Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform

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.