Overestimation of genetic risks owing to small sample sizes in cardiovascular studies

quantitative assessment of the influence of cytochrome P450 1A2 gene polymorphism and colorectal cancer risk

Cytochrome P450 1A2 (CYP1A2) encodes a member of the cytochrome P450 superfamily of enzymes, which play a central role in activating and detoxifying many carcinogens and endogenous compounds thought to be involved in the development of colorectal cancer (CRC). The CYP1A2*C (rs2069514) and CYP1A2*F (rs762551) polymorphism are two of the most commonly studied polymorphisms of the gene for their association with risk of CRC, but the results are conflicting. To derive a more precise estimation of the relationship between CYP1A2 and genetic risk of CRC, we performed a comprehensive meta-analysis which included 7088 cases and 7568 controls from 12 published case-control studies. In a combined analysis, the summary per-allele odds ratio for CRC was 0.91 (95% CI: 0.83-1.00, P = 0.04), and 0.91 (95% CI: 0.68-1.22, P = 0.53), for CYP1A2 *F and *C allele, respectively. In the subgroup analysis by ethnicity, significant associations were found in Asians for CYP1A2*F and CYP1A2*C, while no significant associations were detected among Caucasian populations. Similar results were also observed using dominant genetic model. Potential sources of heterogeneity were explored by subgroup analysis and meta-regression. No significant heterogeneity was detected in most of comparisons. This meta-analysis suggests that the CYP1A2 *F and *C polymorphism is a protective factor against CRC among Asians.

Association of the CCR5Δ32 polymorphism and its ligand RANTES-403G/A polymorphism with coronary artery disease: a meta-analysis

INTRODUCTION

To explore the relationship between polymorphisms in the RANTES and CCR5 genes and the risk of coronary artery disease (CAD).

MATERIALS AND METHODS

We conducted a meta-analysis on two genetic variants (RANTES-403G/A and CCR5Δ32). Publication bias was tested by the Egger's regression test and Begg's test. Sensitivity analysis and subgroup analyses were performed to explore the heterogeneity among studies.

RESULTS

No significant association of RANTES-403G/A polymorphism and CAD risk was observed (dominant model: RR=1.02, 95%CI=0.90-1.06; recessive model: RR=1.27, 95%CI=0.90-1.80). However, after excluding the study conducted by Yangsoo et al., the pooled relative ratio (RR) in the dominant model suggested that the RANTES-403G/A polymorphism was positively associated with CAD risk. The subgroup analyses found that a positive relationship between the polymorphism and CAD risk was restricted to the Caucasian population. A meta-analysis of studies on the CCR5Δ32 polymorphism showed no significant association with CAD risk both in dominant (RR=1.05, 95%CI=0.92-1.21) and recessive (RR=1.27, 95%CI=0.90-1.80) models. Moreover, no association was identified in the subgroup analyses.

CONCLUSIONS

The RANTES-403G/A polymorphism is not associated with CAD risk, but does most likely increase CAD risk in Caucasians. Moreover, no relationship between the CCR5∆32 polymorphism and risk of CAD was found.

Genetic polymorphisms of glutathione S-transferase genes GSTM1, GSTT1 and risk of hepatocellular carcinoma

BACKGROUND

A number of case-control studies were conducted to investigate the association of glutathione S-transferase (GST) genetic polymorphisms and hepatocellular carcinoma (HCC) risk. However, these studies have yielded contradictory results. We therefore performed a meta-analysis to derive a more precise estimation of the association between polymorphisms on GSTM1, GSTT1 and HCC.

METHODOLOGY/PRINICPAL FINDINGS

PubMed, EMBASE, ISI web of science and the CNKI databases were systematically searched to identify relevant studies. Data were abstracted independently by two reviewers. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were used to assess the strength of association. Potential sources of heterogeneity were also assessed by subgroup analysis and meta-regression. Funnel plots and Egger's linear regression were used to test publication bias among the articles. A total of 34 studies including 4,463 cases and 6,857 controls were included in this meta-analysis. In a combined analysis, significantly increased HCC risks were found for null genotype of GSTM1 (OR = 1.29, 95% CI: 1.06-1.58; P = 0.01) and GSTT1 (OR = 1.43, 95% CI: 1.22-1.68; P<10(-5)). Potential sources of heterogeneity were explored by subgroup analysis and meta-regression. Significant results were found in East Asians and Indians when stratified by ethnicity; whereas no significant associations were found among Caucasians and African populations. By pooling data from 12 studies that considered combinations of GSTT1 and GSTM1 null genotypes, a statistically significant increased risk for HCC (OR = 1.88, 95% CI: 1.41-2.50; P<10(-4)) was detected for individuals with combined deletion mutations in both genes compared with positive genotypes.

