Haplotype-based Case-control Study Research Articles

Haplotype-Based Case–Control Study of the Human CYP11B2 Gene and Essential Hypertension in Yi and Hani Minorities of China

This haplotype-based case-control study investigated whether the aldosterone synthase gene (CYP11B2) might be implicated in the pathogenesis of essential hypertension in Yi (226 individuals) and Hani (296 individuals) minorities of China. Four tag SNPs (rs4536, rs4545, rs3097, and rs3802230) and the K173R polymorphism were genotyped using the PCR-RFLP method. In the Hani minority, rs4536 was significantly associated with hypertension, after Bonferroni correction. H9 AGGC constructed by tag SNPs was significantly higher in hypertensives than in controls (P=0.001). Further, we observed that haplotype AGGC remained significantly associated with male hypertension after adjustment for covariates (OR=3.76, P=0.002). In the Yi minority, it was found that the CYP11B2 gene was not significantly associated with hypertension. These results indicated that haplotype AGGC conferred an increased risk for hypertension in the Hani minority male. In addition, CYP11B2 may not be associated with hypertension in the Yi minority of China.

The haplotype of the CACNA1B gene associated with cerebral infarction in a Japanese population

Cerebral infarction (CI) is thought to be a multifactorial disease that is affected by several environmental factors and genetic variants. N-type voltage-gated calcium channels (VGCCs), which are expressed primarily in the neurons, have various roles in neuronal functions and are especially involved with neurotransmitter release at the sympathetic nerve terminals. We considered the α1B subunit of the N-type voltage-gated calcium channel (CACNA1B) to be representative of the general characteristics of this channel type. The aim of the present study was to assess the association of the human CACNA1B gene with the occurrence of CI via a haplotype-based case-control study that used single nucleotide polymorphisms (SNPs) from the Japanese population. A total of 165 CI patients and 314 controls were enrolled in the case-controlled studies that examined three SNPs of the human CACNA1B gene (rs7042521, rs11137351, rs10780199). There were significant differences between the CI and control groups for the overall distribution of the genotypes and the presence of the recessive rs10780199. Multiple logistic regression analyses revealed that even after adjusting for confounding factors (odds ratio: 1.716), the frequencies of the A/G and G/G genotypes of rs10780199 in the CI group were significantly higher than those observed in the control group (p = 0.021). Furthermore, the C-C-G and G-G-G haplotypes of rs7042521-rs11137351-rs10780199 were significantly more frequent in the CI group than in the control group (p = 0.024 and p < 0.000). In conclusion, significant differences were noted between the CI and control patients for the specific SNPs and haplotypes in the CACNA1B gene. The results indicate that these polymorphisms and haplotypes might be genetic markers for CI.

Association of the insulin-like growth factor1 gene with myocardial infarction in Japanese subjects

During adult life, the insulin/insulin-like growth factor1 (IGF1) signaling pathway plays an important role in cardiovascular function. Several reports have suggested that low baseline levels of IGF1 increase the risk of fatal ischemic heart disease. Thus, IGF1 may be involved in cardiovascular disease. The aim of the present study was to investigate the relationship between the human IGF1 gene and myocardial infarction (MI) in the Japanese population via the use of single nucleotide polymorphisms (SNPs). After selecting six SNPs in the human IGF1 gene (rs2162679, rs7956547, rs2288378, rs2072592, rs978458 and rs6218), we performed a case-control study using each of the SNPs and haplotypes in 320 MI patients and 307 non-MI controls. Multiple logistic regression analysis demonstrated that the GG+GA variant of rs2162679 (p=0.009) and the AA+GA variant of rs2072592 (p=0.026) exhibited a resistant effect for MI. The haplotype-based case-control study revealed that the frequency of the A-T-G-G haplotype for rs2162679-rs7956547-rs2072592-rs978458 was significantly higher in the MI group (47.3%) as compared to the non-MI group (41.4%) (p=0.037, odds ratio=1.270). The frequency of the A-T-G-T haplotype for rs2162679-rs7956547-rs978458-rs6218 was also significantly higher in the MI group (47.3%) as compared to the non-MI group (41.3%) (p=0.033, odds ratio=1.276). The current results suggest that specific SNPs and haplotypes can be utilized as genetic markers for MI risk or MI resistance. In addition, IGF1 or a neighboring gene might be associated with increased or decreased susceptibility to MI.

