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International Journal of Clinical and Experimental Medicine logoLink to International Journal of Clinical and Experimental Medicine
. 2015 May 15;8(5):7497–7506.

Association analysis of GWAS and candidate gene loci in a Chinese population with coronary heart disease

Min Gao 1, Haiqin Tang 2, Xiaodong Zheng 3, Fusheng Zhou 3, Wensheng Lu 4
PMCID: PMC4509238  PMID: 26221293

Abstract

Objective: Coronary heart disease (CHD), the most severe form of coronary artery disease (CAD), is a complex disease that involves a variety of genetic and environmental factors. Recently, multiple single nucleotide polymorphisms (SNPs) have been associated with CAD in Caucasians by genome-wide association (GWA) studies.However, the association of these SNPs with CHD in Asian populations has not yet been established. Here, we aim to investigate the genetic etiology of CHD in a Chinese population by genotyping SNPs previously been associated with CHD in other ethic origin in GWAS or candidate gene studies. Methods: Five SNPs, rs17114036, rs9369640, rs515135, rs579459 and rs8055236, from 5 different loci were genotyped using a sequenom Mass array system in 545CHD patients and 1008 unrelated controls from a Chinese population. Results: Our study showed that SNP rs515135 is strongly associated with CHD in a Chinese Han population (P-value=0.00333, OR=1.48). We also detected significant difference of SNP rs579459 in APOB gene in patients withsevere CAD compared to patients with mild CAD. Conclusion: SNP rs515135 is associated with the susceptibility of CHD in Chinese Han population. The location of rs515135 in the APOB gene supports its potential involvement in the pathogenesis of CAD. Our study data also support that SNP rs579459 may be associated with the severity of CHD.

Keywords: Coronary heart disease, genetic variants, case-controlled study, single nucleotide polymorphism

Introduction

Coronary artery disease (CAD) is one of the leading causes of death in the populations both in developed and developing countries. According to the World Health Organization, it was estimated that more than 700,000 people die from CAD each year in China. Coronary heart disease (CHD) is the most severe clinical manifestation of CAD and is the leading cause of death worldwide [1,2]. CHD is a complex disease characterized by the inheritance of multiple genetic variants in addition to environmental factors which worsen the disease state. Epidemiological studies have identified many risk factors for coronary heart disease, including plasma lipid concentrations, blood pressure, smoking, diabetes and markers of inflammation. Among them, a causal role has been proven only for some factors (for example, low-density lipoprotein (LDL) cholesterol and blood pressure) primarily through randomized clinical trials of drug therapy. Twin and family studies have demonstrated that a significant proportion (40-50%) of susceptibility to CHD is inherited [3]. A previous linkage study and candidate gene study have identified genetic factors predisposing to CHD. However, the results of CHD genetic studies have not been very satisfactory. Recently, GWAS have proven to be a powerful tool to identify susceptibility genes for common diseases. To date, GWAS studies in Caucasians identified multiple single nucleotide polymorphisms (SNPs) that associated with coronary artery disease (CAD) [4-12]. However, no independent studies of these SNPs have been reported in a Chinese population with CHD. Here, we intend to identify the associations between genetic variants of CHD, specifically, the associations of the SNPs rs17114036, rs9369640, rs515135, rs579459 and rs8055236 with CHD in a Chinese Han population.

Materials and methods

Patients and controls

A total of 545 blood-unrelated Chinese patients with coronary heart disease and 1008 healthy controls were recruited consecutively from outpatients at the Department of Cardiovascular Internal Medicine at Anhui Provincial Hospital. All subjects were of self-reported Chinese Han ancestry. Coronary heart disease was defined as the following: ① clinical symptoms and an electrocardiogram consistent with the diagnosis of coronary heart disease criteria formulated by the WHO in 1979. ② Coronary angiography revealed that at least 1 coronary artery stenosis was more than or equal to 50%. ③ There was no relationship between cases. Exclusion criteria: ① Associated with other cardiac diseases, such as dilated cardiomyopathy, rheumatic heart disease ② severe disease in the liver and kidney. ③ Previously received intravenous thrombolysis, coronary artery stenting and coronary artery bypass grafting patients. Control subjects were recruited from healthy adult visitors to the hospitals without a history of cardiovascular disease and family history of coronary artery disease (including first-, second- and third-degree relatives), matched for age (up to 6 years older or younger) and sex with the cases. Participants who consented to the study completed a structured questionnaire, attended a health examination, and had a venous blood sample taken. Information about demographic factors, socioeconomic status, lifestyle (smoking, leisure time, physical activity, and dietary patterns), personal and family history of cardiovascular disease, hypertension and diabetes mellitus was obtained. After written informed consent was obtained, peripheral blood samples were collected from all patients and matched healthy controls. All participants provided their written informed consent. At the same time, we promised reporting of the research results to the participants. The study was approved by the Ethical Committee of the Anhui Provincial Hospital and was performed according to the Declaration of Helsinki Principles.

