title: Optimizing cancer genome sequencing and analysis.
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).
authors.affiliation: 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.
authors.forename: Malachi
authors.initials: M
authors.lastname: Griffith
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Miller
authors.affiliation: 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, 63108.
authors.forename: Obi L
authors.initials: OL
authors.lastname: Griffith
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Kilannin
authors.initials: K
authors.lastname: Krysiak
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Zachary L
authors.initials: ZL
authors.lastname: Skidmore
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Avinash
authors.initials: A
authors.lastname: Ramu
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Walker
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Ha X
authors.initials: HX
authors.lastname: Dang
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Lee
authors.initials: L
authors.lastname: Trani
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108.
authors.forename: David E
authors.initials: DE
authors.lastname: Larson
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Ryan T
authors.initials: RT
authors.lastname: Demeter
authors.affiliation: 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.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Wendl
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Joshua F
authors.initials: JF
authors.lastname: McMichael
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Rachel E
authors.initials: RE
authors.lastname: Austin
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Vincent
authors.initials: V
authors.lastname: Magrini
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Sean D
authors.initials: SD
authors.lastname: McGrath
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Amy
authors.initials: A
authors.lastname: Ly
authors.affiliation: 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.
authors.forename: Shashikant
authors.initials: S
authors.lastname: Kulkarni
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Cordes
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Catrina C
authors.initials: CC
authors.lastname: Fronick
authors.affiliation: The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Robert S
authors.initials: RS
authors.lastname: Fulton
authors.affiliation: 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. Louis, MO, USA, 63108.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Maher
authors.affiliation: 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, 63108.
authors.forename: Li
authors.initials: L
authors.lastname: Ding
authors.affiliation: Department of Pathology and Immunology, Washington University, St. Louis, MO, USA, 63108.
authors.forename: Jeffery M
authors.initials: JM
authors.lastname: Klco
authors.affiliation: 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, 63108.
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.affiliation: 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, 63108.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Ley
authors.affiliation: 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, 63108.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson