{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T18:00:44Z","timestamp":1781200844074,"version":"3.54.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T00:00:00Z","timestamp":1781136000000},"content-version":"vor","delay-in-days":41,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"HKSAR Government","award":["7015-23G"],"award-info":[{"award-number":["7015-23G"]}]},{"name":"HKSAR Government","award":["T12-101\/23-N"],"award-info":[{"award-number":["T12-101\/23-N"]}]},{"name":"HKSAR Government","award":["R4012-18"],"award-info":[{"award-number":["R4012-18"]}]},{"name":"HKSAR Government","award":["MHP\/033\/20"],"award-info":[{"award-number":["MHP\/033\/20"]}]},{"name":"HKSAR Government","award":["ITS\/043\/23"],"award-info":[{"award-number":["ITS\/043\/23"]}]},{"DOI":"10.13039\/501100005950","name":"HKUST","doi-asserted-by":"publisher","award":["3030_009"],"award-info":[{"award-number":["3030_009"]}],"id":[{"id":"10.13039\/501100005950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005950","name":"HKUST","doi-asserted-by":"publisher","award":["BGF.001.2023"],"award-info":[{"award-number":["BGF.001.2023"]}],"id":[{"id":"10.13039\/501100005950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005950","name":"HKUST","doi-asserted-by":"publisher","award":["CSSET24SC01"],"award-info":[{"award-number":["CSSET24SC01"]}],"id":[{"id":"10.13039\/501100005950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005950","name":"HKUST","doi-asserted-by":"publisher","award":["OKT26EG06"],"award-info":[{"award-number":["OKT26EG06"]}],"id":[{"id":"10.13039\/501100005950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005950","name":"HKUST","doi-asserted-by":"publisher","award":["Z1056"],"award-info":[{"award-number":["Z1056"]}],"id":[{"id":"10.13039\/501100005950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFE0203200"],"award-info":[{"award-number":["2021YFE0203200"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Structural variants (SVs) are major contributors to genome diversity and disease susceptibility, particularly in cancer. Although third-generation sequencing technologies have substantially improved SV detection sensitivity, accurate detection of complex SVs remains challenging due to fragmented and heterogeneous alignment signals, as well as the dependence of many existing methods on predefined variant models. In this paper, we propose gSV, a general SV detector that integrates alignment-based and assembly-based approaches with the maximum exact match strategy, with particular emphasis on resolving SVs with complex or atypical alignment signatures. Without predefined assumptions about SV types, gSV captures diverse variant signals, enabling the detection of SVs that are usually missed by conventional tools. Benchmarking using both simulated datasets and real long-read sequencing data demonstrates that gSV achieves improved sensitivity and overall detection performance compared with current state-of-the-art SV callers, particularly for simple and complex SV events with complex alignment patterns. Unique SV discoveries in four breast cancer cell lines, particularly in cancer-associated genes, demonstrate the potential biological relevance of gSV-enabled discoveries. Furthermore, analysis of a breast cancer cohort from the Chinese population highlights the utility of gSV for population-scale genomic studies. Collectively, gSV provides a unified framework for comprehensive SV discovery in both research and clinical genomics settings.<\/jats:p>","DOI":"10.1093\/bib\/bbag294","type":"journal-article","created":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T11:20:15Z","timestamp":1779103215000},"source":"Crossref","is-referenced-by-count":0,"title":["gSV: a general structural variant detector using the third-generation sequencing data"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3301-4439","authenticated-orcid":false,"given":"Jingyu","family":"Hao","sequence":"first","affiliation":[{"name":"Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5178-8470","authenticated-orcid":false,"given":"Jiandong","family":"Shi","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, The Chinese University of Hong Kong, Shatin, New Territories , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0773-8329","authenticated-orcid":false,"given":"Sheng","family":"Lian","sequence":"additional","affiliation":[{"name":"Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay , Kowloon, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7905-7269","authenticated-orcid":false,"given":"Zhen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay , Kowloon, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0447-329X","authenticated-orcid":false,"given":"Yongyi","family":"Luo","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5124-7167","authenticated-orcid":false,"given":"Taobo","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Breast