We present a novel semiparametric method for quantitative trait loci (QTL) mapping in experimental crosses. Conventional genetic mapping methods typically assume parametric models with Gaussian errors and obtain parameter estimates through maximum likelihood estimation. In contrast with univariate regression and interval mapping methods, our model requires fewer assumptions and also accommodates various machine learning algorithms. Estimation is performed with targeted maximum likelihood learning methods. We demonstrate our semiparametric targeted learning approach in a simulation study and a well-studied barley dataset.
Wang, Hui; Zhang, Zhongyang; Rose, Sherri; and van der Laan, Mark J., "A Novel Targeted Learning Method for Quantitative Trait Loci Mapping" (July 2014). U.C. Berkeley Division of Biostatistics Working Paper Series. Working Paper 328.