Joint modeling of eQTLs and parent-of-origin effects using an orthogonal framework with RNA-seq data

Extensive studies have been conducted on the analysis of genome function, especially on the expression quantitative trait loci (eQTL). These studies offered promising results for characterization of the functional sequencing variation and understanding of the basic processes of gene regulation. Parent of origin effect (POE) is an important epigenetic phenomenon describing that the expression of certain genes depends on their allelic parent-of-origin and it is known to play important roles in human complex diseases. However, traditional eQTL mapping approaches do not allow for the detection of imprinting, or they focus on modeling the additive genetic effect thereby ignoring the estimation of the dominance genetic effect. In this study, we proposed a statistical framework to test the additive and dominance genetic effects of the candidate eQTLs along with detection of the POE with a functional model and an orthogonal model for RNA-seq data. We demonstrated the desirable power and preserved Type I errors of the methods in most scenarios, especially the orthogonal model with un-biased estimation of the genetic effects and over-dispersion of the RNA-seq data. The application to a HapMap project trio dataset validated existing imprinting genes and discovered two novel imprinting genes with potential dominance genetic effect and RB1 and IGF1R genes. This study provides new insights into the next generation statistical modeling of eQTL mapping for better understanding of the genetic architecture underlying the mechanisms of gene expression regulation.