test [40] and the “set-based analysis” in PLINK [41] use phenotype permutation to naturally correct for biases introduced by LD and gene size; however, these tools require raw genotype data and are computationally demanding, making them better suited for studies of candidate pathways with relatively few genes. Notably, recently-developed methods that accept p-values as input and account for LD through simulations [42, 43] or genotype permutation [32] are computationally efficient and may represent new paradigms as their power is honed and evaluated.
