@article {1171, title = {Bayesian methods for meta-analysis of causal relationships estimated using genetic instrumental variables.}, journal = {Stat Med}, volume = {29}, year = {2010}, month = {2010 May 30}, pages = {1298-311}, abstract = {

Genetic markers can be used as instrumental variables, in an analogous way to randomization in a clinical trial, to estimate the causal relationship between a phenotype and an outcome variable. Our purpose is to extend the existing methods for such Mendelian randomization studies to the context of multiple genetic markers measured in multiple studies, based on the analysis of individual participant data. First, for a single genetic marker in one study, we show that the usual ratio of coefficients approach can be reformulated as a regression with heterogeneous error in the explanatory variable. This can be implemented using a Bayesian approach, which is next extended to include multiple genetic markers. We then propose a hierarchical model for undertaking a meta-analysis of multiple studies, in which it is not necessary that the same genetic markers are measured in each study. This provides an overall estimate of the causal relationship between the phenotype and the outcome, and an assessment of its heterogeneity across studies. As an example, we estimate the causal relationship of blood concentrations of C-reactive protein on fibrinogen levels using data from 11 studies. These methods provide a flexible framework for efficient estimation of causal relationships derived from multiple studies. Issues discussed include weak instrument bias, analysis of binary outcome data such as disease risk, missing genetic data, and the use of haplotypes.

}, keywords = {Bayes Theorem, Biostatistics, C-Reactive Protein, Fibrinogen, Genetic Markers, Humans, Meta-Analysis as Topic, Models, Statistical, Phenotype, Polymorphism, Single Nucleotide}, issn = {1097-0258}, doi = {10.1002/sim.3843}, author = {Burgess, Stephen and Thompson, Simon G and Burgess, S and Thompson, S G and Andrews, G and Samani, N J and Hall, A and Whincup, P and Morris, R and Lawlor, D A and Davey Smith, G and Timpson, N and Ebrahim, S and Ben-Shlomo, Y and Davey Smith, G and Timpson, N and Brown, M and Ricketts, S and Sandhu, M and Reiner, A and Psaty, B and Lange, L and Cushman, M and Hung, J and Thompson, P and Beilby, J and Warrington, N and Palmer, L J and Nordestgaard, B G and Tybjaerg-Hansen, A and Zacho, J and Wu, C and Lowe, G and Tzoulaki, I and Kumari, M and Sandhu, M and Yamamoto, J F and Chiodini, B and Franzosi, M and Hankey, G J and Jamrozik, K and Palmer, L and Rimm, E and Pai, J and Psaty, B and Heckbert, S and Bis, J and Anand, S and Engert, J and Collins, R and Clarke, R and Melander, O and Berglund, G and Ladenvall, P and Johansson, L and Jansson, J-H and Hallmans, G and Hingorani, A and Humphries, S and Rimm, E and Manson, J and Pai, J and Watkins, H and Clarke, R and Hopewell, J and Saleheen, D and Frossard, R and Danesh, J and Sattar, N and Robertson, M and Shepherd, J and Schaefer, E and Hofman, A and Witteman, J C M and Kardys, I and Ben-Shlomo, Y and Davey Smith, G and Timpson, N and de Faire, U and Bennet, A and Sattar, N and Ford, I and Packard, C and Kumari, M and Manson, J and Lawlor, Debbie A and Davey Smith, George and Anand, S and Collins, R and Casas, J P and Danesh, J and Davey Smith, G and Franzosi, M and Hingorani, A and Lawlor, D A and Manson, J and Nordestgaard, B G and Samani, N J and Sandhu, M and Smeeth, L and Wensley, F and Anand, S and Bowden, J and Burgess, S and Casas, J P and Di Angelantonio, E and Engert, J and Gao, P and Shah, T and Smeeth, L and Thompson, S G and Verzilli, C and Walker, M and Whittaker, J and Hingorani, A and Danesh, J} } @article {1251, title = {Association of coagulation-related and inflammation-related genes and factor VIIc levels with stroke: the Cardiovascular Health Study.}, journal = {J Thromb Haemost}, volume = {9}, year = {2011}, month = {2011 Feb}, pages = {267-74}, abstract = {

BACKGROUND: Thrombosis and inflammation are critical in stroke etiology, but associations of coagulation and inflammation gene variants with stroke, and particularly factor VII levels, are inconclusive.

OBJECTIVES: To test the associations between 736 single-nucleotide polymorphisms (SNPs) between tagging haplotype patterns of 130 coagulation and inflammation genes, and stroke events, in the 5888 participants aged >= 65 years of the observational Cardiovascular Health Study cohort.

