Logistic regression model for analyzing extended haplotype data

Exploiting gene-environment independence in haplotype-based inferences for population-based case-control studies with complex sampling

The use of complex sampling in population-based case-control studies is becoming more common. Although most single nucleotide polymorphism-based association studies with complex sampling account for the design complications, many of haplotype-based genetic association studies with complex sampling tend to ignore them when estimating haplotype frequencies, regression coefficients, or both. In this article, we develop innovative one-step and two-step statistical methods that account for the design complications in haplotype-based association studies when cases and/or controls are sampled with complex sampling. Attracted by the efficiency advantage of the retrospective method, we explore the assumptions of Hardy-Weinberg equilibrium and gene-environment independence in the underlying population. Results of our simulation studies demonstrate superior performance of the proposed methods over selected existing methods under various complex sampling designs. An application of the proposed methods is illustrated using a population-based case-control study of kidney cancer.

Genome-wide association study identifies SNPs in the MHC class II loci that are associated with self-reported history of whooping cough

Whooping cough is currently seeing resurgence in countries despite high vaccine coverage. There is considerable variation in subject-specific response to infection and vaccine efficacy, but little is known about the role of human genetics. We carried out a case–control genome-wide association study of adult or parent-reported history of whooping cough in two cohorts from the UK: the ALSPAC cohort and the 1958 British Birth Cohort (815/758 cases and 6341/4308 controls, respectively). We also imputed HLA alleles using dense SNP data in the MHC region and carried out gene-based and gene-set tests of association and estimated the amount of additive genetic variation explained by common SNPs. We observed a novel association at SNPs in the MHC class II region in both cohorts [lead SNP rs9271768 after meta-analysis, odds ratio [95% confidence intervals (CIs)] 1.47 (1.35, 1.6), P-value 1.21E − 18]. Multiple strong associations were also observed at alleles at the HLA class II loci. The majority of these associations were explained by the lead SNP rs9271768. Gene-based and gene-set tests and estimates of explainable common genetic variation could not establish the presence of additional associations in our sample. Genetic variation at the MHC class II region plays a role in susceptibility to whooping cough. These findings provide additional perspective on mechanisms of whooping cough infection and vaccine efficacy.

Revisiting the role of MCL1 in tumorigenesis of solid cancer: gene expression correlates with antiproliferative phenotype in breast cancer cells and its functional regulatory variants are associated with reduced cancer susceptibility

Compared to the well-defined anti-apoptotic role of myeloid cell leukemia sequence 1 (MCL1), its antiproliferative function in tumorigenesis is less studied. We had recently reported that regulatory variants of MCL1 contribute to enhanced promoter activity but reduced risk of lung cancer. We hypothesized that MCL1 expression may manifest antiproliferative phenotype and its functional variations may have etiological relevance for breast cancer. We manipulated MCL1 expression in MCF-7 cells and MDA231 with overexpression and knockdown, analyzed the effects on cell viability and cell cycling phase, and characterized the correlation with expression profiles of key regulators of cell cycle. We further genotyped the -190 insertion polymorphism and the neighboring single nucleotide polymorphisms (SNPs) in 745 breast cancer patients and 537 controls and analyzed their association with cancer risk. We confirmed that heightened expression of MCL1 resulted in decreased proliferation ability of breast cancer cells. We further observed that MCL1 overexpression in breast cancer cells resulted in cell cycle progression arresting in S phase and concomitant enhanced expression of p27, which could be rescued by p27 knockdown with co-transfection of small interfering RNA (siRNA). Furthermore, we found a significant reduction in breast cancer risk [odds ratio (OR) = 0.74; 95 % confidence interval (CI) = 0.59-0.93] associated with -190 insertion genotype; the expression-enhancing regulatory haplotype (OR 0.79; 95 % CI 0.66-0.95) and diplotype (OR 0.71; 95 % CI 0.57-0.89) were consistently associated with decreased cancer susceptibility. The study demonstrates that the expression-enhancing regulatory variants of MCL1 are protective modifiers of breast cancer risk, and reduced cell proliferation and arrested cell cycle progression partly mediated by p27 might be the underlying mechanism.

Environmental tobacco smoke and male sex modify the influence of IL-13 genetic variants on cord blood IgE levels

Elevated cord blood IgE (cIgE) levels enhance the risk of childhood atopic diseases. However, genetic determinants of cIgE elevation and their potential modifiers remain inconclusive. We aimed to investigate the associations of single-nucleotide polymorphisms (SNPs) in the IL-13 gene (IL-13) with cIgE elevation and their interactions with prenatal environmental tobacco smoke (ETS) and neonatal sex. A structured questionnaire regarding prenatal environmental exposures was completed during pregnancy. Birth information was extracted from the medical records. Cord blood from 794 term neonates was genotyped for three SNPs (rs1800925, rs20541, and rs848) of IL-13 and measured for cIgE levels. SNP rs20541 and a 3-SNP haplotype containing rs1800925, rs20541, and rs848 (denoted as h011) were significantly associated with cIgE elevation (p = 0.04 and 0.003, respectively). Two-way interaction analysis revealed that the associations of IL-13 rs20541 and h011 with cIgE elevation were synergistically enhanced by prenatal ETS (p for interaction = 0.03 and 0.03, respectively), but not by male sex. If the association analyses were stratified by prenatal ETS and neonatal sex simultaneously, IL-13 rs20541 and h011 had the highest risks for cIgE elevation in male babies prenatally exposed to ETS, with adjusted odds ratios (95% confidence interval) being 3.03 (1.56-5.88) and 2.81 (1.54-5.15), respectively. When three-way interactions were examined, both IL-13 rs20541 and h011 exhibited significant interactions with male sex and ETS (p for interaction = 0.03 and 0.007, respectively). In conclusion, the influence of IL-13 genetic variants on cIgE elevation was modified by male sex and prenatal ETS.

C-reactive protein and genetic variants and cognitive decline in old age: the PROSPER study

BACKGROUND

Plasma concentrations of C-reactive protein (CRP), a marker of chronic inflammation, have been associated with cognitive impairment in old age. However, it is unknown whether CRP is causally linked to cognitive decline.

METHODS AND FINDINGS

Within the Prospective Study of Pravastatin in the Elderly at Risk (PROSPER) trial, with 5680 participants with a mean age of 75 years, we examined associations of CRP levels and its genetic determinants with cognitive performance and decline over 3.2 years mean follow-up. Higher plasma CRP concentrations were associated with poorer baseline performance on the Stroop test (P = 0.001) and Letter Digit Tests (P<0.001), but not with the immediate and delayed Picture Learning Test (PLT; both P>0.5). In the prospective analyses, higher CRP concentrations associated with increased rate of decline in the immediate PLT (P = 0.016), but not in other cognitive tests (all p>0.11). Adjustment for prevalent cardiovascular risk factors and disease did not change the baseline associations nor associations with cognitive decline during follow-up. Four haplotypes of CRP were used and, compared to the common haplotype, carrierships associated strongly with levels of CRP (all P<0.007). In comparison to strong associations of apolipoprotein E with cognitive measures, associations of CRP haplotypes with such measures were inconsistent.

CONCLUSION

Plasma CRP concentrations associate with cognitive performance in part through pathways independent of (risk factors for) cardiovascular disease. However, lifelong exposure to higher CRP levels does not associate with poorer cognitive performance in old age. The current data weaken the argument for a causal role of CRP in cognitive performance, but further study is warranted to draw definitive conclusions.

Meta-analysis of haplotype-association studies: comparison of methods and empirical evaluation of the literature

Background

Meta-analysis is a popular methodology in several fields of medical research, including genetic association studies. However, the methods used for meta-analysis of association studies that report haplotypes have not been studied in detail. In this work, methods for performing meta-analysis of haplotype association studies are summarized, compared and presented in a unified framework along with an empirical evaluation of the literature.

Results

We present multivariate methods that use summary-based data as well as methods that use binary and count data in a generalized linear mixed model framework (logistic regression, multinomial regression and Poisson regression). The methods presented here avoid the inflation of the type I error rate that could be the result of the traditional approach of comparing a haplotype against the remaining ones, whereas, they can be fitted using standard software. Moreover, formal global tests are presented for assessing the statistical significance of the overall association. Although the methods presented here assume that the haplotypes are directly observed, they can be easily extended to allow for such an uncertainty by weighting the haplotypes by their probability.

Conclusions

An empirical evaluation of the published literature and a comparison against the meta-analyses that use single nucleotide polymorphisms, suggests that the studies reporting meta-analysis of haplotypes contain approximately half of the included studies and produce significant results twice more often. We show that this excess of statistically significant results, stems from the sub-optimal method of analysis used and, in approximately half of the cases, the statistical significance is refuted if the data are properly re-analyzed. Illustrative examples of code are given in Stata and it is anticipated that the methods developed in this work will be widely applied in the meta-analysis of haplotype association studies.

