Figure 2
Validation of SHaploseek with clinical PGT embryo biopsies. We evaluated the accuracy of SHaploseek in 31 embryo biopsies from 12 PGT families. (a) In the four families with a child reference individual, we show the proportion of the 200,484 array SNVs with high-confidence haplotype prediction in non-ROC sites in both Haploseek and SHaploseek (box plots). We show results for both the unsampled sequencing data for the parents and reference child (see Table 1 for the sequencing depth of each individual), as well as for lower depths obtained by down-sampling. For each sequencing depth, the box plot represents 20 data points (two for each of the ten embryos), each showing the result of genome-wide prediction of either the maternal or paternal haplotype of one embryo. (b) Box plots for the haplotype phasing accuracy (measured as the concordance with Haploseek) at SNVs with high-confidence prediction in both Haploseek and SHaploseek, for different sequencing depth categories. (c, d) Same as (a) and (b), respectively, for the eight families with grandparental reference individuals. For each sequencing depth, the box plot represents 24 data points, one for each of the 21 embryos, except the three embryos from Family 31 (Table 1; Table S1) who contributed two data points each, because grandparents from both parents were sequenced.
