Novel Insights into Preimplantation Genetic Testing for Aneuploidy and Non-invasive Prenatal Testing

Aneuploidy (chromosome copy number imbalance) is the leading cause of implantation failure, miscarriage, and live birth aneuploidy. Preimplantation genetic testing for aneuploidy (PGT-A) aims to select chromosomally normal (euploid) embryos produced during in vitro fertilisation (IVF) treatment for transfer. Ensuring that the resulting pregnancy is unaffected by aneuploidy aiming to avoid adverse outcomes and improve IVF success rates. Non-invasive prenatal testing (NIPT), is applied at a later stage of fetal development than PGT-A, after 10 weeks of gestation, to detect predominantly the chromosome abnormalities associated with live births. DNA for both PGT-A and NIPT genetic analysis is most commonly from the same region of the developing fetus, the trophoblast, part of the placenta. For PGT-A the trophectoderm (trophoblast) is currently the preferred site for biopsy, which, after developing into the placenta, the subsequent apoptosis of the trophoblast cells provides cell free fetal DNA for NIPT analysis. PGT-A and NIPT are both considered screening tests for the genetic status of the developing fetus, but genetic variation (or mosaicism) between the placenta and fetus in some instances can lead to false positives and negatives for both PGT-A and NIPT. As such, PGT-A and NIPT have limitations in their degree of accuracy, this has generated criticism regarding their application. With this in mind, the aims of this thesis were to investigate the application of PGT-A and NIPT on success over conventional methods and explore the causes and frequency of false positives and mosaicism.Specifically: 1.Following PGT-A, to assess how often are there no euploid embryos but only a mosaic embryo available for transfer? And if using the CoGEN position statement to rank mosaic embryos, what proportion of these mosaic embryos would be considered for transfer? 2.To investigate if the transfer of embryos after PGT-A results in improved live birth rates over conventional IVF without genetic analysis, and to what extent this varies by centre. 3.To investigate the rates of aneuploidy detected following NIPT, based on referral indication. 4.To test the hypothesis that NIPT cases previously reported with a suspected aneuploidy and found to be discordant suspected common aneuploidies, is caused by the presences of rare autosomal trisomies (RATs) on the untested chromosomes. Results found that 10-11% of PGT-A cases only had a mosaic embryo for transfer, and that around 4% of cases would have a mosaic that would be considered for transfer. PGT-A offers improved live birth rates per embryo transferred for patients over 35 years old, and that there is a large degree of variation between referring centres. This work also found that patients referred following an abnormal ultrasound scan were the most likely to have aneuploidy detected with NIPT. This work also demonstrated that in this instance the false positives following the reporting of a suspected common aneuploidy was not due to RATs on the untested chromosomes. The results presented in this thesis demonstrate that both PGT-A and NIPT offer improved accuracy and in turn better outcomes with continued technological improvements. It also demonstrates that by extending the availability of both genetic screening methods to more patients, improvements could be seen in terms of increased live birth rates for PGT-A and increased detection of live birth aneuploidies for both high and low risk patients.