Sensitivity and specificity of a novel preimplantation genetic test for aneuploidy (PGT-A) test detecting the presence and origin of the error: creation of haploid embryos as controls

Introduction Conventional PGT-A methods using NGS sequencing can not detect polyploidy or haploidy, embryo parental origin, or differentiate between mitotic and meiotic abnormalities. To be detected, SNP analysis is needed. Methods Here, we validated a novel preimplantation genetic test for aneuploidy (PGT-A) approach combining next-generation sequencing (NGS) with ad hoc use of single-nucleotide polymorphism (SNP) genotyping to detect aneuploidy, haploidy, triploidy and embryo parental origin, by using NGS complemented by an SNP panel, in which data were grouped into B-allele frequency categories and analysed using proprietary scoring algorithms to classify ploidy status. In the absence of haploid cell lines for validation purposes, haploid human embryos were generated by artificially activating unfertilised oocytes and we also focused our attention on analysing embryos with normal and abnormal number of pronuclei. Results All diploid and triploid control samples were correctly identified and all embryos derived from parthenogenetically activated eggs showed haploid results (with one ‘inconclusive’ exception). Among the 254 embryos assessed for pronuclear origin, 64% of single pronucleus, 42% of three pronuclei and 99% of two pronuclei embryos were found to be diploid. Parental origin and relationship analysis was found to be 100% concordant with genomic DNA and 99% with the embryo biopsies. Conclusions This approach can prevent the misdiagnosis of triploidy and haploidy, while verifying embryo-parent matching when required. The creation of haploid embryos for validation purposes represents a significant advance in the absence of haploid cell lines and this study thus represents the first time that ‘true control’ samples for haploidy have been used to validate a PGT-A test. Establishing that >50% of zygotes with abnormal pronuclear numbers were diploid and potentially transferable opens up that possibility for PGT-A to increase cumulative pregnancy rates.