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Semiconductor Sequencing for Preimplantation Genetic Testing for Aneuploidy
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Embryo tracking system for high-throughput sequencing-based preimplantation genetic testing.

Wanwisa van Dijk1, Kasper Derks1, Marion Drüsedau1

  • 1Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.

Human Reproduction (Oxford, England)
|September 23, 2022
PubMed
Summary
This summary is machine-generated.

The embryo tracking system (ETS) enhances preimplantation genetic testing (PGT) by reducing sample switching and improving efficiency. This novel approach streamlines PGT procedures, making genetic testing safer and more scalable for clinical applications.

Keywords:
IVF embryosclinical sequencingcopy-number profilinggenotyping-by-sequencinghaplarithmisishaplotypingmassively parallel sequencingpreimplantation genetic testing

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Area of Science:

  • Reproductive Medicine and Genetics
  • Genomic Technologies
  • Assisted Reproductive Technologies

Background:

  • Current sequencing-based preimplantation genetic testing (PGT) methods are labor-intensive, costly, and prone to human error, limiting their widespread adoption.
  • Existing PGT protocols require multiple manual quality control steps to prevent sample switching, impacting efficiency and throughput.
  • Next-generation sequencing (NGS) approaches have advanced PGT, but challenges in library preparation and sample handling persist.

Purpose of the Study:

  • To develop and evaluate an embryo tracking system (ETS) to enhance the safety, efficacy, and scalability of sequencing-based PGT.
  • To assess the impact of ETS on reducing sample switching and improving the overall throughput of PGT procedures.
  • To determine if ETS integration affects the genomic landscape of preimplantation embryos during PGT.

Main Methods:

  • Developed an embryo tracking system (ETS) that tracks embryos from whole-genome amplification (WGA) to full genome haplotype profiles.
  • Compared PGT procedures with and without ETS on both bulk DNA samples (n=563) and WGAed few-cell DNA samples (n=322).
  • Incorporated barcoded DNA fragments prior to library preparation in samples with ETS to assess potential interference with NGS-based PGT workflows.

Main Results:

  • The ETS significantly reduced the number of manual quality control steps required in PGT from six to one, minimizing the risk of human error and sample switching.
  • ETS-PGT demonstrated no adverse effect on the genomic landscape of preimplantation embryos, preserving data integrity.
  • The implementation of ETS led to a substantial increase in the efficacy and throughput of sequencing-based PGT methods.

Conclusions:

  • The embryo tracking system (ETS-PGT) offers a robust solution to improve the safety, efficiency, and scalability of massively parallel sequencing-based PGT.
  • ETS-PGT has broad applicability for various single- and few-cell sequencing applications, particularly where specimen input is limited.
  • This approach can be readily adapted to other sequencing-based diagnostic methods, including PGT for structural rearrangements, aneuploidies, and non-invasive prenatal testing.