A comparison between different designs and tests to detect QTLs in association studies

The availability of different designs and tests to detect QTLs in associati on studies raises questions about the relative merits of the various approa ches. We therefore compared the power of quantitative versus categorical te sts, the power in population samples versus samples with subjects selected on the basis of their trait scores, and the power of tests that control for population stratification using parental genotypes versus tests that do no t control for stratification. In case-control samples the power of quantita tive tests was clearly better than that of categorical tests especially whe n the control group was a population sample. In samples of genotyped trios of cases and their parents, the power of quantitative tests was much poorer . Compared to population samples, selection always improved the power in ca se-control samples where the controls were sampled from the opposite end of the continuum and frequently deteriorated the power when the controls were a population sample, Mainly because subjects with at least one heterozygou s parent need to be selected, the use of tests that control for stratificat ion resulted in a substantial decrease of power. In the final section our p ower calculations were integrated into a more general discussion about opti mizing designs in association studies.