Fig. 2: Embryo classification within genomic regions of consanguinity using the Haploseek “diff plot”.

The diff plot depiction of chr9 from the same children as in Fig. 1. This plot simplifies the diagnosis of autosomal recessive disease in consanguineous families. Results are summarized as “homozygous for pathogenic haplotype,” meaning that child 2/3 is identical in both haplotypes to child 1, or “wild type or heterozygous” meaning that child 2/3 is unlike child 1 in at least one haplotype, and thus should be prioritized for transfer in preimplantation genetic testing for monogenic disease (PGT-M) cases. “Diff plot” indicates the degree of confidence with which the hidden Markov model is reporting a certain embryo classification. A diff plot value of 1 means a high-confidence prediction of a nondiseased embryo (i.e., different in at least one haplotype from child 1). A diff plot value of 0 means high-confidence prediction of a diseased embryo, fully matching child 1. We call sites with diff plot values between 0.01 and 0.99 low confidence. Green dots mark regions of consanguinity (ROCs) in which the parents share both of their haplotypes. The purple rectangle indicates the same evaluation region as in Fig. 1. Note that the “show diff” checkbox on the top left is checked, thereby indicating that diff plot embryo classification is being viewed.