Case:control association testing Logistic regression was used to test for association between SNPs and disease, treating disease status as the response and expected genotype counts from imputation or allele counts from direct genotyping as predictor. Testing was performed using the likelihood ratio statistic. When testing for association using the imputed genotypes, controls were matched to cases based on the informativeness of the imputed genotypes, such that for each case controls of matching informativeness were chosen. Failing to match cases and controls will lead to a highly inflated genomic control factor, and in some cases may lead to spurious false-positive findings.
