IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v456y2008i7218d10.1038_nature07484.html
   My bibliography  Save this article

The diploid genome sequence of an Asian individual

Author

Listed:
  • Jun Wang

    (Beijing Genomics Institute at Shenzhen
    Genome Research Institute, Shenzhen University Medical School
    National Engineering Center for Genomics and Bioinformatics
    University of Southern Denmark)

  • Wei Wang

    (Beijing Genomics Institute at Shenzhen
    National Engineering Center for Genomics and Bioinformatics)

  • Ruiqiang Li

    (Beijing Genomics Institute at Shenzhen
    National Engineering Center for Genomics and Bioinformatics
    University of Southern Denmark)

  • Yingrui Li

    (Beijing Genomics Institute at Shenzhen
    College of Life Sciences, Peking University
    Beijing Genomics Institute, Beijing Institute of Genomics of Chinese Academy of Sciences)

  • Geng Tian

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Laurie Goodman

    (Beijing Genomics Institute at Shenzhen)

  • Wei Fan

    (Beijing Genomics Institute at Shenzhen)

  • Junqing Zhang

    (Beijing Genomics Institute at Shenzhen)

  • Jun Li

    (Beijing Genomics Institute at Shenzhen)

  • Juanbin Zhang

    (Beijing Genomics Institute at Shenzhen)

  • Yiran Guo

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Binxiao Feng

    (Beijing Genomics Institute at Shenzhen)

  • Heng Li

    (Beijing Genomics Institute at Shenzhen
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Yao Lu

    (Beijing Genomics Institute at Shenzhen)

  • Xiaodong Fang

    (Beijing Genomics Institute at Shenzhen)

  • Huiqing Liang

    (Beijing Genomics Institute at Shenzhen)

  • Zhenglin Du

    (Beijing Genomics Institute at Shenzhen)

  • Dong Li

    (Beijing Genomics Institute at Shenzhen)

  • Yiqing Zhao

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Yujie Hu

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Zhenzhen Yang

    (Beijing Genomics Institute at Shenzhen)

  • Hancheng Zheng

    (Beijing Genomics Institute at Shenzhen)

  • Ines Hellmann

    (University of California, Berkeley, California 94720, USA)

  • Michael Inouye

    (The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • John Pool

    (University of California, Berkeley, California 94720, USA)

  • Xin Yi

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Jing Zhao

    (Beijing Genomics Institute at Shenzhen)

  • Jinjie Duan

    (Beijing Genomics Institute at Shenzhen)

  • Yan Zhou

    (Beijing Genomics Institute at Shenzhen)

  • Junjie Qin

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Lijia Ma

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Guoqing Li

    (Beijing Genomics Institute at Shenzhen)

  • Zhentao Yang

    (Beijing Genomics Institute at Shenzhen)

  • Guojie Zhang

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Bin Yang

    (Beijing Genomics Institute at Shenzhen)

  • Chang Yu

    (Beijing Genomics Institute at Shenzhen)

  • Fang Liang

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Wenjie Li

    (Beijing Genomics Institute at Shenzhen)

  • Shaochuan Li

    (Beijing Genomics Institute at Shenzhen)

  • Dawei Li

    (Beijing Genomics Institute at Shenzhen)

  • Peixiang Ni

    (Beijing Genomics Institute at Shenzhen)

  • Jue Ruan

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Qibin Li

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Hongmei Zhu

    (Beijing Genomics Institute at Shenzhen)

  • Dongyuan Liu

    (Beijing Genomics Institute at Shenzhen)

  • Zhike Lu

    (Beijing Genomics Institute at Shenzhen)

  • Ning Li

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Guangwu Guo

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Jianguo Zhang

    (Beijing Genomics Institute at Shenzhen)

  • Jia Ye

    (Beijing Genomics Institute at Shenzhen)

  • Lin Fang

    (Beijing Genomics Institute at Shenzhen)

  • Qin Hao

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Quan Chen

    (Beijing Genomics Institute at Shenzhen
    College of Life Sciences, Peking University)

  • Yu Liang

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Yeyang Su

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • A. san

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Cuo Ping

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Shuang Yang

    (Beijing Genomics Institute at Shenzhen)

  • Fang Chen

    (Beijing Genomics Institute at Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Li Li

    (Beijing Genomics Institute at Shenzhen)

  • Ke Zhou

    (Beijing Genomics Institute at Shenzhen)

  • Hongkun Zheng

    (Beijing Genomics Institute at Shenzhen
    University of Southern Denmark)

  • Yuanyuan Ren

    (Beijing Genomics Institute at Shenzhen)

  • Ling Yang

    (Beijing Genomics Institute at Shenzhen)

  • Yang Gao

    (Beijing Genomics Institute at Shenzhen
    Beijing Genomics Institute, Beijing Institute of Genomics of Chinese Academy of Sciences)

  • Guohua Yang

    (Beijing Genomics Institute at Shenzhen
    Genome Research Institute, Shenzhen University Medical School)

  • Zhuo Li

    (Beijing Genomics Institute at Shenzhen)

  • Xiaoli Feng

    (Beijing Genomics Institute at Shenzhen)

  • Karsten Kristiansen

    (University of Southern Denmark)

  • Gane Ka-Shu Wong

    (Beijing Genomics Institute at Shenzhen
    University of Alberta, Edmonton AB, T6G 2E9, Canada)

  • Rasmus Nielsen

    (University of California, Berkeley, California 94720, USA)

  • Richard Durbin

    (The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Lars Bolund

    (Beijing Genomics Institute at Shenzhen
    Insitute of Human Genetics, University of Aarhus)

  • Xiuqing Zhang

    (Beijing Genomics Institute at Shenzhen
    Beijing Genomics Institute, Beijing Institute of Genomics of Chinese Academy of Sciences)

  • Songgang Li

    (Beijing Genomics Institute at Shenzhen
    Genome Research Institute, Shenzhen University Medical School
    College of Life Sciences, Peking University)

  • Huanming Yang

    (Beijing Genomics Institute at Shenzhen
    Genome Research Institute, Shenzhen University Medical School
    National Engineering Center for Genomics and Bioinformatics)

  • Jian Wang

    (Beijing Genomics Institute at Shenzhen
    Genome Research Institute, Shenzhen University Medical School
    National Engineering Center for Genomics and Bioinformatics)

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.

Suggested Citation

  • 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 L, 2008. "The diploid genome sequence of an Asian individual," Nature, Nature, vol. 456(7218), pages 60-65, November.
    • Handle: RePEc:nat:nature:v:456:y:2008:i:7218:d:10.1038_nature07484
    DOI: 10.1038/nature07484
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature07484
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/nature07484?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Sandor Spisak & Viktoria Tisza & Pier Vitale Nuzzo & Ji-Heui Seo & Balint Pataki & Dezso Ribli & Zsofia Sztupinszki & Connor Bell & Mersedeh Rohanizadegan & David R. Stillman & Sarah Abou Alaiwi & Ala, 2023. "A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:456:y:2008:i:7218:d:10.1038_nature07484. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.