Hybrid bootstrap for mapping quantitative trait loci

The hybrid bootstrap uses resampling ideas to extend the duality approach to interval estimation for a parameter of interest when there are nuisance parameters. The confidence region constructed by the hybrid bootstrap may perform much better than the parametric bootstrap region in situations where the data provide substantial information about the nuisance parameter, but limited information about the parameter of interest. We apply this method to estimate the location of quantitative trait loci (QTL) in interval mapping model. The conditional distribution of quantitative traits, given flanked genetic marker genotypes is often assumed to be the mixture model of two phenotype distributions. The mixing proportions in the model represent the recombination rate between a genetic marker and quantitative trait loci and provides information about the unknown location of the QTL. Since recombination events are unlikely, we will have less information about the location of the QTL than other parameters. This observation makes a hybrid approach to interval estimation for QTL appealing, especially since the necessary distribution theory, which is often a challenge for mixture models, can be handled by bootstrap simulation.