Pedigree disequilibrium tests for multilocus haplotypes

Genetic Epidemiology

Volumn 25, Issue 2, 2003, Pages 115-121

  Dudbridge, Frank ^a  

^a UK Human Genome Mapping Project Resource Centre   (United Kingdom)

Author keywords

Association tests; Family based controls; Haplotype analysis; PDT; TDT

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ARTICLE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; HAPLOTYPE; PEDIGREE; POPULATION DYNAMICS; POPULATION GENETICS; POPULATION STRUCTURE; QUANTITATIVE TRAIT; STATISTICAL ANALYSIS;

ALGORITHMS; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; PEDIGREE;

EID: 0041857847     PISSN: 07410395     EISSN: None     Source Type: Journal    
DOI: 10.1002/gepi.10252     Document Type: Article

References (28)

1. Abecasis GR, Cardon LR, Cookson WO. 2000. A general test of association for quantitative traits in nuclear families. Am J Hum Genet 66:279-292.
2. Bader JS. 2001. The relative power of SNPs and haplotypes as genetic markers for association tests. Pharmacogenomics 2:11-24.
3. Bitti PP, Murgia BS, Ticca A, Ferrai R, Musu L, Piras ML, Puledda E, Campo S, Durando S, Montomoli C, Clayton DG, Mander AP, Bernardinelli L. 2001. Association between the ancestral haplotype HLA A30B18DR3 and multiple sclerosis in central Sardinia. Genet Epidemiol 20:271-283.
4. Breslow NE, Day NE. 1980. The analysis of case-control studies. Volume 1, statistical methods in cancer research. Lyon: IARC.
5. Clayton D. 1999. A generalization of the transmission/disequilibrium test for uncertain-haplotype transmission. Am J Hum Genet 65:1170-1177.
6. 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 1 diabetes. Am J Hum Genet 70:124-141.
7. Curtis D, Sham PC. 1995. A note on the application of the transmission disequilibrium test when a parent is missing. Am J Hum Genet 56:811-812.
8. Dempster AP, Laird NM, Rubin D. 1977. Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc B 39:1-38.
9. Koeleman BP, Dudbridge F, Cordell HJ, Todd JA. 2000. Adaptation of the extended transmission/disequilibrium test to distinguish disease associations of multiple loci: the conditional extended transmission/disequilibrium test. Ann Hum Genet 64:207-213.
10. Li H. 2001. A permutation procedure for the haplotype method for identification of disease-predisposing variants. Ann Hum Genet 65:189-196.
11. Markianos K, Daly MJ, Kruglyak L. 2001. Efficient multipoint linkage analysis through reduction of inheritance space. Am J Hum Genet 68:963-977.
12. Martin ER, Bass MP, Kaplan NL. 2001. Correcting for a potential bias in the pedigree disequilibrium test. Am J Hum Genet 68:1065-1067.
13. Monks SA, Kaplan NL. 2000. Removing the sampling restrictions from family-based tests of association for a quantitative-trait locus. Am J Hum Genet 66:576-592.
14. Morris AP, Whittaker JC, Curnow RN. 1997. A likelihood ratio test for detecting patterns of disease-marker association. Ann Hum Genet 61:335-350.
15. North BV, Curtis D, Sham PC. 2003. A note on the calculation of empirical P values from Monte Carlo procedures. Am J Hum Genet 72:498-499.
16. Sasieni PD. 1997. From genotypes to genes: doubling the sample size. Biometrics 53:1253-1261.
17. Schaid DJ, Sommer SS. 1993. Genotype relative risks: methods for design and analysis of candidate-gene association studies. Am J Hum Genet 53:1114-1126.
18. 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.
19. Sham PC, Curtis D. 1995. An extended transmission/disequilibrium test (TDT) for multi-allele marker loci. Ann Hum Genet 59:323-326.
20. Sinsheimer JS, McKenzie CA, Keavney B, Lange K. 2001. SNPs and snails and puppy dogs' tails: analysis of SNP haplotype data using the gamete competition model. Ann Hum Genet 65:483-490.
21. Spielman RS, Ewens WJ. 1996. The TDT and other family-based tests for linkage disequilibrium and association. Am J Hum Genet 59:983-989.
22. Spielman RS, McGinnis RE, Ewens WJ. 1993. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 52:506-516.
23. Terwilliger JD, Ott J. 1992. A haplotype-based "haplotype relative risk" approach to detecting allelic associations. Hum Hered 42:337-346.
24. Thomson G. 1995. Mapping disease genes: family-based association studies. Am J Hum Genet 57:487-498.
25. 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.
26. Zhang S, Zhang K, Li J, Sun F, Zhao H. 2001. Test of association for quantitative traits in general pedigrees: the quantitative pedigree disequilibrium test. Genet Epidemiol [Suppl] 21:370-375.
27. Zhao JH, Sham PC, Curtis D. 1999. A program for the Monte Carlo evaluation of significance of the extended transmission/disequilibrium test. Am J Hum Genet 64:1484-1485.
28. Zhao JH, Curtis D, Sham PC. 2000. Model-free analysis and permutation tests for allelic associations. Hum Hered 50:133-139.