Schrödinger's Cat in Simulations in Genome-wide Association Studies

Simulations are essential components for testing methods or assumptions in genome wide association studies (GWAS). We show through theory and examples that markers can be both causal and noncausal simultaneously, resulting in a paradox, had simulation not being run properly. We developed a software (ParaPheSim, a paradoxical phenotype simulator) that allows users to create different traits whose genetic correlation is exactly 1 and yet they have no genetic overlap.