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

Shan Wei Ph.D, Zachary R. Weiss B.S, Pallavi Gaur Ph.D, Eric Forman M.D HCLD, Zev Williams M.D Ph.D
doi: https://doi.org/10.1101/274563
Shan Wei Ph.D
aColumbia University Medical Center, New York, New York
bAlbert Einstein College of Medicine, Bronx, New York
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Zachary R. Weiss B.S
aColumbia University Medical Center, New York, New York
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Pallavi Gaur Ph.D
aColumbia University Medical Center, New York, New York
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Eric Forman M.D HCLD
aColumbia University Medical Center, New York, New York
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Zev Williams M.D Ph.D
aColumbia University Medical Center, New York, New York
bAlbert Einstein College of Medicine, Bronx, New York
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Abstract

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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 01, 2018.
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Rapid preimplantation genetic screening (PGS) using a handheld, nanopore-based, DNA sequencer
Shan Wei Ph.D, Zachary R. Weiss B.S, Pallavi Gaur Ph.D, Eric Forman M.D HCLD, Zev Williams M.D Ph.D
bioRxiv 274563; doi: https://doi.org/10.1101/274563
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Rapid preimplantation genetic screening (PGS) using a handheld, nanopore-based, DNA sequencer
Shan Wei Ph.D, Zachary R. Weiss B.S, Pallavi Gaur Ph.D, Eric Forman M.D HCLD, Zev Williams M.D Ph.D
bioRxiv 274563; doi: https://doi.org/10.1101/274563

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