CONCLUSIONS/SIGNIFICANCE

This meta-analysis suggests that the GSTM1 and GSTT1 null genotype may slightly increase the risk of HCC and that interaction between unfavourable GSTs genotypes may exist.

Genetic variants of the monocyte chemoattractant protein-1 gene and its receptor CCR2 and risk of coronary artery disease: a meta-analysis

OBJECTIVE

Monocyte chemoattractant protein-1 (MCP-1) and its receptor chemokine (C-C motif) receptor 2 (CCR2) are implicated in promoting atherosclerosis. Many studies have searched the association between variants of the MCP-1 gene or CCR2 gene and risk of coronary artery disease (CAD), but the results are inconsistent.

METHODS

We conducted a meta-analysis of 20 publications including 24 studies on 2 genetic variants [A-2518G in the MCP-1 and V64I in the CCR2] published before January 2011, including a total of 9844 patients with CAD and 11,821 controls. Publication bias and heterogeneity among studies were explored.

RESULTS

In a combined analysis, the pooled OR for CAD of the -2518G allele was 1.42 (95%CI: 1.06-1.92) compared to wild-type A allele under a recessive model in Caucasian group, but there is an indication of publication bias and heterogeneity among the 9 studies. When the analyses were restricted to 2 large studies (n≥500 cases), the pooled OR was 1.08 (95%CI: 0.85-1.37). Our analyses detected a possibility of publication bias with an overestimate of the true association by smaller studies. A meta-analysis of studies on the CCR2 V64I variant showed no significant association with CAD, the pooled OR of 64I was 1.27 (95%CI: 0.81-1.99) in recessive model and 1.06 (95%CI: 0.95-1.19) in dominant model, respectively.

CONCLUSIONS

The results indicate that MCP-1-2518G allele had probably increased risk of CAD in Caucasian but this is likely to be due to publication bias and insufficient sample size. The CCR2 V64I has not been found any association with CAD.

Four genetic polymorphisms of paraoxonase gene and risk of coronary heart disease: a meta-analysis based on 88 case-control studies

OBJECTIVE

The human paraoxonase (PON) is calcium dependent HDL associated ester hydrolase which has attracted considerable attention as a candidate gene for coronary heart disease based on its enzyme function as a key factor in lipoprotein catabolism pathways. Many studies have examined the association between polymorphisms in the PON gene and risk of coronary heart disease (CHD), but the results have been inconsistent.

METHODS

We conducted a meta-analysis of 88 studies on 4 PON polymorphisms [Q192R, L55M, and T(-107)C in the PON1 and the S311C in the PON2] published before August 2010, including a total of 24,702 CHD cases and 38,232 controls. We also systematically explored potential sources of heterogeneity.

RESULT

In a combined analysis, the summary per-allele odds ratio for CHD of the 192R was 1.11 (95% CI: 1.05-1.17). However, when the analyses were restricted to 10 larger studies (n>500 cases), the summary per-allele odds ratio was 0.96 (95% CI: 0.90-1.02). Our analyses detected a possibility of publication bias with an overestimate of the true association by smaller studies. A meta-analysis of studies on the 55M, (-107)T, and 311C variant showed no significant overall association with CHD, yielding a per-allele odds ratio of 0.94 (95% CI: 0.88-1.00), 1.02 (95% CI: 0.91-1.15) and 1.02 (95% CI: 0.90-1.16) respectively.

CONCLUSIONS

This meta-analysis suggested an overall weak association between the R192 polymorphism and CHD risk.

Lack of replication in polymorphisms reported to be associated with atrial fibrillation

BACKGROUND

Atrial fibrillation (AF) is the most common sustained arrhythmia and has a substantial heritable component. Numerous associations between single nucleotide polymorphisms (SNPs) and AF have been described, but few have been replicated.

