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 S5TM 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.