We considered various combinations of sample size, risk allele frequency (RAF), cumulative disease incidence (proportion of individuals who experienced the disease outcome over the period of follow-up), sampling fraction (for the case-cohort design) and HRs between a single hypothetical SNP and disease, assuming a multiplicative allelic effects model. Sample size was varied over 5000, 10 000 and 25 000 for the cohort study design, and the initial cohort was set to 40 000 for the case-cohort study design. Sampling fractions of 5, 10 and 15% were used in the case-cohort design to generate the subcohort. The additional cases from the initial cohort were then added to create the case-cohort data set. Since the differences between the logistic and Cox model are small for rare diseases,3, 4, 5 we selected cumulative disease incidences of 5, 10 and 15% to reflect common diseases (e.g. CHD and type II diabetes) often seen over a 20-year period for the age group studied in the simulations. The RAFs examined were 0.05, 0.10, 0.25, 0.50, 0.75, 0.90 and 0.95. The strength of the association was varied