OBJECTIVE

We sought to systematically replicate SNPs that are reported to be associated with AF in two large study samples of European descent.

METHODS

We searched PubMed for studies reporting associations between SNPs and AF published before July 1, 2007. SNPs were genotyped in two independent case-control samples from Germany and the United States. Associations between SNPs and AF were assessed using logistic regression models adjusting for age, sex, and hypertension. A meta-analysis of the results from the two studies was performed.

RESULTS

We identified 21 SNPs and the angiotensin-converting enzyme insertion/deletion polymorphism that were reported to be associated with AF in the literature. Nine of these genetic variants were not represented on common genome-wide SNP arrays. We successfully genotyped 21 of these 22 variants in 2,145 cases with AF from the German Competence Network for Atrial Fibrillation and 4,073 controls from the KORA S4 study and 16 variants in 790 cases and 1,330 controls from the Massachusetts General Hospital. None of the SNPs replicated in independent populations with AF.

CONCLUSION

Our results suggest that previously reported associations to AF were likely false positives and highlight the need for systematic replication of genetic associations in large, independent cohorts to accurately detect variants associated with disease.

A1166C genetic variation of the angiotensin II type I receptor gene and susceptibility to coronary heart disease: collaborative of 53 studies with 20,435 cases and 23,674 controls

OBJECTIVE

Angiotensin II induces vasoconstriction and vascular smooth muscle growth via stimulation of the angiotensin II type I receptor (AGTR1). Some studies have reported an association between a genetic variant (A1166C) in the 3' un-translated region of AGTR1 and increased risk of coronary heart disease (CHD), but other have yielded apparently conflicting results.

METHODS

Literature-based meta-analyses were performed on 48 papers including 53 studies published before June 2008 in relation to the A1166C polymorphism (NCBI, dbSNP: rs5186) of the AGTR1, involving a total of 20,435 CHD cases and 23,674 controls. We also explored potential sources of heterogeneity and conducted appropriate stratified analyses.

RESULTS

In a combined analysis, the per-allele odds ratio (OR) for CHD of the A1166C polymorphism was 1.11 (95% confidence interval: 1.03-1.19), but there is an indication of publication bias and heterogeneity among the 53 studies. Sample size and study quality were significant sources of heterogeneity among studies of the A1166C polymorphism with possibly overestimates in studies of smaller sample-size and poor-quality. When the analyses were restricted to 11 larger studies (≥500 cases), and to 8 high-quality studies (quality score: ≥11 points), the summary per-allele odds ratios were 0.992 (95% confidence interval, 0.944-1.042) and 0.990 (95% confidence interval, 0.915-1.072), respectively.

CONCLUSIONS

An overall weak association between the A1166C polymorphism and CHD is observed but this is likely to be due to publication bias and heterogeneity between studies. There were no significant associations among the larger sample-size and high-quality studies which are less prone to selective publication and have greater power to detect a true association.

Angiotensin-converting enzyme insertion/deletion gene polymorphism in a Tunisian healthy and acute myocardial infarction population

INTRODUCTION

The role of the insertion/deletion (I/D) polymorphism in the angiotensin-converting enzyme gene (ACE) on acute myocardial infarction (AMI) is controversial.

OBJECTIVES

To assess the effect of the ACE I/D polymorphism on AMI compared with the healthy controls and its relationship with serum ACE activity in a Tunisian population.

DESIGN AND METHODS

A total of 119 patients with AMI were compared with 238 healthy controls from the same geographical area. ACE genotyping was determined by polymerase chain reaction, and serum ACE activity was measured with N-[3-(2-furylacryloyl]-L-phenylalanyl-L-glycyl-L-glycine as substrate.

RESULTS

The ACE I/D polymorphism was significantly different between patients and controls (p < 0.0001). The frequencies of the DD genotype and the D allele were statistically higher in patients with AMI as compared with the controls and were associated with increased risk of AMI (DD vs. ID and II: odds ratio = 4.27, p < 0.0001, 95% confidence interval = 2.65-6.86; D vs. I: odds ratio = 3.15, p < 0.0001, 95% confidence interval = 2.26-4.40). This association was independent of other cardiovascular risk factors but dyslipidemia (p = 0.002) that was not represented in AMI patients with II genotype and in a lower extent with hypertension (p < 0.05). Serum ACE activity was significantly higher in AMI patients with ACE DD genotype compared with the subjects with ID or II genotype (p = 0.034) and was not correlated with other cardiovascular risk factors.

