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Journal article
OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps
Genome biology, v 18(1), pp 1-19
01 Dec 2017
PMID: 29195502
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, and SVs with or without creating or destroying restriction sites. We show that OMSV has high sensitivity and specificity, with clear performance gains over the latest method. Applying OMSV to a human cell line, we identified hundreds of SVs >2 kbp, with 68% of them missed by sequencing-based callers. Independent experimental validation confirmed the high accuracy of these SVs. The OMSV software is available at http://yiplab.cse.cuhk.edu.hk/omsv/.
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Details
- Title
- OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps
- Creators
- Le Li - Chinese University of Hong KongAlden King-Yung Leung - Chinese University of Hong KongTsz-Piu Kwok - Chinese University of Hong KongYvonne Y. Y. Lai - University of California, San FranciscoIris K. Pang - Chinese University of Hong KongGrace Tin-Yun Chung - Chinese University of Hong KongAngel C. Y. Mak - University of California, San FranciscoAnnie Poon - University of California, San FranciscoCatherine Chu - University of California, San FranciscoMenglu Li - University of Hong KongJacob J. K. Wu - University of Hong KongErnest T. Lam - BioNano GenomicsHan Cao - BioNano GenomicsChin Lin - University of California, San FranciscoJustin Sibert - Drexel UniversitySiu-Ming Yiu - University of Hong KongMing Xiao - Drexel UniversityKwok-Wai Lo - Chinese University of Hong KongPui-Yan Kwok - University of California, San FranciscoTing-Fung Chan - Chinese Univ Hong Kong, Sch Life Sci, Shatin, Hong Kong, Peoples R ChinaKevin Y. Yip - Chinese University of Hong Kong
- Publication Details
- Genome biology, v 18(1), pp 1-19
- Publisher
- Springer Nature
- Number of pages
- 19
- Grant note
- HMRF12110542 / Health and Medical Research Fund of the Food and Health Bureau of the Hong Kong Special Administrative Region (HKSAR) T12-402/13-N; T12-401/13-R / Theme-based Research Scheme of the HKSAR Research Grants Council (RGC) 14102014 / General Research Fund AoE/M-403/16 / Area of Excellence Scheme of the HKSAR RGC
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000416858300001
- Scopus ID
- 2-s2.0-85036526499
- Other Identifier
- 991019167927604721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biotechnology & Applied Microbiology
- Genetics & Heredity