Your browser doesn't support javascript.
loading
Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Chaisson, Mark J P; Sanders, Ashley D; Zhao, Xuefang; Malhotra, Ankit; Porubsky, David; Rausch, Tobias; Gardner, Eugene J; Rodriguez, Oscar L; Guo, Li; Collins, Ryan L; Fan, Xian; Wen, Jia; Handsaker, Robert E; Fairley, Susan; Kronenberg, Zev N; Kong, Xiangmeng; Hormozdiari, Fereydoun; Lee, Dillon; Wenger, Aaron M; Hastie, Alex R; Antaki, Danny; Anantharaman, Thomas; Audano, Peter A; Brand, Harrison; Cantsilieris, Stuart; Cao, Han; Cerveira, Eliza; Chen, Chong; Chen, Xintong; Chin, Chen-Shan; Chong, Zechen; Chuang, Nelson T; Lambert, Christine C; Church, Deanna M; Clarke, Laura; Farrell, Andrew; Flores, Joey; Galeev, Timur; Gorkin, David U; Gujral, Madhusudan; Guryev, Victor; Heaton, William Haynes; Korlach, Jonas; Kumar, Sushant; Kwon, Jee Young; Lam, Ernest T; Lee, Jong Eun; Lee, Joyce; Lee, Wan-Ping; Lee, Sau Peng.
  • Chaisson MJP; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
  • Sanders AD; Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA.
  • Zhao X; European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
  • Malhotra A; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
  • Porubsky D; Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA, 02114, USA.
  • Rausch T; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
  • Gardner EJ; European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, AV, NL-9713, The Netherlands.
  • Rodriguez OL; Center for Bioinformatics, Saarland University and the Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.
  • Guo L; European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
  • Collins RL; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
  • Fan X; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
  • Wen J; The School of Life Science and Technology of Xi'an Jiaotong University, 710049, Xi'an, China.
  • Handsaker RE; MOE Key Lab for Intelligent Networks & Networks Security, School of Electronics and Information Engineering, Xi'an Jiaotong University, 710049, Xi'an, China.
  • Fairley S; Ye-Lab For Omics and Omics Informatics, Xi'an Jiaotong University, 710049, Xi'an, China.
  • Kronenberg ZN; Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA, 02114, USA.
  • Kong X; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, 02115, USA.
  • Hormozdiari F; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
  • Lee D; Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
  • Wenger AM; Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
  • Hastie AR; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
  • Antaki D; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
  • Anantharaman T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
  • Audano PA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
  • Brand H; Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, CT, 06520, USA.
  • Cantsilieris S; Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06520, USA.
  • Cao H; Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, 95616, USA.
  • Cerveira E; UC Davis Genome Center, University of California, Davis, Davis, CA, 95616, USA.
  • Chen C; USTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
  • Chen X; Pacific Biosciences, Menlo Park, CA, 94025, USA.
  • Chin CS; Bionano Genomics, San Diego, CA, 92121, USA.
  • Chong Z; Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA, 92093, USA.
  • Chuang NT; Bionano Genomics, San Diego, CA, 92121, USA.
  • Lambert CC; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
  • Church DM; Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA, 02114, USA.
  • Clarke L; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
  • Farrell A; Bionano Genomics, San Diego, CA, 92121, USA.
  • Flores J; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
  • Galeev T; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
  • Gorkin DU; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
  • Gujral M; Pacific Biosciences, Menlo Park, CA, 94025, USA.
  • Guryev V; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
  • Heaton WH; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
  • Korlach J; Pacific Biosciences, Menlo Park, CA, 94025, USA.
  • Kumar S; 10X Genomics, Pleasanton, CA, 94566, USA.
  • Kwon JY; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
  • Lam ET; USTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
  • Lee JE; Illumina Clinical Services Laboratory, Illumina, Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
  • Lee J; Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, CT, 06520, USA.
  • Lee WP; Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06520, USA.
  • Lee SP; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
Nat Commun ; 10(1): 1784, 2019 04 16.
Article en En | MEDLINE | ID: mdl-30992455
ABSTRACT
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.
Asunto(s)
Texto completo
Imprimir
XML
PubMed Links
Search on Google

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Haplotipos / Genoma Humano / Genómica / Variación Estructural del Genoma Límite: Humans Idioma: En Año: 2019 Tipo del documento: Article
Texto completo
Imprimir
XML
PubMed Links
Search on Google

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Haplotipos / Genoma Humano / Genómica / Variación Estructural del Genoma Límite: Humans Idioma: En Año: 2019 Tipo del documento: Article