Targeting efficiency and capability varied between commercially available exome capture kits. (a) The intended targets of the NimbleGen and Agilent exome kits were 26,227,295 bp and 37,640,396 bp, respectively. Both exome kits captured similarly high amounts (up to about 97%) of their intended targets at 1× depth or greater, but the NimbleGen kit was able to reach saturation of target coverage at 20× depth more efficiently than the Agilent kit. The NimbleGen exome kit required less raw data to provide sufficient coverage of the exome and to support confident genotype analysis. (b) Both exome kits were designed to target exons based on the June 2008 version of CCDS, which consisted of 27,515,053 bp of genomic space. Notably, the NimbleGen target was smaller than the CCDS, while the Agilent target was larger than the CCDS. Based on 1× depth sequence coverage, the Agilent exome kit captured more of the CCDS than the NimbleGen exome kit (97% covered by Agilent versus 88% covered by NimbleGen), but the NimbleGen kit was more efficient at capturing the regions of the CCDS it had the capability to capture.
Parla et al. Genome Biology 2011 12:R97 doi:10.1186/gb-2011-12-9-r97