Fig. 2.

Schema of the analysis pipeline for PPS haplotype discovery, refinement, and validation. BEAGLE phased haplotypes for the chromosome 2 region (36–47 Mb) were excised and analyzed with GERMLINE to detect matching pairwise IBD segments. Overlapping segments that matched across the population were clustered, and then the mean phenotype of cluster members was assessed. One cluster containing a 1.3 Mb haplotype strongly associated to high PPS levels. Careful comparison of haplotypes in that cluster revealed a unique ≈526-kb shared segment carried by 52 individuals. The CRANEFOOT software was used to visualize the ≈526-kb haplotype segregating in three closely related kindreds.