Residual ploidy abnormalities after preimplantation genetic testing for aneuploidy

Next-generation sequencing (NGS)-based preimplantation genetic testing for aneuploidy (PGT-A) is widely used for embryo selection, but conventional copy number-based analysis may fail to detect whole-genome ploidy abnormalities such as haploidy and triploidy. This retrospective study evaluated the frequency of residual ploidy abnormalities detected by single-nucleotide polymorphism (SNP)-based analysis among embryos reported as euploid or mosaic by NGS-based PGT-A. Between May 2022 and January 2025, 5983 blastocysts underwent NGS-based PGT-A at Sugiyama Clinic. Of these, 1601 embryos reported as euploid or mosaic were subjected to additional SNP-based ploidy analysis. SNP-based results were classified as diploid, haploid, triploid, or uncertain. Among the 1601 embryos analysed, 1550 (96.8%) were classified as diploid, 4 (0.3%) as haploid, 11 (0.7%) as triploid and 36 (2.2%) as uncertain. The overall frequency of whole-genome ploidy abnormalities was 0.9% (15/1601). Among the 11 triploid embryos, 4 were derived from intracytoplasmic sperm injection (ICSI) and 7 from conventional in vitro fertilization. All haploid and triploid embryos derived from ICSI showed second polar body extrusion on retrospective time-lapse review. These findings indicate that a small but measurable proportion of embryos reported as euploid or mosaic by NGS-based PGT-A have whole-genome ploidy abnormalities detectable by SNP-based analysis. SNP-based ploidy assessment may provide complementary information in selected clinical workflows.