Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial datasets

In a clinical trial for anti-IL-6 in patients with systemic lupus erythematosus we measured interferon (IFN) status, anti-IL-6 drug exposure and genome-wide gene expression at three time points (379 samples from 157 individuals). <br>We mapped eQTLs by applying a random intercept linear mixed model using the first 25 principal components of gene expression and the first 5 principal components of genotyping as covariates. We used subject as a random effect. <br>We defined cis eQTL as the SNP within 250kb upstream of the GENCODE transcription start site of the gene or 250kb downstream of the transcription end site.<br><br>Expression_levels.txt: Gene expression data log2(cpm+1)<br>eQTL_summary_statistics.txt: Cis eQTL summary statistics for all gene SNP pairs tested