CONCLUSIONS

ACE DD genotype associated with higher serum ACE activity is increased in the studied population and might be clinically useful as markers to assess risk for AMI.

Pharmacogenomics: a new paradigm to personalize treatments in nephrology patients

Although notable progress has been made in the therapeutic management of patients with chronic kidney disease in both conservative and renal replacement treatments (dialysis and transplantation), the occurrence of medication-related problems (lack of efficacy, adverse drug reactions) still represents a key clinical issue. Recent evidence suggests that adverse drug reactions are major causes of death and hospital admission in Europe and the United States. The reasons for these conditions are represented by environmental/non-genetic and genetic factors responsible for the great inter-patient variability in drugs metabolism, disposition and therapeutic targets. Over the years several genetic settings have been linked, using pharmacogenetic approaches, to the effects and toxicity of many agents used in clinical nephrology. However, these strategies, analysing single gene or candidate pathways, do not represent the gold standard, being the overall pharmacological effects of medications and not typically monogenic traits. Therefore, to identify multi-genetic influence on drug response, researchers and clinicians from different fields of medicine and pharmacology have started to perform pharmacogenomic studies employing innovative whole genomic high-throughput technologies. However, to date, only few pharmacogenomics reports have been published in nephrology underlying the need to enhance the number of projects and to increase the research budget for this important research field. In the future we would expect that, applying the knowledge about an individual's inherited response to drugs, nephrologists will be able to prescribe medications based on each person's genetic make-up, to monitor carefully the efficacy/toxicity of a given drug and to modify the dosage or number of medications to obtain predefined clinical outcomes.

ACE D/I polymorphism, migraine, and cardiovascular disease in women

BACKGROUND

Interrelationships among the ACE deletion/insertion (D/I) polymorphism (rs1799752), migraine, and cardiovascular disease (CVD) are biologically plausible but remain controversial.

METHODS

Association study among 25,000 white US women, participating in the Women's Health Study, with information on the ACE D/I polymorphism. Migraine and migraine aura status were self-reported. Incident CVD events were confirmed after medical record review. We used logistic regression to investigate the genotype-migraine association and proportional hazards models to evaluate the interrelationship among genotype, migraine, and incident CVD.

RESULTS

At baseline, 4,577 (18.3%) women reported history of migraine; 39.5% of the 3,226 women with active migraine indicated aura. During 11.9 years of follow-up, 625 CVD events occurred. We did not find an association of the ACE D/I polymorphism with migraine or migraine aura status. There was a lack of association between the ACE D/I polymorphism and incident major CVD, ischemic stroke, and myocardial infarction. Migraine with aura doubled the risk for CVD, but only for carriers of the DD (multivariable-adjusted relative risk [RR] = 2.10; 95% CI = 1.22-3.59; p = 0.007) and DI genotype (multivariable-adjusted RR = 2.31; 95% CI = 1.52-3.51; p < 0.0001). The risk was not significant among carriers of the II genotype, a pattern we observed for myocardial infarction and ischemic stroke.

CONCLUSIONS

Data from this large cohort of women do not suggest an association of the ACE deletion/insertion (D/I) polymorphism with migraine, migraine aura status, or cardiovascular disease (CVD). The increased risk for CVD among migraineurs with aura was only apparent for carriers of the DD/DI genotype. Due to limited number of outcome events, however, future studies are warranted to further investigate this association.

Investigation of 89 candidate gene variants for effects on all-cause mortality following acute coronary syndrome

Background

Many candidate genes have been reported to be risk factors for acute coronary syndrome (ACS), but their impact on clinical prognosis following ACS is unknown.

Methods

We examined the association of putative genetic risk factors with 3-year post-ACS mortality in 811 ACS survivors at university-affiliated hospitals in Kansas City, Missouri. Through a systematic literature search, we first identified genetic variants reported as susceptibility factors for atherosclerosis or ACS. Restricting our analysis to whites, so as to avoid confounding from racial admixture, we genotyped ACS cases for 89 genetic variants in 72 genes, and performed individual Kaplan-Meier survival analyses. We then performed Cox regression to create multivariate risk prediction models that further minimized potential confounding.

