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Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Ebert, Peter; Audano, Peter A; Zhu, Qihui; Rodriguez-Martin, Bernardo; Porubsky, David; Bonder, Marc Jan; Sulovari, Arvis; Ebler, Jana; Zhou, Weichen; Serra Mari, Rebecca; Yilmaz, Feyza; Zhao, Xuefang; Hsieh, PingHsun; Lee, Joyce; Kumar, Sushant; Lin, Jiadong; Rausch, Tobias; Chen, Yu; Ren, Jingwen; Santamarina, Martin; Höps, Wolfram; Ashraf, Hufsah; Chuang, Nelson T; Yang, Xiaofei; Munson, Katherine M; Lewis, Alexandra P; Fairley, Susan; Tallon, Luke J; Clarke, Wayne E; Basile, Anna O; Byrska-Bishop, Marta; Corvelo, André; Evani, Uday S; Lu, Tsung-Yu; Chaisson, Mark J P; Chen, Junjie; Li, Chong; Brand, Harrison; Wenger, Aaron M; Ghareghani, Maryam; Harvey, William T; Raeder, Benjamin; Hasenfeld, Patrick; Regier, Allison A; Abel, Haley J; Hall, Ira M; Flicek, Paul; Stegle, Oliver; Gerstein, Mark B; Tubio, Jose M C.
Afiliación
  • Ebert P; Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
  • Audano PA; Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
  • Zhu Q; The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
  • Rodriguez-Martin B; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
  • Porubsky D; Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
  • Bonder MJ; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
  • Sulovari A; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
  • Ebler J; Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
  • Zhou W; Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
  • Serra Mari R; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.
  • Yilmaz F; Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
  • Zhao X; The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
  • Hsieh P; Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA.
  • Lee J; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Kumar S; Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
  • Lin J; Bionano Genomics, San Diego, CA 92121, USA.
  • Rausch T; Program in Computational Biology and Bioinformatics, Yale University, BASS 432 and 437, 266 Whitney Avenue, New Haven, CT 06520, USA.
  • Chen Y; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
  • Ren J; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
  • Santamarina M; Department of Genetics and Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
  • Höps W; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
  • Ashraf H; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
  • Chuang NT; Department of Zoology, Genetics, and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
  • Yang X; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
  • Munson KM; Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
  • Lewis AP; Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA.
  • Fairley S; School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
  • Tallon LJ; Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
  • Clarke WE; Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
  • Basile AO; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Byrska-Bishop M; Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA.
  • Corvelo A; New York Genome Center, New York, NY 10013, USA.
  • Evani US; New York Genome Center, New York, NY 10013, USA.
  • Lu TY; New York Genome Center, New York, NY 10013, USA.
  • Chaisson MJP; New York Genome Center, New York, NY 10013, USA.
  • Chen J; New York Genome Center, New York, NY 10013, USA.
  • Li C; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
  • Brand H; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
  • Wenger AM; Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA.
  • Ghareghani M; Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA.
  • Harvey WT; Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA.
  • Raeder B; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Hasenfeld P; Pacific Biosciences of California, Menlo Park, CA 94025, USA.
  • Regier AA; Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, 66123 Saarbrücken, Germany.
  • Abel HJ; Saarbrücken Graduate School of Computer Science, Saarland University, Saarland Informatics Campus E1.3, 66123 Saarbrücken, Germany.
  • Hall IM; Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
  • Flicek P; Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
  • Stegle O; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
  • Gerstein MB; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
  • Tubio JMC; Department of Medicine, Washington University, St. Louis, MO 63108, USA.
Science ; 372(6537)2021 04 02.
Article en En | MEDLINE | ID: mdl-33632895
ABSTRACT
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% of the genome 26 million base pairs) integrate all forms of genetic variation, even across complex loci. We identified 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing, and 278 SV hotspots (spanning megabases of gene-rich sequence). We characterized 130 of the most active mobile element source elements and found that 63% of all SVs arise through homology-mediated mechanisms. This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population.
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Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Variación Genética / Haplotipos / Genoma Humano Tipo de estudio: Prognostic_studies Límite: Female / Humans / Male Idioma: En Revista: Science Año: 2021 Tipo del documento: Article País de afiliación: Alemania
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Variación Genética / Haplotipos / Genoma Humano Tipo de estudio: Prognostic_studies Límite: Female / Humans / Male Idioma: En Revista: Science Año: 2021 Tipo del documento: Article País de afiliación: Alemania