It is therefore critical to understand the true effect of MAF on the likelihood of obtaining a false-positive result (e.g., very low p-value) under the null hypothesis of no true association. We hypothesize that MAF affects the likelihood of a specific variant achieving significance thresholds under the null hypothesis. If MAF does affect the probability of achieving a specific significance, this would result in non-comparability of p-values (or test statistics) between SNPs with different MAFs. To address this issue we utilized the Genetic Analysis Workshop 16 simulated data set and performed extensive permutations.
