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Mapping copy number variation by population-scale genome sequencing

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Title:
Mapping copy number variation by population-scale genome sequencing
Affiliation:
AA(Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; These authors contributed equally to this work.), AB(The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; These authors contributed equally to this work.), AC(Department of Biology, Boston College, Boston, Massachusetts, USA; These authors contributed equally to this work.), AD(Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; These authors contributed equally to this work.), AE(The Genome Center at Washington University, St. Louis, Missouri, USA; These authors contributed equally to this work.), AF(Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA; These authors contributed equally to this work.), AG(Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA; These authors contributed equally to this work.), AH(Seaver Autism Center and Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA; These authors contributed equally to this work.), AI(Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands; These authors contributed equally to this work.), AJ(Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden CB10 1XL, UK), AK(The Genome Center at Washington University, St. Louis, Missouri, USA), AL(The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK), AM(Life Technologies, Beverly, Massachusetts, USA), AN(Department of Genetics, Stanford University, Stanford, California, USA), AO(School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada), AP(School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada), AQ(Department of Psychiatry, Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA), AR(Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK), AS(Department of Psychiatry, Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA), AT(Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA), AU(Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA), AV(Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA), AW(Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA; Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut, USA), AX(Department of Biology, Boston College, Boston, Massachusetts, USA), AY(Department of Genetics, Stanford University, Stanford, California, USA), AZ(Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA), BA(BGI-Shenzhen, Shenzhen 518083, China), BB(BGI-Shenzhen, Shenzhen 518083, China), BC(Albert Einstein College of Medicine, Bronx, New York, USA), BD(BGI-Shenzhen, Shenzhen 518083, China), BE(Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA), BF(Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA), BG(Life Technologies, Beverly, Massachusetts, USA), BH(Genome Biology Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany), BI(The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK), BJ(Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA), BK(Department of Biology, Boston College, Boston, Massachusetts, USA), BL(Genome Biology Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany), BM(Department of Genetics, Stanford University, Stanford, California, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, USA), BN(Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA), BO(Department of Biology, Boston College, Boston, Massachusetts, USA), BP(The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK), BQ(Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA), BR(Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA), BS(The Genome Center at Washington University, St. Louis, Missouri, USA; Department of Genetics, Washington University, St Louis, Missouri, USA), BT(Department of Biology, Boston College, Boston, Massachusetts, USA), BU(Department of Statistics, University of Oxford, OX3 7BN, UK), BV(Department of Psychiatry, Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA), BW(Department of Genetics, Stanford University, Stanford, California, USA), BX(BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark), BY(Albert Einstein College of Medicine, Bronx, New York, USA), BZ(Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA), CA(Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA; Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut, USA), CB(The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK), CC(Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA), CD(Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA), CE()
Publication:
Nature, Volume 470, Issue 7332, pp. 59-65 (2011). (Nature Homepage)
Publication Date:
02/2011
Origin:
NATURE
Abstract Copyright:
(c) 2011: Nature
DOI:
10.1038/nature09708
Bibliographic Code:
2011Natur.470...59.

Abstract

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.
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