Abstract
Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most recent standard exome enrichment platforms from Agilent, NimbleGen and Illumina applied to six different DNA samples by two sequencing vendors per platform. Our results suggest that both Agilent and NimbleGen overall perform better than Illumina and that the high enrichment performance of Agilent is stable among samples and between vendors, whereas NimbleGen is only able to achieve vendor- and sample-specific best exome coverage. Moreover, the recent Agilent platform overall captures more coding exons with sufficient read depth than NimbleGen and Illumina. Due to considerable gaps in effective exome coverage, however, the three platforms cannot capture all known coding exons alone or in combination, requiring improvement. Our data emphasize the importance of evaluation of updated platform versions and suggest that enrichment-free whole genome sequencing can overcome the limitations of WES in sufficiently covering coding exons, especially GC-rich regions, and in characterizing structural variants.
Highlights
As a widely used method in genomic research and gene diagnostics, whole exome sequencing (WES) has the potential both to capture the entire coding region of all known genes including flanking intronic regions and to provide sequence data from these enriched genomic regions with sufficient read depth using a high-throughput DNA sequencing technology [1,2,3,4,5,6]
NimbleGen promises to capture the largest portion of the entire RefSeq coding exome (98%) followed by Illumina with 95% and Agilent with
By assessing calling accuracy for indels, which was not analysed in previous studies [2,3,4,5,6], we found that all three platforms failed to detect some small indels, Agilent identified the highest number of indels in region of interest (ROI) (Supplementary Table S20)
Summary
As a widely used method in genomic research and gene diagnostics, whole exome sequencing (WES) has the potential both to capture the entire coding region of all known genes including flanking intronic regions and to provide sequence data from these enriched genomic regions with sufficient read depth using a high-throughput DNA sequencing technology [1,2,3,4,5,6]. Since performance comparisons of three major commercial exome enrichment platforms from Agilent, NimbleGen and Illumina were reported [2,3,4,5,6], new versions of these platforms have been introduced. To date, it has not been shown which new platform is superior in performance and most suitable for diagnostic purposes. For this reason and because our preliminary study (Supplementary Figures S1 and S2) revealed that an updated version does not necessarily lead to performance improvements, we assessed the most recent version (v) of each platform (updated end 2013)
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