We performed power calculations for a range of study designs and disease models. Power is described for the frequency of the risk allele in the general population (the frequency of the risk allele in cases and study controls for different values of K are provided in the table footnotes). Not surprisingly, our results showed that including free genotype data from public controls increases statistical power over studies that do not include these data (Table 1). The single-stage study with both public and study controls noticeably outperformed the replication-based two-stage study using the same samples. Power for the proposed replication-based two-stage design was typically greater than the power of the one-stage design based only on study controls. Overall, the same general patterns of results were observed when varying GRR and frequency of the disease susceptibility allele (Supplementary Figure 1), when analyzing the genotype data using a general (co-dominant) 2-df inheritance model (Supplementary Table 2), and when considering dominant or recessive genetic inheritance models (Supplementary Tables 3 and 4, respectively).
