Predicting the genetic component of gene expression using gene regulatory networks

Abstract

Gene expression prediction plays a vital role in transcriptome-wide association studies (TWAS), which seek to establish associations between tissue gene expression and complex traits. Traditional models rely on genetic variants in close genomic proximity to the gene of interest to predict the genetic component of gene expression. In this study, we propose a novel approach incorporating distal genetic variants acting through gene regulatory networks (GRNs) into gene expression prediction models, in line with the omnigenic model of complex trait inheritance. Using causal and coexpression GRNs reconstructed from genomic and transcriptomic data and modeling the data as a Bayesian network jointly over genetic variants and genes, inference of gene expression from observed genotypic data is achieved through a two-step process. Initially, the expression level of each gene in the network is predicted using its local genetic variants. The residuals, calculated as the differences between the observed and predicted expression levels, are then modeled using the genotype information of parent and/or grandparent nodes in the GRN. The final predicted expression level of the gene is obtained by summing the predictions from the local variants model and the residual model, effectively incorporating both local and distal genetic influences. Using various regularized regression techniques for parameter estimation, we found that GRN-based gene expression prediction outperformed the traditional local-variant approach on simulated data from the DREAM5 Systems Genetics Challenge and real data from the Geuvadis study and an eQTL mapping study in yeast. This study provides important insights into the challenge of gene expression prediction for TWAS. It reaffirms the importance of GRNs for understanding the genetic effects on gene expression and complex traits more generally.