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A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

Author

Listed:
  • Jayne Y. Hehir-Kwa

    (Donders Institute, Radboud University Medical Center)

  • Tobias Marschall

    (Center for Bioinformatics, Saarland University
    Max Plank Institute for Informatics)

  • Wigard P. Kloosterman

    (Center for Molecular Medicine, University Medical Center Utrecht)

  • Laurent C. Francioli

    (Center for Molecular Medicine, University Medical Center Utrecht
    Analytic and Translational Genetics Unit, Massachusetts General Hospital
    The Broad Institute
    Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology)

  • Jasmijn A. Baaijens

    (Life Sciences Group, Centrum Wiskunde & Informatica)

  • Louis J. Dijkstra

    (Life Sciences Group, Centrum Wiskunde & Informatica)

  • Abdel Abdellaoui

    (Vrije Universiteit Amsterdam)

  • Vyacheslav Koval

    (Erasmus Medical Center)

  • Djie Tjwan Thung

    (Donders Institute, Radboud University Medical Center)

  • René Wardenaar

    (European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen
    Groningen Bioinformatics Centre, University of Groningen)

  • Ivo Renkens

    (Center for Molecular Medicine, University Medical Center Utrecht)

  • Bradley P. Coe

    (University of Washington)

  • Patrick Deelen

    (University of Groningen, University Medical Center Groningen)

  • Joep de Ligt

    (Center for Molecular Medicine, University Medical Center Utrecht)

  • Eric-Wubbo Lameijer

    (Leiden University Medical Center)

  • Freerk van Dijk

    (University of Groningen, University Medical Center Groningen
    Genomics Coordination Center, University of Groningen, University Medical Center Groningen)

  • Fereydoun Hormozdiari

    (University of Washington)

  • André G. Uitterlinden

    (Erasmus Medical Center
    Erasmus Medical Center)

  • Cornelia M. van Duijn

    (Erasmus Medical Center)

  • Evan E. Eichler

    (University of Washington)

  • Paul I. W. de Bakker

    (Center for Molecular Medicine, University Medical Center Utrecht
    Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht)

  • Morris A. Swertz

    (University of Groningen, University Medical Center Groningen
    Genomics Coordination Center, University of Groningen, University Medical Center Groningen)

  • Cisca Wijmenga

    (University of Groningen, University Medical Center Groningen)

  • Gert-Jan B. van Ommen

    (Leiden University Medical Center)

  • P. Eline Slagboom

    (Leiden University Medical Center)

  • Dorret I. Boomsma

    (Vrije Universiteit Amsterdam)

  • Alexander Schönhuth

    (Life Sciences Group, Centrum Wiskunde & Informatica)

  • Kai Ye

    (The Genome Institute, Washington University
    School of Electronic and Information Engineering, Xi'an Jiaotong University
    The First Affiliated Hospital, Xi'an Jiaotong University)

  • Victor Guryev

    (European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen)

Abstract

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.

Suggested Citation

  • Jayne Y. Hehir-Kwa & Tobias Marschall & Wigard P. Kloosterman & Laurent C. Francioli & Jasmijn A. Baaijens & Louis J. Dijkstra & Abdel Abdellaoui & Vyacheslav Koval & Djie Tjwan Thung & René Wardenaar, 2016. "A high-quality human reference panel reveals the complexity and distribution of genomic structural variants," Nature Communications, Nature, vol. 7(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12989
    DOI: 10.1038/ncomms12989
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    Cited by:

    1. Michel S. Naslavsky & Marilia O. Scliar & Guilherme L. Yamamoto & Jaqueline Yu Ting Wang & Stepanka Zverinova & Tatiana Karp & Kelly Nunes & José Ricardo Magliocco Ceroni & Diego Lima Carvalho & Carlo, 2022. "Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Jinlong Shi & Zhilong Jia & Jinxiu Sun & Xiaoreng Wang & Xiaojing Zhao & Chenghui Zhao & Fan Liang & Xinyu Song & Jiawei Guan & Xue Jia & Jing Yang & Qi Chen & Kang Yu & Qian Jia & Jing Wu & Depeng Wa, 2023. "Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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