HUMAN MUTATION 29(5), 689^694, 2008 RESEARCH ARTICLE K45R Variant of Squalene Synthase Increases Total Cholesterol Levels in Two Study Samples From a French Canadian Population Ron Do, 1 Guillaume Pare ´, 1,2 Alexandre Montpetit, 2 Thomas J. Hudson, 1–3 Daniel Gaudet, 4,5 and James C. Engert 1,3Ã 1 Department of Human Genetics, McGill University, Montreal, Quebec, Canada; 2 McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, Quebec, Canada; 3 Department of Medicine, McGill University, Montreal, Quebec, Canada; 4 Department of Medicine, University of Montreal, Chicoutimi, Quebec, Canada; 5 Lipid, Diabetes and Atherosclerosis Research Group, Montreal University Community Genomics Research Center, Chicoutimi Hospital, Chicoutimi, Quebec, Canada Communicated by Michael Dean Squalene synthase is an important component of the cholesterol biosynthetic pathway, and inhibitors of this enzyme have been shown to lower plasma cholesterol levels. Previously, we sequenced the squalene synthase gene, FDFT1 (farnesyl-diphosphate farnesyltransferase), and identified several SNPs, including a nonsynon- ymous variant, rs11549147:A4G (K45R). To examine the possible association of K45R with plasma lipid traits, we tested 887 individuals from 149 families from the founder population of Saguenay-Lac St. Jean (SLSJ), Quebec. K45R was associated with increased total cholesterol (TC) (P 5 0.035) and non-high-density lipoprotein cholesterol (non-HDL-C) (P 5 0.01). These results were replicated in an independent sample of unrelated individuals (P 5 0.0008 for TC, P 5 0.004 for non-HDL-C). This SNP also influenced low-density lipoprotein cholesterol (P 5 0.042) and HDL-C (P 5 0.025) in the family-based sample, and triglycerides (TG) (P 5 0.007) in the unrelated subjects. The lysine (K) in codon 45 is conserved across 11 mammals and lies in a potential exonic splicing enhancer (ESE) site. These results suggest that this coding variant in the squalene synthase gene influences plasma cholesterol levels, possibly by affecting the intracellular production of cholesterol. Hum Mutat 29(5), 689–694, 2008. r r 2008 Wiley-Liss, Inc. KEY WORDS: coronary artery disease; cholesterol; association study; FDFT1; squalene synthase INTRODUCTION Coronary heart disease (CHD) is the single leading cause of death in the Western world and is projected to be the number one cause worldwide by 2020 [Murray and Lopez, 1997]. CHD is influenced by a number of risk factors, which in turn, are believed to be dependent on a combination of genetic [reviewed by Watkins and Farrall, 2006] and/or environmental factors (such as diet [Ginsberg et al., 1998], alcohol [Savolainen and Kesaniemi, 1995], and exercise [Gielen et al., 2001]). Classic risk factors for CHD include elevated plasma levels of low-density lipoprotein cholesterol (LDL-C) and triglycerides (TG) [reviewed by Gensini et al., 1998] and decreased HDL cholesterol (HDL-C) [Gordon et al., 1989]. A key pharmacological intervention for reducing plasma LDL-C levels is statin therapy [reviewed by Blumenthal, 2000]. Because statins may have side effects in some individuals [Kashani et al., 2006] and are not effective in others [Davidson, 2007], alternatives are currently being developed. Due to its position in the same metabolic pathway, squalene synthase is an attractive target. Squalene synthase controls an important aspect of cholesterol metabolism by catalyzing the conversion of two molecules of farnesyl diphosphate (FPP) to squalene in the first committed step of the sterol branch of cholesterol biosynthesis [McKenzie et al., 1992; Stamellos et al., 1993]. Squalene synthase inhibitors have been shown to lower plasma cholesterol levels in vitro [Tavridou et al., 2006] and in vivo [Nishimoto et al., 2003] and are currently undergoing phase 3 clinical trials [Burnett, 2006; Perez et al., 2006; Piper et al., 2006]. The squalene synthase gene (farnesyl-diphosphate farnesyltrans- ferase, FDFT1; MIM] 184420) is ubiquitously expressed in humans, with high expression found in the testis and skeletal muscle, but low expression in the liver [Summers et al., 1993; Tansey and Shechter, 2001]. Studies in mice have shown that the homozygous knockout of squalene synthase results in embryonic lethality, while the Published online 18 March 2008 in Wiley InterScience (www.inters- cience.wiley.com). DOI 10.1002/humu.20702 Received 31 July 2007; accepted revised manuscript 15 November 2007. Grant sponsor: Canadian Institutes of Health Research; Genome Quebec/GenomeCanada; BurroughsWellcome Fund;Grant sponsor: ECOGENE-21 Project, Center for Applied Health Research (CAHR) Program; Grant number: CAR43283. Current address for ThomasJ. Hudson: Ontario Institute for Cancer Research, MaRS Centre, SouthTower,101 College Street, Suite 500, Toronto, Ontario, Canada M5G 1L7. Ã Correspondence to: James C. Engert, Ph.D., Departments of Med- icine & Human Genetics, McGill University, Royal Victoria Hospital, H7.30, 687 Pine Avenue West, Montreal, Quebec, Canada H3A 1A1. E-mail: jamie.engert@mcgill.ca r r 2008 WILEY-LISS, INC.