Even within samples of the same ethnicity, there is likely to be discrepancies between the MAFs of a reference sample and the sample that GWAS summary statistics were generated from. However, some summary statistics may not include allele frequencies, and using the same reference panel for standardization across phenotypes has the desirable property of maintaining consistency across summary statistics. To examine the effect of this decision, the betas for 30,000 randomly selected SNPs for the mood phenotype from UKB were standardized using either sample or reference panel MAF. The correlation between the betas was .982, and a linear regression of betas standardized using reference panel MAF predicting standardization using sample MAF revealed near perfect correspondence (slope = 1.044, intercept = −6.54e-6; Supplemental Figure 29).
