Evaluation of targeted next generation sequencing based preimplantation genetic diagnosis of monogenic disease

Capsule:
A methodology of next-generation sequencing was developed for preimplantation genetic diagnosis and found to be highly consistent with two independent methods of single-gene disorder screening.

Authors:
Nathan R. Treff, Ph.D., Anastasia Fedick, B.S., Xin Tao, M.S., Batsal Devkota, Ph.D., Deanne Taylor, Ph.D., Richard T. Scott, Jr., M.D.

Volume 99, Issue 5, Pages 1377-1384.e6, April 2013

Abstract:

Objective:
To investigate the applicability of next-generation sequencing (NGS) to preimplantation genetic diagnosis (PGD), this study aims to evaluate semiconductor-based NGS for genetic analysis of human embryos.

Design:
Blinded.

Setting:
Academic center for reproductive medicine.

Patient(s):
Six couples at risk of transmitting single gene disorders to their offspring.

Intervention(s):
None.

Main Outcome Measure(s):
Embryonic genotype consistency of NGS with 2 independent conventional methods of PGD.

Result(s):
NGS provided 100% equivalent PGD diagnoses of compound point mutations, and small deletions and insertions when compared to both a reference laboratory and internally developed qPCR based analyses. Furthermore, NGS single gene disorder screening could be performed in parallel with qPCR based comprehensive chromosome screening.

Conclusion(s):
NGS can provide blastocyst PGD results with a high level of consistency to established methodologies. This study and its design could serve as a model for further development of this unequivocally important and emerging technology.

  • Nathan Treff

    Hi j.utah. Thank you for your kind comments regarding our recent paper, and well done on the “Point Break” reference screen name (my guess though). We are indeed planning and currently conducting a number of studies to further these initial findings. First, we are adding cases which represent a larger variety of mutation types, adding probes to target informative linked polymorphisms, and titrating the number of samples run per chip to identify the necessary depth of coverage to maintain accuracy. We will also evaluate embryos with previously identified chromosomal aneuploidies in order to develop appropriate thresholds for clinical application.

  • j.utah

    This is an outstanding article providing very promising evidence supporting the diagnostic accuracy using a NGS platform to both detect single gene disorders and aneuploidy rates from blastocyst biopsies in IVF. The authors also discussed the potential cost savings because of the ability to perform PGS and PGD using one technological platform using barcoded samples, which will likely decrease further in the future as NGS costs continue to decrease. The authors mentioned future studies are needed to define thresholds for homozygous and heterozygous sequencing calls, the limits of sequencing depth needed to maintain sequencing accuracy, and and the causes of variation in sequencing depth across different genomic loci before it will be used routinely in the clinical arena. Do the authors have future plans for further studies?

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