Joint eQTL mapping and Inference of Gene Regulatory Network Improves Power of Detecting both cis- and trans-eQTLs

MotivationGenetic variations of expression quantitative trait loci (eQTLs) play a critical role in influencing complex traits and diseases development. Two main factors that affect the statistical power of detecting eQTLs are: 1) relatively small size of samples available, and 2) heavy burden of multiple testing due to a very large number of variants to be tested. The later issue is particularly severe when one tries to identify trans-eQTLs that are far away from the genes they influence. If one can exploit co-expressed genes jointly in eQTL-mapping, effective sample size can be increased. Furthermore, using the structure of the gene regulatory network (GRN) may help to identify trans-eQTLs without increasing multiple testing burden. ResultsIn this paper, we employ the structure equation model (SEM) to model both GRN and effect of eQTLs on gene expression, and then develop a novel algorithm, named sparse SEM, for eQTL mapping (SSEMQ) to conduct joint eQTL mapping and GRN inference. The SEM can exploit co-expressed genes jointly in eQTL mapping and also use GRN to determine trans-eQTLs. Computer simulations demonstrate that our SSEMQ significantly outperforms eight existing eQTL mapping methods. SSEMQ is further employed to analyze a real dataset of human breast tissues, yielding a number of cis- and trans-eQTLs. AvailabilityR package ssemQr is available on https://github.com/Ivis4ml/ssemQr.git.