Definitions

The patients were categorized as the following: the severity of coronary disease was determined to be mild (≤20 points) or severe (>20 points) according to the Gensini scoring system [13]. The family history was considered to be positive if the patient’s first-, second-, and/or third-degree relatives had coronary heart disease; the family history was considered to be negative otherwise.

Genomic DNA extracting and SNP genotyping

After informed consent, genomic DNA was isolated from peripheral blood of the patients using a Qiagen kit (Hilden, Germany). In addition, genomic DNA of 1008 unrelated healthy individuals was extracted as a control. We selected only SNPs in CAD-related genes with minor allele frequencies of 0.05 in Chinese patients in the HapMap database. We used the SNPs effect size in the references, minor allele frequencies of Chinese (based on HapMap database) and the sample size of this study to calculate the power for detecting a positive association. Excluding SNPs with power less than 0.20, we selected five SNPs (rs17114036, rs9369640, rs515135, rs579459 and rs8055236), which have been shown to significantly associate with CAD, but have not yet been tested in a Chinese population.

All SNPs were genotyped using the Sequenom iPlex platform (Sequenom, Inc., San Diego, CA, USA) at the State Key Laboratory Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui, China. Each genotyping cluster of five selected SNPs is good, especially the genotyping cluster of rs515135 as shown in Figure 1. Besides, the primers designed for sequencing of this study are shown below (Table 1).

Figure 1.

Figure 1

The genotyping cluster of rs515135.

Table 1.

Primer sequences of amplification and extension

SNP Amplification primersequences Primer sequences of extension
rs17114036 1) ACGTTGGATGCCTATCAGCAAGAGCTGAAG aTAAGTTTTCAGGAAAAAGTAGTC
2) ACGTTGGATGCGAGAACCTGGTTTCTTGAC
rs9369640 1) ACGTTGGATGTGGGCTACTGGAGAATAAGG gACTGTTGCAAAATCACTGTTAG
2) ACGTTGGATGCGGTGTGTAGATACTGTTGC
rs515135 1) ACGTTGGATGGAACCATCTTGTTACTGCAC tAAAAACAGCCAAAATGGAACCAAAGA
2) ACGTTGGATGAGGGCTTACAGCCAAGTAAC
rs579459 1) ACGTTGGATGTTCTGGTTTGCATGTGTTGG cGGTTTCTTTTCGCTACACCA
2) ACGTTGGATGGAAGTAAAAGTGACTTGCTG
rs8055236 1) ACGTTGGATGGCCAGGCTATTTGTGCATCT gtCTTTGTTTTTTTTCATCTTCCACTCG
2) ACGTTGGATGTCCATACAGTCATTGAGGC

Statistical analysis

Hardy Weinberg equilibrium tests of the genotyping data were performed using PLINK (version 1.07). The power of the study population was estimated using the power calculatorfor genome wide association studies program (http://www.sph.umich.edu/csg/abecasis/CaTS/). For allelic association between a SNP and CHD, the p-value and corresponding odds ratio (OR) with a 95% confidence interval were computed by Chi-square tests using Pearson’s 2X2 contingency tables as implemented in PLINK version 1.07.

For the stratified analysis, differences between the cases and controls in terms of the genotype frequency were tested using the chi squared test and by calculating the odds ratios (ORs) and 95% confidence intervals (CIs).

Results

Characters of the study cohorts

The demographic details for the patients and control subjects are shown in Table 2. Except the means of sex and the frequency of presence of alcohol intake, other characteristics in Table 2, CHD patient were significantly different from those in controls.

Table 2.

Characters of the study cohorts

CHD patient Control

Characteristic (n=545) (n=1008)
Age (SD)* 61.5 57.5
Sex (Male/Female) 354/191 605/403
BMI 24.5 23.8
History of HT (%) 40.18% 21.53%
History of T2D (%) 12.29% 3.08%
Current Smoking (%) 57.25% 40.18%
Alcohol intake (%) 38.35% 37.10%
HDL-C mmol/L* 1.02 1.13
LDL-C mmol/L* 2.53 2.27
TG mmol/L* 1.63 1.65
TC mmol/L* 4.55 4.59

CHD, Coronary heart disease; BMI, body mass index (kg/m2); HT, hypertension; T2D, type 2 diabetes; HDL-C, high-density lipoprotein cholesterol; LDL-C, low-density lipoprotein cholesterol; TG, triglycerides; TC, total cholesterol;.

