Multikernel linear mixed model with adaptive lasso for complex phenotype prediction

Linear mixed models (LMMs) and their extensions have been widely used for high‐dimensional genomic data analyses. While LMMs hold great promise for risk prediction research, the high dimensionality of the data and different effect sizes of genomic regions bring great analytical and computational challenges. In this work, we present a multikernel linear mixed model with adaptive lasso (KLMM‐AL) to predict phenotypes using high‐dimensional genomic data. We develop two algorithms for estimating parameters from our model and also establish the asymptotic properties of LMM with adaptive lasso when only one dependent observation is available. The proposed KLMM‐AL can account for heterogeneous effect sizes from different genomic regions, capture both additive and nonadditive genetic effects, and adaptively and efficiently select predictive genomic regions and their corresponding effects. Through simulation studies, we demonstrate that KLMM‐AL outperforms most of existing methods. Moreover, KLMM‐AL achieves high sensitivity and specificity of selecting predictive genomic regions. KLMM‐AL is further illustrated by an application to the sequencing dataset obtained from the Alzheimer's disease neuroimaging initiative.