TY - JOUR
T1 - Optimizing Cancer Genome Sequencing and Analysis
AU - Griffith, Malachi
AU - Miller, Christopher A.
AU - Griffith, Obi L.
AU - Krysiak, Kilannin
AU - Skidmore, Zachary L.
AU - Ramu, Avinash
AU - Walker, Jason R.
AU - Dang, Ha X.
AU - Trani, Lee
AU - Larson, David E.
AU - Demeter, Ryan T.
AU - Wendl, Michael C.
AU - McMichael, Joshua F.
AU - Austin, Rachel E.
AU - Magrini, Vincent
AU - McGrath, Sean D.
AU - Ly, Amy
AU - Kulkarni, Shashikant
AU - Cordes, Matthew G.
AU - Fronick, Catrina C.
AU - Fulton, Robert S.
AU - Maher, Christopher A.
AU - Ding, Li
AU - Klco, Jeffery M.
AU - Mardis, Elaine R.
AU - Ley, Timothy J.
AU - Wilson, Richard K.
N1 - Funding Information:
We thank the McDonnell Genome Institute’s LIMS, Analysis Pipeline, and Systems groups for developing and maintaining the automated sequence analysis pipelines. M.G. was supported by a NIH, National Human Genome Research Institute (NHGRI) grant (K99HG007940). O.L.G. was supported by a National Cancer Institute (NCI) grant (K22CA188163). C.A. Maher was supported by NCI grants (R21CA185983 and R00CA149182). This work was funded by grants to T.J.L. from the NCI (PO1CA101937) and to R.K.W. from the NHGRI (U54HG003079).
Publisher Copyright:
© 2015 Elsevier Inc.
PY - 2015/9/23
Y1 - 2015/9/23
N2 - Summary 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 ∼312x) whole genome sequencing and exome capture (up 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 ∼200,000 putative SNVs by sequencing them to depths of ∼1,000x. Additional targeted sequencing provided over 10,000x coverage and ddPCR assays provided up 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).
AB - Summary 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 ∼312x) whole genome sequencing and exome capture (up 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 ∼200,000 putative SNVs by sequencing them to depths of ∼1,000x. Additional targeted sequencing provided over 10,000x coverage and ddPCR assays provided up 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).
UR - http://www.scopus.com/inward/record.url?scp=84942239424&partnerID=8YFLogxK
U2 - 10.1016/j.cels.2015.08.015
DO - 10.1016/j.cels.2015.08.015
M3 - Article
C2 - 26645048
AN - SCOPUS:84942239424
VL - 1
SP - 210
EP - 223
JO - Cell Systems
JF - Cell Systems
SN - 2405-4712
IS - 3
M1 - 35
ER -