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

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

Publication date: Nov 06, 2019

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.

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.

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

Supplementary data are available at Bioinformatics online.

Li, J., Lu, Q., and Wen, Y. Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data. 05722. 2019 Bioinformatics.

Concepts Keywords
Alzheimer Imaging
Genome Genomics
Kernel Genome
Lasso Simulation
Neuroimaging
Omics
PET Imaging
Phenotype
Precision Medicine
Predictive Modeling
Simulation

Semantics

Type Source Name
disease MESH Multi
gene UNIPROT PTPN5
drug DRUGBANK Coenzyme M

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