This choice of gene analysis model is motivated by a balance of statistical and practical concerns. This multiple regression model ensures that LD between SNPs is fully accounted for. It also offers the flexibility to accommodate additional covariates and interaction terms as needed without changing the model. At the same time, since the F-test has a known asymptotic sampling distribution the gene p-values take very little time to compute, making the gene analysis much faster than permutation-based alternatives.