Results

Of 89 variants tested, 16 were potentially associated with mortality (P < 0.1 for all), of which 6 were significantly associated (P < 0.05) with mortality following ACS. While these findings are not more than what would be expected by chance (P = 0.28), even after Bonferroni correction and adjustment for traditional cardiac risk factors, the IRS1 972Arg variant association (P = 0.001) retained borderline statistical significance (P < 0.1).

Conclusion

With the possible exception of IRS1, we conclude that multiple candidate genes were not associated with post-ACS mortality in our patient cohort. Because of power limitations, the 16 gene variants with P values < 0.1 may warrant further study. Our data do not support the hypothesis that the remaining 73 genes have substantial, clinically significant association with mortality after an ACS.

Quantitative assessment of the effect of angiotensinogen gene polymorphisms on the risk of coronary heart disease

BACKGROUND

Angiotensinogen, a key protein in the renin-angiotensin system, plays an important role in cardiovascular hemostasis. Many studies have examined the association between polymorphisms in the angiotensinogen gene and risk of coronary heart disease (CHD), but the results have been inconsistent.

METHODS AND RESULTS

We performed a meta-analysis of 43 associations studies on 2 angiotensinogen polymorphisms (M235T and T174M) and risk of CHD published before March 2007, including a total of 13,478 CHD cases and 17,024 controls. We also explored potential sources of heterogeneity. In a combined analysis, the summary per-allele odds ratio for CHD of the M235T polymorphism was 1.11 (95% confidence interval, 1.03 to 1.19). However, when the analyses were restricted to 4 larger studies (n >500 cases), the summary per-allele odds ratio was 0.99 (95% confidence interval, 0.94 to 1.04). Our analyses detected a possibility of publication bias with an overestimate of the true association by smaller studies. A meta-analysis of studies on the 174M variant showed no significant overall association with CHD, yielding a per-allele odds ratio of 1.07 (95% confidence interval, 0.93 to 1.22).

CONCLUSIONS

This meta-analysis suggested an overall weak association between the M235T polymorphism and CHD risk. However, the association was not observed in several larger studies, suggesting a publication bias. Additional very large-scale studies are warranted to provide conclusive evidence on the effects of the angiotensinogen gene and other genes within the renin-angiotensin system on risk of CHD.

Angiotensin-Converting Enzyme Genotype Interacts With Systolic Blood Pressure to Determine Coronary Heart Disease Risk in Healthy Middle-Aged Men

The impact of the ACE I/D polymorphism on coronary heart disease (CHD) risk is modest at most, however it may act as a modifier gene. ACE genotype was determined in 2711 healthy middle-aged men (mean age 56 years) followed for 15 years. No genotype-CHD risk association was found, but when analyzed by quartiles of systolic blood pressure (SBP), compared with II homozygotes, carriage of each additional D allele was protective at lower SBP, but in the highest quartile (SBP >150 mm Hg) conferred almost 1.5 times the risk for CHD (genotype interaction P=0.003). When SBP was analyzed as a continuous variable, again a highly significant association was seen, with the hazard ratio ([95% CI]) for a 1 SD increase in SBP being 0.90 [0.70 to 1.15] for IIs and 1.40 [1.21 to 1.61] for ID/DD (genotype SBP interaction P=0.002). The D allele was protective against CHD at lower SBP but would overtake the II risk at higher SBP. In hypertension, the proinflammatory or prohypertrophic properties of angiotensin II may explain this association. The LPL S447X polymorphism also impacts on CHD risk through interaction with hypertension, and there was an additive action of these 2 polymorphisms and SBP on CHD risk (hazard ratio for 1 SD increase in SBP for combined genotypes 1.78 [1.30 to 2.45]). Thus in the presence of hypertension, common variation in "modifier" genes confers significant CHD risk.

