Optimizing Cancer Genome Sequencing and Analysis

被引：146

作者：

Griffith, Malachi ^{[1
,2
,3
,4
]}

Miller, Christopher A. ^{[1
,4
]}

Griffith, Obi L. ^{[1
,2
,3
]}

Krysiak, Kilannin ^{[1
]}

Skidmore, Zachary L. ^{[1
]}

Ramu, Avinash ^{[1
]}

Walker, Jason R. ^{[1
]}

Dang, Ha X. ^{[1
,4
]}

Trani, Lee ^{[1
]}

Larson, David E. ^{[1
,2
]}

Demeter, Ryan T. ^{[1
]}

Wendl, Michael C. ^{[1
,2
,5
]}

McMichael, Joshua F. ^{[1
]}

Austin, Rachel E. ^{[1
]}

Magrini, Vincent ^{[1
]}

McGrath, Sean D. ^{[1
]}

Ly, Amy ^{[1
]}

Kulkarni, Shashikant ^{[2
,6
,7
]}

Cordes, Matthew G. ^{[1
]}

Fronick, Catrina C. ^{[1
]}

Fulton, Robert S. ^{[1
]}

Maher, Christopher A. ^{[1
,3
,4
,8
]}

Ding, Li ^{[1
,2
,3
,4
]}

Klco, Jeffery M. ^{[6
]}

Mardis, Elaine R. ^{[1
,2
,3
,4
]}

Ley, Timothy J. ^{[1
,2
,3
,4
]}

Wilson, Richard K. ^{[1
,2
,3
,4
]}

机构：

[1] Washington Univ, McDonnell Genome Inst, St Louis, MO 63108 USA

[2] Washington Univ, Dept Genet, St Louis, MO 63108 USA

[3] Washington Univ, Siteman Canc Ctr, St Louis, MO 63108 USA

[4] Washington Univ, Dept Med, St Louis, MO 63108 USA

[5] Washington Univ, Dept Math, St Louis, MO 63108 USA

[6] Washington Univ, Dept Pathol & Immunol, St Louis, MO 63108 USA

[7] Washington Univ, Div Hematol Oncol, Dept Pediat, St Louis, MO 63108 USA

[8] Washington Univ, Dept Biomed Engn, St Louis, MO 63108 USA

来源：

CELL SYSTEMS | 2015年 / 1卷 / 03期

关键词：

D O I：

10.1016/j.cels.2015.08.015

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Tumors are typically sequenced to depths of 75x-100x (exome) or 30x-50x (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 similar to 312x) whole genome sequencing and exome capture (up to similar to 433x) 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 similar to 200,000 putative SNVs by sequencing them to depths of similar to 1,000x. Additional targeted sequencing provided over 10,000x coverage and ddPCR assays provided up to similar to 250,000x 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: phs000159).

引用

页码：210 / 223

页数：14

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