Testing association between disease and multiple SNPs in a candidate gene

Genetic Epidemiology

Volumn 31, Issue 5, 2007, Pages 383-395

  Gauderman, W James ^a   Murcray, Cassandra ^a   Gilliland, Frank ^a   Conti, David V ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Complex trait; Genotypes; Haplotypes; Principal components

Indexed keywords

GLUTATHIONE TRANSFERASE P1; TUMOR NECROSIS FACTOR ALPHA;

ARTICLE; COMPARATIVE STUDY; DISEASE ASSOCIATION; DISEASE PREDISPOSITION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ANALYSIS; GENETIC LINKAGE; GENETIC MODEL; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; POPULATION MODEL; PRINCIPAL COMPONENT ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; SYMPTOM;

ASTHMA; CASE-CONTROL STUDIES; CHILD; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; GLUTATHIONE S-TRANSFERASE PI; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS;

EID: 34447315844     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20219     Document Type: Article

References (34)

1. Barrett JC, Fry B, Maller J, Daly MJ. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265.
2. 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.
3. Chapman NH, Wijsman EM. 1998. Genome screens using linkage disequilibrium tests: optimal marker characteristics and feasibility. Am J Hum Genet 63:1872-1885.
4. Clayton D, Chapman J, Cooper J. 2004. Use of unphased multilocus genotype data in indirect association studies. Genet Epidemiol 27:415-428.
5. Conti DV, Gauderman W. 2004. SNPs, haplotypes, and model selection in a candidate gene region: the SIMPle analysis for multilocus data. Genet Epidemiol 27:429-441.
6. Daly M, Rioux J, Schaffner S, Hudson T, Lander E. 2001. High-resolution haplotype structure in the human genome. Nat Genet 29:229-232.
7. Durrant C, Morris AP. 2005. Linkage disequilibrium mapping via cladistic analysis of phase-unknown genotypes and inferred haplotypes in the Genetic Analysis Workshop 14 simulated data. BMC Genet 1 (6 Suppl):S100.
8. Durrant C, Zondervan KT, Cardon LR, Hunt S, Deloukas P, Morris AP. 2004. Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes. Am J Hum Genet 75:35-43.
9. Epstein MP, Satten GA. 2003. Inference on haplotype effects in case-control studies using unphased genotype data. Am J Hum Genet 73:1316-1329.
10. Fallin D, Schork NJ. 2000. Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am J Hum Genet 67:947-959.
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. Fan R, Knapp M. 2003. Genome association studies of complex diseases by case-control designs. Am J Hum Genet 72: 850-868.
13. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. 2002. The structure of haplotype blocks in the human genome. Science 296:2225-2229.
14. Gauderman W. 2002. Sample size requirements for association studies of gene-gene interaction. Am J Epidemiol 155:478-484.
15. Gauderman W, Morrison J. 2006. QUANTO 1.2. A computer program for power and sample size calculations for genetic-epidemiology studies: Freely available at http://hydra.usc. edu/gxe.
16. Gilliland F, McConnell R, Peters J, Gong Jr H. 1999. A theoretical basis for investigating ambient air pollution and children's respiratory health. Env Health Perspect 107:403-407.
17. Johnson R, Wichern D. 1982. Applied Multivariate Analysis. Englewood Cliffs, NJ: Prentice-Hall, Inc.
18. Kaplan N, Morris R. 2001. Prospects for association-based fine mapping of a susceptibility gene for a complex disease. Theor Popul Biol 60:181-191.
19. Kolonel LN, Henderson BE, Hankin JH, Nomura AM, Wilkens LR, Pike MC, Stram DO, Monroe KR, Earle ME, Nagamine FS. 2000. A multiethnic cohort in Hawaii and Los Angeles: baseline characteristics. Am J Epidemiol 151:346-357.
20. Kolonel LN, Altshuler D, Henderson BE. 2004. The multiethnic cohort study: exploring genes, lifestyle and cancer risk. Nat Rev Cancer 4:519-527.
21. Kraft P, Cox DG, Paynter RA, Hunter D, De Vivo I. 2005. Accounting for haplotype uncertainty in matched association studies: a comparison of simple and flexible techniques. Genet Epidemiol 28:261-272.
22. Lin Z, Altman RB. 2004. Finding haplotype tagging SNPs by use of principal components analysis. Am J Hum Genet 75:850-861.
23. McConnell R, Berhane K, Gilliland F, Molitor J, Thomas D, Lurmann F, Avol E, Gauderman WJ, Peters JM. 2003. Prospective Study of Air Pollution and Bronchitic Symptoms in Children with Asthma. Am J Respir Crit Care Med 168: 790-797.
24. Meng Z, Zaykin DV, Xu CF, Wagner M, Ehm MG. 2003. Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes. Am J Hum Genet 73: 115-130.
25. Peters J, Avol E, Navidi W, London S, Gauderman W, Lurmann F, Linn W, Margolis H, Rappaport E, Gong HJ, Thomas D. 1999. A study of twelve southern California communities with differing levels and types of air pollution I. Prevalence of respiratory morbidity. Am J Respir Crit Care Med 159: 760-767.
26. Satten GA, Epstein MP. 2004. Comparison of prospective and retrospective methods for haplotype inference in case-control studies. Genet Epidemiol 27:192-201.
27. Schaid DJ. 2002. Relative efficiency of ambiguous vs. directly measured haplotype frequencies. Genet Epidemiol 23: 426-443.
28. 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.
29. Schork NJ, Nath SK, Fallin D, Chakravarti A. 2000. Linkage disequilibrium analysis of biallelic DNA markers, human quantitative trait loci, and threshold-defined case and control subjects. Am J Hum Genet 67:1208-1218.
30. Sha Q, Dong J, Jiang R, Zhang S. 2005. Tests of association between quantitative traits and haplotypes in a reduced-dimensional space. Ann Hum Genet 69:715-732.
31. Stram D, Pearce L, Bretsky P, Freedman M, Hirschhorn J, Altshuler D, Kolonel L, Henderson B, Thomas D. 2003. Modeling 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.
32. Stram DO. 2004. Tag SNP selection for association studies. Genet Epidemiol 27:365-374.
33. 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.
34. Zhao LP, Li SS, 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.