{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:44Z","timestamp":1772138024060,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,1,17]],"date-time":"2024-01-17T00:00:00Z","timestamp":1705449600000},"content-version":"vor","delay-in-days":56,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hong Kong Research Grants Council Collaborative Research Fund","award":["C4057-18E"],"award-info":[{"award-number":["C4057-18E"]}]},{"name":"Innovation and Technology Commission, Hong Kong Special Administrative Region Government to the State Key Laboratory of Agrobiotechnology"},{"name":"Government of the Hong Kong Special Administrative Region or the Innovation and Technology Commission"},{"name":"Hong Kong Research Grants Council Collaborative Research Funds","award":["C4015-20E"],"award-info":[{"award-number":["C4015-20E"]}]},{"name":"Hong Kong Research Grants Council Collaborative Research Funds","award":["C4045-18W"],"award-info":[{"award-number":["C4045-18W"]}]},{"name":"Hong Kong Research Grants Council Collaborative Research Funds","award":["C7044-19G"],"award-info":[{"award-number":["C7044-19G"]}]},{"name":"General Research Funds","award":["14170217"],"award-info":[{"award-number":["14170217"]}]},{"name":"General Research Funds","award":["14203119"],"award-info":[{"award-number":["14203119"]}]},{"name":"Hong Kong Epigenomics Project"},{"name":"Chinese University of Hong Kong Young Researcher Award"},{"name":"Outstanding Fellowship and Project Impact Enhancement Fund"},{"name":"National Institute of Health","award":["P30 CA030199-41"],"award-info":[{"award-number":["P30 CA030199-41"]}]},{"name":"National Institute of Health","award":["U54 AG079758-01"],"award-info":[{"award-number":["U54 AG079758-01"]}]},{"name":"National Institute of Health","award":["R21 AG075483-01S1"],"award-info":[{"award-number":["R21 AG075483-01S1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the Cancer Optical Mapping for detecting Structural Variations (COMSV) method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample.<\/jats:p>","DOI":"10.1093\/bib\/bbad520","type":"journal-article","created":{"date-parts":[[2023,12,19]],"date-time":"2023-12-19T19:42:23Z","timestamp":1703014943000},"source":"Crossref","is-referenced-by-count":2,"title":["Accurate identification of structural variations from cancer samples"],"prefix":"10.1093","volume":"25","author":[{"given":"Le","family":"Li","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenyang","family":"Hong","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , Chicago, Illinois 60208 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claire Yik-Lok","family":"Chung","sequence":"additional","affiliation":[{"name":"School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alden King-Yung","family":"Leung","sequence":"additional","affiliation":[{"name":"School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Delbert Almerick T","family":"Boncan","sequence":"additional","affiliation":[{"name":"School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lixin","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kwok-Wai","family":"Lo","sequence":"additional","affiliation":[{"name":"Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul B S","family":"Lai","sequence":"additional","affiliation":[{"name":"Department of Surgery, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Wong","sequence":"additional","affiliation":[{"name":"Department of Surgery, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingying","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Biomedical Sciences, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alfred Sze-Lok","family":"Cheng","sequence":"additional","affiliation":[{"name":"School of Biomedical Sciences, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting-Fung","family":"Chan","sequence":"additional","affiliation":[{"name":"School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"},{"name":"Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"},{"name":"Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng","family":"Yue","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , Chicago, Illinois 60208 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevin Y","family":"Yip","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"},{"name":"Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"},{"name":"Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong , Shatin, New Territories , Hong Kong"},{"name":"Sanford Burnham Prebys Medical Discovery Institute , La Jolla, California 92037 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,1,16]]},"reference":[{"issue":"3","key":"2024011719290057200_ref1","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/nrc1299","article-title":"A census of human cancer genes","volume":"4","author":"Andrew Futreal","year":"2004","journal-title":"Nat Rev Cancer"},{"issue":"7793","key":"2024011719290057200_ref2","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/s41586-019-1913-9","article-title":"Patterns of somatic structural variation in human cancer genomes","volume":"578","author":"Li","year":"2020","journal-title":"Nature"},{"issue":"1","key":"2024011719290057200_ref3","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.tig.2011.10.002","article-title":"Characterizing complex structural 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