The diploid genome sequence of an Asian individual

Jun Wang; Wei Wang; Ruiqiang Li; Yingrui Li; Geng Tian; Laurie Goodman; Wei Fan; Junqing Zhang; Jun Li; Juanbin Zhang; Yiran Guo; Binxiao Feng; Heng Li; Yao Lu; Xiaodong Fang; Huiqing Liang; Zhenglin Du; Dong Li; Yiqing Zhao; Yujie Hu; Zhenzhen Yang; Hancheng Zheng; Ines Hellmann; Michael Inouye; John Pool; Xin Yi; Jing Zhao; Jinjie Duan; Yan Zhou; Junjie Qin; Lijia Ma; Guoqing Li; Zhentao Yang; Guojie Zhang; Bin Yang; Chang Yu; Fang Liang; Wenjie Li; Shaochuan Li; Dawei Li; Peixiang Ni; Jue Ruan; Qibin Li; Hongmei Zhu; Dongyuan Liu; Zhike Lu; Ning Li; Guangwu Guo; Jianguo Zhang; Jia Ye; Lin Fang; Qin Hao; Quan Chen; Yu Liang; Yeyang Su; A San; Cuo Ping; Shuang Yang; Fang Chen; Li Li; Ke Zhou; Hongkun Zheng; Yuanyuan Ren; Ling Yang; Yang Gao; Guohua Yang; Zhuo Li; Xiaoli Feng; Karsten Kristiansen; Gane Ka-Shu Wong; Rasmus Nielsen; Richard Durbin; Lars Bolund; Xiuqing Zhang; Songgang Li; Huanming Yang; Jian Wang

doi:10.1038/nature07484

The diploid genome sequence of an Asian individual

Jun Wang, Wei Wang, Ruiqiang Li, Yingrui Li, Geng Tian, Laurie Goodman, Wei Fan, Junqing Zhang, Jun Li, Juanbin Zhang, Yiran Guo, Binxiao Feng, Heng Li, Yao Lu, Xiaodong Fang, Huiqing Liang, Zhenglin Du, Dong Li, Yiqing Zhao, Yujie HuZhenzhen Yang, Hancheng Zheng, Ines Hellmann, Michael Inouye, John Pool, Xin Yi, Jing Zhao, Jinjie Duan, Yan Zhou, Junjie Qin, Lijia Ma, Guoqing Li, Zhentao Yang, Guojie Zhang, Bin Yang, Chang Yu, Fang Liang, Wenjie Li, Shaochuan Li, Dawei Li, Peixiang Ni, Jue Ruan, Qibin Li, Hongmei Zhu, Dongyuan Liu, Zhike Lu, Ning Li, Guangwu Guo, Jianguo Zhang, Jia Ye, Lin Fang, Qin Hao, Quan Chen, Yu Liang, Yeyang Su, A San, Cuo Ping, Shuang Yang, Fang Chen, Li Li, Ke Zhou, Hongkun Zheng, Yuanyuan Ren, Ling Yang, Yang Gao, Guohua Yang, Zhuo Li, Xiaoli Feng, Karsten Kristiansen, Gane Ka-Shu Wong, Rasmus Nielsen, Richard Durbin, Lars Bolund, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang

Computational and RNA Biology

714 Citations (Scopus)

Abstract

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.

Original language	English
Journal	Nature
Volume	456
Issue number	7218
Pages (from-to)	60-65
Number of pages	5
ISSN	0028-0836
DOIs	https://doi.org/10.1038/nature07484
Publication status	Published - 2008

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Wang, J, Wang, W, Li, R, Li, Y, Tian, G, Goodman, L, Fan, W, Zhang, J, Li, J, Zhang, J, Guo, Y, Feng, B, Li, H, Lu, Y, Fang, X, Liang, H, Du, Z, Li, D, Zhao, Y, Hu, Y, Yang, Z, Zheng, H, Hellmann, I, Inouye, M, Pool, J, Yi, X, Zhao, J, Duan, J, Zhou, Y, Qin, J, Ma, L, Li, G, Yang, Z, Zhang, G, Yang, B, Yu, C, Liang, F, Li, W, Li, S, Li, D, Ni, P, Ruan, J, Li, Q, Zhu, H, Liu, D, Lu, Z, Li, N, Guo, G, Zhang, J, Ye, J, Fang, L, Hao, Q, Chen, Q, Liang, Y, Su, Y, San, A, Ping, C, Yang, S, Chen, F, Li, L, Zhou, K, Zheng, H, Ren, Y, Yang, L, Gao, Y, Yang, G, Li, Z, Feng, X, Kristiansen, K, Wong, GK-S, Nielsen, R, Durbin, R, Bolund, L, Zhang, X, Li, S, Yang, H & Wang, J 2008, 'The diploid genome sequence of an Asian individual', Nature, vol. 456, no. 7218, pp. 60-65. https://doi.org/10.1038/nature07484

