Genetics of the human metabolome, what is next?

• Metabolite-GWAS provide insight in the genetics of biochemical conversions.
• Pathway analysis using prior knowledge improves interpretation of mGWAS data.
• Systems biology will further interpretation of mGWAS data and disease associations.

Increases in throughput and decreases in costs have facilitated large scale metabolomics studies, the simultaneous measurement of large numbers of biochemical components in biological samples. Initial large scale studies focused on biomarker discovery for disease or disease progression and helped to understand biochemical pathways underlying disease. The first population-based studies that combined metabolomics and genome wide association studies (mGWAS) have increased our understanding of the (genetic) regulation of biochemical conversions. Measurements of metabolites as intermediate phenotypes are a potentially very powerful approach to uncover how genetic variation affects disease susceptibility and progression. However, we still face many hurdles in the interpretation of mGWAS data. Due to the composite nature of many metabolites, single enzymes may affect the levels of multiple metabolites and, conversely, levels of single metabolites may be affected by multiple enzymes. Here, we will provide a global review of the current status of mGWAS. We will specifically discuss the application of prior biological knowledge present in databases to the interpretation of mGWAS results and discuss the potential of mathematical models. As the technology continuously improves to detect metabolites and to measure genetic variation, it is clear that comprehensive systems biology based approaches are required to further our insight in the association between genes, metabolites and disease. This article is part of a Special Issue entitled: From Genome to Function.