Variance heterogeneity analysis for detection of potentially interacting genetic loci: Method and its limitations

Background: Presence of interaction between a genotype and certain factor in determination of a trait's value, it is expected that the trait's variance is increased in the group of subjects having this genotype. Thus, test of heterogeneity of variances can be used as a test to screen for potentially interacting single-nucleotide polymorphisms (SNPs). In this work, we evaluated statistical properties of variance heterogeneity analysis in respect to the detection of potentially interacting SNPs in a case when an interaction variable is unknown.Results: Through simulations, we investigated type I error for Bartlett's test, Bartlett's test with prior rank transformation of a tr

Estrogen use and early onset Alzheimer's disease: a population-based study

Estrogen use may be protective for Alzheimer's disease with late onset. However, the effects on early onset Alzheimer's disease are unclear. This issue was studied in a population based setting. For each female patient, a female control was matched on age (within 5 years) and place of residence. Information on estrogen use and other risk factors were, for cases (n=109) and controls (n=119), collected from the next of kin by structured interview. The strength of the association between estrogen use and early onset Alzheimer's disease was studied using conditional logistic regression with adjustment for age and education level. There was an inverse association between estrogen use and early onset Alzheimer's disease (adjusted odds ratio 0.34; 95% confidence interval 0.12-0.94). The study therefore suggests that estrogen use is beneficial to Alzheimer's disease with early onset

Reproductive period and risk of dementia in postmenopausal women

CONTEXT: Exogenous estrogen use may lower risk of dementia in postmenopausal women. A relationship between long-term exposure to endogenous estrogens and incident dementia has been hypothesized but not studied. OBJECTIVE: To determine whether a longer reproductive period, as an indicator of longer exposure to endogenous estrogens, is associated with lower risk of dementia and Alzheimer disease (AD) in women who have natural menopause. DESIGN AND SETTING: The Rotterdam Study, a population-based prospective cohort study conducted in the Netherlands. PARTICIPANTS: A total of 3601 women aged 55 years or older who did not have dementia at baseline (1990-1993) and had information on age at menarche

Heritabilities, proportions of heritabilities explained by GWAS findings, and implications of cross-phenotype effects on PR interval

Electrocardiogram (ECG) measurements are a powerful tool for evaluating cardiac function and are widely used for the diagnosis and prediction of a variety of conditions, including myocardial infarction, cardiac arrhythmias, and sudden cardiac death. Recently, genome-wide association studies (GWASs) identified a large number of genes related to ECG parameter variability, specifically for the QT, QRS, and PR intervals. The aims of this study were to establish the heritability of ECG traits, including indices of left ventricular hypertrophy, and to directly assess the proportion of those heritabilities explained by GWAS variants. These analyses were conducted in a large, Dutch family-based cohort study, the Erasmus Rucphen Family study using variance component methods implemented in the SOLAR (Sequential Oligogenic Linkage Analysis Routines) software package. Heritability estimates ranged from 34 % for QRS and Cornell voltage product to 49 % for 12-lead sum. Trait-specific GWAS findings for each trait explained a fraction of their heritability (17 % for QRS, 4 % for QT, 2 % for PR, 3 % for Sokolow–Lyon index, and 4 % for 12-lead sum). The inclusion of all ECG-associated single nucleotide polymorphisms explained an additional 6 % of the heritability of PR. In conclusion, this study shows that, although GWAS explain a portion of ECG trait variability, a large amount of heritability remains to be explained. In addition, larger GWAS for PR are likely to detect loci already identified, particularly those observed for QRS and 12-lead sum

Retinal vessel diameters and risk of impaired fasting glucose or diabetes: the Rotterdam study

