title: Comparison of three targeted enrichment strategies on the SOLiD sequencing platform.
abstract: 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 20× 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.
authors.affiliation: 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
authors.forename: Dale J
authors.initials: DJ
authors.lastname: Hedges
authors.forename: Toumy
authors.initials: T
authors.lastname: Guettouche
authors.forename: Shan
authors.initials: S
authors.lastname: Yang
authors.forename: Guney
authors.initials: G
authors.lastname: Bademci
authors.forename: Ashley
authors.initials: A
authors.lastname: Diaz
authors.forename: Ashley
authors.initials: A
authors.lastname: Andersen
authors.forename: William F
authors.initials: WF
authors.lastname: Hulme
authors.forename: Sara
authors.initials: S
authors.lastname: Linker
authors.forename: Arpit
authors.initials: A
authors.lastname: Mehta
authors.forename: Yvonne J K
authors.initials: YJ
authors.lastname: Edwards
authors.forename: Gary W
authors.initials: GW
authors.lastname: Beecham
authors.forename: Eden R
authors.initials: ER
authors.lastname: Martin
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Pericak-Vance
authors.forename: Stephan
authors.initials: S
authors.lastname: Zuchner
authors.forename: Jeffery M
authors.initials: JM
authors.lastname: Vance
authors.forename: John R
authors.initials: JR
authors.lastname: Gilbert
mesh_terms: D000483:Alleles; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D017931:DNA Primers / Q000737:chemistry; D005260:Female; D005838:Genotype; D006579:Heterozygote; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D016133:Polymerase Chain Reaction / Q000379:methods; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D017931:DNA Primers