The choice of ancestry PC covariates to include in each super-population GWAS was determined by stepwise linear regression for the specific phenotype being analyzed. Non-ancestry covariates (sex and age) were forced to be kept in the model while ancestry covariates were kept if they were retained in the best fitting model as measured by AIC. This approach, of only keeping PCs significant to a specific ancestry and phenotype, increases parsimony and minimizes risk of over-fitting. We have shown that there is no evidence of genomic inflation when this parsimonious approach is taken.
