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. Show more
Permanent link
https://doi.org/10.3929/ethz-b-000103097Publication status
publishedExternal links
Journal / series
Nucleic Acids ResearchVolume
Pages / Article No.
Publisher
Oxford University PressOrganisational unit
02207 - Functional Genomics Center Zurich / Functional Genomics Center Zurich
08828 - Schlapbach, Ralph (Tit.-Prof.)
Notes
It was possible to publish this article open access thanks to a Swiss National Licence with the publisherMore
Show all metadata