Comparison of Whole Exome Sequencing Commercial Kits Performance Across Diverse Tissue Sources

Whole exome sequencing (WES) is a standard, relevant diagnostic strategy in medical genetics. However, commercial WES library preparation kits vary significantly in design and covered regions. Very few studies have assessed DNA tissue of origin's impact on WES performance, which relates to preanalytical factors that may compromise DNA quality. We evaluated three WES commercial solutions using eight DNA samples extracted from peripheral blood, amniotic fluid, fetal tissue, and fibroblasts. A second set of 24 previously sequenced samples was resequenced using the highest-performing kit to validate results. A comprehensive bioinformatics pipeline was applied to evaluate key metrics such as coverage uniformity, duplication rates, or estimated library size, among others. Twist Exome 2.0 capture kit demonstrated the best overall performance, achieving more uniform coverage, lower duplication rates (8% vs. 16-17%), and a larger estimated library size (243 M vs. 102-129 M). Additionally, this kit achieved 93% of regions covered at the standard threshold of 38x (compared to ~80% in the other two solutions). Notably, Twist Exome 2.0 capture consistently delivered superior results for DNA extracted from non-peripheral blood tissues. This study suggests that Twist Exome 2.0 provides robust performance and is particularly well-suited for samples where DNA quality may be compromised due to preanalytical limitations.