Genetic analysis of 103 candidate genes for coronary artery disease and associated phenotypes in a founder population reveals a new association between endothelin-1 and high-density lipoprotein cholesterol

K45R variant of squalene synthase increases total cholesterol levels in two study samples from a French Canadian population

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 nonsynonymous variant, rs11549147:A>G (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=0.035) and non-high-density lipoprotein cholesterol (non-HDL-C) (P=0.01). These results were replicated in an independent sample of unrelated individuals (P=0.0008 for TC, P=0.004 for non-HDL-C). This SNP also influenced low-density lipoprotein cholesterol (P=0.042) and HDL-C (P=0.025) in the family-based sample, and triglycerides (TG) (P=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.

The value of HDL genetics

PURPOSE OF REVIEW

To review studies on hereditary disorders of high-density lipoprotein (HDL) metabolism and studies on HDL genetics in mice, which have both provided valuable insight into the pathways of this intriguing lipoprotein and moreover revealed targets to raise HDLc to reduce atherosclerosis.

RECENT FINDINGS

To date, as many as 11 genes are considered key players in the synthesis, maturation, conversion and/or catabolism of HDL. Five of these genes have been identified in humans, APOA1, LCAT, ABCA1, LIPC, and CETP, whereas the other six genes have been identified in mice, SCARB1, ABCG1, ATPB5, PLTP, LIPG and APOM. Genetic association studies are as yet the best line of evidence of the roles of the 'murine genes' in human HDL pathways. In addition to recent genetic association studies, a third section describes exciting news on six newly proposed HDL genes VNN1, GALNT2, MMAB/MVK, CTalpha, BMP-1 and SIRT1.

SUMMARY

This review provides a summary of the current literature on the genetics of HDL. New information from this research area may assist us in obtaining a better understanding of HDL biology and identifying novel pharmacological targets.

Association of methylenetetrahydrofolate reductase (MTHFR-677 and MTHFR-1298) genetic polymorphisms with occlusive artery disease and deep venous thrombosis in Macedonians

AIM

To analyze the association of methylenetetrahydrofolate reductase polymorphisms (MTHFR-677 and MTHFR-1298) with occlusive artery disease and deep venous thrombosis in Macedonians.

METHODS

We examined 83 healthy respondents, 76 patients with occlusive artery disease, and 67 patients with deep venous thrombosis. Blood samples were collected and DNA was isolated from peripheral blood leukocytes. Identification of MTHFR mutations was done with CVD StripAssay (ViennaLab, Labordiagnostika GmbH, Vienna, Austria) and the population genetics analysis package, PyPop, was used for the analysis. Pearson P values, crude odds ratio, and Wald's 95% confidence intervals were calculated.

RESULTS

The frequency of C alleles of MTHFR-677 was 0.575 in patients with deep venous thrombosis, 0.612 in patients with occlusive artery disease, and 0.645 in healthy participants. The frequency of T allele of MTHFR-677 was lower in healthy participants (0.355) than in patients with occlusive artery disease (0.388) and deep venous thrombosis (0.425). The frequency of A allele for MTHFR-1298 was 0.729 in healthy participants, 0.770 in patients with occlusive artery disease, and 0.746 in patients with deep venous thrombosis. The frequency of C allele of MTHFR-1298 was 0.271 in healthy participants, 0.230 in patients with occlusive artery disease, and 0.425 in patients with deep venous thrombosis. No association of MTHFR-677 and MTHFR-1289 polymorphisms with occlusive artery disease and deep venous thrombosis was found, except for the protective effect of MTHFR/CA:CC diplotype for occlusive artery disease.

CONCLUSION

We could not confirm a significant association of MTHFR-677 and MTHFR-1289 polymorphisms with occlusive artery disease or deep venous thrombosis in Macedonians, except for the protective effect of MTHFR/CA:CC diplotype against occlusive artery disease.

