Fast and Accurate Genome-Wide Association Test of Multiple Quantitative Traits

Multiple correlated traits are often collected in genetic studies. By jointly analyzing multiple traits, we can increase power by aggregating multiple weak effects and reveal additional insights into the genetic architecture of complex human diseases. In this article, we propose a multivariate linear regression-based method to test the joint association of multiple quantitative traits. It is flexible to accommodate any covariates, has very accurate control of type I errors, and offers very competitive performance. We also discuss fast and accurate significance p value computation especially for genome-wide association studies with small-to-medium sample sizes. We demonstrate through extensive numerical studies that the proposed method has competitive performance. Its usefulness is further illustrated with application to genome-wide association analysis of diabetes-related traits in the Atherosclerosis Risk in Communities (ARIC) study. We found some very interesting associations with diabetes traits which have not been reported before. We implemented the proposed methods in a publicly available R package

Risk of Type 2 Diabetes and Obesity Is Differentially Associated with Variation in FTO in Whites and African-Americans in the ARIC Study

Single nucleotide polymorphisms (SNPs) in the fat mass and obesity associated (FTO) gene are associated with body mass index (BMI) in populations of European descent. The FTO rs9939609 variant, first detected in a genome-wide association study of diabetes, conferred an increased disease risk that was abolished after adjustment for BMI, suggesting that the association may be due to variation in adiposity. The relationship between diabetes, four previously identified FTO polymorphisms that span a 19.6-kb genomic region, and obesity was therefore evaluated in the biracial population-based Atherosclerosis Risk in Communities Study with the goal of further refining the association by comparing results between the two ethnic groups. The prevalence of diabetes and obesity (BMI ≥30 kg/m2) was established at baseline, and diabetes was determined by either self-report, a fasting glucose level ≥126 mg/dL, or non-fasting glucose ≥200 mg/dL. There were 1,004 diabetes cases and 10,038 non-cases in whites, and 670 cases and 2,780 non-cases in African-Americans. Differences in mean BMI were assessed by a general linear model, and multivariable logistic regression was used to predict the risk of diabetes and obesity. For white participants, the FTO rs9939609 A allele was associated with an increased risk of diabetes (odds ratio (OR)  = 1.19, p<0.001) and obesity (OR = 1.22, p<0.001) under an additive genetic model that was similar for all of the SNPs analyzed. In African-Americans, only the rs1421085 C allele was a determinant of obesity risk (OR = 1.17, p = 0.05), but was found to be protective against diabetes (OR = 0.79, p = 0.03). Adjustment for BMI did not eliminate any of the observed associations with diabetes. Significant statistical interaction between race and the FTO variants suggests that the effect on diabetes susceptibility may be context dependent

The Relationship Between Self-Reported History of Endodontic Therapy and Coronary Heart Disease in the Atherosclerosis Risk in Communities Study

Results from numerous studies have suggested links between periodontal disease and coronary heart disease (CHD), but endodontic disease has not been studied extensively in this regard

Hospitalized Infection as a Trigger for Acute Ischemic Stroke

Acute triggers for ischemic stroke, which may include infection, are understudied, as is whether background cardiovascular disease (CVD) risk modifies such triggering. We hypothesized that infection increases acute stroke risk, especially among those with low CVD risk

Evidence for Three Novel QTLs for Adiposity on Chromosome 2 With Epistatic Interactions: The NHLBI Family Heart Study

We sought to identify quantitative trait loci (QTLs) by genome-wide linkage analysis for BMI and waist circumference (WC) exploring various strategies to address heterogeneity including covariate adjustments and complex models based on epistatic components of variance. Because cholesterol-lowering drugs and diabetes medications may affect adiposity and risk of coronary heart disease, we excluded subjects medicated for hypercholesterolemia and hyperglycemia. The evidence of linkage increased on 2p25 (BMI: lod = 1.59 vs. 2.43, WC: lod = 1.32 vs. 2.26). Because environmental and/or genetic components could mask the effect of a specific locus, we investigated further whether a QTL could influence adiposity independently of lipid pathway and dietary habits. Strong evidence of linkage on 2p25 (BMI: lod = 4.31; WC: lod = 4.23) was found using Willet’s dietary factors and lipid profile together with age and sex in adjustment. It suggests that lipid profile and dietary habits are confounding factors for detecting a 2p25 QTL for adiposity. Because evidence of linkage has been previously detected for BMI on 7q34 and 13q14 in National Heart, Lung, and Blood Institute Family Heart Study (NHLBI FHS), and for diabetes on 15q13, we investigated epistasis between chromosome 2 and these loci. Significant epistatic interactions were found between QTLs 2p25 and 7q34, 2q37 and 7q34, 2q31 and 13q14, and 2q31–q36 and 15q13. These results suggest multiple pathways and factors involving genetic and environmental effects influencing adiposity. By taking some of these known factors into account, we clarified our linkage evidence of a QTL on 2p25 influencing BMI and WC. The 2p25, 2q24–q31, and 2q36–q37 showed evidence of epistatic interaction with 7q34, 13q14, and 15q13

Association of Glycemic Index and Glycemic Load With Risk of Incident Coronary Heart Disease Among Whites and African Americans With and Without Type 2 Diabetes: The Atherosclerosis Risk in Communities Study

This study examined whether high glycemic index (GI) and glycemic load (GL) diets are associated with increased risk of developing CHD in Whites and African Americans with and without type 2 diabetes

Role of BMI in the Association of the TCF7L2 rs7903146 Variant with Coronary Heart Disease: The Atherosclerosis Risk in Communities (ARIC) Study

We examined the association of variation in the type 2 diabetes risk-conferring TCF7L2 gene with the risk of incident coronary heart disease (CHD) among the lean, overweight, and obese members of the Atherosclerosis Risk in Communities (ARIC) Study cohort. Cox proportional hazard regression analyses were performed using a general model, with the major homozygote as the reference category. For 9,865 whites, a significant increase in the risk of CHD was seen only among lean ( BMI < 25 kg/m2) individuals homozygous for the T allele of the TCF7L2 rs7903146 gene risk variant (hazard ratio 1.42; 95% CI 1.03,1.97; P = .01). No association was found among 3,631 blacks, regardless of BMI status. An attenuated hazard ratio was observed among the nondiabetic ARIC cohort members. This study suggests that body mass modifies the association of the TCF7L2 rs7903146 T allele with CHD risk

Prediabetes and Diabetes Are Associated With Arterial Stiffness in Older Adults: The ARIC Study

To determine whether prediabetes and diabetes in older adults are associated with arterial stiffness measured in central and peripheral arteries and to examine characteristics that modify these associations

Chocolate consumption is inversely associated with prevalent coronary heart disease: The National Heart, Lung, and Blood Institute Family Heart Study

Epidemiologic studies have suggested beneficial effects of flavonoids on cardiovascular disease. Cocoa and particularly dark chocolate are rich in flavonoids and recent studies have demonstrated blood pressure lowering effects of dark chocolate. However, limited data are available on the association of chocolate consumption and the risk of coronary heart disease (CHD). We sought to examine the association between chocolate consumption and prevalent CHD