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An integrated map of structural variation in 2,504 human genomes.
Sudmant, Peter H; Rausch, Tobias; Gardner, Eugene J; Handsaker, Robert E; Abyzov, Alexej; Huddleston, John; Zhang, Yan; Ye, Kai; Jun, Goo; Fritz, Markus Hsi-Yang; Konkel, Miriam K; Malhotra, Ankit; Stütz, Adrian M; Shi, Xinghua; Casale, Francesco Paolo; Chen, Jieming; Hormozdiari, Fereydoun; Dayama, Gargi; Chen, Ken; Malig, Maika; Chaisson, Mark J P; Walter, Klaudia; Meiers, Sascha; Kashin, Seva; Garrison, Erik; Auton, Adam; Lam, Hugo Y K; Mu, Xinmeng Jasmine; Alkan, Can; Antaki, Danny; Bae, Taejeong; Cerveira, Eliza; Chines, Peter; Chong, Zechen; Clarke, Laura; Dal, Elif; Ding, Li; Emery, Sarah; Fan, Xian; Gujral, Madhusudan; Kahveci, Fatma; Kidd, Jeffrey M; Kong, Yu; Lameijer, Eric-Wubbo; McCarthy, Shane; Flicek, Paul; Gibbs, Richard A; Marth, Gabor; Mason, Christopher E; Menelaou, Androniki.
Afiliação
  • Sudmant PH; Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195-5065, USA.
  • Rausch T; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.
  • Gardner EJ; Institute for Genome Sciences, University of Maryland School of Medicine, 801 W Baltimore Street, Baltimore, MD 21201, USA.
  • Handsaker RE; Department of Genetics, Harvard Medical School, Boston, 25 Shattuck Street, Boston, MA 02115, USA.
  • Abyzov A; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
  • Huddleston J; Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
  • Zhang Y; Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195-5065, USA.
  • Ye K; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
  • Jun G; Program in Computational Biology and Bioinformatics, Yale University, BASS 432&437, 266 Whitney Avenue, New Haven, CT 06520, USA.
  • Fritz MH; Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 266 Whitney Ave, New Haven, CT 06520, USA.
  • Konkel MK; The Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, USA.
  • Malhotra A; Department of Genetics, Washington University in St. Louis, 4444 Forest Park Ave, St. Louis, MO 63108, USA.
  • Stütz AM; Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
  • Shi X; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler St., Houston, TX 77030, USA.
  • Casale FP; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.
  • Chen J; Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.
  • Hormozdiari F; The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Ave, Farmington, CT 06030, USA.
  • Dayama G; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.
  • Chen K; Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA.
  • Malig M; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
  • Chaisson MJP; Program in Computational Biology and Bioinformatics, Yale University, BASS 432&437, 266 Whitney Avenue, New Haven, CT 06520, USA.
  • Walter K; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA.
  • Meiers S; Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195-5065, USA.
  • Kashin S; Department of Computational Medicine & Bioinformatics, University of Michigan, 500 S. State Street, Ann Arbor, MI 48109, USA.
  • Garrison E; The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
  • Auton A; Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195-5065, USA.
  • Lam HYK; Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195-5065, USA.
  • Mu XJ; The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
  • Alkan C; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.
  • Antaki D; Department of Genetics, Harvard Medical School, Boston, 25 Shattuck Street, Boston, MA 02115, USA.
  • Bae T; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
  • Cerveira E; Department of Biology, Boston College, 355 Higgins Hall, 140 Commonwealth Ave, Chestnut Hill, MA 02467, USA.
  • Chines P; Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.
  • Chong Z; Bina Technologies, Roche Sequencing, 555 Twin Dolphin Drive, Redwood City, CA 94065, USA.
  • Clarke L; Program in Computational Biology and Bioinformatics, Yale University, BASS 432&437, 266 Whitney Avenue, New Haven, CT 06520, USA.
  • Dal E; Cancer Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
  • Ding L; Department of Computer Engineering, Bilkent University, 06800 Ankara, Turkey.
  • Emery S; University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093, USA.
  • Fan X; Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
  • Gujral M; The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Ave, Farmington, CT 06030, USA.
  • Kahveci F; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA.
  • Kidd JM; The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
  • Kong Y; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
  • Lameijer EW; Department of Computer Engineering, Bilkent University, 06800 Ankara, Turkey.
  • McCarthy S; The Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, USA.
  • Flicek P; Department of Genetics, Washington University in St. Louis, 4444 Forest Park Ave, St. Louis, MO 63108, USA.
  • Gibbs RA; Department of Medicine, Washington University in St. Louis, 4444 Forest Park Ave, St. Louis, MO 63108, USA.
  • Marth G; Siteman Cancer Center, 660 South Euclid Ave, St. Louis, MO 63110, USA.
  • Mason CE; Department of Human Genetics, University of Michigan, 1241 Catherine Street, Ann Arbor, MI 48109, USA.
  • Menelaou A; The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
Nature ; 526(7571): 75-81, 2015 Oct 01.
Article em En | MEDLINE | ID: mdl-26432246
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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Variação Genética / Genoma Humano / Mapeamento Físico do Cromossomo Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Ano de publicação: 2015 Tipo de documento: Article
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Variação Genética / Genoma Humano / Mapeamento Físico do Cromossomo Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Ano de publicação: 2015 Tipo de documento: Article