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

Rapid preimplantation genetic screening was successfully performed on trophectoderm biopsy samples using a hand-held nanopore sequencer. Sequencing for aneuploidy screening could be performed on a single sample in 20 minutes and on five samples under 2 hours.

Volume 110, Issue 5, Pages 910–916.e2


Shan Wei, Ph.D., Zachary R. Weiss, B.S., Pallavi Gaur, Ph.D., Eric Forman, M.D., H.C.L.D., Zev Williams, M.D., Ph.D.



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.

Main Outcome Measure(s)

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 45 minutes. Sequencing on a single sample was completed within 20 minutes and 5 samples were simultaneously sequenced in under 2 hours. 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 20 minutes and on 5 samples, simultaneously, within 2 hours. 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.

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