Non-invasive prenatal screening (NIPS) uses fetal cell-free DNA (cfDNA) in maternal plasma to detect aneuploidies early in pregnancy. Because most cfDNA originates from the mother and NIPS is widely used, these datasets offer a large potential resource for genome-wide association studies (GWAS) and polygenic risk score (PRS) analyses. As the NIPS workflow entails generating low-coverage (0.1-0.2×) sequencing, genotype imputation is required before downstream analyses. This thesis evaluates the p