Newly identified loci that influence lipid concentrations and risk of coronary artery disease

To identify genetic variants influencing plasma lipid concentrations, we first used genotype imputation and meta-analysis to combine three genome-wide scans totaling 8,816 individuals and comprising 6,068 individuals specific to our study (1,874 individuals from the FUSION study of type 2 diabetes and 4,184 individuals from the SardiNIA study of aging-associated variables) and 2,758 individuals from the Diabetes Genetics Initiative, reported in a companion study in this issue. We subsequently examined promising signals in 11,569 additional individuals. Overall, we identify strongly associated variants in eleven loci previously implicated in lipid metabolism (ABCA1, the APOA5-APOA4-APOC3-APOA1 and APOE-APOC clusters, APOB, CETP, GCKR, LDLR, LPL, LIPC, LIPG and PCSK9) and also in several newly identified loci (near MVK-MMAB and GALNT2, with variants primarily associated with high-density lipoprotein (HDL) cholesterol; near SORT1, with variants primarily associated with low-density lipoprotein (LDL) cholesterol; near TRIB1, MLXIPL and ANGPTL3, with variants primarily associated with triglycerides; and a locus encompassing several genes near NCAN, with variants strongly associated with both triglycerides and LDL cholesterol). Notably, the 11 independent variants associated with increased LDL cholesterol concentrations in our study also showed increased frequency in a sample of coronary artery disease cases versus controls.

Personalized medicine: a reality within this decade

Personalized medicine is defined as individualized treatment based on the individual's genetic variants. Such treatment has the potential to enable pharmacogenetics, such as the prevention of 100,000 deaths per year in the USA because of adverse drug reactions or specify treatment in heart failure such at the beta 1 adrenergic receptor polymorphisms. It is claimed that coronary artery disease (CAD) is at least 50% because of genetic predisposition. Identification of the genes predisposing to CAD would greatly facilitate prevention, early treatment, and more specific therapies. The arrival of the multimillion single nucleotide polymorphism (SNP) array provides the high throughput genotyping required to perform genome-wide Association (GWA) studies. These studies require markers (SNPs) at intervals of 6,000 bp and sample size of several thousands. Platforms are available to genotype and process millions of genotypes per day. The GWA performed by the Ottawa Heart Genomic Study identified the first deoxyribonucleic acid region (9p21) predisposing to CAD after replication in six independent populations totaling 23,000. This was subsequently confirmed in several independent studies totally more than 45,000 individuals. The region confers a risk for CAD independent of known risk factors. 9p21 occurs in heterozygous form in 40 to 50% of Caucasians with increased risk of 15 to 20% and in homozygous form in 25% of Caucasians with increased risk of 40%. Identification of the genes predisposing to CAD is a prerequisite for personalized care of these patients. It is anticipated that most of the genes predisposing to CAD will be identified in the next 5 to 8 years. The 9p21, in addition to conferring increased risk, provides the bonus of being independent of known risk factors. Thus, 9p21 is likely to provide the impetus and nidus for a major research effort over the next few years. It has the potential to not only provide for early genetic screening but also as a target for novel therapy.

Correction of population stratification in large multi-ethnic association studies

BACKGROUND

The vast majority of genetic risk factors for complex diseases have, taken individually, a small effect on the end phenotype. Population-based association studies therefore need very large sample sizes to detect significant differences between affected and non-affected individuals. Including thousands of affected individuals in a study requires recruitment in numerous centers, possibly from different geographic regions. Unfortunately such a recruitment strategy is likely to complicate the study design and to generate concerns regarding population stratification.

METHODOLOGY/PRINCIPAL FINDINGS

We analyzed 9,751 individuals representing three main ethnic groups - Europeans, Arabs and South Asians - that had been enrolled from 154 centers involving 52 countries for a global case/control study of acute myocardial infarction. All individuals were genotyped at 103 candidate genes using 1,536 SNPs selected with a tagging strategy that captures most of the genetic diversity in different populations. We show that relying solely on self-reported ethnicity is not sufficient to exclude population stratification and we present additional methods to identify and correct for stratification.

CONCLUSIONS/SIGNIFICANCE

Our results highlight the importance of carefully addressing population stratification and of carefully "cleaning" the sample prior to analyses to obtain stronger signals of association and to avoid spurious results.

Polymorphisms in the endothelin-1 (EDN1) are associated with asthma in two populations

Endothelin-1 (EDN1) has been reported to be implicated in the pathophysiology of asthma. Literature results on the genetic association of EDN1 in asthma are inconsistent. Eleven single nucleotide polymorphisms in EDN1 were genotyped in 342 and 100 families from UK and Norway, respectively. Asthma, bronchial hyperreactivity (BHR) and atopic asthma phenotypes were analyzed for the family-based association. Five single nucleotide polymorphisms (SNPs) were associated with asthma (0.0017<or=P<or=0.0291), five with BHR (0.0026<or=P<or=0.0315) and three with atopic asthma (0.0016<or=P<or=0.041) in the UK population. Three SNPs were associated with asthma (0.0041<or=P<or=0.019), seven with BHR (0.0018<or=P<or=0.041) and two with atopic asthma (0.0123<or=P<or=0.0153) in the Norwegian population. A polymorphism (rs1800541) in the promoter region of EDN1 was replicated in the two populations. A nonsynonymous coding polymorphism (rs5370) resulting in a change of amino acid Asn to Lys at position 198 was also replicated. The results of haplotype-based association analyses strongly supported the ones of single SNP associations. This study demonstrates the significant evidence of association between polymorphisms in EDN1 and asthma.

Identification of a chromosome 8p locus for early-onset coronary heart disease in a French Canadian population

Susceptibility to coronary heart disease (CHD) has long been known to exhibit familial aggregation, with heritability estimated to be greater than 50%. The French Canadian population of the Saguenay-Lac Saint-Jean region of Quebec, Canada is descended from a founder population that settled this region 300-400 years ago and this may provide increased power to detect genes contributing to complex traits such as CHD. Probands with early-onset CHD, defined by angiographically determined coronary stenosis, and their relatives were recruited from this population (average sibship size of 6.4). Linkage analysis was performed following a genome-wide microsatellite marker scan on 42 families with 284 individuals. Nonparametric linkage (NPL) analysis provided suggestive evidence for a CHD susceptibility locus on chromosome 8 with an NPL score of 3.14 (P=0.001) at D8S1106. Linkage to this locus was verified by fine mapping in an enlarged sample of 50 families with 320 individuals. This analysis provided evidence of linkage at D8S552 (NPL score=3.53, P=0.0003), a marker that maps to the same location as D8S1106. Candidate genes in this region, including macrophage scavenger receptor 1, farnesyl-diphosphate farnesyltransferase 1, fibrinogen-like 1, and GATA-binding protein 4, were resequenced in all coding exons in both affected and unaffected individuals. Association studies with variants in these and five other genes did not identify a disease-associated mutation. In conclusion, a genome-wide scan and additional fine mapping provide evidence for a locus on chromosome 8 that contributes to CHD in a French Canadian population.

Apolipoprotein E and lipoprotein lipase gene polymorphisms interaction on the atherogenic combined expression of hypertriglyceridemia and hyperapobetalipoproteinemia phenotypes

The combination of hypertriglyceridemia (hyperTG) and hyperapobetalipoproteinemia (hyperapoB) is associated with an increased coronary artery disease (CAD) risk. Apolipoprotein (apo) E and lipoprotein lipase (LPL) genes are involved in the catabolism of triglycerides (TG)-rich apoB-containing lipoproteins (VLDL). Several apoE and LPL gene variants affecting CAD risk, plasma TG or apoB concentrations have an allelic frequency of >5% in the general population. This study examined the combined effect of frequent apoE and LPL gene polymorphisms on the expression of hyperTG and hyperapoB. ApoE (E2, E3, and E4) and LPL (D9N, N291S, G188E, and P207L) were genotyped and fasting lipid profiles were assessed among 1,441 French-Canadian subjects. Multivariate analyses were performed to estimate the relationship between apoE and LPL gene variants and the risk of hyperTG (TG>1.7 mmol/l) and hyperapoB (apoB>0.9 g/l). Compared to apoE3 carriers, the apoE4 allele significantly increased the risk of expressing the "hyperTG/hyperapoB" phenotype [odds ratio (OR)=1.95; p=0.014]. This risk was significantly exacerbated (OR=4.69; p=0.017) by the presence of frequent deleterious LPL gene variants in this population. The apoE2 allele was negatively associated with hyperTG/hyperapoB (OR=0.49; p=0.002) in the absence of a deleterious LPL gene variant. These results suggest that epistasis is a phenomenon to consider while assessing the CAD risk associated with gene variants or the effect of frequent alleles on high-risk lipid profiles.