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

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, Ivo Renkens, Bradley P. Coe, Patrick Deelen, Joep de Ligt, Eric-Wubbo Lameijer, Freerk van Dijk, Fereydoun Hormozdiari, André G. Uitterlinden, Cornelia M. van Duijn, Evan E. Eichler, Paul I. W. de Bakker, Morris A. Swertz, Cisca Wijmenga, Gert-Jan B. van Ommen, P. Eline Slagboom, Dorret I. Boomsma, Alexander Schönhuth (), Kai Ye () and Victor Guryev ()
Additional contact information
Jayne Y. Hehir-Kwa: Donders Institute, Radboud University Medical Center
Tobias Marschall: Center for Bioinformatics, Saarland University
Wigard P. Kloosterman: Center for Molecular Medicine, University Medical Center Utrecht
Laurent C. Francioli: Center for Molecular Medicine, University Medical Center Utrecht
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
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
Fereydoun Hormozdiari: University of Washington
André G. Uitterlinden: 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
Morris A. Swertz: 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
Victor Guryev: European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen

Nature Communications, 2016, vol. 7, issue 1, 1-10

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms12989

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