*

Data are means (SD).

Results of the case-controlled study

To demonstrate the genetic susceptibility of SNPs with CHD in a Chinese population, 5 SNPs were genotyped in 545 CHD patients and 1008 controls. Allele distribution and minor allele frequency in these patients and controls are shown in Figure 2. All of the SNPs were in Hardy-Weinberg equilibrium. Association between the SNPs and CHD is shown in Table 3. In five SNPs, rs515135 was significantly associated with CHD in a Chinese population. The scatter plots of the suggestive association evidence within 2p24-p23 (APOB) for CHDare shown in Figure 3. There is still significant association after adjustment of age, sex and BMI. There was no statistically significant association of rs17114036, rs9369640 Z, rs579459 and rs8055236 with CHD in the Chinese population.

Figure 2.

Figure 2

Allele distribution and minor allele frequency of 5 SNPs in the study patients and controls. A and B are SNP LOGO of 545 blood-unrelated Chinese patients and 1008 healthy controls respectively. (1, 3, 5, 7, 9 shows the minor allele proportion of five SNPs, and 2, 4, 6, 8, 10 shows the major one). C. Minor allele frequency of five SNPs in patients (F_A) and controls (F_U).

Table 3.

Association between single-nucleotide polymorphisms and coronary artery diseasesusceptibility in Chinese population coronary artery disease patients (all) versus controls

SNP Allele(risk) Mode Odds ratio (95% CI) P-value power
rs17114036 G/A (A) Dominant 1.003 (0.999-1.007) 0.523 5
Recessive 2.040 (1.124-3.701) 0.017 67
Allele 2.093 (1.165-3.761) 0.01167 41.7
rs9369640 C/A (A) Dominant 1.284 (0.116-14.208) 1 4.7
Recessive 1.846 (1.062-3.209) 0.028 49.6
Allele 1.787 (1.049-3.044) 0.03043 32
rs515135 G/A (A) Dominant 1.638 (1.227-2.187) 0.001 91.4
Recessive 0.698 (0.214-2.281) 0.776 8.2
Allele 1.48 (1.138-1.925) 0.00333 54.3
rs579459 C/T (T) Dominant 1.477 (0.861-2.533) 0.155 28.9
Recessive 1.285 (0.999-1.652) 0.05 49.9
Allele 1.261 (1.024-1.554) 0.02917 33.6
rs8055236 G/T (T) Dominant 1.575 (0.453-5.472) 0.471 87.1
Recessive 1.337 (0.998-1.791) 0.051 8.1
Allele 1.305 (0.9978-1.707) 0.05139 28.4

Figure 3.

Figure 3

The scatter plots of the suggestive association evidences within 2p24-p23 (APOB) for CHD.

Stratified analysis

Stratified analysis revealed that rs579459 is strongly associated with severe coronary heart disease. Associations between coronary heart disease severity relative to the controls were not observed for the other four SNPs (Table 4).

Table 4.

Associations between single-nucleotide polymorphisms and coronary artery disease susceptibility in the Chinese population relative to the controls

SNP Allele (risk) Mode Odds ratio (95% CI) P-value Power
1) Mild- moderatecoronary artery disease vs control
rs17114036 G/A (A) Dominant 1.00 (0.999-1.007) 1 NA
Recessive 3.49 (1.070-11.379) 0.032 70
Allele 3.55 (1.099-11.490) 0.02386 49
rs9369640 C/A (A) Dominant 1.00 (0.999-1.007) 1 NA
Recessive 1.59 (0.706-3.582) 0.259 39
Allele 1.63 (0.734-3.631) 0.2253 27
rs515135 G/A (A) Dominant 1.64 (1.082-2.49) 1.90E-02 98
Recessive 0.52 (0.065-4.126) 1 12
Allele 1.47 (1.005-2.145) 0.04601 67
rs579459 C/T (T) Dominant 1.25 (0.575-2.700) 0.577 16
Recessive 0.95 (0.661-1.371) 0.791 7
Allele 1.00 (0.745-1.349) 0.989 5
rs8055236 G/T (T) Dominant 1.70 (1.134-2.561) 0.01 99
Recessive 0.93 (0.108-7.997) 1 5
Allele 1.56 (1.079-2.260) 0.01742 83
2) Severe coronary artery disease vs control
rs17114036 G/A (A) Dominant 1.00 (0.999-1.007) 1 NA
Recessive 1.38 (0.574-3.298) 0.472 22
Allele 1.42 (0.602-3.366) 0.4181 17
rs9369640 C/A (A) Dominant 0.35 (0.032-3.894) 0.386 34
Recessive 2.30 (0.814-6.489) 0.117 58
Allele 1.87 (0.737-4.719) 0.1813 32
rs515135 G/A (A) Dominant 1.51 (0.956-2.393) 0.076 84
Recessive 1.01 (1.005-1.023) 0.37 NA
Allele 1.33 (0.871-2.030) 0.1852 32
rs579459 C/T (T) Dominant 2.03 (0.717-5.754) 0.216 50
Recessive 1.79 (1.160-2.757) 0.008 97
Allele 1.68 (1.154-2.436) 0.00623 90
rs8055236 G/T (T) Dominant 1.07 (0.656-1.740) 0.792 7
Recessive 1.14 (0.132-9.873) 1 4
Allele 1.06 (0.678-1.671) 0.7871 6

