Abstract
Metabolite quantitative traits carry great promise for epidemiological studies, and their genetic background has been addressed using Genome-Wide Association Studies (GWAS). Thus far, the role of less common variants has not been exhaustively studied. Here, we set out a GWAS for metabolite quantitative traits in serum, followed by exome sequence analysis to zoom in on putative causal variants in the associated genes. 1H Nuclear Magnetic Resonance (1H-NMR) spectroscopy experiments yielded successful quantification of 42 unique metabolites in 2,482 individuals from The Erasmus Rucphen Family (ERF) study. Heritability of metabolites were estimated by SOLAR. GWAS was performed by linear mixed models, using HapMap imputations. Based on physical vicinity and pathway analyses, candidate genes were screened for coding region variation using exome sequence data. Heritability estimates for metabolites ranged between 10% and 52%. GWAS replicated three known loci in the metabolome wide significance: CPS1 with glycine (P-value = 1.27×10−32), PRODH with proline (P-value = 1.11×10−19), SLC16A9 with carnitine level (P-value = 4.81×10−14) and uncovered a novel association between DMGDH and dimethyl-glycine (P-value = 1.65×10−19) level. In addition, we found three novel, suggestively significant loci: TNP1 with pyruvate (P-value = 1.26×10−8), KCNJ16 with 3-hydroxybutyrate (P-value = 1.65×10−8) and 2p12 locus with valine (P-value = 3.49×10−8). Exome sequence analysis identified potentially causal coding and regulatory variants located in the genes CPS1, KCNJ2 and PRODH, and revealed allelic heterogeneity for CPS1 and PRODH. Combined GWAS and exome analyses of metabolites detected by high-resolution 1H-NMR is a robust approach to uncover metabolite quantitative trait loci (mQTL), and the likely causative variants in these loci. It is anticipated that insight in the genetics of intermediate phenotypes will provide additional insight into the genetics of complex traits.
Highlights
Intermediary metabolites in bodily fluids seem a direct reflection of our genetic constituency in interaction with the environment, which includes eating habits, life style and other external factors
Heritability estimates and genome-wide association studies (GWAS) results The study was conducted in the Erasmus Rucphen Family (ERF) population using fasting serum samples
Regional plots of the 8 loci are shown in S2 Fig. Four of these loci were significant after correction for the number of metabolites analyzed (P-value,1.1061029) and three of these were previously shown to associate with the same metabolites: rs715 located in the 39UTR of the carbamoyl-phosphate synthase 1 (CPS1) gene associated with glycine level (P-value = 1.27610232) [8], rs2540641 35 Kb distant from proline dehydrogenase 1 (PRODH) gene (P-value = 1.11610219) associated with proline levels [9] and rs1171614 in the 5’UTR of SLC16A9 associated with carnitine level (P-value = 4.81610214) [9,10,11]
Summary
Intermediary metabolites in bodily fluids seem a direct reflection of our genetic constituency in interaction with the environment, which includes eating habits, life style and other external factors. Genome-wide screens enriched for common intergenic variants may miss causal genetic variations directly changing the protein sequence. To investigate this further, we zoomed into regions of interest and tested whether the association signals obtained in the first stage were direct, or whether they represent causal variations, which were not captured in the initial panel. We zoomed into regions of interest and tested whether the association signals obtained in the first stage were direct, or whether they represent causal variations, which were not captured in the initial panel These subsequent tests showed that protein coding and regulatory variations are involved in metabolite levels. Our novel loci are of interest for further research to investigate the causal relation to for instance type 2 diabetes and cardiovascular disease
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