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Shared effect modeling reveals that a fraction of autoimmune disease associations are consistent with eQTLs in three immune cell types

By Sung Chun, Alexandra Casparino, Nikolaos Patsopoulos, Damien C. Croteau-Chonka, Benjamin A. Raby, Philip L De Jager, Shamil R. Sunyaev, Chris Cotsapas

Posted 12 May 2016
bioRxiv DOI: 10.1101/053165 (published DOI: 10.1038/ng.3795)

The majority of autoimmune disease risk effects identified by genome-wide association studies (GWAS) localize to open chromatin with gene regulatory activity. GWAS loci are also enriched for expression quantitative trait loci (eQTLs), suggesting that most disease risk variants exert their pathological effects by altering gene expression. However, because causal variants are difficult to identify and cis-eQTLs occur frequently, it remains challenging to translate this bulk observation into specific instances of a disease risk variant driving changes to gene regulation. Here, we use a novel joint likelihood framework with higher resolution than previous methods to identify loci where disease risk and an eQTL are driven by a single, shared genetic effect as opposed to distinct effects in close proximity. We find that 22 approximately 25% of autoimmune disease loci harbor an eQTL driven by the same genetic effect, but the majority of loci do not. Thus, we uncover a fraction of gene regulatory changes as strong mechanistic hypotheses for disease risk.

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