An unknown fraction of the genome participates in the metabolism of sterols and vitamin D, two classes of lipids with diverse physiological and pathophysiological roles. Here, we used mass spectrometry to measure the abundance of >60 sterol and vitamin D derivatives in 3,230 serum samples from a well-phenotyped patient population. Twenty-nine of these lipids were detected in a majority of samples at levels that varied over thousands of fold in different individuals. Pairwise correlations between sterol and vitamin D levels revealed evidence for shared metabolic pathways, additional substrates for known enzymes, and transcriptional regulatory networks. Serum levels of multiple sterols and vitamin D metabolites varied significantly by sex, ethnicity, and age. A genome-wide association study identified 16 loci that were associated with levels of 19 sterols and 25-hydroxylated derivatives of vitamin D (P < 10
−7). Resequencing, expression analysis, and biochemical experiments focused on one such locus (CYP39A1), revealed multiple loss-of-function alleles with additive effects on serum levels of the oxysterol, 24S-hydroxycholesterol, a substrate of the encoded enzyme. Body mass index, serum lipid levels, and hematocrit were strong phenotypic correlates of interindividual variation in multiple sterols and vitamin D metabolites. We conclude that correlating population-based analytical measurements with genotype and phenotype provides productive insight into human intermediary metabolism.human genetics | genotype-phenotype correlation L ipids are an important component of serum and there play essential roles in energy metabolism, signaling, and transport. A recent survey revealed an unexpectedly large complexity in the human serum lipidome, which was found to be composed of hundreds of different molecular species in each major lipid class (1). For example, cholesterol and other sterols were detected in concentrations ranging from milligrams per milliliter to nanograms per milliliter, and over 200 different triglyceride species were found. A pooled plasma sample derived from multiple individuals was analyzed in this study; thus, whether the observed complexity reflected functional diversity in the roles played by different lipids, was environmentally driven or was genetically determined could not be ascertained.To address these issues with respect to sterols and vitamin D metabolites (secosteroids), we developed analytical methods to measure more than 60 different types of these lipids in small volumes (<200 μL) of human serum (2). An initial analysis of 200 human serum samples showed that 22 of the >60 compounds were routinely detected and began to define the ranges and distributions of these analytes in the population (2).The steady-state concentration of a given lipid is determined by rates of formation and degradation, the kinetics of movement into and out of cells and tissues, the levels of lipoproteins that transport sterols through the bloodstream, their availability in the diet, and the physiological state of the...