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

Abstract

ObjectiveTo determine if a handheld, nanopore-based DNA sequencer can be used for rapid preimplantation genetic screening (PGS).\n\nDesignRetrospective study.\n\nSettingAcademic medical center.\n\nPatient(s)Amplified genomic DNA from euploid and aneuploid trophectoderm biopsy samples (n=9) that was also tested using traditional next generation sequencing (NGS).\n\nIntervention(s)Short-read DNA library preparation and nanopore-based sequencing using a hand-held MinION sequencer.\n\nMain outcome measure(s)Comparison of cytogenetic testing result from NGS and nanopore-based sequencing and the time required for library preparation and sequencing.\n\nResult(s)Multiplexed short-read DNA library preparation was completed in 45 minutes. Sequencing times varied from 1 to 2 hours. These times compare favorably with NGS library preparation (>3.5 hours) and sequencing (>12 hours) times. Whole-chromosome aneuploidy screening results obtained from nanopore-based sequencing were identical to those obtained using NGS.\n\nConclusion(s)Methods for PGS of embryos have evolved from FISH to microarrays and most recently to NGS. Here we report the first application of nanopore-based sequencing for PGS on trophecoderm biopsy samples using a rapid multiplex short-read nanopore sequencing library preparation. Aneuploidy screening could be performed on 5 samples in one nanopore flowcell with 1 to 2 hour sequencing times. Overall, nanopore sequencing is a promising tool to perform rapid PGS assay onsite with a rapid turnover time, enabling same day testing and embryo transfer thus obviating the need for complex, large and expensive DNA sequencers or frozen embryos.