To address the multiple testing problem, a minimal number of haplotype-tagging SNPs present on the Illumina chip were selected for analysis using LDSelect (DOCK3: n=10, r2>0.8; SLC9A9: n=79, r2>0.64) (Carlson et al., 2004). A subset of these tagging SNPs were also selected as TaqMan assays (Applied Biosystems) to type in the more recently ascertained study participants to increase sample size, and ultimately power in the data set. All DOCK3 SNPs (n=10) and a subset of the SLC9A9 SNPs (n=15) were included in the expanded screen. SLC9A9 SNPs were selected if they tagged at least one additional SNP or were positioned close to an intron/exon border. Quality control for TaqMan genotype data was as follows: (i) two Centre d’Etude du Polymorphism Humain controls and blinded duplicates were used for every 94 samples and required to match 100%, and (ii) pedigree inconsistencies were identified using PEDCHECK (O’Connell and Weeks, 1998); families were excluded from subsequent analyses for markers if the inconsistencies could not be resolved.
