A cautionary note about combining case–control and family-based samples is worthwhile. While mCLR controls for ancestry, it cannot control for hidden biases inherent in the designs. For example, family-based studies require relatively intact families [37], which could impose conditions quite different from those inherent in a case–control collection. Combining the data by mCLR has advantages for a genetic study only when case–control and family-based samples are not strongly differentiated for risk factors correlated with the genetics of risk.
