Fig. 3: Clinical utility of Haploseek for preimplantation genetic testing for monogenic disease (PGT-M) using only a single grandparent of the embryo for haplotype phasing.

(a) A pedigree of family 24, in which the mother and maternal grandmother (of embryo 68e-1) are both heterozygous for a germline 0.5-Mb duplication on chr16. For haplotype phasing of the mother, the maternal grandmother’s DNA was genotyped. (b) DNA microarray analysis demarcates the location of the duplication on chr16 in both the mother and the maternal grandmother (genomic coordinates indicated on top). The panel shows the microarray analysis suite (Chas) screen capture of the chr16p duplication in both individuals. (c) Screen captures of Haploseek haplotype prediction plots for the familial chr16 duplication in embryo biopsy 68e-1 of family 24. The approximate location of the duplication is marked by a dashed vertical line. The plot shows haplotype predictions in the +/−2 Mb genomic region flanking the chr16 duplication. Overall, the results are depicted in similar fashion to that in Fig. 1, except that the haplotype predictions are defined with respect to grandparental reference (see legend on the top right), as opposed to the child 1 reference. The pictured sample exhibits a high-confidence maternal grandfather haplotype at the familial pathogenic variant site. Since the maternal grandfather does not carry the chr16 duplication, the embryo is wild type. This result and all other clinical applications of Haploseek using grandparent references (summarized in Table S2) were validated by polymerase chain reaction (PCR)-based PGT-M. Note that paternal grandparents were not genotyped, and hence the paternal haplotype of the embryo is equally likely to be grandpaternal or grandmaternal (marginal probability equals 0.5 for the entire paternal haplotype and therefore the paternal haplotype prediction should be ignored).