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Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

Author

Listed:
  • Søren Besenbacher

    (Bioinformatics Research Center, Aarhus University)

  • Siyang Liu

    (BGI Europe
    University of Copenhagen)

  • José M. G. Izarzugaza

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Jakob Grove

    (Bioinformatics Research Center, Aarhus University
    Centre for Integrative Sequencing, iSEQ, Aarhus University
    The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH
    Aarhus University)

  • Kirstine Belling

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Jette Bork-Jensen

    (The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen)

  • Shujia Huang

    (BGI Europe
    School of Bioscience and Biotechnology, South China University of Technology)

  • Thomas D. Als

    (Centre for Integrative Sequencing, iSEQ, Aarhus University
    The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH
    Aarhus University)

  • Shengting Li

    (BGI Europe
    Centre for Integrative Sequencing, iSEQ, Aarhus University
    The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH
    Aarhus University)

  • Rachita Yadav

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Arcadio Rubio-García

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Francesco Lescai

    (Centre for Integrative Sequencing, iSEQ, Aarhus University
    The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH
    Aarhus University)

  • Ditte Demontis

    (Centre for Integrative Sequencing, iSEQ, Aarhus University
    The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH
    Aarhus University)

  • Junhua Rao

    (BGI Europe)

  • Weijian Ye

    (BGI Europe)

  • Thomas Mailund

    (Bioinformatics Research Center, Aarhus University
    Centre for Integrative Sequencing, iSEQ, Aarhus University)

  • Rune M. Friborg

    (Bioinformatics Research Center, Aarhus University
    Centre for Integrative Sequencing, iSEQ, Aarhus University)

  • Christian N. S. Pedersen

    (Bioinformatics Research Center, Aarhus University)

  • Ruiqi Xu

    (BGI Europe)

  • Jihua Sun

    (BGI Europe)

  • Hao Liu

    (BGI Europe)

  • Ou Wang

    (BGI Europe)

  • Xiaofang Cheng

    (BGI Europe)

  • David Flores

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Emil Rydza

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Kristoffer Rapacki

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • John Damm Sørensen

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Piotr Chmura

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • David Westergaard

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Piotr Dworzynski

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Thorkild I. A. Sørensen

    (The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen
    Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospitals, The Capital Region)

  • Ole Lund

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Torben Hansen

    (The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen
    Faculty of Health Sciences, University of Southern Denmark)

  • Xun Xu

    (BGI Europe)

  • Ning Li

    (BGI Europe)

  • Lars Bolund

    (Centre for Integrative Sequencing, iSEQ, Aarhus University
    Aarhus University)

  • Oluf Pedersen

    (The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen)

  • Hans Eiberg

    (Panum Institute, University of Copenhagen)

  • Anders Krogh

    (University of Copenhagen
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen)

  • Anders D. Børglum

    (Centre for Integrative Sequencing, iSEQ, Aarhus University
    The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH
    Aarhus University)

  • Søren Brunak

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Karsten Kristiansen

    (University of Copenhagen)

  • Mikkel H. Schierup

    (Bioinformatics Research Center, Aarhus University
    Centre for Integrative Sequencing, iSEQ, Aarhus University)

  • Jun Wang

    (BGI Europe
    University of Copenhagen
    Centre for Integrative Sequencing, iSEQ, Aarhus University)

  • Ramneek Gupta

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Palle Villesen

    (Bioinformatics Research Center, Aarhus University
    Centre for Integrative Sequencing, iSEQ, Aarhus University)

  • Simon Rasmussen

    (Center for Biological Sequence Analysis, Technical University of Denmark)

Abstract

Building a population-specific catalogue of single nucleotide variants (SNVs), indels and structural variants (SVs) with frequencies, termed a national pan-genome, is critical for further advancing clinical and public health genetics in large cohorts. Here we report a Danish pan-genome obtained from sequencing 10 trios to high depth (50 × ). We report 536k novel SNVs and 283k novel short indels from mapping approaches and develop a population-wide de novo assembly approach to identify 132k novel indels larger than 10 nucleotides with low false discovery rates. We identify a higher proportion of indels and SVs than previous efforts showing the merits of high coverage and de novo assembly approaches. In addition, we use trio information to identify de novo mutations and use a probabilistic method to provide direct estimates of 1.27e−8 and 1.5e−9 per nucleotide per generation for SNVs and indels, respectively.

Suggested Citation

  • Søren Besenbacher & Siyang Liu & José M. G. Izarzugaza & Jakob Grove & Kirstine Belling & Jette Bork-Jensen & Shujia Huang & Thomas D. Als & Shengting Li & Rachita Yadav & Arcadio Rubio-García & Franc, 2015. "Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios," Nature Communications, Nature, vol. 6(1), pages 1-9, May.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms6969
    DOI: 10.1038/ncomms6969
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    Cited by:

    1. Frank R. Wendt & Gita A. Pathak & Renato Polimanti, 2022. "Phenome-wide association study of loci harboring de novo tandem repeat mutations in UK Biobank exomes," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Kitty Sherwood & Joseph C. Ward & Ignacio Soriano & Lynn Martin & Archie Campbell & Raheleh Rahbari & Ioannis Kafetzopoulos & Duncan Sproul & Andrew Green & Julian R. Sampson & Alan Donaldson & Kai-Re, 2023. "Germline de novo mutations in families with Mendelian cancer syndromes caused by defects in DNA repair," Nature Communications, Nature, vol. 14(1), pages 1-10, December.

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