Surgery, Peking University People\u2019s Hospital , No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8015-2319","authenticated-orcid":false,"given":"Toyotaka","family":"Ishibashi","sequence":"additional","affiliation":[{"name":"Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay , Kowloon, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9014-710X","authenticated-orcid":false,"given":"Depeng","family":"Wang","sequence":"additional","affiliation":[{"name":"GrandOmics Inc, Zhongguancun Life Science Park, Changping District , Beijing, 102206,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8651-4795","authenticated-orcid":false,"given":"Shu","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Breast Surgery, Peking University People\u2019s Hospital , No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2744-9030","authenticated-orcid":false,"given":"Xiaodan","family":"Fan","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, The Chinese University of Hong Kong, Shatin , New Territories, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5510-6916","authenticated-orcid":false,"given":"Weichuan","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, 999077,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,11]]},"reference":[{"key":"2026061113321266800_ref1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-017-1158-6","article-title":"Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome","volume":"18","author":"Collins","year":"2017","journal-title":"Genome Biol"},{"key":"2026061113321266800_ref2","volume-title":"PBSV","author":"PacificBiosciences","year":"2017"},{"key":"2026061113321266800_ref3","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1038\/s41592-018-0001-7","article-title":"Accurate detection of complex structural variations using single-molecule sequencing","volume":"15","author":"Sedlazeck","year":"2018","journal-title":"Nat Methods"},{"key":"2026061113321266800_ref4","doi-asserted-by":"crossref","first-page":"2907","DOI":"10.1093\/bioinformatics\/btz041","article-title":"SVIM: structural variant identification using mapped long reads","volume":"35","author":"Heller","year":"2019","journal-title":"Bioinformatics"},{"key":"2026061113321266800_ref5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-020-02107-y","article-title":"Long-read-based human genomic structural variation detection with cuteSV","volume":"21","author":"Jiang","year":"2020","journal-title":"Genome Biol"},{"key":"2026061113321266800_ref6","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/s41467-023-35996-1","article-title":"Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak","volume":"14","author":"Chen","year":"2023","journal-title":"Nat Commun"},{"key":"2026061113321266800_ref7","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1038\/s41467-021-21395-x","article-title":"Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads","volume":"12","author":"Xin Zhou","year":"2021","journal-title":"Nat Commun"},{"key":"2026061113321266800_ref8","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/s41592-022-01674-1","article-title":"SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads","volume":"20","author":"Denti","year":"2023","journal-title":"Nat Methods"},{"key":"2026061113321266800_ref9","doi-asserted-by":"crossref","first-page":"1230","DOI":"10.1038\/s41592-022-01609-w","article-title":"SVision: a deep learning approach to resolve complex structural variants","volume":"19","author":"Lin","year":"2022","journal-title":"Nat Methods"},{"key":"2026061113321266800_ref10","doi-asserted-by":"publisher","DOI":"10.1038\/s41587--024--02190--7","article-title":"De novo and somatic structural variant discovery with SVision-pro","volume":"42","author":"Wang","year":"2025","journal-title":"Nat Biotechnol"},{"key":"2026061113321266800_ref11","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1109\/TPAMI.2012.132","article-title":"Moving object detection by detecting contiguous outliers in the low-rank representation","volume":"35","author":"Zhou","year":"2012","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"key":"2026061113321266800_ref12","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41592-019-0669-3","article-title":"Fast and accurate long-read assembly with wtdbg2","volume":"17","author":"Ruan","year":"2020","journal-title":"Nat Methods"},{"key":"2026061113321266800_ref13","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2026061113321266800_ref14","doi-asserted-by":"crossref","first-page":"btad313","DOI":"10.1093\/bioinformatics\/btad313","article-title":"copMEM2: robust and scalable maximum exact match