Very recently researchers from Stanford University systematically investigated performance of the most widely used exome enrichment platforms:
- Roche/NimbleGen’s Seq Cap EZ Exome Library v2.0 (44 Mbp)
- Agilent’s Sure Select Human All Exon (50 Mbp)
- Illumina’s Tru Seq Exome (61 Mbp)
One of the findings of the study is: When comparing coverage efficiency at constant read depth (80 million reads each) NimbleGen Sequence capture is by far better than the other two platforms. With NimbleGen sequence capture 98.6 % of all targeted bases were covered at least 10x, while Agilent’s Sure Select and Illumina’s Tru Seq covered only 89.6 % and 90.0 % of all bases at least 10x. In my opinion, the different target sizes of the exomes should have been taken into account. In this case the read depth should have been normalized according to the exome sizes. Independent of the missing normalisation it is however clearly shown in the paper that the NimbleGen technology enriched a much higher percentage of the targeted bases than the other two products..
Other criteria that were compared are the off-target enrichment rate (NimbleGen performed best) as well as the enrichment bias owing to GC content (Agilent performed best).
The decision, which platform is best for a specific scientific question should also be influenced by the individual target regions covered by different Exome kits. Agilent’s and NimbleGen’s exomes share 38 Mbp of their target regions. Apart from that Agilent’s Exome covers better Ensembl genes, while NimbleGen’s Exome covers a greater portion of miRNAs. Illumina’s exome, although displaying low coverage efficiency, is designed to capture UTRs in addition, which by now are almost not covered by the other designs and is therefore the choice, if those regions are of interest.
Differences in the performance come from the different oligonucleotide designs. I therefore postulate similar key parameters when using the customised versions of the capture technologies.