Tiffin N, Okpechi I, Perez-Iratxeta C, Andrade-Navarro MA, Ramesar R. Prioritization of candidate disease genes for metabolic syndrome by computational analysis of its defining phenotypes. Physiol Genomics 35: 55-64, 2008. First published July 8, 2008 doi:10.1152/physiolgenomics.90247.2008.-There is a rapid increase in the world-wide burden of disease attributed to metabolic syndrome, as defined by co-occurrence of an array of phenotypes including abdominal obesity, dysglycemia, hypertriglyceridemia, low levels of high density lipoprotein cholesterol, and hypertension. Familial studies clearly indicate a genetic component to the disease and many linkage studies have identified a large number of linked loci. No disease-causing genes, however, have been conclusively identified, most likely because this is a multigenic disease for which effects of many causative genes may be small and combined with environmental effects. To assist empirical identification of metabolic syndrome associated genes, we present here a novel computational approach to prioritize candidate genes. We have used linkage studies and the clinical and population-specific presentation of the disease to select a final candidate gene list of 19 most likely disease-causing genes. These are predominantly involved in chylomicron processing, transmembrane receptor activity, and signal transduction pathways. We propose here that information about the clinical presentation of a complex trait can be used to effectively inform computational prioritization of disease-causing genes for that trait. candidate genes; complex disease METABOLIC SYNDROME IS AN INCREASINGLY common complex disease that is defined by co-occurrence of an array of metabolic phenotypes. These phenotypes have been classified in multiple ways (Ref. 2 and reviewed in Ref. 49) to provide a list of simple clinical markers that can diagnose individuals with the syndrome. The guidelines of the 2001 National Cholesterol Education Program-Adult Treatment Panel III are in common use and characterize metabolic syndrome as the co-occurrence of any three of the five following phenotypes: abdominal obesity, dysglycemia including insulin resistance/hyperinsulinemia, increased triglycerides, decreased high-density lipoprotein (HDL) cholesterol, hypertension (2,17,22,44). Currently, ϳ25% of North Americans are thought to be affected by metabolic syndrome (15). Obesity is the prevalent phenotype and is rising as a global epidemic (1) that is likely to result in a concurrent increase in metabolic syndrome incidence (42, 54) and related morbidity and mortality.Familial studies clearly indicate a heritable component to metabolic syndrome (reviewed in Ref. 49); however, multiple linkage studies have generated a large number of metabolic syndrome-associated loci (Supplementary Data File S1) 1 without subsequent identification of etiological genes. To date, existing approaches have in general failed to identify genes underlying complex diseases or traits such as metabolic syndrome, as they often present with ...