Genome-wide association studies using haplotype clustering with a new haplotype similarity

Association analysis, with the aim of investigating genetic variations, is designed to detect genetic associations with observable traits, which has played an increasing part in understanding the genetic basis of diseases. Among these methods, haplotype-based association studies are believed to possess prominent advantages, especially for the rare diseases in case-control studies. However, when modeling these haplotypes, they are subjected to statistical problems caused by rare haplotypes. Fortunately, haplotype clustering offers an appealing solution. In this research, we have developed a new befitting haplotype similarity for "affinity propagation" clustering algorithm, which can account for the rare haplotypes primely, so as to control for the issue on degrees of freedom. The new similarity can incorporate haplotype structure information, which is believed to enhance the power and provide high resolution for identifying associations between genetic variants and disease. Our simulation studies show that the proposed approach offers merits in detecting disease-marker associations in comparison with the cladistic haplotype clustering method CLADHC. We also illustrate an application of our method to cystic fibrosis, which shows quite accurate estimates during fine mapping.

Polymorphisms of MLH1 and MSH2 genes and the risk of lung cancer among never smokers

Mismatch repair (MMR) plays an important role in repairing nucleotide mismatches during DNA replication. Defects in MMR genes are associated with some sporadic tumors. MLH1 and MSH2 are two of the MMR genes. We conducted a case-control study to investigate the associations between the risk of lung cancer and genetic polymorphisms in the MLH1 and MSH2 genes. The SNP genotypes were determined in 730 lung cancer patients and 730 healthy controls that were frequency matched for the age, gender, and smoking status. Among the SNP polymorphisms, -93A>G (rs1800734), which is located in the promoter region of MLH1, was significantly associated with the risk of lung cancer. The GG genotype for MLH1 -93A>G was associated with a significantly increased risk of lung cancer compared with the AA genotype among the never-smoking group (adjusted OR=1.64, 95% CI=1.10-2.44; P=0.013). Consistently, the haplotype of MLH1 with one -93G risk allele was associated with the risk of lung cancer compared with the AA haplotype among the never-smoking group. Furthermore, the risk of MLH1 -93A>G polymorphism in the never-smoking group related to lung adenocarcinoma was modulated by environmental tobacco smoke (ETS) exposure status, with a significant gene-ETS interaction (P=0.042). No evidence was found of the association between MSH2 and the lung cancer risk. In conclusion, our data suggest that the MLH1 -93A>G polymorphism may contribute to the etiology of lung cancer, particularly in never smokers. This study also suggests that MLH1 -93A>G polymorphisms and ETS exposure have a role in the tumorigenesis of lung adenocarcinoma among never smokers.

Gene variation of the transient receptor potential cation channel, subfamily M, members 6 (TRPM6) and 7 (TRPM7), and type 2 diabetes mellitus: a case-control study

Transient receptor potential cation channel, subfamily M, members 6 (TRPM6) and 7 (TRPM7), have been implicated in inflammatory disorders including diabetes, a major source of morbidity and mortality in developing and Western society. We hypothesized that gene variation of TRPM6 and TRPM7 may play a role in type 2 diabetes mellitus (T2DM) Using a case-control population sample of the Boston metropolitan area (all whites, 455 controls and 467 cases), we assessed the relationship of 29 TRPM6 and 11 TRPM7 tag-single nucleotide polymorphisms (SNPs) with (1) several diabetes-related intermediate phenotypes (fasting insulin levels, fasting glucose levels, hemoglobin A1c, and homeostatic model assessment) and (2) the presence of T2DM. All SNPs examined were in Hardy-Weinberg equilibrium. Overall, genotype distributions were similar between cases and controls. Linear regression analysis, adjusted for potential risk factors/confounders, showed no evidence of an association of any SNPs tested with the aforementioned diabetes-related intermediate phenotypes after correcting for multiple testing. Marker-by-marker multivariable logistic regression analysis showed no evidence of an association of any SNPs tested with the presence of T2DM after correcting for multiple testing. Continued investigation using an entropy-blocker-defined haplotype-based approach showed similar null findings. If corroboration occurs in future large prospective investigations, then the present investigation further suggests that TRPM6 and TRPM7 gene variation may not be useful predictors for T2DM risk assessment.

Variation in the CBP gene involved in epigenetic control associates with cognitive function

Research into the pathologic mechanisms of neurodegenerative diseases has revealed that CREB binding protein (CBP) plays an important role in cognitive dysfunction. Loss of one copy of this gene leads to a syndrome with severe cognitive dysfunction. We investigated the association between four common variants in the CBP gene and cognitive function in 5804 participants of the PROspective Study of Pravastatin in the Elderly at Risk (PROSPER). Baseline associations between genetic variation and cognitive function were assessed with linear regression. Longitudinal associations were assessed with linear mixed models. All analyses were adjusted for sex, age, education, country, version of test, and pravastatin use. The intron 4CT and intron 3AC polymorphisms in the CBP gene were associated with better cognitive performance at baseline and during follow-up. Furthermore, the haplotype with the variant alleles of these two polymorphisms also showed a protective effect on cognitive function in all cognitive domains (all p<0.03). Genetic variation in the CBP gene is associated with better cognitive performance in an elderly population. Future research is necessary to investigate the effect of these polymorphisms on the expression of CBP levels and how these polymorphisms affect the gene expression mediated by CBP.

ATM polymorphisms and risk of lung cancer among never smokers

The ataxia-telangiectasia mutated (ATM) gene, an important caretaker of overall genome stability, is thought to play a role in the development of human malignancy. Therefore, we hypothesized that sequence variants in ATM may influence the disposition to lung cancer. In this hospital-based matched case-control study, nine ATM single nucleotide polymorphisms (rs189037, rs228597, rs228592, rs664677, rs609261, rs599558, rs609429, rs227062, and rs664982) were genotyped in 730 lung cancer patients and 730 healthy controls. Pairwise linkage disequilibrium among nine polymorphisms in the ATM gene was very high. None of the main effects of any of the ATM polymorphisms were related to the risk of lung cancer. Interestingly, ATM polymorphisms were significantly associated with lung cancer among never smokers, and the association was modulated by low-level exposure to carcinogens such as environmental tobacco smoke. When the haplotypes of nine ATM polymorphism sites were studied, no overall association between ATM haplotypes and risk of lung cancer was found. However, the frequency distribution of haplotypes between lung cancer cases and controls was significant in the never smokers (P=0.009), demonstrating that haplotypes have a significant effect on the risk of lung cancer. In conclusion, we found that never smokers with sequence variants of the ATM gene may be at increased risk for lung cancer. Our data also suggest this association may be further modified by exposure to environmental tobacco smoke. This study suggests support to the literature that ATM polymorphisms and environmental tobacco smoke exposure have a role in lung carcinogenesis among never smokers.

A polymorphism in the APE1 gene promoter is associated with lung cancer risk

Apurinic/apyrimidinic endonuclease 1 (APE1) is an essential enzyme in the base excision repair pathway, which is the primary mechanism for the repair of DNA damage caused by oxidation and alkylation. We hypothesized that polymorphisms of APE1 are associated with risk for lung cancer. In the hospital-based matched case-control study, a total of 730 lung cancer cases and 730 cancer-free controls were genotyped for four APE1 haplotype-tagging polymorphisms (that is, -656T>G, 400A>G, 630T>C, and 1350T>G). Among them, the single-nucleotide polymorphism -656T>G located in the promoter region of APE1 was significantly associated with risk for lung cancer. We found that, compared with -656 TT homozygotes, the variant genotypes were associated with a significantly decreased risk [adjusted odds ratio, 0.51; 95% confidence interval (95% CI), 0.33-0.79 for -656 TG; adjusted odds ratio, 0.43; 95% CI, 0.25-0.76 for -656 GG, respectively]. Furthermore, we found a statistically significant reduced risk of -656T>G variants among heavy smokers (adjusted odds ratio, 0.52; 95% CI, 0.30-0.93 for -656 TG; adjusted odds ratio, 0.27; 95% CI, 0.13-0.57 for -656 GG, respectively), with a significant gene-smoking interaction (P = 0.013). A similar gene-smoking interaction in the context of APE1 haplotypes was also observed. The in vitro promoter assay revealed that the -656 G allele had a significantly higher transcriptional activity than that of the -656 T allele. Together, our results suggest that polymorphisms of the APE1 gene possibly interact with smoking and may contribute to the development of lung cancer.