Renin-angiotensin system haplotypes and the risk of myocardial infarction and stroke in pharmacologically treated hypertensive patients

The products of the renin-angiotensin system (RAS) play an important role in the pathogenesis of cardiovascular disease. Studies examining RAS gene variants and cardiovascular disease have focused on single-nucleotide polymorphisms (SNPs) rather than haplotypes, which better characterize the patterns of genetic variation. The authors conducted a population-based, case-control study at Group Health (Seattle, Washington) between 1995 and 1999 to determine whether common haplotypes in the angiotensinogen gene (AGT), the renin gene, the angiotensin-converting enzyme gene, and the angiotensin II receptor type 1 and receptor type 2 genes were associated with the risk of myocardial infarction and stroke among pharmacologically treated hypertensive patients. SNP discovery was done using 23 European-origin samples. Thirty tagSNPs (the minimum sets of SNPs that capture most of the haplotype diversity within a block) were genotyped in cases and controls. Haplotypes were inferred using the program PHASE (http://www.stat.washington.edu/stephens/software.html). The authors used weighted logistic regression to estimate associations and conducted a permutation test to estimate the probability of a chance finding. AGT haplotype B was associated with the risk of myocardial infarction (odds ratio = 1.58, 95% confidence interval: 1.06, 2.35); however, results were not statistically significant given the number of tests performed (permutation p = 0.17). In this case-control study, RAS gene haplotypes were not significantly associated with increased risks of myocardial infarction or stroke.

Relevance of Genetics and Genomics for Prevention and Treatment of Cardiovascular Disease

Atherosclerotic cardiovascular disease (CVD) is a major health problem in the United States and around the world. Evidence accumulated over decades convincingly demonstrates that family history in a parent or a sibling is associated with atherosclerotic CVD, manifested as coronary heart disease, stroke, and/or peripheral arterial disease. Although there are several mendelian disorders that contribute to CVD, most common forms of CVD are believed to be multifactorial and to result from many genes, each with a relatively small effect working alone or in combination with modifier genes and/or environmental factors. The identification and the characterization of these genes and their modifiers would enhance prediction of CVD risk and improve prevention, treatment, and quality of care. This scientific statement describes the approaches researchers are using to advance understanding of the genetic basis of CVD and details the current state of knowledge regarding the genetics of myocardial infarction, atherosclerotic CVD, hypercholesterolemia, and hypertension. Current areas of interest and investigation--including gene-environment interaction, pharmacogenetics, and genetic counseling--are also discussed. The statement concludes with a list of specific recommendations intended to help incorporate usable knowledge into current clinical and public health practice, foster and guide future research, and prepare both researchers and practitioners for the changes likely to occur as molecular genetics moves from the laboratory to clinic.

The use of meta-analysis risk estimates for candidate genes in combination to predict coronary heart disease risk

Although the risk for coronary heart disease (CHD) associated with single SNPs is modest it has been suggested that, in combination, several common risk-associated alleles could lead to a substantially better heart disease risk prediction. We have modelled this using 10 SNPs in ten candidate genes (APOB, NOS3, APOE, ACE, SERPINE1, MTHFR, ITGA2B, PON 1, LPL, and CETP) and their predicted summary risk estimates from meta-analysis. Based on published allele frequencies, approximately 29% of the general population would be expected to carry less than three risk alleles, approximately 55% would carry 3 or 4 risk alleles, 4% would have 6 and 1% 7 or more risk alleles. Compared to the mean of those with 3 or 4 risk associated genotypes, those with 6 and 7-or-more alleles have a significantly higher risk odds ratio (OR) of CHD (mean OR (95% Confidence Intervals), 1.70 (1.14 to 2.55); and 4.51 (2.89 to 7.04) respectively), while compared to those in the lowest decile of risk, those in the highest decile have a CHD odds ratio in the range of 3.05 (2.24 to 4.14). Taking into account age and the risk alleles carried, the mean 10 year probability for developing CHD for a 55 year old man was calculated to be 15% (8.6% to 24.8%), with nearly 1 in 5 having more than 20% risk. Whether this particular group of 10 SNPs will improve the accuracy of CHD predictions over the combination of classical risk factors in clinical use requires further experimental evidence.

Genetic associations in preterm birth: a primer of marker selection, study design, and data analysis

Spontaneous preterm birth (PTB; delivery before 37 weeks gestation) is a primary risk factor for infant morbidity and mortality. The etiology is unclear, but there is evidence that there is a genetic predisposition to PTB. Armed with the suggestion of genetic risk factors and the failure to identify useful biomarkers, investigators are starting to actively pursue the role of genetic predisposition in PTB. Several studies have been done to date assessing the role of single gene variants. However, positive findings have failed to replicate. We argue that heterogeneity in study designs, definition of phenotype, single-nucleotide polymorphism (SNP) selection, population selection, and sample size makes data interpretation difficult in complex phenotypes such as PTB. In this review, we introduce general concepts of study designs in genetic epidemiology, selection of candidate genes and markers for analysis, and analytical methodologies. We also introduce how the concept of gene-gene interactions (biologic epistasis) and gene-environment interactions may affect the predisposition to PTB.

