Technically, WES aims at a complete enrichment of all known coding regions and generation of highly uniform sequencing coverage to ensure optimal data quality for all applications. WES protocols are continuously being improved and the quest for a more precise exome that enables more confident variant calling is ongoing. Consequently, this TechNote is intended to address key quality metrics such as probe design efficiency, on-target rate, sequencing coverage, and uniformity of coverage of four WES protocols. We tested three newly released exome protocols on the market: Agilent SureSelect Human All Exon V7 (as Protocol Y herein), Illumina-IDT xGen Exome Research Panel v1.0 (as Protocol Z), and Twist Human Core Exome (as Protocol W). Agilent SureSelect Human All Exon V6 (as Protocol X) was used to benchmark their performance. The same DNA sources were used for this test, all procedures were carried out according to vendor’s original protocol, and reads were downsampled to mimic equivalent sequencing.
Based on the hg19 build, protocol X, Y, Z, or W is designed to target 38, 36, 39, or 33 Mb of highly conserved protein-coding regions, respectively. To enrich target regions, vendors design capture baits/probes either directly on or close to the desired regions.