Genotyping, imputation and quality control has been previously reported.37 Genotyping of 3414 individuals from 598 families was performed at the Center for Inherited Disease Research using the Illumina 2.5M array (Illlumina, San Diego, CA, USA). SNPs with a genotyping rate <98% or that violated Hardy–Weinberg equilibrium (P<10−6) or with minor allele frequency (MAF) <3% were excluded from the analyses. Mendelian inconsistencies were removed,38 after which data were imputed to 1000 genomes (hg19) using SHAPEIT39 and IMPUTE2.40 Following imputation, genotype probabilities ⩾ 0.90 were changed to genotypes. Mendelian errors in the imputed SNPs were reviewed and resolved as described in Wetherill et al.37 All SNPs with an imputation information score <0.30 or MAF <0.03 were excluded from subsequent association analysis.40
