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Diabetes-associated metabolites may aid the identification of new risk variants for type 2 diabetes. Using targeted metabolomics within a subsample of the German EPIC-Potsdam study (n = 2500), we tested previously published SNPs for their association with diabetes-associated metabolites and conducted an additional exploratory analysis using data from the exome chip including replication within 2,692 individuals from the German KORA F4 study. We identified a total of 16 loci associated with diabetes-related metabolite traits, including one novel association between rs499974 ( MOGAT2 ) and a diacyl-phosphatidylcholine ratio (PC aa C40:5/PC aa C38:5). Gene-based tests on all exome chip variants revealed associations between  GFRAL  and PC aa C42:1/PC aa C42:0,  BIN1  and SM (OH) C22:2/SM C18:0 and  TFRC  and SM (OH) C22:2/SM C16:1). Selecting variants for gene-based tests based on functional annotation identified one additional association between  OR51Q1  and hexoses. Among single genetic variants consistently associated with diabetes-related metabolites, two (rs174550 ( FADS1 ), rs3204953 ( REV3L )) were significantly associated with type 2 diabetes in large-scale meta-analysis for type 2 diabetes. In conclusion, we identified a novel metabolite locus in single variant analyses and four genes within gene-based tests and confirmed two previously known mGWAS loci which might be relevant for the risk of type 2 diabetes.

Genetic variants including markers from the exome chip and metabolite traits of type 2 diabetes