Correcting for population stratification in genomewide association studies

Journal of the American Statistical Association

Volumn 106, Issue 495, 2011, Pages 997-1008

  Lin, D Y ^a   Zeng, D ^a  

^a University of North Carolina at Chapel Hill   (United States)

Author keywords

B spline; Case control study; Principal components; Propensity score; Semiparametric logistic regression; Single nucleotide polymorphism

Indexed keywords

EID: 80054708839     PISSN: 01621459     EISSN: None     Source Type: Journal    
DOI: 10.1198/jasa.2011.tm10294     Document Type: Article

References (25)

1. Bickel, P. J., Klaassen, C. A. J., Ritov, Y., and Wellner, J. A. (1993), Efficient and Adaptive Estimation for Semiparametric Models, Baltimore: Johns Hopkins University Press. [1006]
2. Chen, H.-S., Zhu, X., Zhao, H., and Zhang, S. (2003), "Qualitative Semi-Parametric Test for Genetic Associations in Case-Control Designs Under Structured Populations, " Annals of Human Genetics, 67, 250-264. [997,1001]
3. de Boor, C. (1978), A Practical Guide to Splines, New York: Springer. [1006]
4. Devlin, B., and Roeder, K. (1999), "Genomic Control for Association Studies, " Biometrics, 55, 997-1004. [997,1000]
5. Epstein, M. P., Allen, A. S., and Satten, G. A. (2007), "A Simple and Improved Correction for Population Stratification in Case-Control Studies, " American Journal of Human Genetics, 80, 921-930. [997]
6. Lander, E., and Schork, N. (1994), "Genetic Dissection of Complex Traits, " Science, 265, 2037-2048. [997]
7. Lee, A. B., Luca, D., Klei, L., Devlin, B., and Roeder, K. (2010), "Discovering Genetic Ancestry Using Spectral Graph Theory, " Genetic Epidemiology, 34, 51-59. [1000]
8. Lee, S., Sullivan, P. F., Zou, F., and Wright, F. A. (2008), "Comment on a Simple and Improved Correction for Population Stratification, " American Journal of Human Genetics, 80, 524-531. [998,1001]
9. Lehmann, E. L., and Casella, G. (1998), Theory of Point Estimation, NewYork: Springer. [1006]
10. Lin, D. Y., and Zeng, D. (2006), "Likelihood-Based Inference on Haplotype Effects in Genetic Association Studies" (with discussion), Journal of the American Statistical Association, 101, 89-118. [1005]
11. Prentice, R. L., and Pyke, R. (1979), "Logistic Disease Incidence Models and Case-Control Studies, " Biometrika, 66, 403-411. [998]
12. Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., and Reich, D. (2006), "Principal Components Analysis Corrects for Stratification in Genome-Wide Association Studies, " Nature Genetics, 38, 904-909. [997,1001,1003]
13. Pritchard, J. K., Stephens, M., Rosenberg, N. A., and Donnelly, P. (2000), "Association Mapping in Structured Populations, " American Journal of Human Genetics, 67, 170-181. [997]
14. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P., de Bakker, P. I., Daly, M. J., and Sham, P. C. (2007), "PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses, " American Journal of Human Genetics, 81, 559-575. [1002]
15. Risch, N., and Merikangas, K. (1996), "The Future of Genetic Studies of Complex Human Diseases, " Science, 273, 1516-1517. [997]
16. Rosenbaum, P. R., and Rubin, D. B. (1983), "The Central Role of the Propensity Score in Observational Studies for Causal Effects, " Biometrika, 70, 41-55. [998,999]
17. Sarasua, S. M., Collins, J. S., Williamson, D. M., Satten, G. A., and Allen, A. S. (2009), "Effect of Population Stratification on the Identification of Significant Single-Nucleotide Polymorphisms in Genome-Wide Association Studies, " BMC Proceedings, 3 (Suppl 7), S13. [1001]
18. Schumaker, L. L. (2007), Spline Functions: Basic Theory, Cambridge: Cambridge University Press. [1006]
19. The International HapMap Consortium (2005), "A Haplotype Map of the Human Genome, " Nature, 437, 1299-1320. [997]
20. TheWellcome Trust Case Control Consortium (2007), "Genome-Wide Association Study of 14,000 Cases of Seven Common Diseases and 3,000 Shared Controls, " Nature, 447, 661-678. [1001]
21. Tracy, C., and Widom, H. (1994), "Level-Spacing Distributions and the Airy Kernel, " Communications in Mathematical Physics, 159, 151-174. [1003]
22. van der Vaart, A. W., and Wellner, J. A. (1996), Weak Convergence and Empirical Processes, New York: Springer. [1006,1007]
23. Zhang, J., Niyogi, P., and McPeek, M. S. (2009), "Laplacian Eigenfunctions Learn Population Structure, " PLoS ONE, 4 (12), e7928. [1000]
24. Zhang, S., Zhu, X., and Zhao, H. (2003), "On a Semiparametric Test to Detect Associations Between Quantitative Traits and Candidate Genes Using Unrelated Individuals, " Genetic Epidemiology, 24, 44-56. [997]
25. Zhao, H., Rebbeck, T. R., and Mitra, N. (2009), "A Propensity Score Approach to Correction for Bias Due to Population Stratification Using Genetic and Non-Genetic Factors, " Genetic Epidemiology, 33, 679-690. [998]