In order to systematically compare polygenic prediction methods across a wide range of settings, we conducted a number of secondary simulation studies: (1) sampling SNP effect sizes using a point-normal model with heritability fixed at 0.2 or 0.8; (2) sampling SNP effect sizes using a point-t model with heavy tails (a mixture of a point mass at zero and a Student’s t-distribution with 4 degrees of freedom); (3) sampling SNP effect sizes using a point-gamma model (a mixture of a point mass at zero and a gamma distribution with the shape parameter set to 2), which produces an effect size distribution that is asymmetric about zero and positively skewed with the right tail being long and thin and the left tail being short and fat; (4) using the combined UK Biobank validation and testing data sets (N = 6000) as an in-sample LD reference panel in the point-normal simulations. For each setting and training sample size considered (10,000, 20,000, 50,000, and 100,000), and the simulation was repeated 20 times.
