SNPs, haplotypes, and model selection in a candidate gene region: The SIMPle analysis for multilocus data

Genetic Epidemiology

Volumn 27, Issue 4, 2004, Pages 429-441

  Conti, David V ^a   Gauderman, W James ^b  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b NONE

Author keywords

Association analysis; Bayes model averaging; Genotypes; Haplotypes; SNPs

Indexed keywords

ANALYTIC METHOD; ARTICLE; BAYES THEOREM; GENETIC MODEL; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; POLYMORPHIC LOCUS; RISK ASSESSMENT; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; UNCERTAINTY;

BAYES THEOREM; CHROMOSOME MAPPING; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; GENOME, HUMAN; GENOTYPE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 10044292874     PISSN: 07410395     EISSN: None     Source Type: Journal    
DOI: 10.1002/gepi.20039     Document Type: Article

References (32)

1. Ayres KL, Balding DJ. 2001. Measuring gametic disequilibrium from multilocus data. Genetics 157:413-423.
2. Bader JS. 2001. The relative power of SNPs and haplotype as genetic markers for association tests.[comment]. Pharmacogenomics 2:11-24.
3. Chapman JM, Cooper JD, Todd JA, Clayton DG. 2003. Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum Hered 56:18-31.
4. Chipman H. 1996. Bayesian variable selection with related predictors. Can J Stat 24:17-36.
5. Chipman HA, George EI, McCulloch RE. 2001. Managing multiple models. In: Jaakkola T, Richardson T, editors. Artificial Intelligence and Statistics 2001. Morgan Kaufman. p 11-18.
6. Conti DV, Witte JS. 2003. Hierarchical modeling of linkage disequilibrium: genetic structure and spatial relations. Am J Hum Genet 72:351-363.
7. Conti DV, Cortessis V, Molitor J, Thomas DC. 2003. Bayesian modeling of complex metabolic pathways. Hum Hered 56:83-93.
8. Cordell HJ, Clayton DG. 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 I diabetes. Am J Hum Genet 70:124-141.
9. Devlin B, Roeder K, Wasserman L. 2003. Analysis of multilocus models of association. Genet Epidemiol 25:36-47.
10. Excoffier L, Slatkin M. 1995. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927.
11. Fallin D, Cohen A, Essioux L, Chumakov I, Blumenfeld M, Cohen D, Schork NJ. 2001. Genetic analysis of case/control data using estimated haplotype frequencies: application to APOE locus variation and Alzheimer's disease. Genome Res 11:143-151.
12. George EI, Foster DP. 2000. Calibration and empirical Bayes variable selection. Biometrika 87:731-747.
13. George EI, McCulloch RE. 1993. Variable selection via Gibbs sampling. JASA 88:881-889.
14. Haiman CA, Stram DO, Pike MC, Kolonel LN, Burtt NP, Altshuler D, Hirschhorn J, Henderson BE. 2003. A comprehensive haplotype analysis of CYP19 and breast cancer risk: the Multiethnic Cohort. Hum Mol Genet 12:2679-2692.
15. Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337-338.
16. International HapMap Project. 2003. Nature 426:789-796.
17. Kass R, Raftery A. 1995. Bayes factors. J Am Stat Assoc 90:773-795.
18. Loukola A, Chadha M, Penn SG, Rank D, Conti DV, Thompson D, Cicek M, Love B, Bivolarevic V, Yang Q, Jiang Y, Hanzel DK, Paris PL, Casey G, Witte JS. 2004. Comprehensive evaluation of the association between prostate cancer and genotypes/haplotypes in CYP17A1, CYP3A4, SRD5A2 and the Androgen receptor. Eur J Hum Genet 12:321-332.
19. McCullagh P, Nelder JA. 1989. Generalized linear models. Boca Raton: Chapman.
20. Morris A, Pedder A, Ayres K. 2003. Linkage disequilibrium assessment via log-linear modeling of SNP haplotype frequencies. Genet Epidemiol 25:106-114.
21. Morris RW, Kaplan NL. 2002. On the advantage of haplotype analysis in the presence of multiple disease susceptibility alleles. Genet Epidemiol 23:221-233.
22. Ott J. 1989. Statistical properties of the haplotype relative risk. Genet Epidemiol 6:127-130.
23. R Development Core Team. 2003. R: A language and environment for statistical Computing. R Development Core Team. Vienna, Austria: R Foundation for Statistical Computing.
24. Schaid D, Sommer S. 1993. Genotype relative risks: methods for design and analysis of candidate-gene association studies. Am J Hum Genet 53:1114-1126.
25. Schaid DJ. 1996. General score tests for associations of genetic markers with disease using cases and their parents. Genet Epidemiol 13:423-449.
26. Schaid DJ. 2002. Relative efficiency of ambiguous vs. directly measured haplotype frequencies. Genet Epidemiol 23:426-443.
27. Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. 2002. Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70:425-434.
28. Smouse PE. 1974. Likelihood analysis of recombinational disequilibrium in multiple-locus gametic frequencies. Genetics 76:557-565.
29. Speigelhalter DJ, Thomas A, Best NG. 1999. WinBUGS Version 1.2 User Manual. Cambridge: Medical Research Council Biostatistics Unit.
30. Stram DO. 2004. Tag SNP selection for association studies. Genet Epidemiol 27:365-374 (this issue).
31. Stram DO, Haiman CA, Hirschhorn JN, Altshuler D, Kolonel LN, Henderson BE, Pike MC. 2003. 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.
32. Zaykin DV, Westfall PH, Young SS, Karnoub MA, Wagner MJ, Ehm MG. 2002. Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum Hered 53:79-91.