A systematic analysis of contemporary whole exome sequencing capture kits to optimise high-coverage capture of CCDS regions

Whole exome sequencing (WES) is a well-established tool for clinical diagnostics, is more cost-effective and faster to analyse than whole genome sequencing and has been implemented to uplift diagnostic rates in human disease. However, challenges remain to achieve comprehensive and uniform coverage of targets, and high sensitivity and specificity. Differences in genomic target regions and exome capture mechanism between kits may lead to differences in overall coverage uniformity and capture efficiency. Here, we analyse the efficiency of a range of off-the-shelf exome sequencing (ES) kits in capturing their reported targets and the consensus coding sequence (CCDS) regions. Our results show Twist Custom Exome, Twist Human Comprehensive Exome, and Roche KAPA HyperExome V1 perform particularly well at capturing their target regions at 10X and 20X coverage and achieve the highest capture efficiency of CCDS regions upon read downsampling. This was the case despite both Twist kits targeting less than 37Mb in the genome. Our analysis highlights the impact of kit target design on capture efficiency in WES, with kit target size and uniformity of coverage impacting the capture efficiency of CCDS regions. This benchmark will help researchers to make an informed decision based on their needs.