Because all cohorts used the same genotyping chip, the genotyped marker panel was analysed, but in the Australian and Scottish cohorts imputed genotypes were used where cases and SNPs were missing within samples. This ensured that the full panel of markers was available in each cohort. The HapMap phase II CEU data (NCBI build 36 (UCSC hg18)) was used as the reference sample for imputation using MACH software. In the Australian and Scottish cohorts, SNPs with low imputation (r2 < .30) were excluded, and in all cohorts, SNPs with low minor allele frequency (MAF < .01) were excluded.
