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

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 Ma, Justin Sibert, Ramakrishnan Rajagopalan, Nana Jin, Eugene Y. C. Chow, Catherine Chu, Annie Poon, Chin Lin, Ahmed Naguib, Wei-Ping Wang, Han Cao, Ting-Fung Chan, Kevin Y. Yip, Ming Xiao and Pui-Yan Kwok ()
Additional contact information
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
Kevin Y. Yip: The Chinese University of Hong Kong
Ming Xiao: Drexel University
Pui-Yan Kwok: University of California–San Francisco

Nature Communications, 2019, vol. 10, issue 1, 1-14

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-019-08992-7

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