@article{100e5070f75411ddbf70000ea68e967b,

title = "The diploid genome sequence of an Asian individual",

abstract = "Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.",

author = "Jun Wang and Wei Wang and Ruiqiang Li and Yingrui Li and Geng Tian and Laurie Goodman and Wei Fan and Junqing Zhang and Jun Li and Juanbin Zhang and Yiran Guo and Binxiao Feng and Heng Li and Yao Lu and Xiaodong Fang and Huiqing Liang and Zhenglin Du and Dong Li and Yiqing Zhao and Yujie Hu and Zhenzhen Yang and Hancheng Zheng and Ines Hellmann and Michael Inouye and John Pool and Xin Yi and Jing Zhao and Jinjie Duan and Yan Zhou and Junjie Qin and Lijia Ma and Guoqing Li and Zhentao Yang and Guojie Zhang and Bin Yang and Chang Yu and Fang Liang and Wenjie Li and Shaochuan Li and Dawei Li and Peixiang Ni and Jue Ruan and Qibin Li and Hongmei Zhu and Dongyuan Liu and Zhike Lu and Ning Li and Guangwu Guo and Jianguo Zhang and Jia Ye and Lin Fang and Qin Hao and Quan Chen and Yu Liang and Yeyang Su and A San and Cuo Ping and Shuang Yang and Fang Chen and Li Li and Ke Zhou and Hongkun Zheng and Yuanyuan Ren and Ling Yang and Yang Gao and Guohua Yang and Zhuo Li and Xiaoli Feng and Karsten Kristiansen and Wong, {Gane Ka-Shu} and Rasmus Nielsen and Richard Durbin and Lars Bolund and Xiuqing Zhang and Songgang Li and Huanming Yang and Jian Wang",

year = "2008",

doi = "10.1038/nature07484",

language = "English",

volume = "456",

pages = "60--65",

journal = "Nature",

issn = "0028-0836",

publisher = "nature publishing group",

number = "7218",

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TY - JOUR

T1 - The diploid genome sequence of an Asian individual

AU - Wang, Jun

AU - Wang, Wei

AU - Li, Ruiqiang

AU - Li, Yingrui

AU - Tian, Geng

AU - Goodman, Laurie

AU - Fan, Wei

AU - Zhang, Junqing

AU - Li, Jun

AU - Zhang, Juanbin

AU - Guo, Yiran

AU - Feng, Binxiao

AU - Li, Heng

AU - Lu, Yao

AU - Fang, Xiaodong

AU - Liang, Huiqing

AU - Du, Zhenglin

AU - Li, Dong

AU - Zhao, Yiqing

AU - Hu, Yujie

AU - Yang, Zhenzhen

AU - Zheng, Hancheng

AU - Hellmann, Ines

AU - Inouye, Michael

AU - Pool, John

AU - Yi, Xin

AU - Zhao, Jing

AU - Duan, Jinjie

AU - Zhou, Yan

AU - Qin, Junjie

AU - Ma, Lijia

AU - Li, Guoqing

AU - Yang, Zhentao

AU - Zhang, Guojie

AU - Yang, Bin

AU - Yu, Chang

AU - Liang, Fang

AU - Li, Wenjie

AU - Li, Shaochuan

AU - Li, Dawei

AU - Ni, Peixiang

AU - Ruan, Jue

AU - Li, Qibin

AU - Zhu, Hongmei

AU - Liu, Dongyuan

AU - Lu, Zhike

AU - Li, Ning

AU - Guo, Guangwu

AU - Zhang, Jianguo

AU - Ye, Jia

AU - Fang, Lin

AU - Hao, Qin

AU - Chen, Quan

AU - Liang, Yu

AU - Su, Yeyang

AU - San, A

AU - Ping, Cuo

AU - Yang, Shuang

AU - Chen, Fang

AU - Li, Li

AU - Zhou, Ke

AU - Zheng, Hongkun

AU - Ren, Yuanyuan

AU - Yang, Ling

AU - Gao, Yang

AU - Yang, Guohua

AU - Li, Zhuo

AU - Feng, Xiaoli

AU - Kristiansen, Karsten

AU - Wong, Gane Ka-Shu

AU - Nielsen, Rasmus

AU - Durbin, Richard

AU - Bolund, Lars

AU - Zhang, Xiuqing

AU - Li, Songgang

AU - Yang, Huanming

AU - Wang, Jian

PY - 2008

Y1 - 2008

N2 - Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.

AB - Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.

U2 - 10.1038/nature07484

DO - 10.1038/nature07484

M3 - Journal article

C2 - 18987735

SN - 0028-0836

VL - 456

SP - 60

EP - 65

JO - Nature

JF - Nature

IS - 7218

ER -

The diploid genome sequence of an Asian individual

Abstract

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