published-online":{"date-parts":[[2021,5,11]]},"reference":[{"key":"2023051608282287500_btab343-B1","doi-asserted-by":"crossref","first-page":"D571","DOI":"10.1093\/nar\/gku1207","article-title":"NCBI viral genomes resource","volume":"43","author":"Brister","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023051608282287500_btab343-B2","doi-asserted-by":"crossref","first-page":"2050","DOI":"10.1101\/gr.222109.117","article-title":"GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly","volume":"27","author":"Cameron","year":"2017","journal-title":"Genome Res"},{"key":"2023051608282287500_btab343-B3","doi-asserted-by":"crossref","first-page":"3240","DOI":"10.1038\/s41467-019-11146-4","article-title":"Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software","volume":"10","author":"Cameron","year":"2019","journal-title":"Nat. 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