The association between a smaller retinal arteriolar-to-venular ratio (AVR) and incident diabetes may be due to arteriolar narrowing, venular dilatation, or both. We investigated associations between baseline vessel diameters and incident impaired fasting glucose or diabetes in a population-based cohort (aged > or =55 years). Baseline retinal vessel diameters (1990-1993) were measured on digitized images of 2,309 subjects with a normal glucose tolerance test (postload glucose or =7.0 mmol/l and/or antidiabetic medication use. Odds ratios (ORs) per SD increase in venular diameters were 1.13 (95% CI 1.00-1.29) for impaired fasting glucose and 1.09 (0.90-1.33) for diabetes. ORs per SD decrease in arteriolar diameters were 1.12 (0.98-1.27) and 1.08 (0.89-1.31) and per SD decrease in AVR were 1.29 (1.13-1.46) and 1.19 (0.98-1.45). After adjustment for cardiovascular risk factors, the associations were unaltered for venules and disappeared for arterioles. After stratification on age, associations between venular dilatation and impaired fasting glucose (1.23 [1.02-1.47]) or diabetes (1.18 [0.89-1.56]) were mainly present in participants aged <70 years. In conclusion, in our study, the risk of impaired fasting glucose and diabetes with AVR was explained by venular dilatation rather than arteriolar narrowing, warranting more focus on the causes of this dilatation

Performance of Framingham cardiovascular disease (CVD) predictions in the Rotterdam Study taking into account competing risks and disentangling CVD into coronary heart disease (CHD) and stroke

AbstractBackgroundTo evaluate the performance of Framingham predictions of cardiovascular disease (CVD) risk corrected for the competing risk of non-CVD death, in an independent European cohort of older individuals and subsequently extend the predictions by disentangling CVD into coronary heart disease (CHD) and stroke separately.MethodsWe used the Rotterdam Study data, a prospective cohort study of individuals aged 55years and older (N=6004), to validate the Framingham predictions of CVD, defined as first occurrence of myocardial infarction, coronary death or stroke during 15years of follow-up, corrected for the competing risk of non-CVD death. We subsequently estimated the risks of CHD and stroke separately, and used the sum as a predictor for the total CVD risk. Calibration plots and c-statistics were used to evaluate the performance of the models.ResultsPerformance of the Framingham predictions was good in the low- to intermediate risk (≤30%, 15-year CVD risk) (17.5% observed vs. 16.6% expected) but poorer in the higher risk (>30%) categories (36.3% observed vs. 44.1% expected). The c-statistic increased from 0.66 to 0.69 after refitting. Separately estimating CHD and stroke revealed considerable heterogeneity with regard to the contribution of CHD and stroke to total CVD risk.ConclusionsFramingham CVD risk predictions perform well in the low- to intermediate risk categories in the Rotterdam Study. Disentangling CVD into CHD and stroke separately provides additional information about the individual contribution of CHD and stroke to total individual CVD risk

Prolonged QTc Interval and Risk of Sudden Cardiac Death in a Population of Older Adults

ObjectivesThis study sought to investigate whether prolongation of the heart rate-corrected QT (QTc) interval is a risk factor for sudden cardiac death in the general population.BackgroundIn developed countries, sudden cardiac death is a major cause of cardiovascular mortality. Prolongation of the QTc interval has been associated with ventricular arrhythmias, but in most population-based studies no consistent association was found between QTc prolongation and total or cardiovascular mortality. Only very few of these studies specifically addressed sudden cardiac death.MethodsThis study was conducted as part of the Rotterdam Study, a prospective population-based cohort study that comprises 3,105 men and 4,878 women aged 55 years and older. The QTc interval on the electrocardiogram was determined during the baseline visit (1990 to 1993) and the first follow-up examination (1993 to 1995). The association between a prolonged QTc interval and sudden cardiac death was estimated using Cox proportional hazards analysis.ResultsDuring an average follow-up period of 6.7 years (standard deviation, 2.3 years) 125 patients died of sudden cardiac death. An abnormally prolonged QTc interval (>450 ms in men, >470 ms in women) was associated with a three-fold increased risk of sudden cardiac death (hazard ratio, 2.5; 95% confidence interval, 1.3 to 4.7), after adjustment for age, gender, body mass index, hypertension, cholesterol/high-density lipoprotein ratio, diabetes mellitus, myocardial infarction, heart failure, and heart rate. In patients with an age below the median of 68 years, the corresponding relative risk was 8.0 (95% confidence interval 2.1 to 31.3).ConclusionsAbnormal QTc prolongation on the electrocardiogram should be viewed as an independent risk factor for sudden cardiac death

