Building the sequence map of the human pan-genome

Ruiqiang Li; Yingrui Li; Hancheng Zheng; Ruibang Luo; Hongmei Zhu; Qibin Li; Wubin Qian; Yuanyuan Ren; Geng Tian; Jinxiang Li; Guangyu Zhou; Xuan Zhu; Honglong Wu; Junjie Qin; Xin Jin; Dongfang Li; Hongzhi Cao; Xueda Hu; Hélène Blanche; Howard Cann; Xiuqing Zhang; Songgang Li; Lars Bolund; Karsten Kristiansen; Huanming Yang; Jun Wang; Jian Wang

doi:10.1038/nbt.1596

Building the sequence map of the human pan-genome

Ruiqiang Li, Yingrui Li, Hancheng Zheng, Ruibang Luo, Hongmei Zhu, Qibin Li, Wubin Qian, Yuanyuan Ren, Geng Tian, Jinxiang Li, Guangyu Zhou, Xuan Zhu, Honglong Wu, Junjie Qin, Xin Jin, Dongfang Li, Hongzhi Cao, Xueda Hu, Hélène Blanche, Howard CannXiuqing Zhang, Songgang Li, Lars Bolund, Karsten Kristiansen, Huanming Yang, Jun Wang, Jian Wang

Department of Biology

147 Citations (Scopus)

Abstract

Here we integrate the de novo assembly of an Asian and an African genome with the NCBI reference human genome, as a step toward constructing the human pan-genome. We identified ∼5 Mb of novel sequences not present in the reference genome in each of these assemblies. Most novel sequences are individual or population specific, as revealed by their comparison to all available human DNA sequence and by PCR validation using the human genome diversity cell line panel. We found novel sequences present in patterns consistent with known human migration paths. Cross-species conservation analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain 19-40Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing to the genetic variation of the pan-genome indicates the importance of using complete genome sequencing and de novo assembly.

Original language	English
Journal	Nature Biotechnology
Volume	28
Issue number	1
Pages (from-to)	57-63
Number of pages	7
ISSN	1087-0156
DOIs	https://doi.org/10.1038/nbt.1596
Publication status	Published - Jan 2010

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Li, R, Li, Y, Zheng, H, Luo, R, Zhu, H, Li, Q, Qian, W, Ren, Y, Tian, G, Li, J, Zhou, G, Zhu, X, Wu, H, Qin, J, Jin, X, Li, D, Cao, H, Hu, X, Blanche, H, Cann, H, Zhang, X, Li, S, Bolund, L, Kristiansen, K, Yang, H, Wang, J & Wang, J 2010, 'Building the sequence map of the human pan-genome', Nature Biotechnology, vol. 28, no. 1, pp. 57-63. https://doi.org/10.1038/nbt.1596

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title = "Building the sequence map of the human pan-genome",

abstract = "Here we integrate the de novo assembly of an Asian and an African genome with the NCBI reference human genome, as a step toward constructing the human pan-genome. We identified ∼5 Mb of novel sequences not present in the reference genome in each of these assemblies. Most novel sequences are individual or population specific, as revealed by their comparison to all available human DNA sequence and by PCR validation using the human genome diversity cell line panel. We found novel sequences present in patterns consistent with known human migration paths. Cross-species conservation analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain 19-40Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing to the genetic variation of the pan-genome indicates the importance of using complete genome sequencing and de novo assembly.",

author = "Ruiqiang Li and Yingrui Li and Hancheng Zheng and Ruibang Luo and Hongmei Zhu and Qibin Li and Wubin Qian and Yuanyuan Ren and Geng Tian and Jinxiang Li and Guangyu Zhou and Xuan Zhu and Honglong Wu and Junjie Qin and Xin Jin and Dongfang Li and Hongzhi Cao and Xueda Hu and H{\'e}l{\`e}ne Blanche and Howard Cann and Xiuqing Zhang and Songgang Li and Lars Bolund and Karsten Kristiansen and Huanming Yang and Jun Wang and Jian Wang",

note = "Keywords: Animals; Base Sequence; Genetics, Population; Genome, Human; Humans; Sequence Alignment; Sequence Analysis, DNA; Species Specificity",

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doi = "10.1038/nbt.1596",

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AU - Zhu, Hongmei

AU - Li, Qibin

AU - Qian, Wubin

AU - Ren, Yuanyuan

AU - Tian, Geng

AU - Li, Jinxiang

AU - Zhou, Guangyu

AU - Zhu, Xuan

AU - Wu, Honglong

AU - Qin, Junjie

AU - Jin, Xin

AU - Li, Dongfang

AU - Cao, Hongzhi

AU - Hu, Xueda

AU - Blanche, Hélène

AU - Cann, Howard

AU - Zhang, Xiuqing

AU - Li, Songgang

AU - Bolund, Lars

AU - Kristiansen, Karsten

AU - Yang, Huanming

AU - Wang, Jun

AU - Wang, Jian

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PY - 2010/1

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N2 - Here we integrate the de novo assembly of an Asian and an African genome with the NCBI reference human genome, as a step toward constructing the human pan-genome. We identified ∼5 Mb of novel sequences not present in the reference genome in each of these assemblies. Most novel sequences are individual or population specific, as revealed by their comparison to all available human DNA sequence and by PCR validation using the human genome diversity cell line panel. We found novel sequences present in patterns consistent with known human migration paths. Cross-species conservation analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain 19-40Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing to the genetic variation of the pan-genome indicates the importance of using complete genome sequencing and de novo assembly.

AB - Here we integrate the de novo assembly of an Asian and an African genome with the NCBI reference human genome, as a step toward constructing the human pan-genome. We identified ∼5 Mb of novel sequences not present in the reference genome in each of these assemblies. Most novel sequences are individual or population specific, as revealed by their comparison to all available human DNA sequence and by PCR validation using the human genome diversity cell line panel. We found novel sequences present in patterns consistent with known human migration paths. Cross-species conservation analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain 19-40Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing to the genetic variation of the pan-genome indicates the importance of using complete genome sequencing and de novo assembly.

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Building the sequence map of the human pan-genome

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