Shrinkage Estimators for Robust and Efficient Inference in Haplotype-Based Case-Control Studies

Case-control association studies often aim to investigate the role of genes and gene-environment interactions in terms of the underlying haplotypes (i.e., the combinations of alleles at multiple genetic loci along chromosomal regions). The goal of this article is to develop robust but efficient approaches to the estimation of disease odds-ratio parameters associated with haplotypes and haplotype-environment interactions. We consider "shrinkage" estimation techniques that can adaptively relax the model assumptions of Hardy-Weinberg-Equilibrium and gene-environment independence required by recently proposed efficient "retrospective" methods. Our proposal involves first development of a novel retrospective approach to the analysis of case-control data, one that is robust to the nature of the gene-environment distribution in the underlying population. Next, it involves shrinkage of the robust retrospective estimator toward a more precise, but model-dependent, retrospective estimator using novel empirical Bayes and penalized regression techniques. Methods for variance estimation are proposed based on asymptotic theories. Simulations and two data examples illustrate both the robustness and efficiency of the proposed methods.

Variation in the GST mu locus and tobacco smoke exposure as determinants of childhood lung function

RATIONALE

The glutathione S-transferases (GSTs) are important detoxification enzymes.

OBJECTIVES

To investigate effects of variants in GST mu genes on lung function and assess their interactions with tobacco smoke exposure.

METHODS

In this prospective study, 14,836 lung function measurements were collected from 2,108 children who participated in two Southern California cohorts. For each child, tagging single nucleotide polymorphisms in GSTM2, GSTM3, GSTM4, and GSTM5 loci were genotyped. Using principal components and haplotype analyses, the significance of each locus in relation to level and growth of FEV1, maximum midexpiratory flow rate (MMEF), and FVC was evaluated. Interactions between loci and tobacco smoke on lung function were also investigated.

MEASUREMENTS AND MAIN RESULTS

Variation in the GST mu family locus was associated with lower FEV1 (P = 0.01) and MMEF (0.04). Two haplotypes of GSTM2 were associated with FEV1 and MMEF, with effect estimates in opposite directions. One haplotype in GSTM3 showed a decrease in growth for MMEF (-164.9 ml/s) compared with individuals with other haplotypes. One haplotype in GSTM4 showed significantly decreased growth in FEV1 (-51.3 ml), MMEF (-69.1 ml/s), and FVC (-44.4 ml), compared with all other haplotypes. These results were consistent across two independent cohorts. Variation in GSTM2 was particularly important for FVC and FEV(1) among children whose mothers smoked during pregnancy.

CONCLUSIONS

Genetic variation across the GST mu locus is associated with 8-year lung function growth. Children of mothers who smoked during pregnancy and had variation in GSTM2 had lower lung function growth.

Polymorphisms in advanced glycosylation end product-specific receptor (AGER) gene, insulin resistance, and type 2 diabetes mellitus

BACKGROUND

Variants in the advanced glycosylation end product-specific receptor (AGER) gene have been associated with diabetic vasculopathy, however their role in the pathogenesis of insulin resistance and type 2 diabetes mellitus (T2DM) are uncertain. We investigated the relationship of 3 polymorphisms (rs1800625, rs1800624 and rs2070600) in the AGER gene and their haplotypes with T2DM as well as insulin resistance.

METHODS

A case-control study from community-based population sample of the Boston metropolitan area was performed in 637 diabetic patients and 596 controls (non-diabetic). The relationships between genotypes and T2DM were evaluated by linear and logistic regression models. Associations with insulin resistance [using corrected insulin response (CIR-30), insulin sensitivity index (ISI-120) and oral glucose tolerance test] were also examined among controls.

RESULTS

We found no consistent association between prevalent type 2 diabetes mellitus, and "insulin indices" (CIR-30, ISI-120 and oral glucose tolerance test) and the AGER polymorphisms. The A allele in the rs1800624 was modestly associated with a progressive decrease in CIR-30 levels only among Black controls (p=0.03).

CONCLUSIONS

A suggestive association between the A allele in the rs1800624 and CIR-30 levels was found. Further large and multiethnic studies should be performed to clarify these relationships.

Association of an EGFR intron 1 SNP with never-smoking female lung adenocarcinoma patients

Epidermal growth factor receptor (EGFR) plays an important role in the development and progression of a variety of malignant tumors. To test single nucleotide polymorphisms (SNPs) and haplotypes of the EGFR in modulating the lung cancer susceptibility, we conducted a matched case-control study of 730 lung cancer patients and 730 healthy controls for examining the association in Taiwanese population. Fourteen tag SNPs distributed in EGFR were selected for genotyping and one SNP 8227G>A (rs763317) located in the intron 1 of EGFR was significantly associated with lung cancer (P=0.009). Interestingly, the increase of lung cancer risk is significantly associated with never-smoking female adenocarcinoma patients harboring 8227A allele. In never-smoking female population, ORs for 8227G>A were significantly increased in adenocarcinoma subtype (adjusted odds ratio (OR) for GA genotype=1.23, 95% confidence interval (CI)=0.87-1.75; and adjusted OR for AA genotype=3.52, 95% CI=1.32-9.37, respectively). The ORs in dominant or recessive genetic model were also significantly increased in female lung adenocarcinoma subtype (adjusted OR=1.35, 95% CI=1.05-1.90; and adjusted OR=3.26, 95% CI=1.24-8.62, respectively). Haplotype analyses of 14 EGFR SNPs revealed that haplotype comprising the rare allele of 8227G>A and the common allele of the other 13 SNPs was associated with a significantly increased risk of female adenocarcinoma (OR=2.81, 95% CI=1.02-7.77). Together, our results suggest that polymorphisms or haplotypes of the EGFR play an important role in the development of lung cancer in Taiwan, particularly in never-smoking female lung adenocarcinoma.

Genetic variants within the interleukin-1 gene cluster, and risk of incident myocardial infarction, and ischemic stroke: a nested case-control approach

BACKGROUND AND PURPOSE

Recent findings implicating specific gene polymorphisms of the interleukin-1 superfamily gene cluster in the risk of developing athero-thrombotic disorders have generated great interest. However, to date, no prospective, genetic-epidemiological data are available.

METHODS

Using DNA samples collected at baseline in a prospective cohort of 14,916 initially healthy American men, we evaluated seven gene polymorphisms within the interleukin-1 gene cluster among 599 individuals who subsequently developed athero-thrombotic event and among 599 age- and smoking-matched individuals who remained free of reported cardiovascular disease during follow-up (341 incident myocardial infarction matched case-control pairs and 258 incident ischemic stroke matched case-control pairs).

RESULTS

Overall, we observed little evidence of association between the polymorphisms tested and risk of incident athero-thrombotic events. Further adjustment for traditional cardiovascular risk factors yielded similar null findings. Of note, a modest association of rs1143623 with reduced risk of incident MI was found (recessive model: OR=0.455, 95% CI=0.215-0.960, uncorrected p=0.039). However, this finding was not corrected for multiple testing, and thus requires cautious interpretation.

CONCLUSION

In contrast to prior retrospective studies, our prospective data suggest that the IL-1 cluster gene variation is not associated with risk of athero-thrombotic disorders.

Scrapie resistance in ARQ sheep

Variation in the ovine prion protein amino acid sequence influences scrapie progression, with sheep homozygous for A(136)R(154)Q(171) considered susceptible. This study examined the association of survival time of scrapie-exposed ARQ sheep with variation elsewhere in the ovine prion gene. Four single nucleotide polymorphism alleles were associated with prolonged survival. One nonsynonymous allele (T112) was associated with an additional 687 days of survival for scrapie-exposed sheep compared to M112 sheep (odds ratio, 42.5; P = 0.00014). The only two sheep homozygous for T112 (TARQ) did not develop scrapie, suggesting that the allelic effect may be additive. These results provide evidence that TARQ sheep are genetically resistant to development of classical scrapie.

Genetic variants of tumor necrosis factor superfamily, member 4 (TNFSF4), and risk of incident atherothrombosis and venous thromboembolism

BACKGROUND

Recent data have implicated tumor necrosis factor (ligand) superfamily, member 4 (TNFSF4) gene variation in myocardial infarction in women; however, no prospective data are available on either incident arterial or venous disorders.

METHODS

We evaluated 2 previously characterized TNFSF4 gene variants (-921C>T and dbSNP rs3850641) with a) incident arterial events using a prospective case-cohort design with 344 incident CVD cases and 2254 control participants, all white, drawn from the Women's Health Study cohort with 10 years of follow-up, and b) venous thromboembolism (VTE) risk using a nested, matched case-control design of 108 white male pairs (drawn from the Physicians' Health Study cohort) and a case-cohort design of white female participants consisting of 125 cases and 2269 controls (drawn from the Women's Health Study cohort), analyzed separately.

RESULTS

Genotype distributions were in Hardy-Weinberg equilibrium. Results from a marker-by-marker regression analysis, adjusting for traditional risk factors, showed a significant association of -921C>T with an increased risk of VTE in women (additive: odds ratio 1.86; 95% CI 1.17-2.92, P = 0.008) in women. Furthermore, using a haplotype-based regression analysis, haplotype C-G was associated with a reduced risk of VTE relative to the referent haplotype, C-A (odds ratio 0.50; 95% CI 0.27-0.92; P = 0.02). In contrast, we found little evidence for an association of the variants/haplotypes with risk of VTE in men or CVD risk in women (as previously reported).