Abbreviations: CI, confidence interval; SNP, single-nucleotidepolymorphism.

Discussion

CHD is the result of a combination of genetic and environmental factors. Until recently, the underlying mechanisms of coronary heart disease formation are only partially understood. More than 200 risk factors have been associated with CHD and, among these, randomized controlled trials have shown that low-density lipoprotein cholesterol (LDL-c) and blood pressure (BP) is causally related to CHD [14-16]. A key factor in reducing the global burden of CAD is early prediction of the disease to target preventive interventions.

Several studies have investigated a number of genes for polymorphisms or mutations that may be associated with coronary heart disease [17]. However, the results genetic studies of coronary heart disease have not been very satisfactory. Recent GWAS studies have identified several genetic variants that are associated with CAD [18-21]. The present study was performed in a Chinese population to determine the positive association signals identified in the GWAS studies with CAD in Caucasians.

We have shown that, there was a significant association of the SNP rs515135 with CHD after age, sex and BMI adjustment in a Chinese population. No association was found betweenSNPs rs17114036, rs9369640, rs579459 and rs8055236 and susceptibility of coronary heart disease.

The SNP rs515135 is located on chromosome 2p23-24 where locates the APOB gene. APOB is the main apolipoprotein component of LDL-C and it plays a central role in lipid metabolism as the major protein component of very-low-density lipoprotein (VLDL) and LDL, and serves as the ligand for the removal of LDL from circulation [22]. The gene encoding for APOB has been cloned and sequenced. It is 43 kb in length with 29 exons [23]. The APOB gene is known to have several sequences that serve as recognition sites for various restriction enzymes. Several polymorphisms have been identified in the APOB gene, which can result in the deletion of amino acids from the signal peptide and have been postulated to affect APOB secretion and assembly with lipids. In our study, polymorphisms of rs515135 in the APOB gene in CHD patients were significantly higher compared to healthy controls, suggesting that these variants increase the risk of CHD.

Stratified analysis of rs579459 revealed that in the recessive mode of inheritance (where C/T+C/C is compared with T/T), the severe coronary artery disease group had significant ORs compared with both the controls and the groupwith mild coronary artery disease. The ORs were maintained after Bonferroni’s correction (OR: 1.79, 95% CI: 1.16-2.76, p-value 0.008, respectively). The ratio of the severe tomild OR for rs579459 (recessive model) is presented in Table 4 (1.79/0.95=1.88). The result indicates that rs579459 is strongly associated with severe coronary artery disease. No association was detected for the other four SNPs regarding the severity of coronary artery disease.

The ABO SNP rs579459 had strong association with severe coronary artery disease in our data. Other GWAS studies have also identified ABO as a locus for low density lipoprotein (LDL-C)[24], type-2 diabetes [25], inflammatory risk biomarkers E-selectin, P-selectin, and sol-ICAM1 [25-27]. These findings suggested that ABO might modulate multiple pathways relating to cardiovascular risk factors, atherosclerosis and thrombosis. The genetic variation(s) in ABO might affect low density lipoprotein and coronary artery disease formation, although further studies are needed to explore its precise role in the development of CHD. There is limitation in the present study, as the cohort is of a limited size, and may not have sufficient power to detect SNPs with a small effect with a true association. Further studies in other ethnic groups and functional studies of the selected SNPs are needed in order to provide more insights into the biological relevance of CHD.

Acknowledgements

We are grateful to all the members who are willingly to participate in this study. This work was funded by the Anhui Provincial Natural Science Foundation (1208085QH155).

Disclosure of conflict of interest

None.

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