Genetic biomarkers and origins of aneuploidy: evaluating embryonic competence
Creators: name: Rana, Bhavini R.
Publisher: name: No Publisher Supplied
Year: 2024

description: Infertility affects approximately 10-15% of couples of reproductive age. Assisted reproductive technologies (ART), particularly in vitro fertilization (IVF), has been able to significantly improve live birth rates in couples struggling with infertility. For some couples, the use of preimplantation genetic testing for aneuploidy (PGT-A) may be warranted to transfer a single chromosomally normal (euploid) embryo, increasing the chances of a successful pregnancy outcome. However, even with the use of PGT-A, pregnancy loss and adverse pregnancy outcomes may persist, with some couples experiencing recurrent pregnancy loss (RPL). This thesis focuses on two markers that may help evaluate embryonic competence to provide the greatest chance of a successful IVF outcome. The first is a new genetic marker that predisposes couples to the risk of early and late miscarriages known as the M2 haplotype, and the second allows prediction of the origins of aneuploidy. The M2 haplotype consists of four point mutations in the core promoter of the Annexin A5 gene which decreases Annexin A5 protein (ANXA5) levels. Decreased ANXA5 increases the risk for thrombophilia in the placenta leading to placental mediated pregnancy complications. Forty-four percent of couples attempting in vitro fertilization (IVF) are carriers of the M2 haplotype compared to 15% in the general population. Importantly, evidence suggests the M2 haplotype is embryonal, and that the risks of pregnancy complications originate with the carrier status of the embryo. A novel qPCR based genotyping method was developed and validated to screen IVF patients as well as preimplantation genetic embryos for the M2 haplotype with an accuracy of 100% and 97-100%, respectively. In addition, using large data banks, population wide phenotypic associations were made to characterize the M2 haplotype. Imputation methods were validated to infer the M2 genotypes of the UK Biobank (UKBB) data set with an accuracy of 97%. Validated imputation methods were applied to the UKBB and severe pre-eclampsia was reported in M2 carriers at a frequency of 31% compared to 22% in non-carriers. The utility of PGT in carrier patients will be assessed as a means for embryo selection as opposed to conventional low molecular weight heparin (LMWH) treatment. A clinical trial recruited 166 couples, 23 of those couples elected for PGT for M2 to select non carrier embryos, and 11 IVF outcomes have been reported. In addition to screening for the M2 Haplotype, improvements to PGT-A may help increase the success of IVF. The use of PGT-A has become increasingly common over the last few years. However, most methods of PGT-A are limited to copy number analyses that can lead to false positive diagnosis of mosaicism. Mosaicism, defined as the presence of mitotic errors in the embryo, has been difficult to classify and report with current PGT-A methods and is currently being overreported by many PGT laboratories. The second focus of this thesis is to improve PGT-A methods using both copy number and SNP genotyping data to predict the parental and cell division origins of aneuploidy. This may lead to determining the true prevalence of mosaic embryos and provide more accurate diagnoses of preimplantation embryos. After validating a method to predict the origins of trisomies with 99%-100% accuracy on truth models it was applied to a cohort of embryos where parental DNA was available and meiotic aneuploidy was responsible for 27% of aneuploidy and mitotic aneuploidy only 2%. With the development and validation of both methodologies, embryonic competence may be evaluated providing patients with a higher chance of IVF success.