A phenomics-based strategy identifies loci on APOC1, BRAP, and PLCG1 associated with metabolic syndrome phenotype domains

Despite evidence of the clustering of metabolic syndrome components, current approaches for identifying unifying genetic mechanisms typically evaluate clinical categories that do not provide adequate etiological information. Here, we used data from 19,486 European American and 6,287 African American Candidate Gene Association Resource Consortium participants to identify loci associated with the clustering of metabolic phenotypes. Six phenotype domains (atherogenic dyslipidemia, vascular dysfunction, vascular inflammation, pro-thrombotic state, central obesity, and elevated plasma glucose) encompassing 19 quantitative traits were examined. Principal components analysis was used to reduce the dimension of each domain such that >55% of the trait variance was represented within each domain. We then applied a statistically efficient and computational feasible multivariate approach that related eight principal components from the six domains to 250,000 imputed SNPs using an additive genetic model and including demographic covariates. In European Americans, we identified 606 genome-wide significant SNPs representing 19 loci. Many of these loci were associated with only one trait domain, were consistent with results in African Americans, and overlapped with published findings, for instance central obesity and FTO. However, our approach, which is applicable to any set of interval scale traits that is heritable and exhibits evidence of phenotypic clustering, identified three new loci in or near APOC1, BRAP, and PLCG1, which were associated with multiple phenotype domains. These pleiotropic loci may help characterize metabolic dysregulation and identify targets for intervention.
Author Summary The metabolic syndrome represents a clustering of metabolic phenotypes (e.g. elevated blood pressure, cholesterol levels, and plasma glucose, as well as abdominal obesity) and is associated with an increased risk of atherosclerosis and type 2 diabetes. Although multiple genes influencing the specific metabolic syndrome components have been reported, few studies have evaluated the genetic underpinnings of the syndrome as a whole. Here, we describe an approach to evaluate multiple clustered traits, which allows us to test whether common genetic variants influence the co-occurrence of one or more metabolic phenotypes. By examining approximately 20,000 European American and 6,200 African American participants from five studies, we show that three regions on chromosomes 12, 19, and 20 are associated with multiple metabolic phenotypes. These genetic variants are highly intriguing candidates that may increase our understanding of the biologic basis of the clustering of metabolic phenotypes and help identify targets for early intervention.