The array-genotyped SNP data were acquired with the following Illumina (San Diego, CA, USA) arrays: Yale-Penn-1 by the HumanOmni1-Quad v1.0; Yale-Penn-2 by the HumanCore Exome BeadChip; and SAGE by the Human 1M. IMPUTEv2 software40 was used to impute additional SNPs for each array. The 1000 Genomes June 2011 (http://www.1000genomes.org/) release was used as the reference for imputation. The 1000 Genomes reference included phased haplotypes for 1094 individuals of diverse ancestries, including samples of European descent, Asian descent, African descent, and an admixed American sample.41 SNPs with imputed information scores < 0.80 and minor allele frequencies < 2.5 percent (for both imputed and directly genotyped SNPs) were excluded from the GWAS analysis. To evaluate our GWAS finding of association between NicW and PCDH-α, -β and –γ gene cluster variation, the laboratory subjects were genotyped for rs31746 with a 2 μl TaqMan allelic discrimination assay (Applied Biosystems, Foster City, CA, USA). We considered rs31746 to be the “best” SNP to select for follow-up studies in the laboratory sample because in contrast to the other two SNPS, rs31746 was directly genotyped by all
