SHaploseek: A sequencing-only high-resolution implementation of comprehensive preimplantation genetic testing

Abstract

AbstractPurposeWe previously developed Haploseek, a clinically-validated, variant-agnostic comprehensive preimplantation genetic testing (PGT) solution. Haploseek is based on microarray genotyping of the embryo’s parents and relatives, combined with low-pass sequencing of the embryos. Here, to increase throughput and versatility, we aimed to develop a sequencing-only implementation of Haploseek.MethodsWe developed SHaploseek, a universal PGT method to determine genome-wide haplotypes of each embryo based on low-pass (≤5x) sequencing of the parents and relative(s) along with ultra-low pass (0.2-0.4x) sequencing of the embryos. We used SHaploseek to analyze five single lymphoblast cells and 31 embryos from 14 families. We validated the genome-wide haplotype predictions against either bulk DNA, Haploseek, or, at focal genomic sites, PCR-based PGT results.ResultsSHaploseek achieved >99% concordance with bulk DNA in two families from which single cells were derived from grown-up children. In embryos from 12 PGT families, all of SHaploseek’s focal site haplotype predictions were concordant with clinical PCR-based PGT results. Genome-wide, there was >99% median concordance between Haploseek and SHaploseek’s haplotype predictions. Concordance remained high at all assayed sequencing depths ≥2x, as well as with only 1ng of parental DNA input. In subtelomeric regions, significantly more haplotype predictions were high-confidence in SHaploseek compared to Haploseek.ConclusionAs a single-platform comprehensive PGT solution with higher sensitivity in subtelomeric regions, SHaploseek constitutes a significantly improved, accurate, and cost-effective re-embodiment of Haploseek.