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CCmed: cross-condition mediation analysis for identifying robust trans-eQTLs and assessing their effects on human traits

By Fan Yang, Kevin J. Gleason, Jiebiao Wang, The GTEx consortium, Jubao Duan, Xin He, Brandon L. Pierce, Lin S. Chen

Posted 13 Oct 2019
bioRxiv DOI: 10.1101/803106

Trans-eQTLs collectively explain a substantial proportion of expression variation, yet are challenging to detect and replicate since their effects are individually weak. Many trans-effects are mediated by cis-gene expression and some of those effects are shared across tissue types/conditions. To detect robust cis-mediated trans-associations at the gene-level and for specific single nucleotide polymorphisms (SNPs), we proposed two Cross-Condition Mediation methods -- CCmed-gene and CCmed-GWAS, respectively. We analyzed data from 13 brain tissue types from the Genotype-Tissue Expression (GTEx) project, and identified trios with cis-eQTLs of a cis-gene having associations with a trans-gene, many of which show evidence of replication in other datasets. By applying CCmed-GWAS, we identified trans-genes associated with known schizophrenia susceptibility loci. We further conducted validation analyses assessing the schizophrenia-risk-associations of the identified trans-genes, by harnessing GWAS summary statistics from the Psychiatric Genomics Consortium and multitissue eQTL statistics from GTEx.

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