Haplotype analysis of the CYP2J2 gene associated with myocardial infarction in a Chinese Han population

The cytochromes P450 epoxygenases CYP2J2 synthesize epoxyeicosatrienoic, which regulate endothelial function. The aim of this study was to assess the association between the human CY2J2 gene and myocardial infarction (MI) in a Chinese population using a haplotype-based case-control study. There were 440 Chinese Han MI patients and 440 age-matched control subjects genotyped for three SNPs (rs2271800, rs11572223, and rs14493270) of the human CYP2J2 gene. Haplotypes were constructed and their frequencies compared between the MI patients and the controls. The CC genotype of rs2271800 was found more frequently in the MI group than in the control group (p = 0.004). The frequency of the C-C-G haplotype was significantly higher in MI patients than in control subjects (p < 0.001). The present results indicate that MI is associated with the CC genotype of rs2271800 in the human CYP2J2 gene. The C-C-G haplotype appears to be a useful genetic marker of MI in Chinese Han people.

Haplotype-Based Case-Control Study on Human Apurinic/Apyrimidinic Endonuclease 1/Redox Effector Factor-1 Gene and Essential Hypertension

Oxidative DNA damage is involved in the pathophysiology of essential hypertension (EH), which is a multifactorial disorder. Apurinic/apyrimidinic endonuclease 1/redox effector factor-1 (APE1/REF-1) is an essential endonuclease in the base excision repair pathway of oxidatively damaged DNA, in addition to having reducing properties that promote the binding of redox-sensitive transcription factors. Blood pressure in APE1/REF-1-knockout mice is reported to be significantly higher than in wild-type mice. The aim of this study was to investigate the relationship between EH and the human APE1/REF-1 gene through a haplotype-based case-control study using single-nucleotide polymorphisms (SNPs). We selected five SNPs in the human APE1/REF-1 gene (rs1760944, rs3136814, rs17111967, rs3136817, and rs1130409), and performed case-control studies in 265 EH patients and 266 age-matched normotensive (NT) subjects. rs17111967 was found to show nonheterogeneity among Japanese subjects. There were no significant differences in the overall distribution of genotypes or alleles for each SNP between EH and NT groups. In the overall distribution of the haplotype-based case-control study constructed based on rs1760944, rs3136817, and rs1130409, the frequency of the G-T-T haplotype was significantly higher in the EH group than in the NT group (2.1% vs. 0.0%, P = 0.001). Multiple logistic regression analysis also revealed significant differences for the G-T-T haplotype, even after adjustment for confounding factors (OR = 8.600, 95% CI: 1.073-68.951, P = 0.043). Based on the present results, the G-T-T haplotype appears to be a genetic marker of EH, and the APE1/REF-1 gene appears to be a susceptibility gene for EH.

환자-대조군 연구에서 인구집단 층화가 일배체형 경향성 검정에 미치는 영향

환자-대조군 연관성 연구에서 후보 유전자와 질병이 연관되어 있지 않더라도 인구집단 층화로 인해 가짜 연관성이 발생할 수도 있다. 본 연구에서는 일배체형에 기초한 환자-대조군 연관성 연구에서 인구집단 층화로 인한 가짜 연관성을 해결하기 위한 방법으로, Zaykin 등 (2002)이 제안한 일배체형 경향성 모형에 인구집단 층화에 대한 정보를 추가하고자 한다. Zaykin 등 (2002)의 모형과 제안한 모형에 기초한 일배체형의 유의성 검정에서 인구집단 층화와 인구집단에 대한 관측 오차가 제1종 오류율에 미치는 영향을 모의실험을 통해 살펴보았다. 인구집단이 층화되어 있지만 각 개체가 속한 인구집단을 정확히 알 수 있을 때, Zaykin 등 (2002)의 모형에 기초한 검정은 제1종 오류율을 잘 조절하지 못했지만 본 연구에서 제안한 모형에 기초한 검정은 제1종 오류율을 잘 조절하는 것으로 나타났다. 그러나 인구집단이 층화되어 있고 관측 오차가 존재하면 제안한 모형에 기초한 검정도 제1종 오류율을 조절하지 못하고 명목 유의수준보다 큰 값을 갖는 것으로 나타났다. 따라서 단일염기다형성에 기초한 환자-대조군 연관성 연구와 마찬가지로 일배체형에 기초한 환자-대조군 연관성 연구에서도 인구집단 층화에 대한 정보를 갖고 있다할지라도 그 속에 관측 오차가 존재하면 위양성을 피하기 어렵다는 것을 알 수 있었다. Population stratification can cause spurious associations between genetic markers and disease locus. In order to handle this population stratification in haplotype-based case-control association studies, we added population indicators as covariates to the haplotype trend regression model proposed by Zaykin et al. (2002). We investigated through simulations how both population stratification and measurement error in the estimation of true population of each individual affect type I error probabilities of the association tests based on both Zaykin et al.'s (2002) model and the proposed model. Based on those results, in the situation that there exists population stratification but there is no error in population classification of each individual, our proposed model does satisfy a type I error probability whereas Zaykin et al.'s (2002) model does not. However, as the measurement error increases, a type I error probability of our model correspondingly becomes larger than a nominal significance level. It implies that as long as uncertainty in the estimation of true population of each individual still remains, it is nearly impossible to avoid false positive in case-control association studies based on haplotypes.