Investigating the Genetic Determinants of Cardiovascular Disease Using Candidate Genes and Meta-analysis of Association Studies

Coronary artery disease (CAD) has a polygenic basis, and identification of CAD susceptibility genes has the potential to aid the development of new treatments and enhance prediction of disease risk. Thus far, the strategy has firstly been to choose "candidate" genes coding for important "rate-limiting" proteins in the homeostatic systems involved in maintaining cardiovascular health; secondly to identify common variants in these candidate genes; thirdly to carry out genotyping and statistical analysis using genetic association studies; and finally to test the functional effects of the identified variants in vitro and in vivo. However, lack of reproducibility of genetic association studies has led to uncertainty about the nature and number of genes involved. In part this is because many of the studies conducted have not been adequately powered to detect small risk effects, or to permit adequate exploration of gene-gene or gene-environment interactions in a robust manner. Spurious positive and negative associations due to type I and type II statistical errors are likely to co-exist with real associations in the published literature. By utilising all available data to increase statistical power, meta-analysis of genetic association studies is increasingly being used to identify genotypic risk with a greater degree of precision. Though potentially powerful, this approach may be prone to publication bias. Therefore, very large genetic association studies will also be required to identify risk genes for CAD. This review lays out the framework for the candidate gene approach for CAD and illustrates this with published results from a UK prospective study of 3000 middle-aged men.

ACE-DD genotype is associated with the occurrence of acute coronary syndrome in postmenopausal women

The insertion/deletion (I/D) polymorphism of the angiotensin converting enzyme (ACE), the A1166C polymorphism in the angiotensin type 1 receptor (AT1R), and the M235T polymorphism of the angiotensinogen gene are associated with cardiovascular disease mostly in men. Few data are available on the effects of these genetic variations in postmenopausal women according to hormone replacement therapy (HRT) use. In this case-control study, we determine the frequency of mutant alleles in the ACE I/D, M235T and A1166C polymorphisms in postmenopausal Caucasian women with and without a diagnosis of acute coronary syndrome (ACS). Data from 198 women with ACS (63+/-10 years) and 149 controls (62+/-7 years) showed that ACE-DD genotype was more prevalent in women with ACS compared to controls (30% vs. 19%, P<0.05). There was no difference in genotype distributions for either the M235T or the A1166C polymorphisms between groups. The difference in ACE genotype distribution between ACS women and controls was driven by current HRT users with 30% of ACS and 15% of controls carrying the ACE-DD genotype (P<0.05). The oligenic combination of ACE-DD and M235T-TT genotypes was higher in ACS compared to controls. Among carriers of M235T-TT, 7% of ACS and 1% of controls also had the ACE-DD genotype, P<0.05. Thus, the ACE-DD genotype may be associated with ACS in postmenopausal women, particularly in HRT users.

The choice of a genetic model in the meta-analysis of molecular association studies

BACKGROUND

To evaluate gene-disease associations, genetic epidemiologists collect information on the disease risk in subjects with different genotypes (for a bi-allelic polymorphism: gg, Gg, GG). Meta-analyses of such studies usually reduce the problem to a single comparison, either by performing two separate pairwise comparisons or by assuming a specific underlying genetic model (recessive, co-dominant, dominant). A biological justification for the choice of the genetic model is seldom available.

METHODS

We present a genetic model-free approach, which does not assume that the underlying genetic model is known in advance but still makes use of the information available on all genotypes. The approach uses OR(GG), the odds ratio between the homozygous genotypes, to capture the magnitude of the genetic effect, and lambda, the heterozygote log odds ratio as a proportion of the homozygote log odds ratio, to capture the genetic mode of inheritance. The analysis assumes that the same unknown genetic model, i.e. the same lambda, applies in all studies, and this is investigated graphically. The approach is illustrated using five examples of published meta-analyses.

