- Linear regression
- Confounding factor
A common technique to control for confounding factors in practice is by regression adjustment. There are various versions of regression modeling in the literature, and in this paper we considered four approaches often seen in genetic association studies. We carried out both analytical and simulation studies comparing the bias of effect size estimates and examining the test sizes under the null hypothesis of no association between an outcome and an exposure. Further, we compared the methods in a nonsynonymous genome-wide scan for plasma lipoprotein(a) levels using a dataset from the Dallas Heart Study. We found that a widely employed approach that models the covariate-adjusted outcome and the exposure leads to an infranominal test size and underestimation of the exposure effect size. In conclusion, we recommend either using multiple regression models or modeling the covariate-adjusted outcome and the covariate-adjusted exposure to control for confounding factors.
Copyright © 2011 S. Karger AG, Basel
- Rothman KJ, Greenland S, Lash TL: Modern Epidemiology, ed 3. Philadelphia, Lippincott Williams & Wilkins, 2008.
- Rosenbaum PR, Rubin DB: The central role of the propensity score in observational studies for causal effects. Biometrika 1983;70:41–55.
- Rosenbaum PR, Rubin DB: Reducing bias in observational studies using subclassification on the propensity score. J Am Stat Assoc 1984;79:516–524.
- Spielman RS, McGinnis RE, Ewens WJ: Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 1993;52:506–516.
- Devlin B, Roeder K: Genomic control for association studies. Biometrics 1999;55:997–1004.
- Pritchard JK, Stephens M, Rosenberg NA, Donnelly P: Association mapping in structured populations. Am J Hum Genet 2000;67:170–181.
- Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D: Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006;38:904–909.
- Satten GA, Flanders WD, Yang Q: Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model. Am J Hum Genet 2001;68:466–477.
- Allen AS, Satten GA: Control for confounding in case-control studies using the stratification score, a retrospective balancing score. Am J Epidemiol 2011;173:752–760.
- Epstein MP, Allen AS, Satten GA: A simple and improved correction for population stratification in case-control studies. Am J Hum Genet 2007;80:921–930.
- Zhao H, Rebbeck TR, Mitra N: A propensity score approach to correction for bias due to population stratification using genetic and non-genetic factors. Genet Epidemiol 2009;33:679–690.
- Xing C, Cohen JC, Boerwinkle E: A weighted false discovery rate control procedure reveals alleles at FOXA2 that influence fasting glucose levels. Am J Hum Genet 2010;86:440–446.
- Deo RC, Reich D, Tandon A, Akylbekova E, Patterson N, Waliszewska A, Kathiresan S, Sarpong D, Taylor HA Jr, Wilson JG: Genetic differences between the determinants of lipid profile phenotypes in African and European Americans: the Jackson Heart Study. PLoS Genet 2009;5:e1000342.
- Paschou P, Drineas P, Lewis J, Nievergelt CM, Nickerson DA, Smith JD, Ridker PM, Chasman DI, Krauss RM, Ziv E: Tracing sub-structure in the European American population with PCA-informative markers. PLoS Genet 2008;4:e1000114.
- The 1000 Genomes Project Consortium: A map of human genome variation from population-scale sequencing. Nature 2010;467:1061–1073.
- Su Z, Marchini J, Donnelly P: Hapgen2: simulation of multiple disease SNPs. Bioinformatics 2011;27:2304–2305.
- Guyton JR, Dahlen GH, Patsch W, Kautz JA, Gotto AM Jr: Relationship of plasma lipoprotein lp(a) levels to race and to apolipoprotein b. Arteriosclerosis 1985;5:265–272.
- Boerwinkle E, Leffert CC, Lin J, Lackner C, Chiesa G, Hobbs HH: Apolipoprotein(a) gene accounts for greater than 90% of the variation in plasma lipoprotein(a) concentrations. J Clin Invest 1992;90:52–60.
- Boerwinkle E, Menzel HJ, Kraft HG, Utermann G: Genetics of the quantitative lp(a) lipoprotein trait. III. Contribution of lp(a) glycoprotein phenotypes to normal lipid variation. Hum Genet 1989;82:73–78.
- Victor RG, Haley RW, Willett DL, Peshock RM, Vaeth PC, Leonard D, Basit M, Cooper RS, Iannacchione VG, Visscher WA, Staab JM, Hobbs HH: The Dallas Heart Study: a population-based probability sample for the multidisciplinary study of ethnic differences in cardiovascular health. Am J Cardiol 2004;93:1473–1480.
- Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager PL, Mignault AA, Yi Z, De The G, Essex M, Sankale JL, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T, Sninsky JJ, Hafler DA, Altshuler D, Gilbert DA, O’Brien SJ, Reich D: A high-density admixture map for disease gene discovery in African Americans. Am J Hum Genet 2004;74:1001–1013.
- Romeo S, Kozlitina J, Xing C, Pertsemlidis A, Cox D, Pennacchio LA, Boerwinkle E, Cohen JC, Hobbs HH: Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat Genet 2008;40:1461–1465.
- Seber GAF, Lee AJ: Linear Regression Analysis, ed 2. Hoboken, John Wiley & Sons, Inc., 2003.
- Rosenbaum PR, Rubin DB: Difficulties with regression analyses of age-adjusted rates. Biometrics 1984;40:437–443.
- Cox DR, Hinkley DV: Theoretical Statistics, ed 1. Chapman & Hall/CRC, 1974.
- Vandaele W: Wald, likelihood ratio, and Lagrange multiplier tests as an F test. Economics Letters 1981;8:361–365.
- Neuhaus JM: Estimation efficiency with omitted covariates in generalized linear models. J Am Stat Assoc 1998;93:1124–1129.
- Xing G, Xing C: Adjusting for covariates in logistic regression models. Genet Epidemiol 2010;34:769–771; author reply 772.
Chao Xing, PhD
MC 8591, University of Texas Southwestern Medical Center
5323 Harry Hines Boulevard
Dallas, TX 75390 (USA)
Tel. +1 214 648 1695, E-Mail email@example.com
Received: July 22, 2011
Accepted after revision: September 1, 2011
Published online: November 11, 2011
Number of Print Pages : 12
Number of Figures : 5, Number of Tables : 2, Number of References : 28
Human Heredity (International Journal of Human and Medical Genetics)
Vol. 72, No. 3, Year 2011 (Cover Date: November 2011)
Journal Editor: Devoto M. (Philadelphia, Pa./Rome)
ISSN: 0001-5652 (Print), eISSN: 1423-0062 (Online)
For additional information: http://www.karger.com/HHE
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