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A complete reference genome improves analysis of human genetic variation.
Aganezov, Sergey; Yan, Stephanie M; Soto, Daniela C; Kirsche, Melanie; Zarate, Samantha; Avdeyev, Pavel; Taylor, Dylan J; Shafin, Kishwar; Shumate, Alaina; Xiao, Chunlin; Wagner, Justin; McDaniel, Jennifer; Olson, Nathan D; Sauria, Michael E G; Vollger, Mitchell R; Rhie, Arang; Meredith, Melissa; Martin, Skylar; Lee, Joyce; Koren, Sergey; Rosenfeld, Jeffrey A; Paten, Benedict; Layer, Ryan; Chin, Chen-Shan; Sedlazeck, Fritz J; Hansen, Nancy F; Miller, Danny E; Phillippy, Adam M; Miga, Karen H; McCoy, Rajiv C; Dennis, Megan Y; Zook, Justin M; Schatz, Michael C.
Afiliação
  • Aganezov S; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
  • Yan SM; Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
  • Soto DC; Department of Biochemistry and Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA.
  • Kirsche M; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
  • Zarate S; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
  • Avdeyev P; Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA.
  • Taylor DJ; Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
  • Shafin K; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
  • Shumate A; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
  • Xiao C; National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.
  • Wagner J; National Institute of Standards and Technology, Gaithersburg, MD, USA.
  • McDaniel J; National Institute of Standards and Technology, Gaithersburg, MD, USA.
  • Olson ND; National Institute of Standards and Technology, Gaithersburg, MD, USA.
  • Sauria MEG; Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
  • Vollger MR; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • Rhie A; Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA.
  • Meredith M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
  • Martin S; Department of Computer Science and Biofrontiers Institute, University of Colorado, Boulder, CO, USA.
  • Lee J; Bionano Genomics, San Diego, CA, USA.
  • Koren S; Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA.
  • Rosenfeld JA; Cancer Institute of New Jersey, New Brunswick, NJ, USA.
  • Paten B; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
  • Layer R; Department of Computer Science and Biofrontiers Institute, University of Colorado, Boulder, CO, USA.
  • Chin CS; DNAnexus, Mountain View, CA, USA.
  • Sedlazeck FJ; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
  • Hansen NF; Comparative Genomics Analysis Unit, National Human Genome Research Institute, Rockville, MD, USA.
  • Miller DE; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • Phillippy AM; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA.
  • Miga KH; Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA.
  • McCoy RC; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
  • Dennis MY; Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
  • Zook JM; Department of Biochemistry and Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA.
  • Schatz MC; National Institute of Standards and Technology, Gaithersburg, MD, USA.
Science ; 376(6588): eabl3533, 2022 04.
Article em En | MEDLINE | ID: mdl-35357935
ABSTRACT
Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Variação Genética / Genoma Humano / Análise de Sequência de DNA / Genômica Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Revista: Science Ano de publicação: 2022 Tipo de documento: Article
Texto completo
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Variação Genética / Genoma Humano / Análise de Sequência de DNA / Genômica Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Revista: Science Ano de publicação: 2022 Tipo de documento: Article