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Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

机译：丹麦150个基因组的测序和从头组装

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摘要

Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits(1-4). Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly(2,5-7). However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology(4,8-13). We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.
机译：现在正在对数十万个人类基因组进行测序，以表征遗传变异，并利用这些信息来增强对复杂疾病和其他表型特征的关联作图研究（1-4）。遗传变异主要是通过将短读段映射到参考基因组或通过进行局部组装来鉴定的（2,5-7）。但是，这些方法偏向于发现结构变异和基因组更复杂部分的变异。因此，需要大规模的从头组装。在这里，我们表明可以通过覆盖范围高达20千碱基对的伴侣对文库，从高覆盖率的测序中构建出色的从头组装。我们报告了来自GenomeDenmark项目的150个参与者（50个三重奏）的从头汇编。这些组件的质量类似于使用更昂贵的长读技术获得的组件（4,8-13）。我们使用这些程序集来识别一组丰富的结构变异，包括许多新颖的插入物，并演示此变异目录如何实现对已知关联映射信号的进一步解密。我们利用程序集提供100种完全解析的主要组织相容性复杂单倍型并解析Y染色体的主要部分。我们的研究提供了一个区域参考基因组，我们期望该基因组将改善未来的关联图谱研究的能力，从而为精密医学计划铺平道路，目前在包括丹麦在内的许多国家已经启动了精确医学计划。

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  • 来源
    《Nature》 |2017年第7665期|87-91|共5页
  • 作者

    Maretty Lasse; Jensen Jacob Malte; Petersen Bent; Sibbesen Jonas A. Ndreas; Liu Siyang; Villesen Palle; Kov Laurits S.; Belling Kirstine; Have Christian T. Heil; Izarzugaza Jose M. G.; Rosjean Marie G.; Bork-Jensen Jette; Rove Jakob G.; Ls Thomas D. A.; Huang Shujia; Chang Yuqi; Xu Ruiqi; Ye Weijian; Rao Junhua; Guo Xiaosen; Sun Jihua; Cao Hongzhi; Ye Chen; van Beusekom Johan; Espeseth Thomas; Flindt Esben; Friborg Rune M.; Halager Anders E.; Le Hellard Stephanie; Hultman Christina M.; Lescai Francesco; Li Shengting; Lund Ole; Longren Peter; Mailund Thomas; Matey-Hernandez Maria Luisa; Mors Ole; Pedersen Christian N. S.; Icheritz-Ponten Thomas S.; Sullivan Patrick; Syed Ali; Westergaard David; Yadav Rachita; Li Ning; Xu Xun; Hansen Torben; Krogh Anders; Bolund Lars; Sorensen Thorkild I. A.; Pedersen Oluf; Upta Ramneek G.; Rasmussen Simon; Besenbacher Soren; Borglum Anders D.; Wang Jun; Eiberg Hans; Kristiansen Karsten; Brunak Soren; Schierup Mikkel Heide;

  • 作者单位

    Univ Copenhagen, Bioinformat Ctr, Dept Biol, DK-2200 Copenhagen, Denmark;

    Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark|Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Univ Copenhagen, Bioinformat Ctr, Dept Biol, DK-2200 Copenhagen, Denmark;

    Univ Copenhagen, Bioinformat Ctr, Dept Biol, DK-2200 Copenhagen, Denmark|BGI Europe, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark;

    Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark|Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark|Aarhus Univ, Dept Clin Med, DK-8000 Aarhus, Denmark;

    Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark|Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metab Res, Sect Metab Genet, DK-2100 Copenhagen, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metab Res, Sect Metab Genet, DK-2100 Copenhagen, Denmark;

    Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark|Aarhus Univ, Dept Biomed, DK-8000 Aarhus, Denmark|iPSYCH, Lundbeck Fdn Initiat Integrat Psychiat Res, DK-8000 Aarhus, Denmark;

    Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark|Aarhus Univ, Dept Biomed, DK-8000 Aarhus, Denmark|iPSYCH, Lundbeck Fdn Initiat Integrat Psychiat Res, DK-8000 Aarhus, Denmark;

    BGI Shenzhen, Shenzhen 518083, Peoples R China|South China Univ Technol, Sch Biosci & Biotechnol, Guangzhou 510006, Guangdong, Peoples R China;

    BGI Shenzhen, Shenzhen 518083, Peoples R China;

