Rapid preimplantation genetic screening using a handheld, nanopore-based DNA sequencer

Abstract

To determine if a handheld, nanopore-based DNA sequencer can be used for rapid preimplantation genetic screening (PGS). Laboratory study. Academic medical center. Amplified genomic DNA from euploid and aneuploid trophectoderm biopsy samples (n=9) that was also tested using traditional next generation sequencing (NGS). Short-read DNA library preparation and nanopore-based sequencing using a hand-held MinION sequencer. Comparison of cytogenetic testing result from NGS and nanopore-based sequencing and the time required for library preparation and sequencing. Multiplexed short-read DNA library preparation was completed in 45minutes. Sequencing on a single sample was completed within 20minutes and 5 samples were simultaneously sequenced in under 2hours. Whole-chromosome aneuploidy screening results obtained from nanopore-based sequencing were identical to those obtained using NGS. Here we report the first application of nanopore-based sequencing for PGS on trophectoderm biopsy samples using a novel rapid multiplxed short-read nanopore sequencing library preparation protocol. Sequencing for aneuploidy screening could be performed on a single sample in 20minutes and on 5 samples, simultaneously, within 2hours. Overall, nanopore sequencing is a promising tool to perform rapid PGS onsite, enabling same day testing and embryo transfer, thus obviating the need for complex, large and expensive DNA sequencers or embryo freezing.