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Genome maps across 26 human populations reveal population-specific patterns of structural variation.
Levy-Sakin, Michal; Pastor, Steven; Mostovoy, Yulia; Li, Le; Leung, Alden K Y; McCaffrey, Jennifer; Young, Eleanor; Lam, Ernest T; Hastie, Alex R; Wong, Karen H Y; Chung, Claire Y L; Ma, Walfred; Sibert, Justin; Rajagopalan, Ramakrishnan; Jin, Nana; Chow, Eugene Y C; Chu, Catherine; Poon, Annie; Lin, Chin; Naguib, Ahmed; Wang, Wei-Ping; Cao, Han; Chan, Ting-Fung; Yip, Kevin Y; Xiao, Ming; Kwok, Pui-Yan.
Afiliação
  • Levy-Sakin M; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA.
  • Pastor S; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
  • Mostovoy Y; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA.
  • Li L; Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
  • Leung AKY; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.
  • McCaffrey J; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
  • Young E; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
  • Lam ET; Bionano Genomics, San Diego, CA, 92121, USA.
  • Hastie AR; Bionano Genomics, San Diego, CA, 92121, USA.
  • Wong KHY; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA.
  • Chung CYL; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.
  • Ma W; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA.
  • Sibert J; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
  • Rajagopalan R; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
  • Jin N; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.
  • Chow EYC; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.
  • Chu C; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA.
  • Poon A; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA.
  • Lin C; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA.
  • Naguib A; Bionano Genomics, San Diego, CA, 92121, USA.
  • Wang WP; Bionano Genomics, San Diego, CA, 92121, USA.
  • Cao H; Bionano Genomics, San Diego, CA, 92121, USA.
  • Chan TF; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.
  • Yip KY; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
  • Xiao M; Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
  • Kwok PY; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
Nat Commun ; 10(1): 1025, 2019 03 04.
Article em En | MEDLINE | ID: mdl-30833565
ABSTRACT
Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Genoma Humano / Mapeamento Cromossômico / Variação Estrutural do Genoma Idioma: En Ano de publicação: 2019 Tipo de documento: Article
Texto completo
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XML
PubMed Links
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Genoma Humano / Mapeamento Cromossômico / Variação Estrutural do Genoma Idioma: En Ano de publicação: 2019 Tipo de documento: Article