are applied that compare the frequencies of SNP alleles between diseased and non-diseased individuals in a study cohort. Typically, only a very small fraction of SNPs are plausibly related to disease risk. Odds ratios (ORs) may be reported, to display the association strengths for SNPs selected for reporting. A significant SNP-disease risk association may be declared following a single stage study, in which case corresponding reliable OR estimates and confidence intervals (CIs) are needed to assess the magnitude of association and to decide upon next research steps. These could, for example, involve an intensive study of close-by SNPs or neighboring genes. Such a declaration may also take place following an early, intermediate, or late stage of a multistage design. Even the design of the next stage of a multistage design could be influenced by OR estimation, for example, if the sample size calculation for a subsequent stage is based on an overestimated OR, replication stages are likely to be underpowered and more likely to fail [Zhong and Prentice, 2008].
