A cautionary note on design implications when the primary analysis is a stratified analysis of a binary endpoint

When the primary analysis is a stratified analysis of a binary endpoint, the commonly used CMH procedure could produce results that are quite different from those obtained by ignoring the stratification factor altogether. This means that when designing a trial with a primary endpoint that is binary, it is important that one keep in mind how the data will be analyzed. Only when design and analysis are considered in tandem will the study possess the desired properties. The discussion in this paper is illustrated by a hypothetical example, which nevertheless resembles the findings from a confirmatory trial involving the evaluation of a biologic for severe sepsis.