    BGI Europe, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark;

    BGI Europe, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark;

    BGI Europe, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark;

    BGI Shenzhen, Shenzhen 518083, Peoples R China|Univ Copenhagen, Dept Biol, Lab Genom & Mol Biomed, DK-2100 Copenhagen, Denmark;

    BGI Europe, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark|Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metab Res, Sect Metab Genet, DK-2100 Copenhagen, Denmark;

    BGI Shenzhen, Shenzhen 518083, Peoples R China;

    BGI Shenzhen, Shenzhen 518083, Peoples R China;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Univ Oslo, Dept Psychol, N-0317 Oslo, Norway|Univ Bergen, KG Jebsen Ctr Psychosis Res, Dept Clin Sci, NORMENT, N-5021 Bergen, Norway;

    Univ Copenhagen, Dept Biol, Lab Genom & Mol Biomed, DK-2100 Copenhagen, Denmark;

    Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark;

    Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark;

    Univ Bergen, KG Jebsen Ctr Psychosis Res, Dept Clin Sci, NORMENT, N-5021 Bergen, Norway|Haukeland Hosp, Ctr Med Genet & Mol Med, Dr E Martens Res Grp Biol Psychiat, N-5021 Bergen, Norway;

    Karolinska Inst, Dept Med Epidemiol & Biostat, S-17177 Stockholm, Sweden;

    Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark|Aarhus Univ, Dept Biomed, DK-8000 Aarhus, Denmark|iPSYCH, Lundbeck Fdn Initiat Integrat Psychiat Res, DK-8000 Aarhus, Denmark;

    Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark|Aarhus Univ, Dept Biomed, DK-8000 Aarhus, Denmark|iPSYCH, Lundbeck Fdn Initiat Integrat Psychiat Res, DK-8000 Aarhus, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark|Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark|Aarhus Univ, Dept Clin Med, DK-8000 Aarhus, Denmark|iPSYCH, Lundbeck Fdn Initiat Integrat Psychiat Res, DK-8000 Aarhus, Denmark;

    Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark|Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Karolinska Inst, Dept Med Epidemiol & Biostat, S-17177 Stockholm, Sweden|Univ N Carolina, Dept Genet, Chapel Hill, NC 27599 USA;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    BGI Europe, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark;

    BGI Shenzhen, Shenzhen 518083, Peoples R China;

    Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metab Res, Sect Metab Genet, DK-2100 Copenhagen, Denmark;

    Univ Copenhagen, Bioinformat Ctr, Dept Biol, DK-2200 Copenhagen, Denmark;

    BGI Shenzhen, Shenzhen 518083, Peoples R China;

    Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metab Res, Sect Metab Genet, DK-2100 Copenhagen, Denmark|Bispebjerg & Frederiksberg Hosp, Dept Clin Epidemiol, DK-2000 Frederiksberg, Denmark|Univ Copenhagen, Fac Hlth & Med Sci, Dept Publ Hlth, DK-2200 Copenhagen, Denmark;

    Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metab Res, Sect Metab Genet, DK-2100 Copenhagen, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark;

    Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark|Aarhus Univ, Dept Clin Med, DK-8000 Aarhus, Denmark;

    Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark|Aarhus Univ, Dept Biomed, DK-8000 Aarhus, Denmark|iPSYCH, Lundbeck Fdn Initiat Integrat Psychiat Res, DK-8000 Aarhus, Denmark;

    Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark|BGI Shenzhen, Shenzhen 518083, Peoples R China|Univ Copenhagen, Dept Biol, Lab Genom & Mol Biomed, DK-2100 Copenhagen, Denmark;

    Univ Copenhagen, Dept Cellular & Mol Med, DK-2200 Copenhagen, Denmark;

    BGI Shenzhen, Shenzhen 518083, Peoples R China|Univ Copenhagen, Dept Biol, Lab Genom & Mol Biomed, DK-2100 Copenhagen, Denmark;

    Tech Univ Denmark, Dept Bio & Hlth Informat, DTU Bioinformat, DK-2800 Kongens Lyngby, Denmark|Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Prot Res, DK-2200 Copenhagen, Denmark;

    Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark|Aarhus Univ, Ctr Integrat Sequencing, iSEQ, DK-8000 Aarhus, Denmark|Aarhus Univ, Dept Biosci, DK-8000 Aarhus, Denmark;

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