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Cell Syst. 2015 Sep 23;1(3):210-223.

Optimizing cancer genome sequencing and analysis.

Author information

1
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.
2
The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 63108.
3
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.
4
The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108.
5
The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108.
6
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.
7
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.
8
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.
9
Department of Pathology and Immunology, Washington University, St. Louis, MO, USA, 63108.

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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