Haplotype-based case-control study of the human AGTR1 gene and essential hypertension in Han Chinese subjects

Objectives Essential hypertension is considered to be a multifactorial trait resulting from the combined influence of environmental and genetic determinants. The aim of the study is to assess the association between the human AGTR1 gene and essential hypertension (EH) using a haplotype-based case-control study in Han Chinese subjects. Design and methods Seven tag SNPs and the A1166C polymorphism of the AGTR1 gene were genotyped in 510 hypertension subjects and 510 normotensive subjects using PCR-RFLP method. Results Single SNP analyses indicated that the rs12695895 was significantly associated with hypertension, adjusted for covariates. Compared with the other haplotypes, Hap4 (AGGACTT) which carry the susceptible rs12695895 A allele was found to significantly increase the risk of EH with odds ratios equal to 1.84 ( p = 0.0002). Conclusions The present results indicate that rs12695895 might be a genetic marker for EH and Hap4 (AGGACTT) was associated with hypertension in Han Chinese population.

Purinergic receptor P2Y, G-protein coupled, 2 (P2RY2) gene is associated with cerebral infarction in Japanese subjects

G-protein-coupled purinergic receptor P2Y2 (P2RY2) has an important role in the process of atherosclerosis related to cerebral infarction (CI). The aim of this study was to investigate the relationship between the P2RY2 gene and CI through a haplotype-based case-control study, including the separate analysis of two gender groups. A total of 237 CI patients and two control groups (control 1, 254; control 2, 255) were genotyped for five single nucleotide polymorphisms (SNPs) in the human P2RY2 gene (rs4944831, rs1783596, rs4944832, rs4382936, rs10898909). Among women, the distribution of the dominant rs4944832 phenotype (GG vs. GA+AA) differed significantly between the CI patients and the control 1 group (P=0.043) and between the CI patients and the control 2 group (P=0.029). Logistic regression analysis showed that the GG genotype of rs4944832 was significantly more prevalent in the female CI patients than in the control 1 (P=0.021) and control 2 groups (P=0.005). For all subjects, the overall distribution of the haplotype established by rs1783596-rs4382936-rs10898909 was significantly different between the CI patients and the control 1 group (P=0.027). For all subjects, the frequency of the T-A-G haplotype (rs1783596-rs4382936-rs10898909) was also significantly higher (P=0.031), whereas the frequency of the T-C-G haplotype (rs1783596-rs4382936-rs10898909) was significantly lower (P=0.029) in the CI patients than in the control 1 group. The present results indicate that the T-A-G haplotype of the human P2RY2 gene is a susceptibility haplotype for CI in Japanese subjects, and that the GG genotype is a genetic marker for CI, particularly in Japanese women.