CONCLUSIONS

Our present findings, if corroborated in other prospective investigations, suggest that the TNFSF4 variants tested may be useful indicators for assessing the risk of venous thromboembolism.

Glutathione S-transferase P1, maternal smoking, and asthma in children: a haplotype-based analysis

BACKGROUND

Glutathione S-transferase P1 (GSTP1) plays a role in a spectrum of respiratory diseases; however, the effects of sequence variation across the entire locus in asthma pathogenesis have yet to be determined.

OBJECTIVES

This study was designed to investigate whether sequence variations in the GSTP1 coding and promoter regions are associated with asthma and wheezing outcomes and to determine whether variants affect susceptibility to maternal smoking.

METHODS

Four haplotype tagging SNPs were selected that accounted for 83% of the common haplotypic variation in GSTP1. The associations of GSTP1 variants with asthma and wheezing were assessed among white children in the Children's Health Study (CHS).

RESULTS

The Ile105Val allele and a SNP in the upstream promoter region (SNP1: rs6591255, putative transcription factor 1 binding site) were associated with asthma and wheezing outcomes, an association observed in two cohorts of the CHS recruited in different years. Haplotypes that included both the promoter SNP (i.e., rs6591255) and the 105 Val variant were associated with an increased risk for asthma in non-Hispanic whites. Using SNP- and haplotype-based approaches, the effect of maternal smoking on wheezing was largest in children with the Ile105Val allele.

CONCLUSIONS

Variants in both the promoter and coding regions of the GSTP1 locus may contribute to the occurrence of childhood asthma and wheezing and may increase susceptibility to adverse effects of tobacco-smoke exposure.

Conditional likelihood methods for haplotype-based association analysis using matched case-control data

Genetic epidemiologists routinely assess disease susceptibility in relation to haplotypes, that is, combinations of alleles on a single chromosome. We study statistical methods for inferring haplotype-related disease risk using single nucleotide polymorphism (SNP) genotype data from matched case-control studies, where controls are individually matched to cases on some selected factors. Assuming a logistic regression model for haplotype-disease association, we propose two conditional likelihood approaches that address the issue that haplotypes cannot be inferred with certainty from SNP genotype data (phase ambiguity). One approach is based on the likelihood of disease status conditioned on the total number of cases, genotypes, and other covariates within each matching stratum, and the other is based on the joint likelihood of disease status and genotypes conditioned only on the total number of cases and other covariates. The joint-likelihood approach is generally more efficient, particularly for assessing haplotype-environment interactions. Simulation studies demonstrated that the first approach was more robust to model assumptions on the diplotype distribution conditioned on environmental risk variables and matching factors in the control population. We applied the two methods to analyze a matched case-control study of prostate cancer.

SIRT1 gene, age-related diseases, and mortality: the Leiden 85-plus study

The (Silent Information Regulator 2) Sir2 gene has been shown to regulate the life span of several model organisms. In mammals, the evolutionarily conserved homologue (Sirtuin 1) SIRT1 regulates neuroprotection, metabolism, and cell survival in response to stress. Based on these data, we hypothesized that SIRT1 might influence the prevalence of age-related diseases and modify the life span of humans. In order to test this, we genotyped five single nucleotide polymorphisms (SNPs) in 1245 participants of the population-based Leiden 85-plus Study. SIRT1 haplotypes were assessed and tested for association with the risks of mortality, metabolic profile, age-related diseases, and cognitive functioning. These analyses revealed a trend for lower cardiovascular mortality for haplotype 2 and rs3758391 SNP carriers. In further analyses, this trend was not supported by intermediate phenotypes, albeit the rs3758391 T-allele carriers had better cognitive functioning. In conclusion, our results indicate a role for SIRT1 in cognitive functioning, but the role in life span remains to be elucidated.

Polymorphisms of CAK genes and risk for lung cancer: A case–control study in Chinese population

The incidence of lung cancer has been increasing over recent decades. Previous studies show that polymorphisms of the genes involved in carcinogen-detoxication, DNA repair and cell cycle control compose of the risk factors for lung cancer. Recent observations reveal that the components of CAK: Cdk7, MAT1 and cyclin H, may play important roles in cell cycle control, transcriptional control, and DNA repairing process, all of which are important in carcinogenesis. To test whether the genetic variants of CAK genes modify the risk of lung cancer, we compared the manifestation of 25 single nucleotide polymorphisms (SNPs) and the haplotypes of Cdk7, MAT1 and cyclin H between 500 patients with lung cancer and 517 healthy controls. Our results indicated that the genotype frequency of MAT1 79023A/G (p = 0.042) and MAT1 85693C/T (p = 0.005) of cases significantly differed from those of the controls. Further analyses revealed that cyclin H 11817C/T, MAT1 12199A/G, MAT1 70650A/G, MAT1 79023A/G and MAT1 85693C/T significantly influenced the susceptibility of lung cancer in a dominant genetic model while cyclin H 12128A/T and MAT1 42172A/G did in a recessive model. Strongest association between cyclin H alleles and lung cancer patients was found in the non-smoke subpopulation. The haplotype 'TAC' (p = 0.007) increased and the haplotype 'TTC' (p = 0.043) decreased the risk of lung cancer. The potential gene-gene and gene-environmental interactions on lung cancer risk was evaluated using MDR software. A significant interaction between the three CAK component genes was identified and the combination of smoking status and genetic factors barely increased the accuracy. Our results suggested that genetic variants in CAK genes, Cdk7, cyclin H, MAT1, might modulate the risk of lung cancer in a gene-gene interaction mode, which consist to the biochemical interaction of corresponding proteins.

Intercellular adhesion molecule 1 (ICAM1) Lys56Met and Gly241Arg gene variants, plasma-soluble ICAM1 concentrations, and risk of incident cardiovascular events in 23,014 initially healthy white women

BACKGROUND AND PURPOSE

The objective of this study was to examine the association of 2 nonsynonymous intercellular adhesion molecule 1 (ICAM1) gene variants (Lys56Met and Gly241Arg) with baseline plasma soluble ICAM1 concentrations and with risk of total and selected cardiovascular disease (CVD) events in a prospective cohort of 23 014 apparently healthy white American women followed for 10 years. ICAM1 variations have been associated with plasma soluble ICAM1 concentrations and inflammatory conditions, including atherosclerosis. However, to date, no large prospective, genetic-epidemiological data set is available that would allow evaluation of the degree of association of these gene variants with risk of CVD.

METHODS

ICAM1 genotypes and baseline plasma soluble ICAM1 concentrations were determined. The primary outcome measure was a composite CVD end point (incident ischemic stroke, myocardial infarction, or death due to ischemic CVD); other measures were incident ischemic stroke, myocardial infarction, and coronary revascularization. During follow-up, 751 total incident CVD events, 187 incident myocardial infarction cases, 203 incident ischemic stroke cases, and 433 coronary revascularization events occurred.

RESULTS

All observed genotype frequencies were in Hardy-Weinberg equilibrium across the whole sample population. We found baseline plasma soluble ICAM1 concentrations to be significantly reduced among carriers of Met56 allele (P<0.0001) and Arg241 allele (P<0.0001) as compared with the respective noncarriers of these variants. However, the polymorphisms tested and the respective haplotypes were neither associated with overall risk nor with risk with risk for selected CVD events regardless of whether analyses were adjusted for traditional CVD risk factors/confounders (all P values >0.10).

CONCLUSIONS

In this large prospective study, we found an association of the nonsynonymous gene variants tested with reduced baseline plasma soluble ICAM1 concentrations. However, no evidence was found for an association of the gene variants tested with the overall or selected CVD end points examined, suggesting that these variants may not add useful aids to current risk predictors for early assessment of cardiovascular events.

C-reactive protein gene variation and type 2 diabetes mellitus: a case-control study

OBJECTIVE

C-reactive protein (CRP) gene variation, in particular an rs2794521 variant was recently associated with type 2 diabetes mellitus (T2DM) in Pima Indians.

RESEARCH DESIGN AND METHODS

The present investigation was conducted to replicate this previous association, and to further examine the potential association of a set of common CRP gene variants with the prevalence of T2DM in a case-control investigation. A total of 629 T2DM cases (476 Whites, and 153 Blacks), and 579 controls (481 Whites, and 98 Blacks) were examined. Seven CRP variants were evaluated: rs3093059, rs2794521, rs3091244, rs1417938, rs1800947, rs1130864, and rs1205.

RESULTS

Using a marker-by-marker logistic regression analysis, adjusting for age, smoking, gender, and body mass index, we found an association of rs3093059 (recessive: OR, 7.01; 95% CI, 1.16-42.22; p=0.03) with T2DM in the white study population, and an association, albeit not statistically significant, of rs2794521 with T2DM in the Black study population. Moreover, further analysis using a haplotype-based analysis showed no evidence for an association of the haplotypes tested with T2DM.

