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

Yingrui Li; Hancheng Zheng; Ruibang Luo; Honglong Wu; Hongmei Zhu; Ruiqiang Li; Hongzhi Cao; Boxin Wu; Shujia Huang; Haojing Shao; Hanzhou Ma; Fan Zhang; Shuijian Feng; Wei Zhang; Hongli Du; Geng Tian; Jingxiang Li; Xiuqing Zhang; Songgang Li; Lars Bolund; Karsten Kristiansen; Adam J de Smith; Alexandra I F Blakemore; Lachlan J M Coin; Huanming Yang; Jian Wang; Jun Wang; Jun Wang

doi:10.1038/nbt.1904

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

Yingrui Li, Hancheng Zheng, Ruibang Luo, Honglong Wu, Hongmei Zhu, Ruiqiang Li, Hongzhi Cao, Boxin Wu, Shujia Huang, Haojing Shao, Hanzhou Ma, Fan Zhang, Shuijian Feng, Wei Zhang, Hongli Du, Geng Tian, Jingxiang Li, Xiuqing Zhang, Songgang Li, Lars BolundKarsten Kristiansen, Adam J de Smith, Alexandra I F Blakemore, Lachlan J M Coin, Huanming Yang, Jian Wang, Jun Wang, Jun Wang

Department of Biology

93 Citations (Scopus)

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

Original language	English
Journal	Nature Biotechnology
Volume	29
Issue number	8
Pages (from-to)	723-730
Number of pages	8
ISSN	1087-0156
DOIs	https://doi.org/10.1038/nbt.1904
Publication status	Published - Aug 2011

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Li, Y., Zheng, H., Luo, R., Wu, H., Zhu, H., Li, R., Cao, H., Wu, B., Huang, S., Shao, H., Ma, H., Zhang, F., Feng, S., Zhang, W., Du, H., Tian, G., Li, J., Zhang, X., Li, S., ... Wang, J. (2011). Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nature Biotechnology, 29(8), 723-730. https://doi.org/10.1038/nbt.1904

Li, Y, Zheng, H, Luo, R, Wu, H, Zhu, H, Li, R, Cao, H, Wu, B, Huang, S, Shao, H, Ma, H, Zhang, F, Feng, S, Zhang, W, Du, H, Tian, G, Li, J, Zhang, X, Li, S, Bolund, L, Kristiansen, K, de Smith, AJ, Blakemore, AIF, Coin, LJM, Yang, H, Wang, J, Wang, J & Wang, J 2011, 'Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly', Nature Biotechnology, vol. 29, no. 8, pp. 723-730. https://doi.org/10.1038/nbt.1904

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

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 ",

author = "Yingrui Li and Hancheng Zheng and Ruibang Luo and Honglong Wu and Hongmei Zhu and Ruiqiang Li and Hongzhi Cao and Boxin Wu and Shujia Huang and Haojing Shao and Hanzhou Ma and Fan Zhang and Shuijian Feng and Wei Zhang and Hongli Du and Geng Tian and Jingxiang Li and Xiuqing Zhang and Songgang Li and Lars Bolund and Karsten Kristiansen and {de Smith}, {Adam J} and Blakemore, {Alexandra I F} and Coin, {Lachlan J M} and Huanming Yang and Jian Wang and Jun Wang and Jun Wang",

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doi = "10.1038/nbt.1904",

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T1 - Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

AU - Li, Yingrui

AU - Zheng, Hancheng

AU - Luo, Ruibang

AU - Wu, Honglong

AU - Zhu, Hongmei

AU - Li, Ruiqiang

AU - Cao, Hongzhi

AU - Wu, Boxin

AU - Huang, Shujia

AU - Shao, Haojing

AU - Ma, Hanzhou

AU - Zhang, Fan

AU - Feng, Shuijian

AU - Zhang, Wei

AU - Du, Hongli

AU - Tian, Geng

AU - Li, Jingxiang

AU - Zhang, Xiuqing

AU - Li, Songgang

AU - Bolund, Lars

AU - Kristiansen, Karsten

AU - de Smith, Adam J

AU - Blakemore, Alexandra I F

AU - Coin, Lachlan J M

AU - Yang, Huanming

AU - Wang, Jian

AU - Wang, Jun

PY - 2011/8

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N2 - 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

AB - 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

U2 - 10.1038/nbt.1904

DO - 10.1038/nbt.1904

M3 - Journal article

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SN - 1087-0156

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SP - 723

EP - 730

JO - Nature Biotechnology

JF - Nature Biotechnology

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ER -

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

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