Haplotype-based case–control study of receptor (calcitonin) activity-modifying protein-1 gene in cerebral infarction

Calcitonin gene-related peptide (CGRP) receptor is a complex molecule that consists of calcitonin receptor-like receptor and receptor activity-modifying protein-1 (RAMP1). It was recently reported that RAMP1-deficient mice (RAMP1(-/-)) showed inflammatory responses with a transiently significant increase in serum CGRP levels and proinflammatory cytokines when compared with RAMP1(+/+) mice. The aim of this study was to investigate the relationship between the human RAMP1 gene and cerebral infarction (CI) using single-nucleotide polymorphisms (SNPs) in a Japanese population. We selected six SNPs in the human RAMP1 gene (rs3754701, rs3769048, rs7557078, rs1584243, rs10199956 and rs7590387) and performed a case-control study using each SNP and haplotype in 171 CI patients and 234 controls. There were no significant differences in overall distribution of genotype and allele frequencies of the SNPs between the CI and control groups. However, there was a significant difference in overall distribution between the CI and control groups (P<0.001) in the haplotype-based case-control study with the combinations of rs3754701-rs3769048-rs7590387. The T-A-C susceptibility haplotype for CI was significantly more frequent than in the control group (P=0.0024). The results suggest that the T-A-C haplotype is a genetic marker for CI, and that RAMP1 or neighbouring genes are associated with increased susceptibility to CI.

The purinergic receptor P2Y, G-protein coupled, 2 (P2RY2) gene associated with essential hypertension in Japanese men

P2RY2 has an important function in the regulation of blood pressure by activating adenosine triphosphate (ATP). The aim of this study was to investigate the association between the human P2RY2 gene and essential hypertension (EH) through a haplotype-based case-control study that included two gender groups. The 273 EH patients and 255 age-matched controls were genotyped for five single-nucleotide polymorphisms (SNPs) of the human P2RY2 gene (rs4944831, rs1783596, rs4944832, rs4382936 and rs10898909). Data were analysed for men and women separately and then as a combined total group. For the total and the men only groups, the genotype distribution of the T allele of rs4944831 and the recessive model (GG vs TG+TT) of rs4944831 differed significantly between the EH patients and controls (P=0.028 and 0.019; P=0.009 and 0.008, respectively). Logistic regression showed that for the total and men groups, the TG+TT genotype of rs4944831 was more prevalent in EH patients than in the controls (P=0.026 and 0.011, respectively). For men, the overall distribution of the haplotype (SNP2-SNP4-SNP5) was significantly different between the EH patients and the controls (P=0.006). As compared with controls, the frequency of the T-A-G haplotype was significantly higher, whereas the T-C-G haplotype was significantly lower for the EH patients (P=0.001 and 0.014, respectively). In conclusion, the present results indicate that rs4944831 and the T-A-G haplotype of the human P2RY2 gene might be genetic markers for EH in Japanese men.

Haplotype-based case–control study between human apurinic/apyrimidinic endonuclease 1/redox effector factor-1 gene and cerebral infarction

Objectives The aim of this study was to investigate the relationship between cerebral infarction (CI) and the human apurinic/apyrimidinic endonuclease 1/redox effector factor-1 (APE1/REF-1) gene using single-nucleotide polymorphisms (SNPs) and a haplotype-based case–control study. Design and methods We selected 5 SNPs in the human APE1/REF1 gene (rs1760944, rs3136814, rs17111967, rs3136817 and rs1130409), and performed case–control studies in 177 CI patients and 309 control subjects. Results rs17111967 was found to have no heterogeneity in Japanese. The overall distribution of the haplotype-based case–control study constructed by rs1760944, rs3136814 and rs1130409 showed a significant difference. The frequency of the G-C-T haplotype was significantly higher in the CI group than in the control group (2.5% vs. 0.0%, p > 0.001). Conclusions Based on the results of the haplotype-based case–control-study, the G-C-T haplotype may be a genetic marker of CI, and the APE1/REF-1 gene may be a CI susceptibility gene.

Association on the haplotypes of CYP4F2 gene and myocardial infarction

The aim of this study was to assess the association between human CYP4F2 gene and myocardial infarction (MI), using a haplotype-based case-control study. A separate analysis on gender was also carried out. There were 250 MI patients and 250 control subjects genotyped for 5 SNPs of the human CYP4F2 gene (rs3093105, rs3093135, rs1558139, rs2108622, rs3093200). Data were assessed on 3 separate groups: the total subjects, men and women. For men, G allele was significantly higher in the MI patients than in the control subjects and the overall distribution of the haplotypes was significantly different between the MI patients and the control subjects (P=0.002). Also in men, the frequency of T-C-G haplotype was significantly higher for MI patients than for control subjects (P=0.002), and the frequency of T-C-A haplotype was significantly lower for MI patients than for control subjects (P=0.003). Data from the present results indicated that MI was associated with G allele of rs2108622 in men, suggesting that T-C-G haplotype might serve as genetic marker for MI in men.

