Bayesian methods for instrumental variable analysis with genetic instruments ('Mendelian randomization'): Example with urate transporter SLC2A9 as an instrumental variable for effect of urate levels on metabolic syndrome

International Journal of Epidemiology

Volumn 39, Issue 3, 2010, Pages 907-918

  McKeigue, Paul M ^a   Campbell, Harry ^a   Wild, Sarah ^a   Vitart, Veronique ^b   Hayward, Caroline ^b   Rudan, Igor ^b,c   Wright, Alan F ^b   Wilson, James F ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b WESTERN GENERAL HOSPITAL   (United Kingdom)

^c UNIVERSITY OF SPLIT   (Croatia)

Author keywords

Bayesian analysis; Biomarkers; Causality; Genetics; Human SLC2A9 protein; Monte Carlo method; Randomization; Uric acid

Indexed keywords

BIOLOGICAL MARKER; PROTEIN; SLC2A9 PROTEIN; UNCLASSIFIED DRUG; URATE;

BAYESIAN ANALYSIS; BIOMARKER; BLOOD; DISEASE; EPIDEMIOLOGY; GENETIC ANALYSIS; GENETIC VARIATION; GENOTYPE; INDIVIDUAL VARIATION; METABOLISM; MONTE CARLO ANALYSIS; MORTALITY; NITROGEN COMPOUND; POLYMORPHISM; PROTEIN;

ARTICLE; BAYES THEOREM; CROSS-SECTIONAL STUDY; DISEASE ASSOCIATION; GENETIC LINKAGE; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; METABOLIC SYNDROME X; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED KINGDOM; URIC ACID BLOOD LEVEL;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; BAYES THEOREM; BIOLOGICAL MARKERS; CAUSALITY; FEMALE; GENOTYPE; GLUCOSE TRANSPORT PROTEINS, FACILITATIVE; HUMANS; LOD SCORE; LOGISTIC MODELS; MENDELIAN RANDOMIZATION ANALYSIS; METABOLIC SYNDROME X; MIDDLE AGED; MONTE CARLO METHOD; POLYMORPHISM, SINGLE NUCLEOTIDE; URIC ACID; YOUNG ADULT;

EID: 77955755708     PISSN: 03005771     EISSN: 14643685     Source Type: Journal    
DOI: 10.1093/ije/dyp397     Document Type: Article

References (47)