CONCLUSION

Further studies are needed to examine the possible involvement of C-reactive protein gene variation in the pathogenesis of type 2 diabetes mellitus.

Purinergic receptor P2Y, G-protein coupled, 12 gene variants and risk of incident ischemic stroke, myocardial infarction, and venous thromboembolism

Recent data have implicated a haplotype of the purinergic receptor P2Y, G-protein coupled, 12 gene (P2RY12), as potential risk determinant for atherothrombosis. However, to date, no prospective, genetic-epidemiological data are available. Using DNA samples collected at baseline in a prospective cohort of 14,916 initially healthy American men, we examined the possible association of P2RY12 genetic variants, in particular a haplotype H2 (constituted by dbSNP rs10935838, rs2046934, rs5853517, and rs6809699) amongst 708 white males who subsequently developed a thromboembolic event (incident myocardial infarction (MI), ischemic stroke, or deep venous thromboembolism/pulmonary embolism (DVT/PE)) and amongst an equal number of age- and smoking-matched white males who remained free of reported vascular disease during follow-up (controls). The P2RY12 gene variants tested were in linkage disequilibrium. The haplotype H2 distribution was significantly different between the DVT/PE cases (12%) and their matched controls (21%), p-permuted=0.02. In an adjusted conditional logistic regression analysis, the haplotype H2 was significantly associated with a lower risk of incident DVT/PE as compared to the reference haplotype H1 (odds ratio=0.50, 95% CI=0.27-0.93, p=0.028). However, we found no evidence for an association of the P2RY12 variants or the haplotype H2 with incident MI or ischemic stroke. The present investigation provides evidence for an association of the P2RY12 haplotype H2 with lower risk of DVT/PE; however these findings require replication in other well-designed studies.

Retrospective analysis of haplotype-based case control studies under a flexible model for gene environment association

Genetic epidemiologic studies often involve investigation of the association of a disease with a genomic region in terms of the underlying haplotypes, that is the combination of alleles at multiple loci along homologous chromosomes. In this article, we consider the problem of estimating haplotype-environment interactions from case-control studies when some of the environmental exposures themselves may be influenced by genetic susceptibility. We specify the distribution of the diplotypes (haplotype pair) given environmental exposures for the underlying population based on a novel semiparametric model that allows haplotypes to be potentially related with environmental exposures, while allowing the marginal distribution of the diplotypes to maintain certain population genetics constraints such as Hardy-Weinberg equilibrium. The marginal distribution of the environmental exposures is allowed to remain completely nonparametric. We develop a semiparametric estimating equation methodology and related asymptotic theory for estimation of the disease odds ratios associated with the haplotypes, environmental exposures, and their interactions, parameters that characterize haplotype-environment associations and the marginal haplotype frequencies. The problem of phase ambiguity of genotype data is handled using a suitable expectation-maximization algorithm. We study the finite-sample performance of the proposed methodology using simulated data. An application of the methodology is illustrated using a case-control study of colorectal adenoma, designed to investigate how the smoking-related risk of colorectal adenoma can be modified by "NAT2," a smoking-metabolism gene that may potentially influence susceptibility to smoking itself.

Haplotypes in the human Foxo1a and Foxo3a genes; impact on disease and mortality at old age

Recently, the Daf-16 gene has been shown to regulate the lifespan of nematodes and flies. In mammals, the Daf-16 homologues are forkhead (FOXO) transcription factors, of which specific functions have been identified for Foxo1a and Foxo3a. Despite that, their influence on human age-related trajectories and lifespan is unknown. Here, we analysed the effect of genetic variance in Foxo1a and Foxo3a on metabolic profile, age-related diseases, fertility, fecundity and mortality. This study was carried out in the prospective population-based Leiden 85-plus Study, which includes 1245 participants, aged 85 years or more. The mean follow-up time was 4.4 years. Haplotype analyses of Foxo1a revealed that carriers of haplotype 3 'TCA' have higher HbA1c levels (P=0.025) and a 1.14-fold higher all-cause mortality risk (P=0.021). This increase in mortality was attributable to death from diabetes, for which a 2.43-fold increase was observed (P=0.025). The analyses with Foxo3a haplotypes revealed no differences in metabolic profile, fertility or fecundity. However, increased risks of stroke were observed for Foxo3a block-A haplotype 2 'GAGC' (P=0.007) and haplotype 4 'AAAT' (P=0.014) carriers. In addition, the haplotype 2 'GAGC' carriers had a 1.13-fold increased risk for all-cause mortality (P=0.036) and 1.19-fold increased risk for cardiovascular mortality (P=0.052). In conclusion, this study shows that genetic variation in evolutionarily conserved Foxo1a and Foxo3a genes influences lifespan in our study population.

Risk of human T-lymphotropic virus type I-associated diseases in Jamaica with common HLA types

Human T-lymphotropic virus-I (HTLV-I) causes adult T-cell leukemia/lymphoma (ATL) and HTLV-associated myelopathy/tropical spastic paraparesis (HAM/TSP). We postulated a higher disease risk for people with common human leukocyte antigen (HLA) types, due to a narrower immune response against viral or neoplastic antigens, compared to people with uncommon types. HLA class-I (A,B) and class-II (DRB1, DQB1) allele and haplotype frequencies in 56 ATL patients, 59 HAM/TSP patients and 190 population-based, asymptomatic HTLV-I-infected carriers were compared by logistic regression overall (score test) and with odds ratios (ORs) for common types (prevalence >50% of asymptomatic carriers) and by prevalence quartile. HTLV-I proviral load between asymptomatic carriers with common versus uncommon types was compared by t-test. ATL differed from asymptomatic carriers in overall DQB1 allele and class-I haplotype frequencies (p </=</= 0.04). ATL risk was increased significantly with common HLA-B (OR 2.25, 95% CI 1.19-4.25) and DRB1 (OR 2.11, 95% CI 1.13-3.40) alleles. Higher prevalence HLA-B alleles were associated with higher ATL risk (OR 1.14 per quartile, p(trend) = 0.02). Asymptomatic carriers with common HLA-B alleles had marginally higher HTLV-I proviral load (p = 0.057). HAM/TSP risk did not differ consistently with common HLA types. Thus, ATL risk, but not HAM/TSP risk, was increased with higher prevalence HLA-B alleles. Perhaps breadth of cellular immunity affects risk of this viral leukemia/lymphoma.

The differential effects of age on the association of KLOTHO gene polymorphisms with coronary artery disease

The Klotho knockout mouse is thought to be a good animal model for human aging. Recent studies have reported on the association of KLOTHO gene mutation with cardiovascular disease in humans. We observed the frequencies of single nucleotide polymorphisms, that is, G-395A in the promoter region, C1818T in exon 4, and a functional variant, KL-VS, of KLOTHO gene in Koreans, and we investigated their relationships with the presence of coronary artery disease (CAD) in patients who had undergone coronary angiograms. A total of 274 subjects who underwent coronary angiograms because of chest pain were enrolled, and their blood pressure, body mass index, fasting blood glucose level, and lipid profiles were measured. Genotypings were performed on samples of their blood with real-time polymerase chain reaction. Two single nucleotide polymorphisms, G-395A and C1818T, complied with Hardy-Weinberg equilibrium. For the KL-VS genotype, 1 homozygote subject for the adverse allele was detected among the entire population (GG for F352V and CC for C370S). When the subjects were classified into 4 groups according to the number of stenotic vessels, there were no differences among the mean values of the cardiovascular risk factors, except for age and the fasting blood glucose levels, which showed a significant difference between that of the normal and the diseased vessel groups. There were no differences in the prevalence of CAD according to the genotypes of the G-395A polymorphism; however, for the C1818T polymorphism, those subjects with the T allele showed a lower prevalence of CAD than those with the CC genotype. When the subjects were divided into 2 groups according to age, in the group younger than 60 years, T allele carriers of the C1818T polymorphism showed a lower prevalence of CAD than did the noncarriers. In the group older than 60 years, A allele carriers of the G-395A polymorphism showed a lower prevalence of CAD than did the noncarriers. On the haplotype analysis, the GG-CC haplotype showed an increased risk for CAD with an odds ratio of 2.594 (95% confidence interval, 1.385-4.858; P = 0.003). Differential effects of age were observed in the association of KLOTHO G-395A and C1818T polymorphisms with CAD in Koreans. The KL-VS variant seems to be rarely found in the Korean population. These results infer the possibility of the KLOTHO gene being a candidate gene of atherosclerosis in humans, and further research on this topic needs to be done.

Association of adiponectin gene variations with risk of incident myocardial infarction and ischemic stroke: a nested case-control study

BACKGROUND

Adiponectin (ADIPOQ) gene variations are associated with risk of cardiovascular disease in patients with diabetes. No prospective data are available, however, on the risk of atherothrombotic disorders in persons with ADIPOQ variations who do not have diabetes.

