Statistical methods for haplotype-based matched case-control association studies

Genetic Epidemiology

Volumn 31, Issue 4, 2007, Pages 316-326

  Zhang, Han ^a   Zhang, Hong ^a,b   Li, Zhaohai ^c,d   Zheng, Gang ^e  

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

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c GEORGE WASHINGTON UNIVERSITY   (United States)

^d NATIONAL CANCER INSTITUTE   (United States)

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

Author keywords

Bias; Estimation; Haplotype analysis; Matching; Wald test

Indexed keywords

ARTICLE; CONTROLLED STUDY; DISEASE ASSOCIATION; GENETIC ASSOCIATION; GENETIC EPIDEMIOLOGY; GENETIC RISK; HAPLOTYPE; HUMAN; INTERMETHOD COMPARISON; POPULATION GENETICS; PROBABILITY; PROCESS DEVELOPMENT; RISK ASSESSMENT; SIMULATION; STATISTICAL ANALYSIS;

CASE-CONTROL STUDIES; COMPUTER SIMULATION; GENETIC PREDISPOSITION TO DISEASE; HAPLOTYPES; HUMANS; LIKELIHOOD FUNCTIONS; LOGISTIC MODELS; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 34247326370     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20212     Document Type: Article

References (31)

1. ACCESS Research Group. 1999. Design of a case control etiologic study of sarcoidosis (ACCESS). J Clinical Epidemiol 52:1173-1186.
2. Akaike H. 1972. Information theory and an extension of maximum likelihood principle. Proceedings of the Second International Symposium on Information Theory. Suppl. to Problems of Control and Information Theory. p 267-281.
3. Botstein D, Risch N. 2003. Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nat Genet 33:228-237.
4. Breslow N, Day N. 1980. Statistical Methods in Cancer Research. Lyon, France: IARC Scientific Publications.
5. Chatterjee N, Carroll R. 2005. Semiparametric maximum-likelihood estimation exploiting gene-environment independence in case-control studies. Biometrika 92:399-418.
6. Chee M, Yang R, Hubbell E, Huang X, Stern D, Winkler J, Lockhart D, Morris M, Fodor S. 1996. Accessing genetic information with high-density DNA arrays. Science 274:610-614.
7. Cordell H, Clayton D. 2002. A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: application to HLA in type 1 diabetes. Am J Hum Genet 70:124-141.
8. Cox D. 1972. Regression models and life-tables (with discussion). J R Stat Soc B 34:187-220.
9. De Vivo I, Huggins G, Hankinson S, Lescault P, Boezen M, Colditz G, Hunter D. 2002. A functional polymorphism in the promoter of the progesterone receptor gene associated with endometrial cancer risk. Proc Natl Acad Sci, USA 99:12263-12268.
10. Epstein M, Satten G. 2003. Inference on haplotype effects in case-control studies using unphased genotype data. Am J Hum Genet 73:1316-1329.
11. Heinonen O, Albanes D, Virtamo J, Taylor P, Huttunen J, Hartman A, Haapakoski J, Malila N, Rautalahti M, Ripatti S, et al. 1998. Prostate cancer and supplementation with alpha-tocopherol and beta-carotene: incidence and mortality in a controlled trial. J Natl Cancer Inst 90:440-446.
12. Kraft P, Cox D, Paynter R, Hunter D, DeVivo I. 2005. Accounting for haplotype uncertainty in matched association studies: a comparison of simple and flexiable techniques. Genet Epidemiol 28:261-272.
13. Lake S, Lyon H, Tantisra K, Silverman E, Weiss S, Laird N, Schaid D. 2003. Estimation and tests of haplotype-environment interaction when linkage phase is ambiguous. Hum Hered 55:56-65.
14. Liddell F, McDonald J, Thomas D. 1977. Methods of cohort analysis: appraisal by application to asbestos mining. J R Stat Soc A 140:469-491.
15. Lin D, Zeng D. 2006. Likelihood-based inference on haplotype effects in genetic association studies (with discussion). J Am Stat Assoc 101:89-104.
16. Pike M, Hill A, Smith P. 1980. Bias and efficiency in logistic analyses of stratified case-control studies. Int J Epidemiol 9:89-95.
17. Risch N. 2000. Searching for genetic determinants in the new millennium. Nature 405:847-856.
18. Risch N, Merikangas K. 1996. The future of genetic studies of complex human diseases. Science 273:1516-1517.
19. Satten G, Epstein M. 2004. Comparison of prospective and retrospective methods for haplotype inference in case-control studies. Genet Epidemiol 27:192-201.
20. Schaid D. 2004. Evaluating associations of haplotypes with traits. Genet Epidemiol 27:348-364.
21. Schaid D, Rowland C, Tines D, Jacobson R, Poland G. 2002. Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70:425-434.
22. Schwartz G. 1986. Estimating the dimension of a model. Ann Stat 6:461-464.
23. Spinka C, Carroll R, Chatterjee N. 2005. Analysis of case-control studies of genetic and environmental factors with missing genetic information and haplotype-phase ambiguity. Genet Epidemiol 29:108-127.
24. Stram D, Pearce C, Bretsky P, Freedman M, Hirschhorn J, Altshuler D, Kolonel L, Henderson B, Thomas D. 2003a. Modelling and E-M estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals. Hum Hered 55:179-190.
25. Stram D, Haiman C, Hirschhorn J, Altshuler D, Kolonel L, Henderson B, Pike M. 2003b. Choosing haplotype-tagging SNPs based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the multiethnic cohort study. Hum Hered 55:27-36.
26. Tibshirani R. 1996. Regression shrinkage and selection via the lasso. J R Stat Soc B 58:267-288.
27. Valle T, Tuomilehto J, Bergman R, Ghosh S, Hauser E, Eriksson J, Nylund S, Kohtamaki K, Toivanen L, Vidgren G, and others. 1998. Mapping genes for NIDDM: design of the Finland-United States Investigation of NIDDM Genetics (FUSION) study. Diabetes Care 21:949-958.
28. Wang D, Fan J, Siao C, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, et al. 1998. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077-1082.
29. Zaykin D, Westfall P, Young S, Karnoub M, Wagner M, Ehm M. 2002. Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum Hered 53:79-91.
30. Zhang H, Zheng G, Li Z. 2006. Statistical analysis for haplotype-based matched case-control studies. Biometrics 62:1124-1131.
31. Zhao L, Li S, Khalid N. 2003. A method for the assessment of disease associations with single-nucleotide polymorphism haplotypes and environmental variables in case-control studies. Am J Hum Genet 72:1231-1250.