Aneuploidy is the largest contributor to pregnancy loss. Here I identify genetic associations with aneuploidy incidence across a sample of day-5 IVF embryos.

Using published clinical data from PGT-A, we identify possible ranges of meiotic and mitotic error rates that best explain ratios of euploid, mosaic, and aneuploid embryos.

Using very low-coverage single-cell DNA sequencing data of gametes originating from a single diploid donor, rhapsodi (1) phases the diploid donor haplotypes, (2) imputes missing gamete genotypes, and (3) discovers gamete-specific meiotic recombination events. I applied this method to >40,000 of single-cell sperm DNA from 25 donors to investigate signatures of transmission distortion.