RESULTS

Analyses based on specific genetic models can produce misleading estimates of the odds ratios when an inappropriate model is assumed. The genetic model-free approach gives appropriately wider confidence intervals than genetic model-based analyses because it allows for uncertainty about the genetic model. In terms of assessment of model fit, it performs at least as well as a bivariate pairwise analysis in our examples.

CONCLUSIONS

The genetic model-free approach offers a unified approach that efficiently estimates the genetic effect and the underlying genetic model. A bivariate pairwise analysis should be used if the assumption of a common genetic model across studies is in doubt.

Modifier genes in cystic fibrosis

Although over 1,000 disease-causing mutations in the CFTR gene have been described, the highly variable disease phenotype in cystic fibrosis (CF) cannot be explained on the basis of this gene alone. Both the environment and other non-CFTR genes are likely to be important. The increased understanding of pathophysiological processes in the CF lung has led to several studies on genes in these pathways, including those involved in host defense, mucin production, and airway responsiveness. Additionally, candidate modifiers of the gastrointestinal manifestations of CF have been explored. One of the major aims of such studies is to produce targets for novel drug developments. This review will summarize the field to date and discuss some of the methodological issues important in the design and interpretation of such studies.

The PlA1/A2 polymorphism of platelet glycoprotein IIIa is not associated with the risk of type 2 diabetes. The Ludwigshafen Risk and Cardiovascular Health study

AIMS/HYPOTHESIS

The PlA1/A2 polymorphism of platelet glycoprotein IIIa (GPIIIa) has been implicated in the pathogenesis of type 2 diabetes. We studied this polymorphism in a homogenous, extensively phenotyped cohort using the candidate gene approach.

METHODS

The PlA1/A2 polymorphism was determined in 1051 patients with type 2 diabetes and in 2247 individuals without type 2 diabetes.

RESULTS

In patients with type 2 diabetes, genotype frequencies were as follows: PlA1/A1 71.4%, PlA1/A2 26.0%, and PlA2/A2 2.7%. In individuals without type 2 diabetes, genotype frequencies were 71.6%, 25.7% and 2.8%, respectively. The PlA2 allele was not associated with fasting and postprandial glucose, glycated haemoglobin, insulin, proinsulin, C-peptide and calculated indices of insulin resistance or pancreatic beta cell function. The PlA2 allele was also not significantly associated with angiographic CHD (adjusted odds ratio [OR] 1.13; 95% CI, 0.93-1.39) or with a history of previous myocardial infarction (adjusted OR 1.09; 95% CI, 0.87-1.37).

CONCLUSIONS/INTERPRETATION

The GPIIIa PlA1/A2 polymorphism is not associated with type 2 diabetes, glucose metabolism, angiographic CHD or myocardial infarction.

The effects of the ACE gene insertion/deletion polymorphism on glucose tolerance and insulin secretion in elderly people are modified by birth weight

The I allele of an insertion/deletion (I/D) polymorphism in the angiotensin-converting enzyme gene (ACE) appears to be protective against the complications of type 2 diabetes. Low birth weight, a marker of an adverse intrauterine environment, is associated with higher rates of type 2 diabetes. We examined whether the ACE I/D polymorphism could explain or modify the association between low birth weight and adulthood glucose tolerance. We measured plasma glucose and insulin concentrations after an oral glucose challenge in a group of 423 men and women, ages 65-75 yr, with measurements at birth recorded. The presence of the I allele was associated with shorter duration of gestation (P = 0.006) and, relative to gestational age, higher birth weight (P = 0.008) and length (P = 0.02). The I allele was associated with lower glucose at 120 min (P = 0.04) and a greater insulin response (P = 0.03 for insulin at 30 min and P = 0.06 for insulin area under the curve) to a standard oral glucose tolerance test. However, the associations between the ACE genotype and adulthood insulin secretion were only present in people with low birth weight (P for interaction birth weight * ACE genotype on insulin at 30 min = 0.003 and on insulin area under the curve = 0.05). The ACE I allele is associated with shorter duration of gestation and higher birth weight. The association between the presence of the ACE I allele and increased indices of adult insulin secretion is confined to subjects with low birth weight. We suggest that these findings reflect interactions between genotype and intrauterine environment with resulting changes in gene expression.