Assessing concordance of genetic parameters between trophectoderm and inner cell mass in morphologically scored day-5 embryos via NGS.

Abstract: Preimplantation genetic testing for aneuploidy (PGT-A) is used for embryo selection, on a 5-10 cell biopsy from the trophectoderm (TE), which later forms the placenta. Whether this biopsy reflects the inner cell mass (ICM), which develops into the fetus, is still a subject of debate. Various parameters were previously evaluated, many of which have been proposed as potential biomarkers based on their observed associations, including the mitochondrial DNA (mtDNA) copy number. Here, we analysed thirty-two donated blastocysts, dissected into TE and ICM, with low-pass whole-genome sequencing. For 14 of these 32 embryos, PGT-A on TE biopsy was previously performed. Ploidy status, mtDNA copy number and the morphology of TE and ICM were evaluated. 81% of blastocysts showed full ploidy concordance, and 19% showed partial concordance between their ICM and TE. Out of the 14 embryos with previous PGT-A results, 86% showed full concordance, and 14% showed partial concordance. Non-euploid blastocysts showed a significantly higher mtDNA copy number in both ICM and TE. Interestingly, among euploid blastocysts, the higher rates of mtDNA were observed in those with the best morphology of the TE alone. These results suggest that TE ploidy correctly reflects ICM, and a TE biopsy is suitable for embryo status prediction. A high mtDNA copy number in TE or ICM alone may also be indicative of aneuploidy, but a euploid embryo with a high mtDNA copy number could be suggestive of a better implantation potential. Our data support the clinical utility of PGT-A, especially when combined with additional biomarkers. Lay summary: Genetic testing before implantation is a technique used after in vitro fertilisation to check whether an embryo has the correct number of chromosomes, by testing a few cells from the outside layer that will form the placenta. One common concern is whether these cells accurately represent the actual cells that will develop into the baby. Here, we compared these two cell groups and observed a high consistency. We also investigated the amount of DNA copies in the cell's energy-producing parts. Embryos with abnormal chromosome number were found to have a higher number of DNA copies than embryos with normal chromosome number. Among embryos in the latter group, those with the healthiest external appearance had the highest number of DNA copies in these energy-producing regions. These findings suggest that genetic testing before implantation is helpful and that choosing the best embryos could be further improved by considering additional biological factors.