Aggregative trans-eQTL analysis detects trait-specific target gene sets in whole blood

Abstract

Large scale genetic association studies have identified many trait-associated variants and understanding the role of these variants in downstream regulation of gene-expressions can uncover important mediating biological mechanisms. In this study, we propose Aggregative tRans assoCiation to detect pHenotype specIfic gEne-sets (ARCHIE), as a method to establish links between sets of known genetic variants associated with a trait and sets of co-regulated gene-expressions through trans associations. ARCHIE employs sparse canonical correlation analysis based on summary statistics from trans-eQTL mapping and genotype and expression correlation matrices constructed from external data sources. A resampling based procedure is then used to test for significant trait-specific trans-association patterns in the background of highly polygenic regulation of gene-expression. Simulation studies show that compared to standard trans-eQTL analysis, ARCHIE is better suited to identify “core”-like genes through which effects of many other genes may be mediated and which can explain disease specific patterns of genetic associations. By applying ARCHIE to available trans-eQTL summary statistics reported by the eQTLGen consortium, we identify 71 gene networks which have significant evidence of trans-association with groups of known genetic variants across 29 complex traits. Around half (50.7%) of the selected genes do not have any strong trans-associations and could not have been detected by standard trans-eQTL mapping. We provide further evidence for causal basis of the target genes through a series of follow-up analyses. These results show ARCHIE is a powerful tool for identifying sets of genes whose trans regulation may be related to specific complex traits. The method has potential for broader applications for identification of networks of various types of molecular traits which mediates complex traits genetic associations.