METHODS

From a group of DNA samples collected at baseline in a prospective cohort of 14 916 initially healthy American men, we assessed the presence of 5 ADIPOQ genetic variants (rs266729, rs182052, rs822396, rs2241766, and rs1501299) in samples from 600 Caucasian men who subsequently suffered an atherothrombotic event (incident myocardial infarction or ischemic stroke) and from 600 age- and smoking-matched Caucasian men who remained free of reported vascular disease during follow-up (controls).

RESULTS

Genotype distributions for the variations tested were in Hardy-Weinberg equilibrium. Marker-by-marker conditional logistic regression analysis, adjusted for potential risk factors, showed an association of rs266729 [recessive: odds ratio (OR), 0.26; 95% confidence interval (CI), 0.10-0.64; P=0.004] and rs182052 (recessive: OR, 0.40; 95% CI, 0.21-0.76; P=0.006) with decreased risk of ischemic stroke. These findings remained significant after Bonferroni correction. Haplotype-based (constituted by rs266729, rs182052, and rs822396) conditional logistic regression analysis, adjusted for the same potential risk factors, showed an association of haplotype G-A-G (OR, 0.28; 95% CI, 0.09-0.87; P=0.03) with decreased risk of ischemic stroke. Prespecified analysis limited to participants without baseline diabetes showed similar significant findings.

CONCLUSIONS

The present prospective investigation provides further evidence for a protective role of adiponectin gene variation in the risk of ischemic stroke that was independent of the presence of diabetes.

Polymorphisms of the Phosphodiesterase 4D, cAMP-Specific ( PDE4D ) Gene and Risk of Ischemic Stroke

Background and Purpose— In an Icelandic population, gene variants of the phosphodiesterase 4D, cAMP-specific ( PDE4D ) gene were reported to be risk predictors for ischemic stroke. Case–control studies in other populations have yielded mixed evidence for association. A recent analysis in a prospective, non-Icelandic study found an association with stroke after stratification by hypertension.

Methods— We evaluated nine PDE4D single nucleotide polymorphisms (SNPs) among 259 incident ischemic stroke cases and 259 controls were matched on age and smoking status and length of follow up since randomization, all drawn from initially healthy white males within the Physicians’ Health Study cohort who were prospectively followed for first-ever stroke events.

Results— Genotype and allele distributions were similar between cases and controls. Results from single-marker conditional logistic regression analysis adjusting for traditional stroke risk factors showed significant association of SNP56 with risk of ischemic stroke (recessive odds ratio [OR], 2.26; 95% confidence interval [CI], 1.11 to 4.61; P =0.03). Among the participants without baseline hypertension, SNP42 (additive OR, 1.68; 95% CI, 0.99 to 2.86, P =0.06), SNP45 (dominant odds ratio, 2.24; 95% CI, 1.00 to 5.00, P =0.05), and SNP56 (additive odds ratio, 1.77; 95% CI, 1.02 to 3.10, P =0.04) showed modest association with increased risk of ischemic stroke.

Conclusions— We found modest associations between several PDE4D gene polymorphisms and risk of incident ischemic stroke in men without baseline hypertension in this prospective, non-Icelandic study. Although of borderline statistical significance, the direction and magnitude of the effect for SNP42 parallels that observed in a recent study evaluating women from an independent, nested case–control study.

Haplotype-based association analysis in cohort and nested case-control studies

Genetic epidemiologic studies often collect genotype data at multiple loci within a genomic region of interest from a sample of unrelated individuals. One popular method for analyzing such data is to assess whether haplotypes, i.e., the arrangements of alleles along individual chromosomes, are associated with the disease phenotype or not. For many study subjects, however, the exact haplotype configuration on the pair of homologous chromosomes cannot be derived with certainty from the available locus-specific genotype data (phase ambiguity). In this article, we consider estimating haplotype-specific association parameters in the Cox proportional hazards model, using genotype, environmental exposure, and the disease endpoint data collected from cohort or nested case-control studies. We study alternative Expectation-Maximization algorithms for estimating haplotype frequencies from cohort and nested case-control studies. Based on a hazard function of the disease derived from the observed genotype data, we then propose a semiparametric method for joint estimation of relative-risk parameters and the cumulative baseline hazard function. The method is greatly simplified under a rare disease assumption, for which an asymptotic variance estimator is also proposed. The performance of the proposed estimators is assessed via simulation studies. An application of the proposed method is presented, using data from the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study.

A prospective assessment of the Y402H variant in complement factor H, genetic variants in C-reactive protein, and risk of age-related macular degeneration

PURPOSE

Two biologically related factors, complement factor H (CFH) and C-reactive protein (CRP), have been associated with AMD. The Y402H variant of CFH is located within the binding site of CFH for CRP. Although plasma CRP levels have been related to AMD and plasma CRP levels are partly determined by genetic variation, there is no information on whether genetic variants in CRP are associated with AMD.

METHODS

A prospective analysis was performed of 111 men who eventually developed AMD and 401 men who remained free of AMD, all participants in the Physicians' Health Study. Genotypes were determined for the common T-->C single nucleotide polymorphism (SNP) in exon 9 of CFH (rs1061170; protein Y402H), as well as seven previously described CRP SNPs (rs3093059, rs2794521, rs3091244, rs1417938, rs1800947, rs1130864, and rs1205). Logistic regression analysis was used to evaluate individual SNPs, as well as six CRP haplotypes for association with AMD.

RESULTS

The high-risk C allele of CFH was present in 45% of cases and 34% of controls. An odds ratio (OR) of 1.46 was observed for AMD (95% confidence interval [CI]: 1.05-2.04) for TC heterozygotes and an OR of 2.13 (95% CI: 1.10-4.16) for CC homozygotes, assuming a multiplicative (log-additive) model and attributable fraction of 25% (95% CI: 1% to 44%) was calculated. For CRP, single-marker or haplotype-based analysis failed to reveal any significant associations with a risk of AMD.

CONCLUSIONS

These prospective data confirmed an association between the Y402H variant of CFH and a risk of AMD. In contrast, although a biologically plausible, genetic variation in CRP does not appear to be associated with a risk of AMD. Further prospective studies of a larger number of subjects are needed to substantiate available information on the genetic epidemiology of AMD.

Polymorphisms in the Advanced Glycosylation End Product–Specific Receptor Gene and Risk of Incident Myocardial Infarction or Ischemic Stroke

Background and Purpose— Recent findings of an association between polymorphisms of advanced glycosylation end product–specific receptor (AGER) and risk of diabetic vasculopathy have generated great interest. However, to date, no genetic–epidemiological data are available on risk of atherothrombotic events among nondiabetic populations.

Methods— Using DNA samples collected at baseline in a prospective cohort of 14 916 initially healthy American men, we evaluated 3 AGER genetic variants: −429T>C, −374T>A, and Gly82Ser, among 600 white individuals who subsequently developed atherothrombotic event (incident myocardial infarction or ischemic stroke) and among 600 age- and smoking-matched white individuals who remained free of reported vascular disease during follow-up (controls).

Results— Genotype distributions for the polymorphisms tested were in Hardy–Weinberg equilibrium. Haplotype-based conditional logistic regression, adjusting for other potential confounders, showed that haplotype C-T-Gly (myocardial infarction: odds ratio [OR], 0.60; 95% CI, 0.41 to 0.90; P =0.01) and haplotype T-A-Gly (ischemic stroke: OR, 0.63; 95% CI, 0.40 to 0.99; P =0.05), compared with the reference haplotype T-T-Gly, were associated with reduced risk of atherothrombosis. Prespecified analysis limited to those without baseline history of diabetes showed similar significant findings.

Conclusions— We found an association of specific AGER promoter gene haplotypes with reduced risk of incident myocardial infarction and ischemic stroke that was independent of the presence of diabetes.

Genetic variants of arachidonate 5-lipoxygenase-activating protein, and risk of incident myocardial infarction and ischemic stroke: a nested case-control approach

BACKGROUND AND PURPOSE

Recent findings have implicated specific gene polymorphisms of arachidonate 5-lipoxygenase-activating protein (ALOX5AP), and 2 at-risk haplotypes (HapA, HapB) in myocardial infarction and stroke. To date, no prospective data are available.

METHODS

We evaluated 10 specific Icelandic ALOX5AP gene variants among 600 male participants with incident atherothrombotic events (myocardial infarction [MI] or ischemic stroke) and among 600 age- and smoking-matched male participants, all white, who remained free of reported cardiovascular disease during follow-up within the Physicians' Health Study cohort.

RESULTS

Overall allele, genotype, and haplotype distributions were similar between cases and controls. Single-marker conditional logistic regression analysis adjusted for potential risk factors found no association with risk of atherothrombotic events. Further investigation using a haplotype-based approach showed similar null findings with MI (HapA: odds ratio [OR]=1.18, 95% CI, 0.76 to 1.85; P=0.46; HapB: odds ratio=0.62, 95% CI, 0.36 to 1.07; P=0.08), and with ischemic stroke (HapA: odds ratio=1.11, 95% CI, 0.65 to 1.89; P=0.71; HapB: odds ratio=0.82, 95% CI, 0.47 to 1.42; P=0.47).

