We restricted the number of SNPs for follow-up analysis in stage 2 to be values that approximate numbers that would typically be considered given today’s currently available commercial genotyping platforms. Namely, we considered follow-up platforms of size 100, 1,500, 7,500, and 16,500 SNPs. For each follow-up genotyping platform, we found the optimal proportion of cases, πcases, to be genotyped in stage 1 that optimized the power of the two-stage design. Specifically, we used the “optimize” function in R to search for the maximum power in the continuous space of πcases. This method combines the golden section search and successive parabolic interpolation algorithms.
