Evaluation of a hybridization capture-based hereditary cancer panel for the ion semiconductor-based next-generation sequencing system

Abstract Background There is an unmet need to use the ThermoFisher Ion sequencing platform with a hybridization capture-based next-generation sequencing (NGS) panel. However, the analytical performance of combining an ion semiconductor-based sequencing system and a hybridization capture-based NGS panel has not been thoroughly evaluated. Therefore, we compared the analytic performance of Illumina's NextSeq and Ion S5 XL using a hybridization capture-based target enrichment method. Methods We included 31 clinical samples and NA12878 reference material for comparing two different NGS instruments using a hybridization capture-based panel. The hybridization-based capture hereditary cancer predisposition (HCP) panel was designed for Ion S5 XL Sequencer and Illumina platforms, respectively. Results We obtained comparable data involving sequencing run metrics and analytical performance of two different NGS systems using a hybridization-based capture panel designed for each NGS platform. The sensitivity, specificity, and accuracy of single-nucleotide variant and indel calling were 97.06%, 100%, and 100% for the Ion S5™ XL system and 98.53%, 100%, and 100% for NextSeq 550Dx platform, respectively. Conclusions This study demonstrated that a hybrid capture panel kit can be successfully implemented using the ThermoFisher Scientific Ion S5 XL instrument and offers the opportunity to select a variety of hybridization-based capture panels from various manufacturers.