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Optimizing cancer genome sequencing and analysis.
Griffith, Malachi; Miller, Christopher A; Griffith, Obi L; Krysiak, Kilannin; Skidmore, Zachary L; Ramu, Avinash; Walker, Jason R; Dang, Ha X; Trani, Lee; Larson, David E; Demeter, Ryan T; Wendl, Michael C; McMichael, Joshua F; Austin, Rachel E; Magrini, Vincent; McGrath, Sean D; Ly, Amy; Kulkarni, Shashikant; Cordes, Matthew G; Fronick, Catrina C; Fulton, Robert S; Maher, Christopher A; Ding, Li; Klco, Jeffery M; Mardis, Elaine R; Ley, Timothy J; Wilson, Richard K.
Afiliación
  • Griffith M; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108 ; Siteman Cancer Center, Washington University, St. Louis, MO, USA, 63108.
  • Miller CA; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 63108.
  • Griffith OL; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108 ; Siteman Cancer Center, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 6
  • Krysiak K; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Skidmore ZL; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Ramu A; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Walker JR; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Dang HX; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 63108.
  • Trani L; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Larson DE; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108.
  • Demeter RT; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Wendl MC; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108 ; Department of Mathematics, Washington University, St. Louis, MO, USA, 63108.
  • McMichael JF; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Austin RE; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Magrini V; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • McGrath SD; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Ly A; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Kulkarni S; Department of Genetics, Washington University, St. Louis, MO, USA, 63108 ; Department of Pathology and Immunology, Washington University, St. Louis, MO, USA, 63108 ; Department of Pediatrics, Division of Hematology/Oncology, Washington University, St. Louis, MO, USA, 63108.
  • Cordes MG; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Fronick CC; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Fulton RS; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
  • Maher CA; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Siteman Cancer Center, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 63108 ; Department of Biomedical Engineering, Washington University, St. Lou
  • Ding L; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108 ; Siteman Cancer Center, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 6
  • Klco JM; Department of Pathology and Immunology, Washington University, St. Louis, MO, USA, 63108.
  • Mardis ER; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108 ; Siteman Cancer Center, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 6
  • Ley TJ; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108 ; Siteman Cancer Center, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 6
  • Wilson RK; The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108 ; Siteman Cancer Center, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 6
Cell Syst ; 1(3): 210-223, 2015 Sep 23.
Article en En | MEDLINE | ID: mdl-26645048
ABSTRACT
Tumors are typically sequenced to depths of 75-100× (exome) or 30-50× (whole genome). We demonstrate that current sequencing paradigms are inadequate for tumors that are impure, aneuploid or clonally heterogeneous. To reassess optimal sequencing strategies, we performed ultra-deep (up to ~312×) whole genome sequencing (WGS) and exome capture (up to ~433×) of a primary acute myeloid leukemia, its subsequent relapse, and a matched normal skin sample. We tested multiple alignment and variant calling algorithms and validated ~200,000 putative SNVs by sequencing them to depths of ~1,000×. Additional targeted sequencing provided over 10,000× coverage and ddPCR assays provided up to ~250,000× sampling of selected sites. We evaluated the effects of different library generation approaches, depth of sequencing, and analysis strategies on the ability to effectively characterize a complex tumor. This dataset, representing the most comprehensively sequenced tumor described to date, will serve as an invaluable community resource (dbGaP accession id phs000159).
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Idioma: En Revista: Cell Syst Año: 2015 Tipo del documento: Article
Texto completo
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PubMed Links
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Idioma: En Revista: Cell Syst Año: 2015 Tipo del documento: Article