Association analysis of population-based quantitative trait data: an assessment of ANOVA

The classical analysis of variance (ANOVA) compares the means of different groups under the assumption that the variances within each of the groups are equal. However, for genetic studies of complex disorders, it is not reasonable to assume that variance of a quantitative trait within each genotype at the trait locus will be equal. Thus, the use of ANOVA may lead to misleading association inferences. In this article, we perform a simulation-based study to assess the rate of false positives and the power of ANOVA under various probability distributions of the quantitative trait and different genetic parameters such as allele frequencies and coefficient of linkage disequilibrium.