Blastocyst segmental aneuploidy breakpoints are highly correlated with human genome fragile sites

Are segmental aneuploidies identified in human embryos more likely to occur within known fragile sites of the genome?

Segmental breaks in the autosomes of human preimplantation embryos occur more frequently in known fragile areas of the genome.

Fragile sites represent specific loci in the genome characterized by inhibition of DNA synthesis when exposed to known inhibitors and are particularly sensitive to replication stress and instability.

This was a retrospective analysis of single nucleotide polymorphism (SNP) array-based preimplantation genetic testing data from biopsies performed on 2066 human blastocysts in 98 assisted reproduction laboratories around the world from September 2019 to January 2023.

This multicenter study included eligible patients undergoing IVF with preimplantation genetic testing (PGT), in which at least one embryo was diagnosed with a segmental aneuploidy. The mean maternal age was 36.4 years (SD 4.1), ranging from 25 to 44 years. These samples were processed on high-density SNP arrays. Chromosome level copy number and B allele frequency (BAF) plots from these embryos were used to determine segmental aneuploidy breakpoints. Known fragile sites catalogued by the HumCFS database were used for correlation analyses.

Overall, a side-by-side pairing of observed breakpoints and known fragile sites demonstrated a strong concordance (r = 0.81, 95% CI [0.6, 0.92]). A chi-square test for independence for stratified groups showed a highly significant correlation between all observed breakpoints and known fragile sites (597 expected vs. 848 observed; P < 0.001) and for telomeric breaks alone (521 expected vs. 784 observed; P < 0.001). Observed interstitial breaks alone were not correlated to expected breakpoints (75 expected vs. 64 observed; P > 0.05).

These findings should be interpreted with caution, as limitations in genomic resolution may bias detection and classification of smaller segmental aneuploidies. Additionally, this study touched upon the distribution of meiotic to mitotic breakpoints in human blastocysts as they relate to known fragile sites. Since meiotic aneuploidies increase with advanced maternal age and many IVF patients undergoing PGT-A testing fall in this category, a sampling bias should be considered for this specific metric.

Demonstrating that segmental aneuploidies significantly correlate with known fragile sites highly susceptible to replication stress offers insight into the origin of subchromosomal imbalances and hints at the influence of stressors on reproductive success.

This study received no external funding and was fully supported by the participating authors and their affiliated institutions. The authors declare no conflicts of interest related to this study.

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