finding","volume":"39","author":"Grabowski","year":"2023","journal-title":"Bioinformatics"},{"key":"2026061113321266800_ref15","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1145\/375360.375365","article-title":"A guided tour to approximate string matching","volume":"33","author":"Navarro","year":"2001","journal-title":"ACM computing surveys (CSUR)"},{"key":"2026061113321266800_ref16","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1038\/s41587-023-02024-y","article-title":"Detection of mosaic and population-level structural variants with sniffles2","volume":"42","author":"Smolka","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2026061113321266800_ref17","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"1000 Genomes Project Consortium","year":"2015","journal-title":"Nature"},{"key":"2026061113321266800_ref18","author":"Keskus"},{"key":"2026061113321266800_ref19","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1093\/bioinformatics\/btu828","article-title":"VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications","volume":"31","author":"Mu","year":"2015","journal-title":"Bioinformatics"},{"key":"2026061113321266800_ref20","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btaa835","article-title":"PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores","volume":"37","author":"Ono","year":"2021","journal-title":"Bioinformatics"},{"key":"2026061113321266800_ref21","doi-asserted-by":"crossref","first-page":"giaf095","DOI":"10.1093\/gigascience\/giaf095","article-title":"BVSim: a benchmarking variation simulator mimicking human variation spectrum","volume":"14","author":"Luo","year":"2025","journal-title":"GigaScience"},{"key":"2026061113321266800_ref22","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1093\/bioinformatics\/btz719","article-title":"VISOR: a versatile haplotype-aware structural variant simulator for short-and long-read sequencing","volume":"36","author":"Bolognini","year":"2020","journal-title":"Bioinformatics"},{"key":"2026061113321266800_ref23","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1186\/s13059-022-02840-6","article-title":"Truvari: refined structural variant comparison preserves allelic diversity","volume":"23","author":"English","year":"2022","journal-title":"Genome Biol"},{"key":"2026061113321266800_ref24","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1038\/s41592-022-01753-3","article-title":"Jasmine and iris: population-scale structural variant comparison and analysis","volume":"20","author":"Kirsche","year":"2023","journal-title":"Nat Methods"},{"key":"2026061113321266800_ref25","doi-asserted-by":"crossref","first-page":"14061","DOI":"10.1038\/ncomms14061","article-title":"Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast","volume":"8","author":"Jeffares","year":"2017","journal-title":"Nat Commun"},{"key":"2026061113321266800_ref26","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2026061113321266800_ref27","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1038\/s41587-020-0538-8","article-title":"A robust benchmark for detection of germline large deletions and insertions","volume":"38","author":"Zook","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2026061113321266800_ref28","doi-asserted-by":"crossref","first-page":"2105672","DOI":"10.1002\/advs.202105672","article-title":"HTR1A inhibits the progression of triple-negative breast cancer via TGF-$\\beta $ canonical and noncanonical pathways","volume":"9","author":"Liu","year":"2022","journal-title":"Adv Sci"},{"key":"2026061113321266800_ref29","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1111\/bjd.12969","article-title":"Filaggrin loss-of-function mutations and incident cancer: a population-based study","volume":"171","author":"Skaaby","year":"2014","journal-title":"Br J Dermatol"},{"key":"2026061113321266800_ref30","first-page":"659","article-title":"BEK and FLG, two receptors to members of the FGF family, are amplified in subsets of human breast cancers","volume":"6","author":"Adnane","year":"1991","journal-title":"Oncogene"},{"key":"2026061113321266800_ref31","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet Med"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/3\/bbag294\/68514542\/bbag294.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/3\/bbag294\/68514542\/bbag294.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T17:32:23Z","timestamp":1781199143000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag294\/8706542"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5]]},"references-count":31,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,5,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag294","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,5]]},"published":{"date-parts":[[2026,5]]},"article-number":"bbag294"}}