Efficient approximation of P-value of the maximum of correlated tests, with applications to genome-wide association studies

Annals of Human Genetics

Volumn 72, Issue 3, 2008, Pages 397-406

  Li, Qizhai ^a,b   Zheng, Gang ^c   Li, Zhaohai ^d,e   Yu, Kai ^a,f  

^a NATIONAL CANCER INSTITUTE   (United States)

^b CHINESE ACADEMY OF SCIENCES   (China)

^c NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^d GEORGE WASHINGTON UNIVERSITY   (United States)

^e EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^f NONE   (United States)

Author keywords

Case control; MAX; Robust genome wide scan

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; BREAST CANCER; CONTROLLED STUDY; CORONARY ARTERY DISEASE; CORRELATION ANALYSIS; COVARIANCE; GENETIC ASSOCIATION; GENOME ANALYSIS; GENOTYPE; HUMAN; NON INSULIN DEPENDENT DIABETES MELLITUS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROSTATE CANCER; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL SIGNIFICANCE;

CHROMOSOMES, HUMAN; COMPUTER SIMULATION; CORONARY ARTERY DISEASE; DIABETES MELLITUS; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; HUMANS; MODELS, GENETIC; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 42149115111     PISSN: 00034800     EISSN: 14691809     Source Type: Journal    
DOI: 10.1111/j.1469-1809.2008.00437.x     Document Type: Article

References (28)

1. Conneely, K. N. & Boehnke, M. (2007) So many correlated tests, so little time Rapid adjustment of p-values for multiple correlated tests. Am J Hum Genet 81, 1158-1168.
2. Devlin, B. & Roeder, K. (1999) Genomic control for association studies. Biometrics 55, 997-1004.
3. Efron, B. (1997) The length heuristic for simultaneous hypothesis tests. Biometrika 84, 143-157.
4. Freidlin, B., Podgor, M. J. & Gastwirth, J. L. (1999) Efficiency robust tests for survival or ordered categorical data. Biometrics 55, 883-886
5. Gastwirth, J. L. (1985) The use of maximin efficiency robust tests in combining contingency tables and survival analysis. J Am Stat Assoc 80, 380-384.
6. Hoh, J. & Ott, J. (2003) Mathematical multi-locus approaches to localizing complex human trait genes. Nat Rev Genet 4, 701-709.
7. Hunter, D. J., Kraft, P., Jacobs, K. B., Cox, D. G., Yeager, M., Hankinson, S. E., Wacholder, S., Wang, Z., Welch, R., Hutchinson, A. et al. (2007) A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 39, 870-874.
8. Klein, R. J., Zeiss, C., Chew, E. Y., Tsai, J. Y., Sackler, R. S., Haynes, C., Henning, A. K., SanGiovanni, J. P., Mane, S. M., Mayne, S. T. et al. (2005) Complement factor H polymorphism in aged-related macular degeneration. Science 308, 385-389.
9. Li, Q. Z. & Yu, K. (2008) Improved correction for population stratification in genome-wide association studies by identifying hidden population structures. Genet Epidemiol, (In press).
10. Liang, K. Y. & Zeger, S. L. (1986) longitudinal data analysis using generalized linear models. Biometrika 73, 13-22.
11. Marchini, J., Donnelly, P. & Cardon, L. R. (2005) Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 37, 413-417.
12. Pepe, M. S., Whitaker, B. C. & Seidel, K. (1999) Estimating and comparing univariate associations with application to the prediction of adult obesity. Stat Med 18, 163-173.
13. Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., Reich, D. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38, 904-909.
14. Sasieni, P. D. (1997) From genotypes to genes: Doubling the sample size. Biometrics 53, 1253-1261.
15. Schaid, D. J., McDonnell, S. K., Hebbring, S. J., Cunningham, J. M. & Thibodeau, S. N. (2005) Nonparametric tests of association of multiple genes with human diseases. Am J Hum Genet 76, 780-793.
16. Skol, A. D., Scott, L. J., Abecasis, G. R. & Boehnke, M. (2006) Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 38, 209-213.
17. Sladek, R., Rocheleau, G., Rung, J., Dina, C., Shen, L., Serre, D., Boutin, P., Vincent, D., Belisle, A., Hadjadj, S. et al. (2007) A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445, 881-885.
18. Slager, S. L. & Schaid, D. J. (2001) Case-control studies of genetic markers: Power and sample size approximations for Armitage's test for trend. Hum Hered 52, 149-153.
19. The Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature 447, 661-678.
20. Wang, T., Zhu, X. & Elston, R. C. (2007) Improving power in contrasting linkage-disequilibrium patterns between cases and controls. Am J Hum Genet 80, 911-920.
21. Yan, L. H., Zheng, G. & Li, Z. H. (2008) Two-stage group sequential robust tests in family-based association studies: Controlling type I error. Ann Hum Genet (Tentatively accepted).
22. Yeager, M., Orr, N., Hayes, R. B., Jacobs, K. B., Kraft, P. et al. (2007) Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 39, 645-649.
23. Yu, K., Chatterjee, N., Wheeler, W., Li, Q. Z., Wang, S. et al. (2007) Flexible Design for Following Up Positive Findings. Am J Hum Genet 81, 540-551.
24. Zhang, S., Zhu, X. & Zhao, H. (2003) On a Semiparametric Test to Detect Associations Between Quantitative Traits and Candidate Genes Using Unrelated Individuals. Genet Epidemiol 24, 44-56.
25. Zheng, G., Freidlin, B., Li, Z. H. & Gastwirth, J. L. (2003) Choice of scores in trend tests for case-control studies of candidate gene associations. Biometrical J 45, 335-348.
26. Zheng, G., Friedlin, B. & Gastwirth, J. L. (2006a) Comparison of robust tests for genetic association using case-control studies. IMS Lecture Notes-Monograph Series. 2nd Eric L. Lehmann Symposium - Optimality 49, 253-265.
27. Zheng, G., Freidlin, B. & Gastwirth, J. L. (2006b) Robust genomic control for association studies. Am J Hum Genet 78, 350-356.
28. Zheng, G., Joo, J., Lin, J. P., Stylianou, M. & Waclawiw, M. A. et al. (2007) Robust ranks of true associations in genome-wide case-control association studies. BMC Proceedings 1 (Suppl 1), S165.