An integrated map of structural variation in 2,504 human genomes

Peter H. Sudmant, Tobias Rausch, Eugene J. Gardner, Robert E. Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz, Miriam K. Konkel, Ankit Malhotra, Adrian M. Stütz, Xinghua Shi, Francesco Paolo Casale, Jieming Chen, Fereydoun Hormozdiari, Gargi Dayama, Ken Chen, Maika Malig, Mark J. P. Chaisson, Klaudia Walter, Sascha Meiers, Seva Kashin, Erik Garrison, Adam Auton, Hugo Y. K. Lam, Xinmeng Jasmine Mu, Can Alkan, Danny Antaki, Taejeong Bae, Eliza Cerveira, Peter Chines, Zechen Chong, Laura Clarke, Elif Dal, Li Ding, Sarah Emery, Xian Fan, Madhusudan Gujral, Fatma Kahveci, Jeffrey M. Kidd, Yu Kong, Eric-Wubbo Lameijer, Shane McCarthy, Paul Flicek, Richard A. Gibbs, Gabor Marth, Christopher E. Mason, Androniki Menelaou, Donna M. Muzny, Bradley J. Nelson, Amina Noor, Nicholas F. Parrish, Matthew Pendleton, Andrew Quitadamo, Benjamin Raeder, Eric E. Schadt, Mallory Romanovitch, Andreas Schlattl, Robert Sebra, Andrey A. Shabalin, Andreas Untergasser, Jerilyn A. Walker, Min Wang, Fuli Yu, Chengsheng Zhang, Jing Zhang, Xiangqun Zheng-Bradley, Wanding Zhou, Thomas Zichner, Jonathan Sebat, Mark A. Batzer, Steven A. McCarroll, Ryan E. Mills, Mark B. Gerstein, Ali Bashir, Oliver Stegle, Scott E. Devine, Charles Lee, Evan E. Eichler () and Jan O. Korbel ()
Additional contact information
Peter H. Sudmant: University of Washington
Tobias Rausch: European Molecular Biology Laboratory (EMBL), Genome Biology Unit
Eugene J. Gardner: Institute for Genome Sciences, University of Maryland School of Medicine
Robert E. Handsaker: Harvard Medical School
Alexej Abyzov: Center for Individualized Medicine, Mayo Clinic
John Huddleston: University of Washington
Yan Zhang: Program in Computational Biology and Bioinformatics, Yale University
Kai Ye: The Genome Institute, Washington University School of Medicine
Goo Jun: University of Michigan
Markus Hsi-Yang Fritz: European Molecular Biology Laboratory (EMBL), Genome Biology Unit
Miriam K. Konkel: Louisiana State University
Ankit Malhotra: The Jackson Laboratory for Genomic Medicine
Adrian M. Stütz: European Molecular Biology Laboratory (EMBL), Genome Biology Unit
Xinghua Shi: University of North Carolina at Charlotte
Francesco Paolo Casale: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus
Jieming Chen: Program in Computational Biology and Bioinformatics, Yale University
Fereydoun Hormozdiari: University of Washington
Gargi Dayama: University of Michigan
Ken Chen: The University of Texas MD Anderson Cancer Center
Maika Malig: University of Washington
Mark J. P. Chaisson: University of Washington
Klaudia Walter: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
Sascha Meiers: European Molecular Biology Laboratory (EMBL), Genome Biology Unit
Seva Kashin: Harvard Medical School
Erik Garrison: Boston College
Adam Auton: Albert Einstein College of Medicine
Hugo Y. K. Lam: Bina Technologies, Roche Sequencing
Xinmeng Jasmine Mu: Program in Computational Biology and Bioinformatics, Yale University
Can Alkan: Bilkent University
Danny Antaki: University of California San Diego (UCSD)
Taejeong Bae: Center for Individualized Medicine, Mayo Clinic
Eliza Cerveira: The Jackson Laboratory for Genomic Medicine
Peter Chines: National Human Genome Research Institute, National Institutes of Health
Zechen Chong: The University of Texas MD Anderson Cancer Center
Laura Clarke: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus
Elif Dal: Bilkent University
Li Ding: The Genome Institute, Washington University School of Medicine
Sarah Emery: University of Michigan
Xian Fan: The University of Texas MD Anderson Cancer Center
Madhusudan Gujral: University of California San Diego (UCSD)
Fatma Kahveci: Bilkent University
Jeffrey M. Kidd: University of Michigan
Yu Kong: Albert Einstein College of Medicine
Eric-Wubbo Lameijer: Molecular Epidemiology, Leiden University Medical Center
Shane McCarthy: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
Paul Flicek: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus
Richard A. Gibbs: Baylor College of Medicine
Gabor Marth: Boston College
Christopher E. Mason: The Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine
Androniki Menelaou: University of Oxford
Donna M. Muzny: Icahn School of Medicine, New York School of Natural Sciences
Bradley J. Nelson: University of Washington
Amina Noor: University of California San Diego (UCSD)
Nicholas F. Parrish: Institute for Virus Research, Kyoto University
Matthew Pendleton: Icahn School of Medicine, New York School of Natural Sciences
Andrew Quitadamo: University of North Carolina at Charlotte
Benjamin Raeder: European Molecular Biology Laboratory (EMBL), Genome Biology Unit
Eric E. Schadt: Icahn School of Medicine, New York School of Natural Sciences
Mallory Romanovitch: The Jackson Laboratory for Genomic Medicine
Andreas Schlattl: European Molecular Biology Laboratory (EMBL), Genome Biology Unit
Robert Sebra: Icahn School of Medicine, New York School of Natural Sciences
Andrey A. Shabalin: Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University
Andreas Untergasser: European Molecular Biology Laboratory (EMBL), Genome Biology Unit
Jerilyn A. Walker: Louisiana State University
Min Wang: Baylor College of Medicine
Fuli Yu: Baylor College of Medicine
Chengsheng Zhang: The Jackson Laboratory for Genomic Medicine
Jing Zhang: Program in Computational Biology and Bioinformatics, Yale University
Xiangqun Zheng-Bradley: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus
Wanding Zhou: The University of Texas MD Anderson Cancer Center
Thomas Zichner: European Molecular Biology Laboratory (EMBL), Genome Biology Unit
Jonathan Sebat: University of California San Diego (UCSD)
Mark A. Batzer: Louisiana State University
Steven A. McCarroll: Harvard Medical School
Ryan E. Mills: University of Michigan
Mark B. Gerstein: Program in Computational Biology and Bioinformatics, Yale University
Ali Bashir: Icahn School of Medicine, New York School of Natural Sciences
Oliver Stegle: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus
Scott E. Devine: Institute for Genome Sciences, University of Maryland School of Medicine
Charles Lee: The Jackson Laboratory for Genomic Medicine
Evan E. Eichler: University of Washington
Jan O. Korbel: European Molecular Biology Laboratory (EMBL), Genome Biology Unit

Nature, 2015, vol. 526, issue 7571, 75-81

Abstract: Abstract Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

Date: 2015
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Citations: View citations in EconPapers (16)

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DOI: 10.1038/nature15394

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