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Assembly and diploid architecture of an individual human genome via single-molecule technologies.
Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali.
Affiliation
  • Pendleton M; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
  • Sebra R; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
  • Pang AW; BioNano Genomics, San Diego, California, USA.
  • Ummat A; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
  • Franzen O; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
  • Rausch T; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Stütz AM; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Stedman W; BioNano Genomics, San Diego, California, USA.
  • Anantharaman T; BioNano Genomics, San Diego, California, USA.
  • Hastie A; BioNano Genomics, San Diego, California, USA.
  • Dai H; BioNano Genomics, San Diego, California, USA.
  • Fritz MH; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Cao H; BioNano Genomics, San Diego, California, USA.
  • Cohain A; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
  • Deikus G; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
  • Durrett RE; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA.
  • Blanchard SC; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.
  • Altman R; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA.
  • Chin CS; Pacific Biosciences, Menlo Park, California, USA.
  • Guo Y; Pacific Biosciences, Menlo Park, California, USA.
  • Paxinos EE; Pacific Biosciences, Menlo Park, California, USA.
  • Korbel JO; 1] Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. [2] European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK.
  • Darnell RB; 1] Laboratory of Neuro-Oncology, The Rockefeller University, New York, New York, USA. [2] Howard Hughes Medical Institute, New York, New York, USA.
  • McCombie WR; 1] The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] The Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
  • Kwok PY; Institute for Human Genetics, University of California-San Francisco, San Francisco, California, USA.
  • Mason CE; 1] The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA. [2] Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medical College, New York, New York, USA. [3] The Feil Family Brain an
  • Schadt EE; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
  • Bashir A; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Nat Methods ; 12(8): 780-6, 2015 Aug.
Article in En | MEDLINE | ID: mdl-26121404
ABSTRACT
We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genome, Human / Computational Biology / Polymorphism, Single Nucleotide / High-Throughput Nucleotide Sequencing Type of study: Prognostic_studies Limits: Humans Language: En Journal: Nat Methods Journal subject: TECNICAS E PROCEDIMENTOS DE LABORATORIO Year: 2015 Document type: Article Affiliation country:
Fulltext
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genome, Human / Computational Biology / Polymorphism, Single Nucleotide / High-Throughput Nucleotide Sequencing Type of study: Prognostic_studies Limits: Humans Language: En Journal: Nat Methods Journal subject: TECNICAS E PROCEDIMENTOS DE LABORATORIO Year: 2015 Document type: Article Affiliation country: