PMID- 21559511
OWN - NLM
STAT- MEDLINE
DCOM- 20111128
LR  - 20220316
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 6
IP  - 4
DP  - 2011 Apr 29
TI  - Comparison of three targeted enrichment strategies on the SOLiD sequencing 
      platform.
PG  - e18595
LID - 10.1371/journal.pone.0018595 [doi]
LID - e18595
AB  - Despite the ever-increasing throughput and steadily decreasing cost of next 
      generation sequencing (NGS), whole genome sequencing of humans is still not a 
      viable option for the majority of genetics laboratories. This is particularly 
      true in the case of complex disease studies, where large sample sets are often 
      required to achieve adequate statistical power. To fully leverage the potential 
      of NGS technology on large sample sets, several methods have been developed to 
      selectively enrich for regions of interest. Enrichment reduces both monetary and 
      computational costs compared to whole genome sequencing, while allowing 
      researchers to take advantage of NGS throughput. Several targeted enrichment 
      approaches are currently available, including molecular inversion probe ligation 
      sequencing (MIPS), oligonucleotide hybridization based approaches, and PCR-based 
      strategies. To assess how these methods performed when used in conjunction with 
      the ABI SOLID3+, we investigated three enrichment techniques: Nimblegen 
      oligonucleotide hybridization array-based capture; Agilent SureSelect 
      oligonucleotide hybridization solution-based capture; and Raindance Technologies' 
      multiplexed PCR-based approach. Target regions were selected from exons and 
      evolutionarily conserved areas throughout the human genome. Probe and primer pair 
      design was carried out for all three methods using their respective informatics 
      pipelines. In all, approximately 0.8 Mb of target space was identical for all 3 
      methods. SOLiD sequencing results were analyzed for several metrics, including 
      consistency of coverage depth across samples, on-target versus off-target 
      efficiency, allelic bias, and genotype concordance with array-based genotyping 
      data. Agilent SureSelect exhibited superior on-target efficiency and correlation 
      of read depths across samples. Nimblegen performance was similar at read depths 
      at 20x and below. Both Raindance and Nimblegen SeqCap exhibited tighter 
      distributions of read depth around the mean, but both suffered from lower 
      on-target efficiency in our experiments. Raindance demonstrated the highest 
      versatility in assay design.
FAU - Hedges, Dale J
AU  - Hedges DJ
AD  - John T. MacDonald Department of Human Genetics, Hussman Institute for Human 
      Genomics, University of Miami Miller School of Medicine, Miami, Florida, United 
      States of America. dhedges@med.miami.edu
FAU - Guettouche, Toumy
AU  - Guettouche T
FAU - Yang, Shan
AU  - Yang S
FAU - Bademci, Guney
AU  - Bademci G
FAU - Diaz, Ashley
AU  - Diaz A
FAU - Andersen, Ashley
AU  - Andersen A
FAU - Hulme, William F
AU  - Hulme WF
FAU - Linker, Sara
AU  - Linker S
FAU - Mehta, Arpit
AU  - Mehta A
FAU - Edwards, Yvonne J K
AU  - Edwards YJ
FAU - Beecham, Gary W
AU  - Beecham GW
FAU - Martin, Eden R
AU  - Martin ER
FAU - Pericak-Vance, Margaret A
AU  - Pericak-Vance MA
FAU - Zuchner, Stephan
AU  - Zuchner S
FAU - Vance, Jeffery M
AU  - Vance JM
FAU - Gilbert, John R
AU  - Gilbert JR
LA  - eng
GR  - 3P50NS071674-01S1/NS/NINDS NIH HHS/United States
GR  - RC2 HG005605/HG/NHGRI NIH HHS/United States
GR  - 1RC2HG005605/HG/NHGRI NIH HHS/United States
GR  - P50 NS071674/NS/NINDS NIH HHS/United States
GR  - R01 NS072248/NS/NINDS NIH HHS/United States
PT  - Comparative Study
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20110429
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (DNA Primers)
SB  - IM
MH  - Alleles
MH  - Base Sequence
MH  - Computational Biology/methods
MH  - DNA Primers/chemistry
MH  - Female
MH  - Genotype
MH  - Heterozygote
MH  - Humans
MH  - Male
MH  - Molecular Sequence Data
MH  - Nucleic Acid Hybridization
MH  - Polymerase Chain Reaction/methods
MH  - Reproducibility of Results
MH  - Sequence Analysis, DNA/*methods
MH  - Software
PMC - PMC3084696
COIS- Competing Interests: A portion of the reagents used in this study was provided 
      free of charge by the participating vendors, including Roche-Nimblegen, 
      Raindance, Agilent, and Applied Biosystems. This does not alter the authors' 
      adherence to all the PLoS ONE policies on sharing data and materials.
EDAT- 2011/05/12 06:00
MHDA- 2011/12/13 00:00
PMCR- 2011/04/29
CRDT- 2011/05/12 06:00
PHST- 2011/01/05 00:00 [received]
PHST- 2011/03/04 00:00 [accepted]
PHST- 2011/05/12 06:00 [entrez]
PHST- 2011/05/12 06:00 [pubmed]
PHST- 2011/12/13 00:00 [medline]
PHST- 2011/04/29 00:00 [pmc-release]
AID - PONE-D-11-01617 [pii]
AID - 10.1371/journal.pone.0018595 [doi]
PST - epublish
SO  - PLoS One. 2011 Apr 29;6(4):e18595. doi: 10.1371/journal.pone.0018595.