We repeated the simulations with correlation between SNP effects on incidence and prognosis. For the 5000 SNPs with effects on both, we simulated their effects from a bivariate normal distribution with correlation 0.5, and then from a distribution with correlation 0.9. These led respectively to genome-wide genetic correlations between incidence and prognosis of 0.25 and 0.45. We repeated the simulations with the equivalent negative correlations.
