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Mendelian Randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

By Eleonora Porcu, Sina Rüeger, Kaido Lepik, eQTLGen Consortium, Federico A. Santoni, A Reymond, Zoltán Kutalik

Posted 25 Jul 2018
bioRxiv DOI: 10.1101/377267 (published DOI: 10.1038/s41467-019-10936-0)

Genome-wide association studies (GWAS) identified thousands of variants associated with complex traits, but their biological interpretation often remains unclear. Most of these variants overlap with expression QTLs (eQTLs), indicating their potential involvement in the regulation of gene expression. Here, we propose an advanced transcriptome-wide summary statistics-based Mendelian Randomization approach (called TWMR) that uses multiple SNPs jointly as instruments and multiple gene expression traits as exposures, simultaneously. When applied to 43 human phenotypes it uncovered 2,369 genes whose blood expression is putatively associated with at least one phenotype resulting in 3,913 gene-trait associations; of note, 36% of them had no genome-wide significant SNP nearby in previous GWAS analysis. Using independent association summary statistics (UKBiobank), we confirmed that the majority of these loci were missed by conventional GWAS due to power issues. Noteworthy among these novel links is educational attainment-associated BSCL2, known to carry mutations leading to a mendelian form of encephalopathy. We similarly unraveled novel pleiotropic causal effects suggestive of mechanistic connections, e.g. the shared genetic effects of GSDMB in rheumatoid arthritis, ulcerative colitis and Crohn's disease. Our advanced Mendelian Randomization unlocks hidden value from published GWAS through higher power in detecting associations. It better accounts for pleiotropy and unravels new biological mechanisms underlying complex and clinical traits.

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