Evaluation of newer risk markers for coronary heart disease:The Rotterdam study

Design: Prospective cohort study in the general population of Rotterdam, the Netherlands (The Rotterdam Study). Methods: Data on measurements taken between 1997 and 2001 in 5,933 persons free of CHD (40.6% men; mean age 69.1 years) were collected. We studied the predictive ability of 12 newer risk markers (N-terminal pro-brain natriuretic peptide [NT-proBNP] levels, von Willebrand factor antigen levels, fibrinogen levels, chronic kidney disease, leukocyte count, C-reactive protein levels, homocysteine levels, uric acid levels, coronary artery calcification [CAC] scores obtained by means of CT, carotid intima-media thickness, peripheral arterial disease, and aortic pulse wave velocity). The predictive value was determined by adding a newer marker to a prediction model that was based on traditional cardiovascular risk factors. Results: Risk discrimination improved the most with the addition of CAC scores. A net 23.5% of the individuals who developed CHD were reclassified to a higher risk category, but also 4.2% of those who did not develop CHD. This resulted in a net reclassification improvement (NRI) of 0.193. The CAC score was followed by NT-proBNP (NRI 0.076) in terms of the most improvement to risk classification. Improvements in risk predictions with the other newer markers were marginal. Conclusions: Classification of CHD risk predictions improved most with the addition of the CAC scores to the risk model. Further research is needed to assess whether refinements in risk prediction will actually lead to more effective prevention of cardiovascular disease together with justifiable costs and efforts.</p

Evaluation of newer risk markers for coronary heart disease:The Rotterdam study

Design: Prospective cohort study in the general population of Rotterdam, the Netherlands (The Rotterdam Study). Methods: Data on measurements taken between 1997 and 2001 in 5,933 persons free of CHD (40.6% men; mean age 69.1 years) were collected. We studied the predictive ability of 12 newer risk markers (N-terminal pro-brain natriuretic peptide [NT-proBNP] levels, von Willebrand factor antigen levels, fibrinogen levels, chronic kidney disease, leukocyte count, C-reactive protein levels, homocysteine levels, uric acid levels, coronary artery calcification [CAC] scores obtained by means of CT, carotid intima-media thickness, peripheral arterial disease, and aortic pulse wave velocity). The predictive value was determined by adding a newer marker to a prediction model that was based on traditional cardiovascular risk factors. Results: Risk discrimination improved the most with the addition of CAC scores. A net 23.5% of the individuals who developed CHD were reclassified to a higher risk category, but also 4.2% of those who did not develop CHD. This resulted in a net reclassification improvement (NRI) of 0.193. The CAC score was followed by NT-proBNP (NRI 0.076) in terms of the most improvement to risk classification. Improvements in risk predictions with the other newer markers were marginal. Conclusions: Classification of CHD risk predictions improved most with the addition of the CAC scores to the risk model. Further research is needed to assess whether refinements in risk prediction will actually lead to more effective prevention of cardiovascular disease together with justifiable costs and efforts.</p

A combined linkage and exome sequencing analysis for electrocardiogram parameters in the Erasmus Rucphen family study

Electrocardiogram (ECG) measurements play a key role in the diagnosis and prediction of cardiac arrhythmias and sudden cardiac death. ECG parameters, such as the PR, QRS, and QT intervals, are known to be heritable and genome-wide association studies of these phenotypes have been successful in identifying common variants; however, a large proportion of the genetic variability of these traits remains to be elucidated. The aim of this study was to discover loci potentially harboring rare variants utilizing variance component linkage analysis in 1547 individuals from a large family-based study, the Erasmus Rucphen Family Study (ERF). Linked regions were further explored using exome sequencing. Five suggestive linkage peaks were identified: two for QT interval (1q24, LOD = 2.63; 2q34, LOD = 2.05), one for QRS interval (1p35, LOD = 2.52) and two for PR interval (9p22, LOD = 2.20; 14q11, LOD = 2.29). Fine-mapping using exome sequence data identified a C > G missense variant (c.713C > G, p.Ser238Cys) in the FCRL2 gene associated with QT (rs74608430; P = 2.8 × 10-4, minor allele frequency = 0.019). Heritability analysis demonstrated that the SNP explained 2.42% of the trait's genetic variability in ERF (P = 0.02). Pathway analysis suggested that the gene is involved in cytosolic Ca2+ levels (P = 3.3 × 10-3) and AMPK stimulated fatty acid oxidat