related to the test for association (allele frequencies in cases and controls or in the transmitted and untransmitted alleles in trios, association p-value, odds ratios with standard errors). Reference alleles were assigned as the allele coded 0 in the HapMap release 21 phased consensus haplotypes during genotype imputation in MACH. The QC checks performed on summary file data included consistency in reference allele and strand orientation (see Supplementary Figs. 13−15 online), and imputation quality (see Supplementary Fig. 16 online). SNPs with imputation quality scores below a threshold were removed from the analysis (Rsq < 0.3 or < 0.5 for the Barbados study). QQ plots were visually inspected to compare the distribution of association p-values for genotyped and imputed markers separately for each cohort.
