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

被引：106

作者：

Levy-Sakin, Michal ^{[1
]}

Pastor, Steven ^{[2
]}

Mostovoy, Yulia ^{[1
]}

Li, Le ^{[3
]}

Leung, Alden K. Y. ^{[4
,5
]}

McCaffrey, Jennifer ^{[2
]}

Young, Eleanor ^{[2
]}

Lam, Ernest T. ^{[6
]}

Hastie, Alex R. ^{[6
]}

Wong, Karen H. Y. ^{[1
]}

Chung, Claire Y. L. ^{[4
,5
]}

Ma, Walfred ^{[1
]}

Sibert, Justin ^{[2
]}

Rajagopalan, Ramakrishnan ^{[2
]}

Jin, Nana ^{[4
,5
]}

Chow, Eugene Y. C. ^{[4
,5
]}

Chu, Catherine ^{[1
]}

Poon, Annie ^{[1
]}

Lin, Chin ^{[1
]}

Naguib, Ahmed ^{[6
]}

Wang, Wei-Ping ^{[6
]}

Cao, Han ^{[6
]}

Chan, Ting-Fung ^{[4
,5
,7
]}

Yip, Kevin Y. ^{[3
,7
]}

Xiao, Ming ^{[2
,8
]}

Kwok, Pui-Yan ^{[1
,9
,10
]}

机构：

[1] Univ Calif San Francisco, Cardiovasc Res Inst, San Francisco, CA 94143 USA

[2] Drexel Univ, Sch Biomed Engn, Philadelphia, PA 19104 USA

[3] Chinese Univ Hong Kong, Dept Comp Sci & Engn, Hong Kong, Peoples R China

[4] Chinese Univ Hong Kong, Sch Life Sci, Hong Kong, Peoples R China

[5] Chinese Univ Hong Kong, State Key Lab Agrobiotechnol, Hong Kong, Peoples R China

[6] Bionano Genom, San Diego, CA 92121 USA

[7] Chinese Univ Hong Kong, Hong Kong Bioinformat Ctr, Hong Kong, Peoples R China

[8] Drexel Univ, Inst Mol Med & Infect Dis, Sch Med, Philadelphia, PA 19104 USA

[9] Univ Calif San Francisco, Dept Dermatol, San Francisco, CA 94143 USA

[10] Univ Calif San Francisco, Inst Human Genet, San Francisco, CA 94143 USA

来源：

NATURE COMMUNICATIONS | 2019年 / 10卷 / 1期

基金：

美国国家卫生研究院;

关键词：

SEGMENTAL DUPLICATIONS; NEXT-GENERATION; COPY-NUMBER; EVOLUTION; ORGANIZATION; SOFTWARE; CANCER; TOOL; DNA;

D O I：

10.1038/s41467-019-08992-7

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 similar to 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 similar to 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.

引用

页数：14

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