Adaptation of PCR-based library preparation for MGI platform for cancer mutation testing in clinical setting

MGI platforms hold promise to become a widespread instrument for various clinical next-generation sequencing applications, from whole genome sequencing to COVID-19 genotyping. However, in the clinical oncology setting it is still restricted to large panel sequencing limiting capacity for routine biomarker screening. In this article, we describe our experience of tailoring amplicon-based library construction for the MGI platform. Illumina compatible reagents served as a prototype in order to introduce platform specific adapters. Elaborated reagent kits were used for BRCA1/2 or 34 oncogenes testing both with whole blood and FFPE-derived DNA. Our data show that amplicon-based DNBSEQ-tailored library preparation demonstrates sufficient analytical efficiency in terms of coverage uniformity (average MAPD 1.08 and 1.19 for ABC plus and Atlas plus panels) and amplicon drop-out rate (ranging from 0.3% to 2.5%). Additionally, it shows efficiency in terms of single sample sensitivity, maintaining 99% sensitivity compared to 99% for the Illumina prototype. We show that it also outreaches expected diagnostic parameters of MGI exome sequencing (99% vs 95% for WES). Per-amplicon coverage of sticky-end libraries sequenced on Illumina and MGI were highly correlated demonstrating that the platform itself does not introduce any bias to amplicon coverage. Across three tested variations of library preparation protocol, discordances were related to ligation mix component composition and resulted in underrepresentation of GC-low and GC-high amplicons and low uniformity as a result. Overall, we outline the successful adaptation of PCR-based library preparation for MGI signifying the importance of tailoring component composition of reagent kit for uniform coverage.