1. Smith GD, Ebrahim S. What can Mendelian randomisation tell us about modifiable behavioural and environmental exposures? Br Med J 2005;330:1076-79.
2. Keavney B, Danesh J, Parish S et al. Fibrinogen and coronary heart disease: Fibrinogen and coronary heart disease: test of causality by 'Mendelian randomization'. Int J Epidemiol 2006;35:935-43.
3. Thomas DC, Conti DV. Commentary: the concept of 'Mendelian Randomization'. Int J Epidemiol 2004;33: 21-25.
4. Newhouse JP, McClellan M. Econometrics in outcomes research: the use of instrumental variables. Annu Rev Public Health 1998;19:17-34.
5. Greenland S. An introduction to instrumental variables for epidemiologists. Int J Epidemiol 2000;29: 722-29.
6. Hernán MA, Robins JM. Instruments for causal inference: an epidemiologist's dream? Epidemiology 2006;17: 360-72.
7. Wehby GL, Ohsfeldt RL, Murray JC. 'Mendelian randomization' equals instrumental variable analysis with genetic instruments. Stat Med 2008;27:2745-49.
8. Timpson NJ, Lawlor DA, Harbord RM et al. C-reactive protein and its role in C-reactive protein and its role in metabolic syndrome: Mendelian randomisation study. Lancet 2005;366:1954-59.
9. Lawlor DA, Harbord RM, Sterne JAC, Timpson N, Smith GD. Mendelian randomization: using genes as instruments for making causal inferences in epidemiology. Stat Med 2008;27:1133-328.
10. Chernozhukov V, Hansen C. The reduced form: a simple approach to inference with weak estimators. Econ Lett 2008;100:68-71.
11. Jaynes ET. Confidence intervals vs Bayesian intervals. In: Harper WL, Hooker CA (eds). Foundations of Probability Theory, Statistical Inference and Statistical Theories of Science. Vol. II. Dordrecht: Reidel, 1976, pp. 175-257.
12. Zech G. Frequentist and Bayesian confidence intervals. Eur Phy J 2002;12:1-81.
13. Rassen JA, Schneeweiss S, Glynn RJ, Mittleman MA, Brookhart MA. Instrumental variable analysis for estimation of treatment effects with dichotomous outcomes. Am J Epidemiol 2009;169:273-84.
14. Vansteelandt S, Goetghebeur E. Causal inference with generalized structural mean models. J Roy Stat Soc B 2003;65:817-35.
15. Robins J, Rotnitzky A. Estimation of treatment effects in randomised trials with noncompliance and a dichotomous outcome using structural mean models. Biometrika 2004;91:763-83.
16. Thompson JR, Minelli C, Abrams KR, Tobin MD, Riley RD. Mendelian Meta-analysis of genetic studies using Mendelian randomization-a multivariate approach. Stat Med 2005;24:2241-54.
17. Kleibergen F, Zivot E. Bayesian and classical approaches to instrumental variable regression. J Econ 2003;114: 29-72.
18. Imbens GW, Rubin DB. Bayesian inference for causal effects in randomized experiments with noncompliance. Ann Stat 1997;25:305-27.
19. Conley TG, Hansen CB, McCulloch RE, Rossi PE. A semiparametric Bayesian approach to the instrumental variable problem. J Econ 2008;138:63-103.
20. Vitart V, Rudan I, Hayward C et al. SLC2A9 is a newly identified urate SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout. Nat Genet 2008;40:437-42.
21. Wallace C, Newhouse SJ, Braund P et al. Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia. Am J Hum Genet 2008;82:139-49.
22. Blower DJ. An easy derivation of logistic regression from the Bayesian and maximum entropy perspective. In: Erickson GJ, Zhai Y (eds). 23rd International Workshop on Bayesian Inference and Maximum EntropyMethods in Science and Engineering. Vol. 707. Melville, NY: American Institute of Physics, 2004, pp. 30-43.
23. Jaynes ET. Probability Theory: The Logic of Science. Cambridge, UK: Cambridge University Press, 2003.
24. Andrews DF, Mallows CL. Scale mixtures of normal distributions. J Roy Stat Soc 1974;B36:99-102.
25. Arellano M. Sargans instrumental variables estimation and the generalized method of moments. J Bus Econ Stat 2002;20:450-59.
26. Palmer TM, Thompson JR, Tobin MD, Sheehan NA, Burton PR. Adjusting for bias and unmeasured confounding in Mendelian randomization studies with binary responses. Int J Epidemiol 2008;37:1161-68.
27. Fisher RA. The correlation between relatives on the supposition of Mendelian inheritance. Philos Trans R Soc Edin 1918;52:399-433.
28. Morton NE, MacLean CJ. Analysis of family resemblance. 3. Complex segregation of quantitative traits. Am J Hum Genet 1974;26:489-503.
29. Aulchenko YS, de Koning DJ, Haley C. Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 2007;177: 577-85.
30. MacKay DJC. Information Theory, Inference and Learning Algorithms. Cambridge, UK: Cambridge University Press, 2003.
31. Hoggart CJ, Parra EJ, Shriver MD et al. Control of confounding of genetic associations in stratified populations. Am J Hum Genet 2003;72:1492-504.
32. Grundy SM, Brewer HB, Cleeman JI, Smith SC, Lenfant C. Definition of metabolic syndrome: Report of the National Heart, Lung, and Blood Institute/American Heart Association conference on scientific issues related to definition. Circulation 2004;109: 433-38.
33. Whitfield JB, Martin NG. Inheritance and alcohol as factors influencing plasma uric acid levels. Acta Genet Med Gemellol 1983;32:117-26.
34. Congdon P. Applied Bayesian Modelling. Hoboken, NJ: Wiley, 2003.
35. Birnbaum A. On the foundations of statistical inference. J Am Stat Assoc 1962;57:269-326.
36. Dawid AP. Counterfactuals: help or hindrance? Int J Epidemiol 2002;31:429-30.
37. Hfler M. Causal inference based on counterfactuals. BMC Med Res Methodol 2005;5:28.
38. Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet 2006;2:e190.
39. Thorgeirsson TE, Geller F, Sulem P et al. A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. Nature 2008;452: 638-42.
40. Sargan JD. The estimation of economic relationships using instrumental variables. Econometrica 1958;26: 393-415.
41. Clayton D, McKeigue PM. Epidemiological methods for studying genes and environmental factors in complex diseases. Lancet 2001;358:1356-60.
42. Feig DI, Kang DH, Johnson RJ. Uric acid and cardiovascular risk. N Engl J Med 2008;359:1811-21.
43. Waring WS, Convery A, Mishra V, Shenkin A, Webb DJ, Maxwell SRJ. Uric acid reduces exercise-induced oxidative stress in healthy adults. Clin Sci 2003;105: 425-30.
44. Waring WS, McKnight JA, Webb DJ, Maxwell SRJ. Uric acid restores endothelial function in patients with type 1 diabetes and regular smokers. Diabetes 2006;55: 3127-32.
45. McClellan M, McNeil BJ, Newhouse JP. Does more intensive treatment of acute myocardial infarction in the elderly reduce mortality? Analysis using instrumental variables. JAMA 1994;272:859-66.
46. Holmes CC, Held L. Bayesian auxiliary variable methods for binary and multinomial regression. Bayesian Anal. 2004;1:145-68.
47. Beal MJ, Ghahramani Z. Variational Bayesian learning of directed graphical models with hidden variables. Bayesian Anal 2006;1:793-832.