Response to: Haplotype-based case–control study of the human CYP4F2 gene and essential hypertension in Japanese subjects

Response to: Haplotype-based case–control study of the human CYP4F2 gene and essential hypertension in Japanese subjects

Haplotype-based case–control study of the human CYP4F2 gene and essential hypertension in Japanese subjects

Haplotype-based case–control study of the human CYP4F2 gene and essential hypertension in Japanese subjects

Novel mutations of ABCC6 gene in Japanese patients with Angioid streaks

Angioid streaks (AS) are eye abnormalities caused by breaks in Bruch’s membrane. The condition is often associated with pseudoxanthoma elasticum (PXE). The ATP-binding cassette, sub-family C (CFTR/MRP), member 6 (ABCC6) is reported to be the causal gene for PXE, although there have been no reports on whether the ABCC6 gene is the causal gene for AS. The aims of this study are to isolate the causal mutations for AS using a haplotype-based case-control study. We genotyped 54 Japanese AS patients and 150 controls for 5 single-nucleotide polymorphisms (SNPs). A simple association study using each SNP and a haplotype-based case-control study were performed. Twelve patients with special haplotypes for AS were selected, and were then subjected to gene sequencing. Six variants were successfully identified as causal mutations for AS (p.R419Q, p.E422K, c.2542delG, Del_Exon23, c.3774-3775insC and p.E1427K), and 4 of these were novel. This method can be applied to both identifying susceptibility variants of multifactorial diseases and isolating mutations in single-gene diseases.

Association of the Purinergic Receptor P2Y, G-Protein Coupled, 2 (P2RY2) Gene With Myocardial Infarction in Japanese Men

Atherosclerosis leads to myocardial infarction (MI) and P2RY2 plays an important role in this process. The aim of the present study was to investigate the association between human P2RY2 and MI via a haplotype-based case-control study that additionally analyzed the group by sex. The 310 MI patients and 254 controls were genotyped for 5 single-nucleotide polymorphisms (SNPs) of the human P2RY2 gene (rs4944831, rs1783596, rs4944832, rs4382936, rs10898909). Data were separately analyzed for the total, male, and female subjects. For men, the GA+AA genotype of rs10898909 was significantly higher in MI patients as compared with controls (P=0.040). Logistic regression analysis found a significant difference for the genotype (P=0.016). As compared with controls, the frequencies of the C-A and T-C-A haplotypes were significantly higher (P=0.016, and P=0.045, respectively) in men, whereas the frequencies of the C-G and T-A-A haplotypes were significantly lower (P=0.023, and P=0.025, respectively) in MI patients. The GA+AA genotype, as well as the C-A and T-C-A haplotypes, of human P2RY2 could be genetic markers for MI in Japanese men.

Association of extracellular superoxide dismutase gene with cerebral infarction in women: a haplotype-based case-control study

It has been reported that oxidative stress is a factor in cerebral infarction (CI). Extracellular superoxide dismutase (EC-SOD) is important in preventing oxidative stress, and the cerebral infarct size of EC-SOD knockout mice is significantly larger than that in wild-type controls. The aim of this study was to investigate the relationship between CI and the human EC-SOD gene using single-nucleotide polymorphism (SNP) in Japanese individuals. We selected five single-nucleotide polymorphisms of the human EC-SOD gene (rs13306703, rs699473, rs17881426, rs2536512 and rs1799895) and performed a case-control study using each SNP and haplotype in 175 CI patients (103 men, 72 women) and 299 controls (144 men and 155 women). Among women, there were significant differences between the CI and control group in overall distribution of alleles for rs699473 (men: OR=1.031, 95% CI: 0.705-1.506, women: OR=1.916, 95% CI: 1.196-3.071) and rs2536512 (men: OR=0.774, 95% CI: 0.523-1.146, women: OR=2.107, 95% CI: 1.227-3.462). In a haplotype-based case control on rs13306703, rs699473 and rs1799895 in women, the frequency of the C-C-C haplotype was significantly higher in the CI group than in the control group (men; 51.5% vs 51.4% p=0.9865, women; 62.5% vs 49.7% p=0.0108). Multiple logistic regression analysis also revealed a significant difference in C-C-C haplotype in women, even after adjustment for confounding factors (OR=2.205, 95% CI: 1.069-4.552 p=0.032). The C-C-C haplotypes could be genetic markers for CI, and the EC-SOD gene may be a susceptibility gene for CI in women.

