Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

Li, Yingrui, Zheng, Hancheng, Luo, Ruibang, Wu, Honglong, Zhu, Hongmei, Li, Ruiqiang, Cao, Hongzhi, Wu, Boxin, Huang, Shujia, Shao, Haojing, Ma, Hanzhou, Zhang, Fan, Feng, Shuijian, Zhang, Wei, Du, Hongli, Tian, Geng, Li, Jingxiang, Zhang, Xiuqing, Li, Songgang, Bolund, Lars, Kristiansen, Karsten, de Smith, Adam J., Blakemore, Alexandra I. F., Coin, Lachlan J. M., Yang, Huanming, Wang, Jian and Wang, Jun (2011) Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nature Biotechnology, 29 8: 723-730. doi:10.1038/nbt.1904

Author Li, Yingrui
Zheng, Hancheng
Luo, Ruibang
Wu, Honglong
Zhu, Hongmei
Li, Ruiqiang
Cao, Hongzhi
Wu, Boxin
Huang, Shujia
Shao, Haojing
Ma, Hanzhou
Zhang, Fan
Feng, Shuijian
Zhang, Wei
Du, Hongli
Tian, Geng
Li, Jingxiang
Zhang, Xiuqing
Li, Songgang
Bolund, Lars
Kristiansen, Karsten
de Smith, Adam J.
Blakemore, Alexandra I. F.
Coin, Lachlan J. M.
Yang, Huanming
Wang, Jian
Wang, Jun
Title Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly
Journal name Nature Biotechnology   Check publisher's open access policy
ISSN 1087-0156
Publication date 2011-01-01
Year available 2011
Sub-type Article (original research)
DOI 10.1038/nbt.1904
Open Access Status Not yet assessed
Volume 29
Issue 8
Start page 723
End page 730
Total pages 8
Place of publication New York, NY, United States
Publisher Nature Publishing Group
Language eng
Abstract Here we use whole-genome de novo assembly of second-generation sequencing reads to map structural variation (SV) in an Asian genome and an African genome. Our approach identifies small-and intermediate-size homozygous variants (1-50 kb) including insertions, deletions, inversions and their precise breakpoints, and in contrast to other methods, can resolve complex rearrangements. In total, we identified 277,243 SVs ranging in length from 1-23 kb. Validation using computational and experimental methods suggests that we achieve overall <6% false-positive rate and <10% false-negative rate in genomic regions that can be assembled, which outperforms other methods. Analysis of the SVs in the genomes of 106 individuals sequenced as part of the 1000 Genomes Project suggests that SVs account for a greater fraction of the diversity between individuals than do single-nucleotide polymorphisms (SNPs). These findings demonstrate that whole-genome de novo assembly is a feasible approach to deriving more comprehensive maps of genetic variation.
Keyword Biotechnology & Applied Microbiology
Biotechnology & Applied Microbiology
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID 2011CB809200
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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