As stated above, the total number of individuals genotyped for each SNP varied because of the costs associated with genotyping individuals ascertained after the initial genome screen. Six hundred and twenty-six individuals were genotyped for all 10 DOCK3 SNPs, whereas the number of individuals genotyped for the 79 SLC9A9 SNPs varied (minimum=422 individuals and maximum=626 individuals). SAS 9.1 (SAS Institute, Cary, North Carolina, USA) was used to calculate the MAF using all individuals and, because of our limited sample size, a MAF less than 10% was used as a further exclusion criterion for SNPs selected for analysis. All SNPs were tested for significant deviations from HWE using exact tests by the Genetic Data Analysis Program (Zaykin et al., 1995). HWE was calculated separately for affected and unaffected individuals. Specifically, the first affected and first unaffected individual from each family were used for the analysis.
