Rapid Testing of SNPs and Gene-Environment Interactions in Case-Parent Trio Data Based on Exact Analytic Parameter Estimation

Biometrics

Volumn 68, Issue 3, 2012, Pages 766-773

  Schwender, Holger ^a,b   Taub, Margaret A ^b   Beaty, Terri H ^b   Marazita, Mary L ^c   Ruczinski, Ingo ^b  

^a TU DORTMUND UNIVERSITY   (Germany)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Conditional logistic regression; Family based design; Genome wide association studies; Genotypic transmission disequilibrium test; International Cleft Consortium; MAX test

Indexed keywords

ASSOCIATION REACTIONS; GENES; PARAMETER ESTIMATION; REGRESSION ANALYSIS; STATISTICAL TESTS; STATISTICS;

CONDITIONAL LOGISTIC REGRESSIONS; FAMILY-BASED DESIGN; GENE-ENVIRONMENT INTERACTION; GENOME-WIDE ASSOCIATION STUDIES; GENOTYPIC TRANSMISSION/DISEQUILIBRIUM TEST; INTERNATIONAL CLEAVE CONSORTIUM; LOGISTIC REGRESSION MODELING; MAX TEST; SINGLE NUCLEOTIDE POLYMORPHISMS; TEST STATISTICS;

ITERATIVE METHODS;

GENOTYPE-ENVIRONMENT INTERACTION; LOGISTICS; REGRESSION ANALYSIS;

EID: 84866750913     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/j.1541-0420.2011.01713.x     Document Type: Article

References (24)

1. Beaty, T. H., Murray, J. C., Marazita, M. L., Munger, R. G., Ruczinski, I., Hetmanski, J. B., Liang, K. Y., Wu, T., Murray, T., Fallin, M. D., Redett, R. A., Raymond, G., Schwender, H., Jin, S. C., Cooper, M. E., Dunnwald, M., Mansilla, M. A., Leslie, E., Bullard, S., Lidral, A. C., Moreno, L. M., Menezes, R., Vieira, A. R., Petrin, A., Wilcox, A. J., Lie, R. T., Jabs, E. W., Wu-Chou, Y. H., Chen, P. K., Wang, H., Ye, X., Huang, S., Yeow, V., Chong, S. S., Jee, S. H., Shi, B., Christensen, K., Melbye, M., Doheny, K. F., Pugh, E. W., Ling, H., Castilla, E. E., Czeizel, A. E., Ma, L., Field, L. L., Brody, L., Pangilinan, F., Mills, J. L., Molloy, A. M., Kirke, P. N., Scott, J. M., Arcos-Burgos, M., and Scott, A. F. (2010). A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nature Genetics 42, 525-529.
2. Breslow, N. E., Day, N. E., Halvorsen, K. T., Prentice, R. L., and Sabai, C. (1978). Estimation of multiple relative risk functions in matched case-control studies. American Journal of Epidemiology 108, 299-307.
3. Chatterjee, N., Kalaylioglu, Z., and Carroll, R. J. (2005). Exploiting gene-environment independence in family based control studies: Increased power for detecting associations, interactions and joint effects. Genetic Epidemiology 28, 138-156.
4. Cordell, H. J. (2002). Epistasis: What it means, what it doesn't mean, and statistical methods to detect it in humans. Human Molecular Genetics 11, 2463-2468.
5. Fallin, D., Beaty, T., Liang, K.-Y., and Chen, W. (2002). Power comparisons for genotypic vs. allelic TDT methods with ≥ 2 alleles. Genetic Epidemiology 23, 458-461.
6. Freidlin, B., Zheng, G., Li, Z., and Gastwirth, J. (2002). Trend tests for case-control studies of genetic markers: Power, sample size and robustness. Human Heredity 53, 146-152.
7. Gauderman, W. J., Witte, J. S., and Thomas, D. C. (1999). Family-based association studies. Journal of the National Cancer Institutes Monograph 26, 31-37.
8. Laird, N. M. and Lange, C. (2006). Family-based designs in the age of large-scale gene-association studies. Nature Reviews Genetics 7, 385-394.
9. Li, Z., Gastwirth, J. L., and Gail, M. H. (2005). Power and related statistical properties of conditional likelihood score tests for association studies in nuclear families with parental genotypes. Annals of Human Genetics 69, 296-314.
10. Louis, T. A. and Ruczinski, I. (2010). Efficient evaluation of ranking procedures when the number of units is large, with application to SNP identification. Biometrical Journal 52, 34-49.
11. Maestri, N. E., Beaty, T. H., Hetmanski, J., Smith, E. A., McIntosh, I., Wyszynski, D. F., Liang, K. Y., Duffy, D. L., and VanderKolk, C. (1997). Application of transmission disequilibrium tests to nonsyndromic oral clefts: Including candidate genes and environmental exposures in the models. American Journal of Medical Genetics 73, 337-344.
12. McNemar, Q. (1947). Note on the sampling error of the difference between correlated proportions or percentages. Psychometrika 12, 153-157.
13. R Development Core Team (2010). R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. ISBN 3-900051-07-0.
14. Schaid, D. J. (1996). General score tests for associations of genetic markers with disease using cases and their parents. Genetic Epidemiology 13, 423-449.
15. Schaid, D. J. (1999a). Case-parents design for gene-environment interaction. Genetic Epidemiology 16, 261-273.
16. Schaid, D. J. (1999b). Likelihoods and TDT for the case-parents design. Genetic Epidemiology 16, 250-260.
17. Schaid, D. J. and Sommer, S. S. (1993). Genotype relative risks: Methods for design and analysis of candidate-gene association studies. American Journal of Human Genetics 53, 1114-1126.
18. Self, S. G., Longton, G., and Kopecky, K. J. Liang, K. Y. (1991). On estimating HLA/disease association with application to a study of aplastic anemia. Biometrics 47, 53-61.
19. Sladek, R., Rocheleau, G., Rung, J., Dina, C., Shen, L., Serre, D., Boutin, P., Vincent, D., Belisle, A., Hadjadj, S., Balkau, B., Heude, B., Charpentier, G., Hudson, T. J., Montpetit, A., Pshezhetsky, A. V., Prentki, M., Posner, B. I., Balding, D. J., Meyre, D., Polychronakos, C., and Froguel, P. (2007). A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445, 881-885.
20. Spielman, R. S. and Ewens, W. J. (1996). The TDT and other family-based tests for linkage disequilibrium and association. American Journal of Human Genetics 59, 983-989.
21. Spielman, R. S., McGinnis, R., and Ewens, W. J. (1993). Transmission test for linkage disequilibrium: The insulin gene region and insulin-dependent diabetes mellitus (IDDM). American Journal of Human Genetics 52, 506-516.
22. Wakefield, J. (2009). Bayes factors for genome-wide association studies: Comparison with p-values. Genetic Epidemiology 33, 79-86.
23. Yan, L. K., Zheng, G., and Li, Z. (2008). Two-stage group sequential robust tests in family-based association studies: Controlling type I error. Annals of Human Genetics 72, 557-565.
24. Zheng, G., Freidlin, B., and Gastwirth, J. L. (2002). Robust TDT-type candidate-gene association tests. Annals of Human Genetics 66, 145-155.