CONCLUSIONS

We found no evidence for an association of the specific Icelandic ALOX5P gene variants/at-risk haplotypes tested with risk of incident MI nor ischemic stroke in this prospective, non-Icelandic study.

Endothelin axis polymorphisms in patients with scleroderma

OBJECTIVE

To evaluate the distribution of polymorphisms in the endothelin 1 (EDN1), endothelin receptor A (EDNRA) and endothelin receptor B (EDNRB) genes in systemic sclerosis (SSc; scleroderma) and SSc subsets.

METHODS

Two hundred five patients with SSc and 255 healthy controls were screened for polymorphisms in EDN1, EDNRA, and EDNRB, using sequence-specific primer-polymerase chain reaction. The polymorphisms studied were at the following positions: for EDN1, -1370 (T-1370G) of the promoter, +138 of exon 1 (+138 A/-), +85 of exon 3 (E106E), and +23 of exon 5 (K198N); for EDNRA, -231 of exon 1 (G-231A), and +69(H323H) and +105 (E335E) of exon 6; for EDNRB, +2841 of exon 2 (EDNRB-3), -2547 of exon 3 (EDNRB-2), and -2446 of exon 3 (EDNRB-1).

RESULTS

No significant differences between the SSc group as a whole and control subjects were observed for any of the investigated polymorphisms in EDN1, EDNRA, and EDNRB. However, compared with patients with limited cutaneous SSc, patients with diffuse skin involvement had an increased frequency of allele carriage of EDNRB-1A (76.8% versus 54.4%; P = 0.002), EDNRB-2A (79.7% versus 60.2%; P = 0.006), and EDNRB-3G (79.7% versus 56.6%; P = 0.001). Significantly increased carriage frequencies for EDNRA alleles H323H/C and E335E/A were observed in SSc patients with anti-RNA polymerase (anti-RNAP) antibodies, compared with both anti-RNAP-negative SSc patients (P < 0.05) and control subjects (P < 0.005).

CONCLUSION

The finding of associations between endothelin receptors A and B and distinct clinical and immunologic SSc subsets supports the role of endothelin and its receptors in the pathogenesis of SSc. However, these findings and their functional significance need to be confirmed and investigated in future studies.

Beta-2 adrenergic receptor gene (ADRB2) polymorphism and risk for lung adenocarcinoma: a case-control study in a Chinese population

The incidence of lung adenocarcinoma (AC) has been increasing over recent decades. The tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is one of the most potent carcinogens and reproducibly induces a high incidence of lung AC in laboratory animals. In addition to its genotoxic effects, NNK has also epigenetic effects on lung cells by functioning as an agonist for beta adrenergic receptors and stimulating the signal pathways that lead to lung AC. Beta-2 adrenergic receptor (ADRB2) expressed on bronchial smooth muscle is a well-defined target for asthma treatment that has epidemiological implications in lung cancer development. And biochemical effect and pharmacogenetic relevance of regulatory and coding variants of ADRB2 have been well documented. Aiming to test whether the genetic variants of ADRB2 modify risk of lung AC, we compared the manifestation of three common single nucleotide polymorphisms (SNPs) of ADRB2 (G-1023A, G-654A, and A46G (Gly16Arg)) between 313 patients with lung AC and 321 controls. Overall association was not observed between risk and either individual of the three SNPs or their combined haplotypes. However, in the subgroup of young subjects < or =50 years old, significant association was observed for G-1023A (allele based OR, 1.82; 95% CI, 1.12-2.95), A46G (Gly16Arg) (allele based OR, 0.64; 95% CI, 0.40-1.03), and the haplotype A(-1023)A(46) (OR 2.62; 95% CI 1.30-5.27). Our results do not support a major independent role of ADRB2 polymorphisms in lung AC risk, suggesting that functional variants of other genes involved in the NNK epigenetic pathway of carcinogenesis should be investigated.

Interaction between inflammation-related gene polymorphisms and cigarette smoking on the risk of myocardial infarction in the Physician’s Health Study

Inflammation is known to be a major component of atherosclerosis, and cigarette smoking is known to induce a systemic inflammatory response. We therefore, investigated possible gene-environment interactions between various inflammation-related gene polymorphisms and cigarette smoking on the risk of myocardial infarction (MI) in the Physician's Health Study (PHS), a cohort of initially healthy middle-aged men. We used a nested case-control design consisting of 522 MI cases and 2,089 controls derived from PHS. Eleven inflammatory polymorphisms were studied using logistic regression analysis: eotaxin (ala23thr), intercellular adhesion molecule 1 (gly241arg), interleukin-4 (582C>T), interleukin-4 receptor (ile75val, gln576arg), interleukin-6 (-174G>C), interleukin-10 (-571C>A), P-selectin (val640leu, thr756pro, ser330asn), and vascular cell adhesion molecule 1 (-1594T>C). Interactions of smoking with all the three modes of inheritance (additive, dominant, recessive) were tested. Statistically significant (P<0.05) interaction terms were found for interleukin-4 receptor (ile75val), with odds ratios of 0.52 (95%CI:0.29-0.95) for Ile-Val and 0.34 (95%CI:0.14-0.83) for Val-Val, compared to the wildtype Ile-Ile; for interleukin-6 (-174G>C) with odds ratios of 2.16 (1.14-4.09) for GC and 0.81 (0.31-2.12) for CC, compared to the wildtype GG; and for P-selectin (ser330asn) with odds ratios of 0.48 (0.24-0.95) for Ser-Asn and 1.08 (0.29-3.93) for Asn-Asn, compared to the wildtype Ser-Ser, with these effects occurring only among the smokers. These data raise the possibility of interaction between the smoking status and certain inflammatory polymorphisms on the risk of MI in men. However, these results should be interpreted with caution due to the potential for false positive results that can arise from analyses with multiple comparisons.

Analysis of case-control studies of genetic and environmental factors with missing genetic information and haplotype-phase ambiguity

Case-control studies of unrelated subjects are now widely used to study the role of genetic susceptibility and gene-environment interactions in the etiology of complex diseases. Exploiting an assumption of gene-environment independence, and treating the distribution of environmental exposures as completely nonparametric, Chatterjee and Carroll recently developed an efficient retrospective maximum-likelihood method for analysis of case-control studies. In this article, we develop an extension of the retrospective maximum-likelihood approach to studies where genetic information may be missing on some study subjects. In particular, special emphasis is given to haplotype-based studies where missing data arise due to linkage-phase ambiguity of genotype data. We use a profile likelihood technique and an appropriate expectation-maximization (EM) algorithm to derive a relatively simple procedure for parameter estimation, with or without a rare disease assumption, and possibly incorporating information on the marginal probability of the disease for the underlying population. We also describe two alternative robust approaches that are less sensitive to the underlying gene-environment independence and Hardy-Weinberg-equilibrium assumptions. The performance of the proposed methods is studied using simulation studies in the context of haplotype-based studies of gene-environment interactions. An application of the proposed method is illustrated using a case-control study of ovarian cancer designed to investigate the interaction between BRCA1/2 mutations and reproductive risk factors in the etiology of ovarian cancer.

Intercellular adhesion molecule-1 and childhood asthma

We investigated the role of intercellular adhesion molecule-1 in childhood asthma by examining associations of functional variants at codons 29 (A --> T), 241 (G --> A), and 469 (A --> G) in Children's Health Study participants. Among African-Americans, 469G carriers had lower risk for asthma (ever asthma OR = 0.4, 95% CI 0.2-0.9) but increased risk among 29T carriers (early onset active asthma OR = 2.2, 95% CI 1.0-4.9). Protective associations with the 241A allele were observed among non-Hispanic and Hispanic whites (ever asthma OR = 0.7, 95% CI 0.6-0.9; early onset active asthma OR = 0.5, 95% CI 0.4-0.8), and these associations were not confounded by population stratification. To gauge the potential impact of confounding by population stratification, we performed analyses by ethnic group and in an independent family-based sample. Regional associations were stable across analyses. Haplotype associations of the four common haplotypes (29A/241G/469A, AGG, TGA, and AAG) with asthma showed that Hispanics with the AAG haplotype had lower asthma risk compared to carriers of two copies of AGA haplotype (OR = 0.6, 95% CI 0.4-0.9). Among non-Hispanic whites, the AAG haplotype was associated with reduced risk for active asthma. For African-Americans, who had a low frequency of the AAG haplotype, carrying one copy of the AGG haplotype was associated with a lower risk of asthma (OR = 0.3, 95% CI 0.1-0.8), as compared with two copies of the AGA haplotype. Consistent with information on variant function, the 241A and 469G variants may indicate haplotypes that are associated with reduced risk for asthma.

