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Journal article
Genome maps across 26 human populations reveal population-specific patterns of structural variation
Nature communications, v 10(1), pp 1025-1025
04 Mar 2019
PMID: 30833565
Featured in Collection : UN Sustainable Development Goals @ Drexel
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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Details
- Title
- Genome maps across 26 human populations reveal population-specific patterns of structural variation
- Creators
- Michal Levy-Sakin - University of California, San FranciscoSteven Pastor - Drexel UniversityYulia Mostovoy - University of California, San FranciscoLe Li - Chinese University of Hong KongAlden K Y Leung - Chinese University of Hong KongJennifer McCaffrey - Drexel UniversityEleanor Young - Drexel UniversityErnest T Lam - BioNano GenomicsAlex R Hastie - BioNano GenomicsKaren H Y Wong - University of California, San FranciscoClaire Y L Chung - Chinese University of Hong KongWalfred Ma - University of California, San FranciscoJustin Sibert - Drexel UniversityRamakrishnan Rajagopalan - Drexel UniversityNana Jin - Chinese University of Hong KongEugene Y C Chow - Chinese University of Hong KongCatherine Chu - University of California, San FranciscoAnnie Poon - University of California, San FranciscoChin Lin - University of California, San FranciscoAhmed Naguib - BioNano GenomicsWei-Ping Wang - BioNano GenomicsHan Cao - BioNano GenomicsTing-Fung Chan - Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, ChinaKevin Y Yip - Chinese University of Hong KongMing Xiao - Drexel UniversityPui-Yan Kwok - University of California, San Francisco
- Publication Details
- Nature communications, v 10(1), pp 1025-1025
- Publisher
- Springer Nature
- Grant note
- R01 GM125757 / NIGMS NIH HHS R01 HG005946 / NHGRI NIH HHS T32 HL007731 / NHLBI NIH HHS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000460125400007
- Scopus ID
- 2-s2.0-85062394585
- Other Identifier
- 991019167914804721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Genetics & Heredity