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Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data

MOTIVATION
The use of human genome discoveries and other established factors to build an accurate risk prediction model is an essential step towards precision medicine. While multi-layer high-dimensional omics data provide unprecedented data resources for prediction studies, their corresponding analytical methods are much less developed.


RESULTS
We present a multi-kernel linear mixed model with adaptive lasso (MKpLMM), a predictive modeling framework that extends the standard linear mixed models widely used in genomic risk prediction, for multi-omics data analysis. MKpLMM can capture not only the predictive effects from each layer of omics data but also their interactions via using multiple kernel functions. It adopts a data-driven approach to select predictive regions as well as predictive layers of omics data, and achieves robust selection performance. Through extensive simulation studies, the analyses of PET-imaging outcomes from the Alzheimer's Disease Neuroimaging Initiative study, and the analyses of 64 drug responses, we demonstrate that MKpLMM consistently outperforms competing methods in phenotype prediction.


AVAILABILITY
The R-package is available at https://github.com/YaluWen/OmicPred.


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.