P-560 Characterization of ploidy level and parental genome inheritance abnormalities in preimplantation human embryos
Authors: Picchetta L , Tao X , Ottolini C  S , Mounts E , Mulas F , Caroselli S , Molinaro T , Whitehead C , Zhang Y , Jalas C , Capalbo A 
Published: July 2024

Abstract

Study question
Can preimplantation genetic testing (PGT) platforms with integrated genotyping aid the characterization of genome-wide chromosomal abnormalities in human embryos and factors contributing to their occurrence?

Summary answer
Signatures detected by genotype-criteria-based models in PGT pinpoint origin of haploidy, triploidy and genome-wide uniparental disomy (gwUPD), highlighting recombination deficiencies potentially underpinning these phenomena.

What is known already
While there is a growing body of knowledge on the frequency and origin of individual chromosome abnormalities, very little is known about genome-wide chromosomal abnormalities in human development. Indeed, genome-wide abnormalities are incompatible with normal human development, making the preimplantation stage the ideal time to characterize them. Novel PGT technologies provide the research and clinical opportunity to characterize both known ploidy-level abnormalities (triploid/haploid) and identify theoretical genome-wide abnormalities undetectable at later stages of development.

Study design, size, duration
PGT genotyping data from 96660 embryos were used to assess incidence of ploidy-level abnormalities and correlation with potential predisposing clinical factors. Parental origin of putative haploidy and triploidy was assessed on 14 and 41 embryos with parental genotypes available (trios), respectively. For the 41 triploid trios, meiotic origin and recombination rates were also evaluated. A novel genotype-criteria based model to detect theoretical gwUPD and meiotic origin was developed on a semi-contemporaneous 74009 female embryo dataset.

Participants/materials, setting, methods
PGT was performed with targeted next-generation sequencing, including 5000 genome-wide SNPs. Informative SNPs from trios were used to identify parental origin of haploidy/triploidy. Informative SNPs within 5cM of the centromere were used to evaluate meiotic origin and extended beyond 5cM to identify maternal recombination observing shifts between single (SPH) and biparental (BPH) homologs. gwUPD was predicted when low genome-wide heterozygosity, increased homozygosity in the centromeric region, and decreased similarity to sibling embryos were observed.

Main results and the role of chance
Genome wide ploidy abnormalities were detected in 1.1% (n = 1.063/96.660; CI 95%: 1-1,2%) of embryos. Haploidy was mainly of paternal origin (n = 12/14), whereas triploidy was exclusively maternal in origin (n = 41/41) and prominently due to meiosis II errors (n = 30/41; 73.2%; 95% CI:57.1-85.8%). Advanced maternal age was positively associated with an increased risk of triploid conceptions (OR = 1.059 per year; p &lt; 0.001). Investigation of maternal recombination rates detected by three consecutive SNPs shifting between SPH and BPH (with a calculated genotyping error of 0.16%) in triploid embryos revealed an outlier group of 7 embryos with statistically lower (P &lt; 0.001) identified crossover events (0-2 events genome-wide) compared to the average 23.7 detectable events genome-wide (SD:4.3). Recombinant gwUPD was predicted in 41 out of 74009 human embryos (0.05%; 95% CI:0.04-0.07%). These embryos showed a high homozygosity in pericentromeric regions, as a proof of each pair of chromosomes being the same parental homolog resulting from a faulty meiosis II, but with detectable heterozygosity regions throughout the rest of the genome, indicating that crossovers occurred between the two parental homologs during prophase I. Multifocal biopsies from the same embryos confirmed the reproducibility of identification of the number of recombination events in triploid embryos and the gwUPD prediction.

Limitations, reasons for caution
This assay genotypes only a portion of the genome and underestimation of recombination events is possible. Our current detection of gwUPD is limited to recombinant uniparental isodisomy of MII origin only. Therefore, the exact prevalence of these abnormal gwUPD configurations requires further understanding and analysis.

Wider implications of the findings
Genotyping in routine PGT can identify severe genome-wide abnormalities with associated gestational complications that would otherwise go undiagnosed. Comprehensive characterization of these abnormalities is not possible at later stages of development. Therefore, PGT offers a unique opportunity to delve into their biological origin and identify novel biomarkers for embryo competence.

Trial registration number
not applicable