Tryptophanyl-tRNA synthetase gene polymorphisms and risk of incident myocardial infarction

Tryptophanyl-tRNA synthetase (WARS) gene polymorphisms have been associated with the patho-physiology of vascular angiogenesis and homeostasis. Data from a recent genome-wide linkage analysis suggested a potential role of WARS in the risk of myocardial infarction. However, no genetic-epidemiological data are available. From a prospective cohort of 14,916 initially healthy American men, we evaluated five common polymorphisms within or close to the WARS locus, all with a minor allele frequency >0.10, amongst 386 individuals who subsequently developed myocardial infarction and 386 matched individuals who remained free of reported cardiovascular events during follow-up. The polymorphisms were: a G > C substitution in the 5'-flanking region (dbSNP rs2273804), an A > G substitution in intron 1 (dbSNP rs941931), a 335T > C substitution in exon 10 (dbSNP rs9453), a C > T substitution in intron 10 (dbSNP rs1570305), and a C > T substitution in the C14orf68 region (dbSNP rs3736951). The observed genotypes were in Hardy-Weinberg equilibrium in the control group. Genotype- and haplotype-frequency distributions were similar between cases and controls. Further investigation using a haplotype-based matched logistic regression analysis, adjusting for age, smoking, randomized treatment-assignment (likelihood ratio test: chi(3)(2) = 3.20, p = 0.36) or with additional adjustment for BMI, hypertension, and diabetes (likelihood ratio test: chi(3)(2) = 2.38, p = 0.50) yielded similar null findings. An alternative haplotype analysis based on evolutionary arguments again yielded null results. In conclusion, we found no evidence for an association between the common polymorphisms or haplotypes of the tryptophanyl-tRNA synthetase gene tested and risk of myocardial infarction.

Candidate-gene screening and association analysis at the autism-susceptibility locus on chromosome 16p: evidence of association at GRIN2A and ABAT

Autism is a highly heritable neurodevelopmental disorder whose underlying genetic causes have yet to be identified. To date, there have been eight genome screens for autism, two of which identified a putative susceptibility locus on chromosome 16p. In the present study, 10 positional candidate genes that map to 16p11-13 were examined for coding variants: A2BP1, ABAT, BFAR, CREBBP, EMP2, GRIN2A, MRTF-B, SSTR5, TBX6, and UBN1. Screening of all coding and regulatory regions by denaturing high-performance liquid chromatography identified seven nonsynonymous changes. Five of these mutations were found to cosegregate with autism, but the mutations are not predicted to have deleterious effects on protein structure and are unlikely to represent significant etiological variants. Selected variants from candidate genes were genotyped in the entire International Molecular Genetics Study of Autism Consortium collection of 239 multiplex families and were tested for association with autism by use of the pedigree disequilibrium test. Additionally, genotype frequencies were compared between 239 unrelated affected individuals and 192 controls. Patterns of linkage disequilibrium were investigated, and the transmission of haplotypes across candidate genes was tested for association. Evidence of single-marker association was found for variants in ABAT, CREBBP, and GRIN2A. Within these genes, 12 single-nucleotide polymorphisms (SNPs) were subsequently genotyped in 91 autism trios (one affected individual and two unaffected parents), and the association was replicated within GRIN2A (Fisher's exact test, P<.0001). Logistic regression analysis of SNP data across GRIN2A and ABAT showed a trend toward haplotypic differences between cases and controls.

Haplotype analysis of the beta2 adrenergic receptor gene and risk of myocardial infarction in humans

Polymorphisms in the beta2 adrenergic receptor (ADRB2), in particular G16R, Q27E, and T164I, have been implicated in the pathogenesis of cardiovascular and metabolic phenotypes. However, no prospective, genetic-epidemiological data are available on the risk of cardiovascular disease associated with these variants. Using DNA samples collected at baseline in a prospective cohort of 14,916 initially healthy American men, we evaluated the G16R, Q27E, and T164I polymorphisms among 523 individuals who subsequently developed myocardial infarction and among 2092 individuals who remained free of reported cardiovascular events during follow-up. The haplotype frequency distribution was significantly different among cases and controls (chi(2)(7d.f.) = 20.92, P = 0.0039). Haplotype-based logistic regression, adjusting for age, smoking, and randomized treatment group, indicated that G16-Q27-I164 (odds ratio 0.178, 95% C.I. 0.043-0.737, P = 0.017) and (non-G16-Q27)-T164 (odds ratio 1.235, 95% C.I. 1.031-1.480, P = 0.022) haplotypes were significantly associated with altered risk of myocardial infarction. These findings remained after further adjustment for BMI, history of hypertension, and presence or absence of diabetes. In conclusion, variation in haplotype frequencies for the beta2 adrenergic receptor gene was found to be associated with risk of myocardial infarction.

C-reactive protein gene polymorphisms and the incidence of post-angioplasty restenosis

Recent findings have demonstrated that plasma C-reactive protein levels predict restenosis after coronary angioplasty. Furthermore, C-reactive protein levels have also been shown to be heritable. However, no genetic-epidemiological data are available on the relationship between genetic variants of C-reactive protein (CRP) gene and risk of restenosis after angioplasty. The present study was carried out to examine the possible association of a non-sense exonic 1059G > C and an intronic T > A C-reactive protein gene polymorphisms in a large, previously described, well-characterized cohort of 779 post-angioplasty patients of whom 342 subjects developed restenosis. Genotype distributions were in Hardy-Weinberg equilibrium. Genotype and allele distributions were similar between cases and controls. Haplotype frequency distributions were also similar between cases and controls. Further investigation using a haplotype-based logistic and linear regression analyses, adjusting for potential confounders, yielded similar null results. In conclusion, we found no evidence for an association between the polymorphisms/haplotypes thereof tested and restenosis after angioplasty.

Identification of genetic variants in base excision repair pathway and their associations with risk of esophageal squamous cell carcinoma

The etiology of esophageal squamous cell carcinoma (ESCC) has been shown to be associated with genetic and certain environmental factors that produce DNA damage. Base excision repair (BER) genes are responsible for repair of DNA damage caused by reactive oxygen species and other electrophiles and therefore are good candidate susceptibility genes for ESCC. We first screened eight BER genes for new and potential functional polymorphisms by resequencing 27 DNA samples. We then identified and genotyped for important tagging single nucleotide polymorphisms (SNPs) in a case-control study of 419 patients with newly diagnosed esophageal cancer and 480 healthy controls by frequency matching on age and sex. The association between genotypes and ESCC risk was estimated by unconditional multivariate logistic regression analysis, and stepwise regression procedure was used for constructing the final logistic regression model. We identified 129 SNPs in the eight BER genes, including 18 SNPs that cause amino acid changes. In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala and MBD4 Glu346Lys) and others in noncoding regions (LIG3 A3704G and XRCC1 T-77C), remained as significant predictors for the risk of ESCC. The adjusted odd ratios were 1.25 [95% confidence interval (CI) 1.02-1.53] for the ADPRT 762Ala allele, 1.25 (95% CI 1.02-1.53) for the MBD4 346 Lys allele, 0.78 (95% CI 0.63-0.97) for the LIG3 3704G allele, and 1.38 (95% CI 1.01-1.89) for the XRCC1-77C allele. In addition, we observed a significant gene-gene interaction between XRCC1 Gln399Arg and ADPRT Val762Ala. The results suggest that the polymorphisms in five BER genes may be associated with the susceptibility to ESCC in a Chinese population.

TP53 haplotype-based analysis and incidence of post-angioplasty restenosis

The tumor suppressor gene product, in particular tumor suppressor protein p53 (TP53), has been suggested to play a role in post-angioplasty restenosis. However, no genetic-epidemiological studies relating to TP53 gene polymorphism(s) and the incidence of post-angioplasty restenosis are available. TP53 11951_11966dup16bp, R72P, and 13494G>A polymorphisms were characterized in a cohort of 779 patients, of whom 342 cases had developed restenosis (as defined by >50% loss of lumen compared with immediate post-procedure results) at repeat quantitative coronary angiography at six months post angioplasty. The haplotype-frequency distribution was marginally different between cases and controls with restenosis risk (chi(2)(7df)=13.08, P=0.070). Multivariable haplotype-based logistic regression indicated that haplotypes 16bp(-) -P72-G13494 [corrected], and 16bp(+) -P72-A13494 [corrected] exhibit protective effects on restenosis risk (odds ratio=0.58, 95%CI=0.40-0.83, P=0.0033; odds ratio=0.69, 95%CI=0.48-0.99, P=0.049, respectively). Multivariable haplotype-based linear regression again showed similar, significant association with degree of lumen loss. The present findings indicate protective effects of TP53 16bp(-) -P72-G13494 [corrected], and 16bp(+) -P72-A13494 [corrected] haplotypes in the incidence of restenosis after angioplasty. Furthermore, our study demonstrates that a haplotype-based approach can be more informative than a single-marker or marker-by-marker analysis.