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Genome maps across 26 human populations reveal population-specific patterns of structural variation

Author

Listed:
  • Michal Levy-Sakin

    (University of California–San Francisco)

  • Steven Pastor

    (Drexel University)

  • Yulia Mostovoy

    (University of California–San Francisco)

  • Le Li

    (The Chinese University of Hong Kong)

  • Alden K. Y. Leung

    (The Chinese University of Hong Kong)

  • Jennifer McCaffrey

    (Drexel University)

  • Eleanor Young

    (Drexel University)

  • Ernest T. Lam

    (Bionano Genomics)

  • Alex R. Hastie

    (Bionano Genomics)

  • Karen H. Y. Wong

    (University of California–San Francisco)

  • Claire Y. L. Chung

    (The Chinese University of Hong Kong)

  • Walfred Ma

    (University of California–San Francisco)

  • Justin Sibert

    (Drexel University)

  • Ramakrishnan Rajagopalan

    (Drexel University)

  • Nana Jin

    (The Chinese University of Hong Kong)

  • Eugene Y. C. Chow

    (The Chinese University of Hong Kong)

  • Catherine Chu

    (University of California–San Francisco)

  • Annie Poon

    (University of California–San Francisco)

  • Chin Lin

    (University of California–San Francisco)

  • Ahmed Naguib

    (Bionano Genomics)

  • Wei-Ping Wang

    (Bionano Genomics)

  • Han Cao

    (Bionano Genomics)

  • Ting-Fung Chan

    (The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Kevin Y. Yip

    (The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Ming Xiao

    (Drexel University
    Drexel University)

  • Pui-Yan Kwok

    (University of California–San Francisco
    University of California–San Francisco
    University of California–San Francisco)

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.

Suggested Citation

  • Michal Levy-Sakin & Steven Pastor & Yulia Mostovoy & Le Li & Alden K. Y. Leung & Jennifer McCaffrey & Eleanor Young & Ernest T. Lam & Alex R. Hastie & Karen H. Y. Wong & Claire Y. L. Chung & Walfred M, 2019. "Genome maps across 26 human populations reveal population-specific patterns of structural variation," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-08992-7
    DOI: 10.1038/s41467-019-08992-7
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    Cited by:

    1. Oscar L. Rodriguez & Yana Safonova & Catherine A. Silver & Kaitlyn Shields & William S. Gibson & Justin T. Kos & David Tieri & Hanzhong Ke & Katherine J. L. Jackson & Scott D. Boyd & Melissa L. Smith , 2023. "Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    2. Gabriel E. Rech & Santiago Radío & Sara Guirao-Rico & Laura Aguilera & Vivien Horvath & Llewellyn Green & Hannah Lindstadt & Véronique Jamilloux & Hadi Quesneville & Josefa González, 2022. "Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Yong Zhou & Zhichao Yu & Dmytro Chebotarov & Kapeel Chougule & Zhenyuan Lu & Luis F. Rivera & Nagarajan Kathiresan & Noor Al-Bader & Nahed Mohammed & Aseel Alsantely & Saule Mussurova & João Santos & , 2023. "Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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