SHaploseek is a sequencing-only, high-resolution method for comprehensive preimplantation genetic testing

Area of Science:

• Genetics and Genomics
• Reproductive Medicine
• Bioinformatics

Background:

• Preimplantation genetic testing (PGT) is crucial for reproductive health.
• Existing methods like Haploseek combine microarray and low-pass sequencing.
• There is a need for more versatile and higher-throughput PGT solutions.

Purpose of the Study:

• To develop a sequencing-only implementation of Haploseek for PGT.
• To create SHaploseek, a universal method for genome-wide embryonic haplotype determination.
• To enhance throughput and versatility in comprehensive PGT.

Main Methods:

• Developed SHaploseek using low-pass sequencing (≤5x) of parents/relatives and ultra-low-pass sequencing (0.2-0.4x) of embryos.
• Analyzed single lymphoblast cells and 31 embryos using SHaploseek.
• Validated genome-wide haplotype predictions against bulk DNA, Haploseek, and PCR-based PGT.

Main Results:

• SHaploseek achieved >99% concordance with bulk DNA from single cells.
• All focal site haplotype predictions in embryos were concordant with clinical PCR-based PGT.
• Demonstrated >99% median concordance with Haploseek, maintaining high accuracy with low DNA input and sequencing depth (≥2x).

Conclusions:

• SHaploseek is an accurate, cost-effective, and versatile comprehensive PGT solution.
• It offers improved high-confidence haplotype predictions, especially in subtelomeric regions.
• SHaploseek represents a significant advancement in single-platform PGT technology.