Comparison of two-phase analyses for case-control genetic association studies

Statistics in Medicine

Volumn 27, Issue 24, 2008, Pages 5054-5075

  Zheng, Gang ^a   Meyer, Mark ^a,b   Li, Wentian ^c   Yang, Yaning ^d  

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

^b AMERICAN UNIVERSITY   (United States)

^c FEINSTEIN INSTITUTE FOR MEDICAL RESEARCH   (United States)

^d UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Adaptive approach; Constrained likelihood ratio test; Efficiency robustness; Genetic model selection; MAX; Two phase analysis

Indexed keywords

ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; BREAST CANCER; CANCER GENETICS; CASE CONTROL STUDY; CHI SQUARE TEST; CONTROLLED STUDY; GENETIC ASSOCIATION; GENETIC MODEL; GENOTYPE; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; BIOLOGICAL MODEL; COMPARATIVE STUDY; GENETIC PREDISPOSITION; HUMAN; STATISTICAL MODEL;

CASE-CONTROL STUDIES; DATA INTERPRETATION, STATISTICAL; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL;

EID: 58149292807     PISSN: 02776715     EISSN: 10970258     Source Type: Journal    
DOI: 10.1002/sim.3336     Document Type: Article

References (30)

1. Cochran WG. Some methods for strengthening the common chi-square tests. Biometrics 1954; 10:417-451.
2. Armitage P. Tests for linear trends in proportions and frequencies. Biometrics 1955; 11:375-386.
3. Sasieni PD. From genotypes to genes: doubling the sample size. Biometrics 1997; 53:1253-1261.
4. Freidlin B, Zheng G, Li Z, Gastwirth JL. Trend tests for case-control studies of genetic markers: power, sample size and robustness. Human Heredity 2002; 53:146-152.
5. Zheng G, Freidlin B, Gastwirth JL. Comparison of robust tests for genetic association using case-control studies. Second Lehmann Symposium - Optimality. IMS Lecture Notes - Monograph Series, vol. 49. IMS: Beachwood, OH, 2006; 253-265.
6. Wang K, Sheffield VC. A constrained-likelihood approach to marker-trait association studies. American Journal of Human Genetics 2005; 77:768-780.
7. Skol AD, Scott LJ, Abecasis GR, Boehnke M. Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nature Genetics 2006; 38:209-213.
8. Elston RC, Lin DY, Zheng G. Multistage sampling for genetic studies. Annual Review of Genomics and Human Genetics 2007; 8:327-342.
9. Zheng G, Song K, Elston RC. Adaptive two-stage analysis of genetic association in case-control designs. Human Heredity 2007; 63:175-186.
10. Zheng G, Ng HKT. Genetic model selection in two-stage analysis for case-control association studies. Biostatistics 2008; DOI: 10.1093/biostatistics/kxm039.
11. Song K, Elston RC. A powerful method of combining measures of association and Hardy-Weinberg disequilibrium for fine-mapping in case-control studies. Statistics in Medicine 2006; 25:105-126.
12. Slager SL, Schaid DJ. Case-control studies of genetic markers: power and sample size approximations for Armitage's test for trend. Human Heredity 2001; 52:149-153.
13. Zheng G, Freidlin B, Li Z, Gastwirth JL. Choice of scores in trend tests for case-control studies of candidate-gene associations. Biometrical Journal 2003; 45:335-348.
14. Zheng G, Gastwirth JL. On estimation of the variance in Cochran-Armitage trend tests for genetic association using case-control studies. Statistics in Medicine 2006; 25:3150-3159.
15. Agresti A. Categorical Data Analysis. Wiley: New York, 1990.
16. Balding DJ. A tutorial on statistical methods for population association studies. Nature Review Genetics 2006; 7:781-791.
17. 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 TJ, Montpetit A, Pshezhetsky AV, Prentki M, Posner BI, Balding DJ, Meyre D, Polychronakos C, Froguel P. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 2007; 445:881-885.
18. Gastwirth JL. The use of maximin efficiency robust tests in combining contingency tables and survival analysis. Journal of the American Statistical Association 1985; 80:380-384.
19. Freidlin B, Podgor MJ, Gastwirth JL. Efficiency robust tests for survival or ordered categorical data. Biometrics 1999; 55:883-886.
20. Zaykin DV, Nielsen DM. Hardy-Weinberg disequilibrium (HWD) fine mapping for case-control samples. American Journal of Human Genetics 2000; 67(Suppl.):1238.
21. Wittke-Thompson JK, Pluzhnikov A, Cox NJ. Rational inferences about departure from Hardy-Weinberg equilibrium. American Journal of Human Genetics 2005; 76:967-986.
22. Suh YJ, Li W. Genotype-based case-control analysis, violation of Hardy-Weinberg equilibrium, and phase diagram. Proceedings of the 5th Asia-Pacific Bioinformatics Conference. Imperial College Press: U.K., 2007; 185-194.
23. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J. Complement factor H polymorphism in age-related macular degeneration. Science 2005; 308:385-389.
24. AREDS Research Group. Risk factors associated with age-related macular degeneration: a case-control study in the age-related eye disease study: age related eye disease study report number 3. Ophthalmology 2000; 107:2224-2232.
25. Pooley KA, Healey CS, Smith PL, Pharoah PD, Thompson D, Tee L, West J, Jordan C, Easton DF, Ponder BA, Dunning AM. Association of the progesterone receptor gene with breast cancer risk: a single-nucleotide polymorphism tagging approach. Cancer Epidemiology, Biomarkers and Prevention 2006; 15:675-782.
26. Van Steen K, McQueen MB, Herbert A, Raby B, Lyon H, DeMeo DL, Murphy A, Su J, Datta S, Rosenow C, Christman M, Silverman EK, Laird NM, Weiss ST, Lange C. Genomic screening and replication using the same data set in family-based association testing. Nature Genetics 2005; 37:683-691.
27. The Wellcome Trust Case Control Consortium. Genome-wide association study of 14 000 cases of seven common diseases and 3000 shared controls. Nature 2007; 447:661-683.
28. Zheng G, Joo J, Lin JP, Stylianou M, Waclawiw MA, Geller NL. Robust ranks of true associations in genome-wide case-control association studies. BMC Proceedings 2007; 1(Suppl. 1):S165.
29. Zaykin DV, Zhivotovsky LA. Ranks of genuine associations in whole-genome scans. Genetics 2005; 171:813-823.
30. Gail MH, Pfeiffer RM, Wheeler W, Pee D. Probability of detecting disease-associated single nucleotide polymorphisms in case-control genome-wide association studies. Biostatistics 2008; 9:201-215.