Optimization of a hybridization-based target enrichment protocol for precision oncology

Next-generation sequencing has become an essential tool in precision oncology, enabling comprehensive detection of clinically relevant genomic alterations. This study aimed to optimize a hybridization-based enrichment protocol for formalin-fixed paraffin-embedded (FFPE)-derived DNA and to evaluate its performance relative to commercial hybridization- and amplification-based kits.

Hybridization conditions, including temperature, duration, buffer composition, and the number of capture rounds, were systematically varied to maximize enrichment efficiency and coverage uniformity. Libraries were sequenced using Illumina platforms and analyzed for enrichment metrics, duplicate fraction, target depth, and variant detection. Comparative analyses were performed against commercial hybridization-based and amplification-based kits, as well as a whole-exome capture panel. Two rounds of short hybridization provided the highest enrichment efficiency while maintaining complete target coverage. The optimized protocol demonstrated approximately sixfold higher enrichment than the hybridization-based analogue, ensuring adequate coverage despite increased duplicate rates. Scalability testing showed performance comparable to a commercial whole-exome kit, with maintained enrichment efficiency and target depth across large panels.

The optimized hybridization-based enrichment protocol provides superior target coverage, high variant recall, and flexibility for scaling from small panels to whole-exome sequencing, supporting its suitability for precision oncology applications in challenging FFPE samples.