ImputePGTA: accurate embryo genotyping and polygenic scoring from ultra-low-pass sequencing

Preimplantation genetic testing (PGT) for polygenic risk (PGT-P) holds great promise for reducing lifetime disease burden, but genotyping embryos remains difficult. PGT for aneuploidy (PGT-A) is a routine test used in over half of in vitro fertilization cycles in the United States, typically via ultra-low-pass (ULP) sequencing ([~]0.004x) or, less commonly, genotyping arrays. Here we describe an approach that enables accurate embryo genotyping from PGT-A data when combined with estimated parental haplotypes. We develop a Coupled Hidden Markov Model, ImputePGTA, which jointly infers inheritance patterns from parents to offspring as well as phasing errors in parental haplotypes, along with an inference algorithm that scales linearly with the number of embryos. The performance of our approach depends on the phasing of parental haplotypes, which we improve through a method, phaseGrafter, that combines evidence from short and long reads, further enabling imputation of rare variants. We validate our approach through simulations and comparison of embryo genomes reconstructed from real PGT-A data to post-birth whole genome sequencing data. When using long reads for parental phasing, we achieve a dosage correlation of 0.98 with high-quality post-birth genotypes, and a mean absolute difference of 0.11 standard deviations across 17 disease polygenic scores, lower than from imputation of genotyping array data from reference panels. Uncertainty from imputation from ULP PGT-A data with accurate parental phasing results in only a [~]2% attenuation in expected gains from embryo selection for typical embryo cohort sizes. Our approach removes an important technological barrier to using PGT-P and is already facilitating more widespread adoption.