We find that for most realistic settings of GWA studies, such as modest genetic effects, large sample sizes and high average imputation accuracies, the strategy of regressing the phenotype on the genetic dosages provides adequate performance. In fact, for these settings, small gains from using the full mixture models are rendered negligible by the increased model complexity and associated “cost” of estimating additional parameters. However, when the effect size is large, and imputation accuracy sufficiently poor, we demonstrate an increase in power when utilizing all available information in the posterior distribution in the form of mixture models.
