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Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects.
Regier, Allison A; Farjoun, Yossi; Larson, David E; Krasheninina, Olga; Kang, Hyun Min; Howrigan, Daniel P; Chen, Bo-Juen; Kher, Manisha; Banks, Eric; Ames, Darren C; English, Adam C; Li, Heng; Xing, Jinchuan; Zhang, Yeting; Matise, Tara; Abecasis, Goncalo R; Salerno, Will; Zody, Michael C; Neale, Benjamin M; Hall, Ira M.
Afiliación
  • Regier AA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA.
  • Farjoun Y; Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA.
  • Larson DE; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA.
  • Krasheninina O; Human Genome Sequencing Center, Baylor College of Medicine, Houston, 77030, TX, USA.
  • Kang HM; Department of Biostatistics, University of Michigan, Ann Arbor, 48109, MI, USA.
  • Howrigan DP; Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA.
  • Chen BJ; New York Genome Center, New York, 10013, NY, USA.
  • Kher M; Google, New York, 10011, NY, USA.
  • Banks E; New York Genome Center, New York, 10013, NY, USA.
  • Ames DC; Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA.
  • English AC; DNAnexus Inc, Mountain View, 94040, CA, USA.
  • Li H; Spiral Genetics, Seattle, 98104, WA, USA.
  • Xing J; Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA.
  • Zhang Y; Department of Genetics, Rutgers University, Piscataway, 08854, NJ, USA.
  • Matise T; Department of Genetics, Rutgers University, Piscataway, 08854, NJ, USA.
  • Abecasis GR; Department of Genetics, Rutgers University, Piscataway, 08854, NJ, USA.
  • Salerno W; Department of Biostatistics, University of Michigan, Ann Arbor, 48109, MI, USA.
  • Zody MC; Human Genome Sequencing Center, Baylor College of Medicine, Houston, 77030, TX, USA.
  • Neale BM; New York Genome Center, New York, 10013, NY, USA.
  • Hall IM; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA.
Nat Commun ; 9(1): 4038, 2018 10 02.
Article en En | MEDLINE | ID: mdl-30279509
Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years. These data are more valuable in aggregate: joint analysis of genomes from many sources increases sample size and statistical power. A central challenge for joint analysis is that different WGS data processing pipelines cause substantial differences in variant calling in combined datasets, necessitating computationally expensive reprocessing. This approach is no longer tenable given the scale of current studies and data volumes. Here, we define WGS data processing standards that allow different groups to produce functionally equivalent (FE) results, yet still innovate on data processing pipelines. We present initial FE pipelines developed at five genome centers and show that they yield similar variant calling results and produce significantly less variability than sequencing replicates. This work alleviates a key technical bottleneck for genome aggregation and helps lay the foundation for community-wide human genetics studies.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Secuenciación Completa del Genoma / Genética Humana Límite: Humans Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2018 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Secuenciación Completa del Genoma / Genética Humana Límite: Humans Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2018 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido