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Ekblom K, Marklund SL, Jansson JH, Osterman P, Hallmans G, Weinehall L, Hultdin J. Plasma bilirubin and UGT1A1*28 are not protective factors against first-time myocardial infarction in a prospective, nested case-referent setting. ACTA ACUST UNITED AC 2010; 3:340-7. [PMID: 20562445 DOI: 10.1161/circgenetics.109.861773] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Bilirubin, an effective antioxidant, shows a large variation in levels between individuals and has been positively associated with reduced cardiovascular disease risk. A major reason for the variability is a common promoter polymorphism, UGT1A1*28, which reduces the transcription of the enzyme that conjugates bilirubin, UDP-glucuronosyltransferase 1A1. The aim of the study was to evaluate a possible protective effect of plasma bilirubin and the UGT1A1*28 polymorphism against myocardial infarction in a prospective case-referent setting. METHODS AND RESULTS Subjects (n=618) with a first-ever myocardial infarction (median event age, 60.5 years; median lag time, 3.5 years) and 1184 matched referents were studied. Plasma bilirubin was lower in cases versus referents. Despite a strong gene-dosage effect on bilirubin levels in both cases and referents, the UGT1A1*28 polymorphism did not influence the risk of myocardial infarction. Among multiple other variables, serum iron showed one of the strongest associations with bilirubin levels. CONCLUSIONS We found no evidence for a protective effect of the UGT1A1*28 polymorphism against myocardial infarction and consequently neither for bilirubin. The lower bilirubin levels in cases might be caused by decreased production, increased degradation, or increased elimination.
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Affiliation(s)
- Kim Ekblom
- Clinical Chemistry, Department of Medical Biosciences, Umeå University, Umeå Sweden.
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Yu JT, Yu Y, Zhang W, Wu ZC, Li Y, Zhang N, Tan L. Single nucleotide polymorphism rs1333049 on chromosome 9p21.3 is associated with Alzheimer's disease in Han Chinese. Clin Chim Acta 2010; 411:1204-7. [PMID: 20427016 DOI: 10.1016/j.cca.2010.04.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2010] [Revised: 04/19/2010] [Accepted: 04/20/2010] [Indexed: 12/27/2022]
Abstract
BACKGROUND Chromosome 9p21.3 polymorphism has been shown to affect susceptibility to Alzheimer's disease (AD) in Caucasians, while there are no studies on the association of chromosome 9p21.3 polymorphism with the risk of AD in Asians. METHODS The study investigated 266 sporadic late-onset AD (LOAD) and 323 healthy controls matched for sex and age in a Han Chinese population. The common genetic variant (tagged by rs1333049, G/C) on chromosome 9p21.3 was genotyped using MALDI-TOF mass spectrometry. RESULTS Patients with LOAD had higher frequencies of C allele (56.0% vs. 49.2%) compared with controls [odds ratio (OR) 1.31, 95% confidence interval (CI) 1.04-1.65, P=0.02]. After stratification by APOE epsilon4-carrying status, the C allele of rs1333049 was only significantly associated with LOAD in non-APOE epsilon4 allele carriers (OR 1.47, 95% CI 1.09-1.98, P<0.01). rs1333049 polymorphism was still strongly associated with LOAD [dominant model: OR 1.83, 95% CI 1.17-2.86, P<0.01; additive model: OR 1.38, 95% CI 1.05-1.80, P=0.02] after adjusting for the APOE epsilon4 carrier status and other vascular risk factors. CONCLUSIONS This study demonstrates an association of rs1333049 polymorphism locus on chromosome 9p21.3 with risk for LOAD in Han Chinese.
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Affiliation(s)
- Jin-Tai Yu
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, Shandong Province 266071, PR China
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Saleheen D, Alexander M, Rasheed A, Wormser D, Soranzo N, Hammond N, Butterworth A, Zaidi M, Haycock P, Bumpstead S, Potter S, Blackburn H, Gray E, Di Angelantonio E, Kaptoge S, Shah N, Samuel M, Janjua A, Sheikh N, Haider SR, Murtaza M, Ahmad U, Hakeem A, Memon MA, Mallick NH, Azhar M, Samad A, Rasheed SZ, Gardezi AR, Memon NA, Ghaffar A, Memon FUR, Zaman KS, Kundi A, Yaqoob Z, Cheema LA, Qamar N, Faruqui A, Jooma R, Niazi JH, Hussain M, Kumar K, Saleem A, Kumar K, Daood MS, Memon F, Gul AA, Abbas S, Zafar J, Shahid F, Memon Z, Bhatti SM, Kayani W, Ali SS, Fahim M, Ishaq M, Frossard P, Deloukas P, Danesh J. Association of the 9p21.3 locus with risk of first-ever myocardial infarction in Pakistanis: case-control study in South Asia and updated meta-analysis of Europeans. Arterioscler Thromb Vasc Biol 2010; 30:1467-73. [PMID: 20395598 DOI: 10.1161/atvbaha.109.197210] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To examine variants at the 9p21 locus in a case-control study of acute myocardial infarction (MI) in Pakistanis and to perform an updated meta-analysis of published studies in people of European ancestry. METHODS AND RESULTS A total of 1851 patients with first-ever confirmed MI and 1903 controls were genotyped for 89 tagging single-nucleotide polymorphisms at locus 9p21, including the lead variant (rs1333049) identified by the Wellcome Trust Case Control Consortium. Minor allele frequencies and extent of linkage disequilibrium observed in Pakistanis were broadly similar to those seen in Europeans. In the Pakistani study, 6 variants were associated with MI (P<10(-2)) in the initial sample set, and in an additional 741 cases and 674 controls in whom further genotyping was performed for these variants. For Pakistanis, the odds ratio for MI was 1.13 (95% CI, 1.05 to 1.22; P=2 x 10(-3)) for each copy of the C allele at rs1333049. In comparison, a meta-analysis of studies in Europeans yielded an odds ratio of 1.31 (95% CI, 1.26 to 1.37) for the same variant (P=1 x 10(-3) for heterogeneity). Meta-analyses of 23 variants, in up to 38,250 cases and 84,820 controls generally yielded higher values in Europeans than in Pakistanis. CONCLUSIONS To our knowledge, this study provides the first demonstration that variants at the 9p21 locus are significantly associated with MI risk in Pakistanis. However, association signals at this locus were weaker in Pakistanis than those in European studies.
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Anderson CD, Biffi A, Rost NS, Cortellini L, Furie KL, Rosand J. Chromosome 9p21 in ischemic stroke: population structure and meta-analysis. Stroke 2010; 41:1123-31. [PMID: 20395606 DOI: 10.1161/strokeaha.110.580589] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND AND PURPOSE Sequence variants on chromosome 9p21.3 are implicated in coronary artery disease and myocardial infarction, but studies in ischemic stroke have produced inconsistent results. We investigated whether these conflicting findings were due to false-positive studies confounded by population stratification or false-negative studies that failed to account for effects specific to certain stroke subtypes. METHODS After assessing for population stratification at 9p21.3 using genomewide data, we meta-analyzed 8 ischemic stroke studies. This analysis focused on 2 single nucleotide polymorphisms, rs1537378 and rs10757278, because these variants are in strong linkage disequilibrium with most single nucleotide polymorphisms analyzed in prior studies of the region. RESULTS Principal component analysis of the genomewide data showed no evidence of population stratification at that locus. Meta-analysis confirmed that both rs1537378 and rs10757278 are risk factors for ischemic stroke (ORs, 1.09 [P=0.0014] and 1.11 [P=0.001], respectively). Subtype analysis revealed a substantial increase in the effect of each single nucleotide polymorphism for risk of large artery stroke, achieving an effect size similar to that seen in coronary artery disease/myocardial infarction. CONCLUSIONS Variants on 9p21.3 are associated with ischemic stroke, and restriction of analysis to large artery stroke increases effect size toward that observed in prior association studies of coronary artery disease/myocardial infarction. Previous inconsistent findings are best explained by this subtype specificity rather than any unmeasured confounding by population stratification.
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Affiliation(s)
- Christopher D Anderson
- Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, CPZN-6818, Boston, MA 02114, USA
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Ma L, Yang J, Runesha HB, Tanaka T, Ferrucci L, Bandinelli S, Da Y. Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham heart study data. BMC MEDICAL GENETICS 2010; 11:55. [PMID: 20370913 PMCID: PMC2867786 DOI: 10.1186/1471-2350-11-55] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 04/06/2010] [Indexed: 11/22/2022]
Abstract
Background Cholesterol concentrations in blood are related to cardiovascular diseases. Recent genome-wide association studies (GWAS) of cholesterol levels identified a number of single-locus effects on total cholesterol (TC) and high-density lipoprotein cholesterol (HDL-C) levels. Here, we report single-locus and epistasis SNP effects on TC and HDL-C using the Framingham Heart Study (FHS) data. Results Single-locus effects and pairwise epistasis effects of 432,096 SNP markers were tested for their significance on log-transformed TC and HDL-C levels. Twenty nine additive SNP effects reached single-locus genome-wide significance (p < 7.2 × 10-8) and no dominance effect reached genome-wide significance. Two new gene regions were detected, the RAB3GAP1-R3HDM1-LCT-MCM6 region of chr02 for TC identified by six new SNPs, and the OSBPL8-ZDHHC17 region (chr12) for HDL-C identified by one new SNP. The remaining 22 single-locus SNP effects confirmed previously reported genes or gene regions. For TC, three SNPs identified two gene regions that were tightly linked with previously reported genes associated with TC, including rs599839 that was 10 bases downstream PSRC1 and 3.498 kb downstream CELSR2, rs4970834 in CELSR2, and rs4245791 in ABCG8 that slightly overlapped with ABCG5. For HDL-C, LPL was confirmed by 12 SNPs 8-45 kb downstream, CETP by two SNPs 0.5-11 kb upstream, and the LIPG-ACAA2 region by five SNPs inside this region. Two epistasis effects on TC and thirteen epistasis effects on HDL-C reached the significance of "suggestive linkage". The most significant epistasis effect (p = 5.72 × 10-13) was close to reaching "significant linkage" and was a dominance × dominance effect of HDL-C between LMBRD1 (chr06) and the LRIG3 region (chr12), and this pair of gene regions had six other D × D effects with "suggestive linkage". Conclusions Genome-wide association analysis of the FHS data detected two new gene regions with genome-wide significance, detected epistatic SNP effects on TC and HDL-C with the significance of suggestive linkage in seven pairs of gene regions, and confirmed some previously reported gene regions associated with TC and HDL-C.
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Affiliation(s)
- Li Ma
- Department of Animal Science, University of Minnesota, USA
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Winkelmann BR, von Holt K, Unverdorben M. Smoking and atherosclerotic cardiovascular disease: Part IV: Genetic markers associated with smoking. Biomark Med 2010; 4:321-33. [DOI: 10.2217/bmm.10.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Genes influence smoking behavior, affect the metabolism of nicotine and specific chemicals produced during combustion, and enhance (or diminish) pathomechanistic pathways associated with the atherogenic potential of smoking, including oxidative stress, its inflammatory burden or procoagulant potential. Genome-wide association studies have revolutionized the search for new functional genetic markers with ever increasing marker density and the precision in identifying new genetic loci without the need for prior knowledge of functional pathways. Nevertheless, the statistical challenge remains to identify the few true positives, the need for replication of findings and the tedious work of identifying functional genetic variants and their mode of action. Genetic variation within a gene or in areas of the genetic code that control the expression of such a gene is far from being understood. Major advances include the detection of large-scale copy-number variants in the human genome and the demonstration of the decisive role of ‘miRNA’ in controlling gene expression. The role of the genomic methylation pattern in controlling the transcription of the underlying genetic sequence and its role in interacting with environmental influences have yet to be explored in depth. Although candidate genes and their genetic variants have been associated with atherosclerosis and cigarette smoking, a major breakthrough has still to be made.
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Affiliation(s)
- Bernhard R Winkelmann
- ClinPhenomics GmbH, 67125 Dannstadt, Germany
- Cardiology Group Frankfurt-Sachsenhausen, 60594 Frankfurt, Germany
| | | | - Martin Unverdorben
- Clinical Research Institute, Center for Cardiovascular Diseases, Heinz-Meise-Strasse 100, 36199 Rotenburg an der Fulda, Germany
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Junyent M, Tucker KL, Shen J, Lee YC, Smith CE, Mattei J, Lai CQ, Parnell LD, Ordovas JM. A composite scoring of genotypes discriminates coronary heart disease risk beyond conventional risk factors in the Boston Puerto Rican Health Study. Nutr Metab Cardiovasc Dis 2010; 20:157-164. [PMID: 19501493 PMCID: PMC4031647 DOI: 10.1016/j.numecd.2009.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 03/10/2009] [Accepted: 03/13/2009] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIMS Using a genetic predisposition score (GPS), integrating the additive associations of a set of single nucleotide polymorphisms (SNPs) with CHD, we examined the consequences of the joint presence of a high GPS and conventional risk factors (CRFs). METHODS AND RESULTS We studied 11 SNPs at eight loci in 197 participants with prior CHD and 524 CHD-free subjects from the Boston Puerto Rican Health Study. Each polymorphism contributed 1 unit (high-risk allele homozygous), 0.5 units (heterozygous) and 0 units (low-risk allele homozygous) to the GPS. Odds ratio (OR) of CHD for those at high risk because of GPS (>5) and simultaneous presence of CRFs were estimated, compared with subjects at low risk, for both measurements. The mean score was higher in participants with prior CHD than those CHD-free (P=0.015), and the OR for CHD with a GPS>5 was 2.90 (P<0.001).The joint presence of a high GPS and each CRF was associated with higher risk of CHD. Compared to participants with high GPS, those with low GPS (<or=5) were protected against CHD even if they were smokers (OR=0.44), heavy drinkers (OR=0.43), displayed low physical activity (OR=0.35), had hypertension (OR=0.52) or hyperlipidemia (OR=0.34) (P values ranging from 0.004 to 0.023). CONCLUSION A simple genetic score of 11 polymorphisms may identify those subjects at increased risk of CHD beyond conventional risk factors.
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Affiliation(s)
- M Junyent
- The Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging at Tufts University School of Medicine, Boston, MA 02111, USA.
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Johansen CT, Hegele RA. Predictive genetic testing for coronary artery disease. Crit Rev Clin Lab Sci 2010; 46:343-60. [PMID: 19958218 DOI: 10.3109/07388550903422075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Coronary artery disease (CAD) is an inflammatory-metabolic disease in which atherosclerotic plaques cause stenosis of the coronary arteries, leading to acute clinical complications such as myocardial infarction. Since CAD is a multifactorial, polygenic disease with a substantial environmental component, individual risk prediction and stratification is often difficult. Recent technological advances have resulted in substantial progress elucidating the impact of common genetic variation on CAD progression. The discovery of common genetic variants, including the chromosome 9p21.3 locus as the strongest and most highly replicated independent genetic CAD risk factor, has stimulated interest in genetic testing for CAD-associated risk variants. The ultimate goal of genotype-based CAD risk prediction is to improve upon the discrimination and stratification offered by conventional risk factors alone. Genotype-based CAD risk prediction may eventually have clinical utility, but not without intrinsic complexities. Are genotype variables superior predictors of risk compared to a family history of CAD? Is a 10-year risk prediction window ambitious enough for the predictive power of genotype data? This review will outline the current state of genotype-based CAD risk prediction and highlight challenging issues integral to the successful implementation of genetic testing for CAD.
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Bentley P, Peck G, Smeeth L, Whittaker J, Sharma P. Causal relationship of susceptibility genes to ischemic stroke: comparison to ischemic heart disease and biochemical determinants. PLoS One 2010; 5:e9136. [PMID: 20161734 PMCID: PMC2817726 DOI: 10.1371/journal.pone.0009136] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 01/04/2010] [Indexed: 01/02/2023] Open
Abstract
Interrelationships between genetic and biochemical factors underlying ischemic stroke and ischemic heart disease are poorly understood. We: 1) undertook the most comprehensive meta-analysis of genetic polymorphisms in ischemic stroke to date; 2) compared genetic determinants of ischemic stroke with those of ischemic heart disease, and 3) compared effect sizes of gene-stroke associations with those predicted from independent biochemical data using a mendelian randomization strategy. Electronic databases were searched up to January 2009. We identified: 1) 187 ischemic stroke studies (37,481 cases; 95,322 controls) interrogating 43 polymorphisms in 29 genes; 2) 13 meta-analyses testing equivalent polymorphisms in ischemic heart disease; and 3) for the top five gene-stroke associations, 146 studies (65,703 subjects) describing equivalent gene-biochemical relationships, and 28 studies (46,928 subjects) describing biochemical-stroke relationships. Meta-analyses demonstrated positive associations with ischemic stroke for factor V Leiden Gln506, ACE I/D, MTHFR C677T, prothrombin G20210A, PAI-1 5G allele and glycoprotein IIIa Leu33Pro polymorphisms (ORs: 1.11 – 1.60). Most genetic associations show congruent levels of risk comparing ischemic stroke with ischemic heart disease, but three genes—glycoprotein IIIa, PAI-1 and angiotensinogen—show significant dissociations. The magnitudes of stroke risk observed for factor V Leiden, ACE, MTHFR and prothrombin, but not PAI-1, polymorphisms, are consistent with risks associated with equivalent changes in activated protein C resistance, ACE activity, homocysteine, prothrombin, and PAI-1 levels, respectively. Our results demonstrate causal relationships for four of the most robust genes associated with stroke while also showing that PAI-1 4G/5G polymorphism influences cardiovascular risk via a mechanism not simply related to plasma levels of PAI-1 (or tPA) alone.
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Affiliation(s)
- Paul Bentley
- Imperial College Cerebrovascular Research Unit, Clinical Neurosciences, Charing Cross Hospital, Imperial College London, London, United Kingdom.
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60
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Ye S, Willeit J, Xiao Q, Motterle A, Laxton RC, Oberhollenzer F, Kiechl S, Xu Q. Single nucleotide polymorphism on chromosome 9p21 and endothelial progenitor cells in a general population cohort. Atherosclerosis 2010; 208:451-5. [DOI: 10.1016/j.atherosclerosis.2009.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 07/23/2009] [Accepted: 08/01/2009] [Indexed: 12/23/2022]
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Emanuele E, Fontana JM, Minoretti P, Geroldi D. Preliminary Evidence of a Genetic Association Between Chromosome 9p21.3 and Human Longevity. Rejuvenation Res 2010; 13:23-6. [DOI: 10.1089/rej.2009.0970] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Enzo Emanuele
- Department of Health Sciences, University of Pavia, Pavia, Italy
| | - Jacopo M. Fontana
- Department of Physiology, Section of Human Physiology, University of Pavia, Pavia, Italy
| | | | - Diego Geroldi
- Department of Internal Medicine and Medical Therapeutics, University of Pavia, Pavia, Italy
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Krug T, Manso H, Gouveia L, Sobral J, Xavier JM, Albergaria I, Gaspar G, Correia M, Viana-Baptista M, Simões RM, Pinto AN, Taipa R, Ferreira C, Fontes JR, Silva MR, Gabriel JP, Matos I, Lopes G, Ferro JM, Vicente AM, Oliveira SA. Kalirin: a novel genetic risk factor for ischemic stroke. Hum Genet 2010; 127:513-23. [PMID: 20107840 DOI: 10.1007/s00439-010-0790-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 01/17/2010] [Indexed: 11/27/2022]
Abstract
Cerebrovascular and cardiovascular diseases are the leading causes of death and disability worldwide. They are complex disorders resulting from the interplay of genetic and environmental factors, and may share several susceptibility genes. Several recent studies have implicated variants of the Kalirin (KALRN) gene with susceptibility to cardiovascular and metabolic phenotypes, but no studies have yet been performed in stroke patients. KALRN is involved, among others, in the inhibition of inducible nitric oxide synthase, in the regulation of ischemic signal transduction, and in neuronal morphogenesis, plasticity, and stability. The goal of the present study was to determine whether SNPs in the KALRN region on 3q13, which includes the Ropporin gene (ROPN1), predispose to ischemic stroke (IS) in a cohort of Portuguese patients and controls. We genotyped 34 tagging SNPs in the KALRN and ROPN1 chromosomal region on 565 IS patients and 517 unrelated controls, and performed genotype imputation for 405 markers on chromosome 3. We tested the single-marker association of these SNPs with IS. One SNP (rs4499545) in the ROPN1-KALRN intergenic region and two SNPs in KALRN (rs17286604 and rs11712619) showed significant (P < 0.05) allelic and genotypic (unadjusted and adjusted for hypertension, diabetes, and ever smoking) association with IS risk. Thirty-two imputed SNPs also showed an association at P < 0.05, and actual genotyping of three of these polymorphisms (rs7620580, rs6438833, and rs11712039) validated their association. Furthermore, rs11712039 was associated with IS (0.001 < P < 0.01) in a recent well-powered genomewide association study (Ikram et al. 2009). These studies suggest that variants in the KALRN gene region constitute risk factors for stroke and that KALRN may represent a common risk factor for vascular diseases.
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Affiliation(s)
- Tiago Krug
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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Ronald J, Rajagopalan R, Ranchalis JE, Marshall JK, Hatsukami TS, Heagerty PJ, Jarvik GP. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Lipids Health Dis 2009; 8:52. [PMID: 19951432 PMCID: PMC2794863 DOI: 10.1186/1476-511x-8-52] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 12/01/2009] [Indexed: 11/11/2022] Open
Abstract
Background Genome-wide association studies have identified numerous single nucleotide polymorphisms (SNPs) affecting high density lipoprotein (HDL) or low density lipoprotein (LDL) cholesterol levels; these SNPs may contribute to the genetic basis of vascular diseases. Results We assessed the impact of 34 SNPs at 23 loci on dyslipidemia, key lipid sub-phenotypes, and severe carotid artery disease (CAAD) in a case-control cohort. The effects of these SNPs on HDL and LDL were consistent with those previously reported, and we provide unbiased estimates of the percent variance in HDL (3.9%) and LDL (3.3%) explained by genetic risk scores. We assessed the effects of these SNPs on HDL subfractions, apolipoprotein A-1, LDL buoyancy, apolipoprotein B, and lipoprotein (a) and found that rs646776 predicts apolipoprotein B level while rs2075650 predicts LDL buoyancy. Finally, we tested the role of these SNPs in conferring risk for ultrasonographically documented CAAD stenosis status. We found that two loci, chromosome 1p13.3 near CELSR2 and PSRC1 which contains rs646776, and 19q13.2 near TOMM40 and APOE which contains rs2075650, harbor risk alleles for CAAD. Conclusion Our analysis of 34 SNPs contributing to dyslipidemia at 23 loci suggests that genetic variation in the 1p13.3 region may increase risk of CAAD by increasing LDL particle number, whereas variation in the 19q13.2 region may increase CAAD risk by promoting formation of smaller, denser LDL particles.
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Affiliation(s)
- James Ronald
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA.
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65
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Saarela O, Kulathinal S, Karvanen J. Joint analysis of prevalence and incidence data using conditional likelihood. Biostatistics 2009; 10:575-87. [PMID: 19458343 DOI: 10.1093/biostatistics/kxp013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Disease prevalence is the combined result of duration, disease incidence, case fatality, and other mortality. If information is available on all these factors, and on fixed covariates such as genotypes, prevalence information can be utilized in the estimation of the effects of the covariates on disease incidence. Study cohorts that are recruited as cross-sectional samples and subsequently followed up for disease events of interest produce both prevalence and incidence information. In this paper, we make use of both types of information using a likelihood, which is conditioned on survival until the cross section. In a simulation study making use of real cohort data, we compare the proposed conditional likelihood method to a standard analysis where prevalent cases are omitted and the likelihood expression is conditioned on healthy status at the cross section.
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Affiliation(s)
- Olli Saarela
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Mannerheimintie 166, 00300 Helsinki, Finland.
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66
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Baudhuin LM. Genetics of coronary artery disease: focus on genome-wide association studies. Am J Transl Res 2009; 1:221-234. [PMID: 19956433 PMCID: PMC2776326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 03/05/2009] [Indexed: 05/28/2023]
Abstract
With the advent of the genome-wide association (GWA) study, a promising new avenue for identifying genetic markers for complex diseases like coronary artery disease (CAD) has been opened. This avenue, however, is not without challenges and limitations, including the need for carefully designed and executed studies and the risk of false positive associations. Nonetheless, new markers have been identified through such studies that could potentially revolutionize the ways that individuals with CAD are identified and managed.
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Affiliation(s)
- Linnea M Baudhuin
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, MN
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Samani NJ, Deloukas P, Erdmann J, Hengstenberg C, Kuulasmaa K, McGinnis R, Schunkert H, Soranzo N, Thompson J, Tiret L, Ziegler A. Large scale association analysis of novel genetic loci for coronary artery disease. Arterioscler Thromb Vasc Biol 2009; 29:774-80. [PMID: 19164808 DOI: 10.1161/atvbaha.108.181388] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Combined analysis of 2 genome-wide association studies in cases enriched for family history recently identified 7 loci (on 1p13.3, 1q41, 2q36.3, 6q25.1, 9p21, 10q11.21, and 15q22.33) that may affect risk of coronary artery disease (CAD). Apart from the 9p21 locus, the other loci await substantive replication. Furthermore, the effect of these loci on CAD risk in a broader range of individuals remains to be determined. METHODS AND RESULTS We undertook association analysis of single nucleotide polymorphisms at each locus with CAD risk in 11,550 cases and 11,205 controls from 9 European studies. The 9p21.3 locus showed unequivocal association (rs1333049, combined odds ratio [OR]=1.20, 95% CI [1.16 to 1.25], probability value=2.81 x 10(-21)). We also confirmed association signals at 1p13.3 (rs599839, OR=1.13 [1.08 to 1.19], P=1.44 x 10(-7)), 1q41 (rs3008621, OR=1.10 [1.04 to 1.17], P=1.02 x 10(-3)), and 10q11.21 (rs501120, OR=1.11 [1.05 to 1.18], P=4.34 x 10(-4)). The associations with 6q25.1 (rs6922269, P=0.020) and 2q36.3 (rs2943634, P=0.032) were borderline and not statistically significant after correction for multiple testing. The 15q22.33 locus did not replicate. The 10q11.21 locus showed a possible sex interaction (P=0.015), with a significant effect in women (OR=1.29 [1.15 to 1.45], P=1.86 x 10(-5)) but not men (OR=1.03 [0.96 to 1.11], P=0.387). There were no other strong interactions of any of the loci with other traditional risk factors. The loci at 9p21, 1p13.3, 2q36.3, and 10q11.21 acted independently and cumulatively increased CAD risk by 15% (12% to 18%), per additional risk allele. CONCLUSIONS The findings provide strong evidence for association between at least 4 genetic loci and CAD risk. Cumulatively, these novel loci have a significant impact on risk of CAD at least in European populations.
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