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OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps.
Li, Le; Leung, Alden King-Yung; Kwok, Tsz-Piu; Lai, Yvonne Y Y; Pang, Iris K; Chung, Grace Tin-Yun; Mak, Angel C Y; Poon, Annie; Chu, Catherine; Li, Menglu; Wu, Jacob J K; Lam, Ernest T; Cao, Han; Lin, Chin; Sibert, Justin; Yiu, Siu-Ming; Xiao, Ming; Lo, Kwok-Wai; Kwok, Pui-Yan; Chan, Ting-Fung; Yip, Kevin Y.
Afiliación
  • Li L; Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
  • Leung AK; School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
  • Kwok TP; Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
  • Lai YYY; Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, USA.
  • Pang IK; School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
  • Chung GT; Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
  • Mak ACY; Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, USA.
  • Poon A; Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, USA.
  • Chu C; Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, USA.
  • Li M; Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong.
  • Wu JJK; Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong.
  • Lam ET; BioNano Genomics, San Diego, California, USA.
  • Cao H; BioNano Genomics, San Diego, California, USA.
  • Lin C; Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, USA.
  • Sibert J; School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania, USA.
  • Yiu SM; Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong.
  • Xiao M; School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania, USA.
  • Lo KW; Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
  • Kwok PY; Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, USA.
  • Chan TF; Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.
  • Yip KY; School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. tf.chan@cuhk.edu.hk.
Genome Biol ; 18(1): 230, 2017 Dec 01.
Article en En | MEDLINE | ID: mdl-29195502
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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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Genómica / Variación Estructural del Genoma Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2017 Tipo del documento: Article País de afiliación: Hong Kong
Texto completo
Imprimir
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Genómica / Variación Estructural del Genoma Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2017 Tipo del documento: Article País de afiliación: Hong Kong