A haplotype of the CYP4F2 gene associated with myocardial infarction in Japanese men

This study assessed associations between the CYP4F2 gene and myocardial infarction (MI), using a haplotype-based case-control study of 234 MI patients and 248 controls genotyped for 5 single-nucleotide polymorphisms (rs3093105, rs3093135, rs1558139, rs2108622, rs3093200). For men, G allele frequency of rs2108622 and frequency of the T-C-G haplotype were significantly higher, and frequency of the T-C-A haplotype was significantly lower for MI patients than for controls ( P = 0.006, P = 0.001 and P = 0.002, respectively).

Human uncoupling protein 2 and 3 genes are associated with obesity in Japanese

Human uncoupling proteins (UCPs) are mitochondrial proteins that are involved in the control of energy metabolism and the pathophysiology of obesity. Although there have been several reports on the association between the UCP2/UCP3 locus and the obesity, there have been no haplotype-based case-control studies with gender-specific analysis. The aim of this study was to examine whether there is an association between the UCP2/UCP3 locus and the obesity in the Japanese population when using a single nucleotide polymorphism (SNP)-based and haplotype-based case-control study with gender-specific analysis. We examined a group consisting of 551 subjects, of which 369 were non-obese and 182 were overweight and/or obese. We selected one nonsynonymous SNP (rs660339: Ala55Val) as a genetic marker. Genotyping for all subjects was performed by the TaqMan polymerase chain reaction (PCR) method. Although the overall distributions of genotype and allele were not significantly different between the non-obese and the obese groups, the overall distributions of the genotype were significantly different in men (P = 0.030). In the obese group, male subjects with the Val allele were significantly more frequent in both association studies. There was a significant difference in the overall distribution of the haplotype (UCP3 rs180049, UCP3 rs2075577, UCP2 rs660339) between the weight groups (P = 0.010), and in women, there was a significant difference (P = 0.042) in the overall distribution of the haplotype (UCP3 rs2075577, UCP2 rs660339). Nonsynonymous rs660339 in the human UCP2 gene in men, and the haplotype (UCP3 rs2075577-UCP2 rs660339) in women might be good obesity markers.

A Haplotype of the CYP4F2 Gene is Associated With Cerebral Infarction in Japanese Men

CYP4F2, a member of the cytochrome P450 family, acts mainly as an enzyme and is involved not only in the metabolism of leukotriene B4, but also in that of arachidonic acid. It converts arachidonic acid to 20-hydroxyeicosatetraenoic acid (20-HETE), a metabolite involved in the regulation of the vascular tone in the brain. The aim of this study was to assess the association between the human CYP4F2 gene and cerebral infarction (CI), using a haplotype-based case-control study with separate analyses of data from the gender groups. A total of 175 CI patients and 246 control subjects were genotyped for five single-nucleotide polymorphisms (SNPs) of the human CYP4F2 gene (rs3093105, rs3093135, rs1558139, rs2108622, rs3093200). For data analysis, three separate groups were assessed: all subjects, men, and women. In the male subjects, the G allele frequency for rs2108622 was significantly higher in CI patients as compared to control subjects (P = 0.025). The overall distribution of the haplotypes in the men was significantly different between the CI patients and the control subjects (P = 0.027). Additionally, the frequency of the T-C-G haplotype for men was significantly higher in the CI patients than in the control subjects (P = 0.008). Multiple logistic regression analysis also revealed the significance of the T-C-G haplotype in men, even after adjustment for confounding factors. The results of this study indicate that, in Japanese men, CI is associated with the G allele of rs2108622 and, in addition, that the T-C-G haplotype appears to be a useful genetic marker for CI.