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

Objective: To determine if a handheld, nanopore-based DNA sequencer can be used for rapid preimplantation genetic screening (PGS).

Design: Retrospective study. Setting: Academic medical center.

Patient(s): Amplified genomic DNA from euploid and aneuploid trophectoderm biopsy samples (n=9) that was also tested using traditional next generation sequencing (NGS).

Intervention(s): Short-read DNA library preparation and nanopore-based sequencing using a hand-held MinION sequencer.

Main outcome measure(s): Comparison of cytogenetic testing result from NGS and nanopore-based sequencing and the time required for library preparation and sequencing.

Result(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.

Conclusion(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.