PATIENTS/METHODS: With 16 years of follow-up, age-adjusted and sex-adjusted Cox models were used to estimate associations of SNPs and FVIIc levels with future stroke.

RESULTS: Eight hundred and fifteen strokes occurred in 5255 genotyped participants without baseline stroke (748 ischemic strokes; 586 among whites). Among whites, six SNPs were associated with stroke, with a nominal P-value of < 0.01: rs6046 and rs3093261 (F7); rs4918851 and rs3781387 (HABP2); and rs3138055 (NFKB1A) and rs4648004 (NFKB1). Two of these SNPs were associated with FVIIc levels (units of percentage activity): rs6046 (β = -18.5, P = 2.38 {\texttimes} 10(-83)) and rs3093261 (β = 2.99, P = 3.93 {\texttimes} 10(-6)). After adjustment for age, sex, race, and cardiovascular risk factors, the association of FVIIc quintiles (Q) with stroke were as follows (hazard ratio; 95\% confidence interval): Q1, reference; Q2, 1.4, 1.1-1.9); Q3, 1.1, 0.8-1.5); Q4, 1.5, 1.1-2.0); and Q5, 1.6, 1.2-2.2). Associations between SNPs and stroke were independent of FVIIc levels.

CONCLUSIONS: Variations in FVII-related genes and FVIIc levels were associated with risk of incident ischemic stroke in this elderly cohort, suggesting a potential causal role for FVII in stroke etiology.

}, keywords = {Blood Coagulation Factors, Cardiovascular Diseases, Cohort Studies, Factor VII, Female, Humans, Inflammation, Male, Polymorphism, Single Nucleotide, Prospective Studies, Risk Factors, Stroke}, issn = {1538-7836}, doi = {10.1111/j.1538-7836.2010.04149.x}, author = {Zakai, N A and Lange, L and Longstreth, W T and O{\textquoteright}Meara, E S and Kelley, J L and Fornage, M and Nikerson, D and Cushman, M and Reiner, A P} } @article {8260, title = {Genome-wide meta-analysis of variant-by-diuretic interactions as modulators of lipid traits in persons of European and African ancestry.}, journal = {Pharmacogenomics J}, year = {2019}, month = {2019 Dec 06}, abstract = {

Hypertension (HTN) is a significant risk factor for cardiovascular morbidity and mortality. Metabolic abnormalities, including adverse cholesterol and triglycerides (TG) profiles, are frequent comorbid findings with HTN and contribute to cardiovascular disease. Diuretics, which are used to treat HTN and heart failure, have been associated with worsening of fasting lipid concentrations. Genome-wide meta-analyses with 39,710 European-ancestry (EA) individuals and 9925 African-ancestry (AA) individuals were performed to identify genetic variants that modify the effect of loop or thiazide diuretic use on blood lipid concentrations. Both longitudinal and cross sectional data were used to compute cohort-specific interaction results, which were then combined through meta-analysis in each ancestry. These ancestry-specific results were further combined through trans-ancestry meta-analysis. Analysis of EA data identified two genome-wide significant (p < 5 {\texttimes} 10) loci with single nucleotide variant (SNV)-loop diuretic interaction on TG concentrations (including COL11A1). Analysis of AA data identified one genome-wide significant locus adjacent to BMP2 with SNV-loop diuretic interaction on TG concentrations. Trans-ancestry analysis strengthened evidence of association for SNV-loop diuretic interaction at two loci (KIAA1217 and BAALC). There were few significant SNV-thiazide diuretic interaction associations on TG concentrations and for either diuretic on cholesterol concentrations. Several promising loci were identified that may implicate biologic pathways that contribute to adverse metabolic side effects from diuretic therapy.

}, issn = {1473-1150}, doi = {10.1038/s41397-019-0132-y}, author = {de Las Fuentes, L and Sung, Y J and Sitlani, C M and Avery, C L and Bartz, T M and Keyser, C de and Evans, D S and Li, X and Musani, S K and Ruiter, R and Smith, A V and Sun, F and Trompet, S and Xu, H and Arnett, D K and Bis, J C and Broeckel, U and Busch, E L and Chen, Y-D I and Correa, A and Cummings, S R and Floyd, J S and Ford, I and Guo, X and Harris, T B and Ikram, M A and Lange, L and Launer, L J and Reiner, A P and Schwander, K and Smith, N L and Sotoodehnia, N and Stewart, J D and Stott, D J and St{\"u}rmer, T and Taylor, K D and Uitterlinden, A and Vasan, R S and Wiggins, K L and Cupples, L A and Gudnason, V and Heckbert, S R and Jukema, J W and Liu, Y and Psaty, B M and Rao, D C and Rotter, J I and Stricker, B and Wilson, J G and Whitsel, E A} }