We used Merlin (39) to perform the linkage scan using a nonparametric allele-sharing model. Allele frequencies were estimated by counting all genotyped individuals. The Kong and Cox linear allele-sharing model (43) was used to estimate the lod score. To minimize the inflation of linkage signals caused by marker-marker LD, we grouped SNPs by LD into clusters using the Merlin “--rsq” option (44). Analyses were repeated with r2 thresholds of 0.05, 0.2, and 0.3 to evaluate the robustness of the linkage results. We assessed the thresholds for autosomal genomewide suggestive and significant linkages, and the autosomal genomewide empirical significance of an observed lod score, by 1000 computer simulations, as described previously (28).
