A flexible Bayesian framework for modeling haplotype association with disease, allowing for dominance effects of the underlying causative variants

American Journal of Human Genetics

Volumn 79, Issue 4, 2006, Pages 679-694

  Morris, Andrew P ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DNA;

ALLELE; AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; CAUSAL ATTRIBUTION; CLUSTER ANALYSIS; CORRELATION ANALYSIS; COST; DISEASE ASSOCIATION; DOMINANT GENE; FUNCTIONAL PROTEOMICS; GENE CLUSTER; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC MARKER; GENETIC MODEL; GENETIC PROCEDURES; GENETIC SIMILARITY; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME ANALYSIS; HAPLOTYPE; HUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN FUNCTION; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; STATISTICAL MODEL;

EID: 33749037699     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/508264     Document Type: Article

References (42)

1. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516-1517
2. Zondervan KT, Cardon LR (2004) The complex interplay among factors that influence allelic association. Nat Rev Genet 5:89-100
3. Thomas DC, Haile RW, Duggan D (2005) Recent developments in genomewide association scans: a workshop summary and review. Am J Hum Genet 77:337-345
4. The International HapMap Consortium (2003) The International HapMap Project. Nature 426:789-796
5. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437:1299-1320
6. Clark AG (2004) The role of haplotypes in candidate gene studies. Genet Epidemiol 27:321-333
7. Tavtigian S, Simard J, Teng D, Abtin V, Baumgard M, Beck A, Camp N, et al (2001) A candidate prostate cancer susceptibility gene at chromosome 17p. Nat Genet 27:172-180
8. 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
9. 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
10. Stram DO, Pearce CL, Bretsky P, Freedman M, Hirschhorn JN, Altshuler D, Kolonel LN, Henderson BE, Thomas DC (2003) Modelling and EM estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals. Hum Hered 55:179-190
11. Morris AP (2005) Direct analysis of unphased SNP genotype data in population-based association studies via Bayesian partition modelling of haplotypes. Genet Epidemiol 29:91-107
12. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989
13. Stephens M, Donnelly P (2003) A comparison of Bayesian methods for haplotype reconstruction from population genetic data. Am J Hum Genet 73:1162-1169
14. Templeton AR, Boerwinkle E, Sing CF (1987) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. 1. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics 117:343-351
15. Templeton AR, Sing CF, Kessling A, Humphries S (1988) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations. Genetics 120:1145-1154
16. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619-633
17. Templeton AR, Sing CF (1993) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134:659-669
18. Molitor J, Marjoram P, Thomas D (2003) Application of Bayesian spatial statistical methods to the analysis of haplotype effects and gene mapping. Genet Epidemiol 25:95-105
19. Molitor J, Marjoram P, Thomas D (2003) Fine-scale mapping of disease genes with multiple mutations via spatial clustering techniques. Am J Hum Genet 73:1368-1384
20. Durrant C, Zondervan KT, Cardon LR, Hunt S, Deloukas P, Morris AP (2004) Linkage disequilibrium mapping via cladistic analysis of SNP haplotypes. Am J Hum Genet 75:35-43
21. Waldron ERB, Whittaker JC, Balding DJ (2006) Fine mapping of disease genes by haplotype clustering. Genet Epidemiol 30:170-179
22. Knorr-Held L, Rasser G (2000) Bayesian detection of clusters and discontinuities in disease maps. Biometrics 56:13-21
23. Denison DGT, Holmes CC (2001) Bayesian partitioning for estimating disease risk. Biometrics 57:143-149
24. Excoffier L, Slatkin M (1995) Maximum likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927
25. Clayton D, Chapman J, Cooper J (2004) The use of unphased multilocus genotype data in indirect association studies. Genet Epidemiol 27:415-428
26. Hosking LK, Boyd PR, Xu CF, Nissum M, Cantone K, Purvis IJ, Khakkar R, Barnes MR, Liberwith U, Hagen-Mann K, Enm MG, Riley JH (2002) Linkage disequilibrium mapping identifies a 390kb region association with CYP2D6 poor drug metabolising activity. Pharmacogenomics J 2:165-175
27. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teuer AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087-1092
28. Hastings WK (1970) Monte-Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109
29. Green PJ (1995) Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732
30. Gammerman D (1997) Markov chain Monte Carlo: stochastic simulation for Bayesian inference. Chapman and Hall, London
31. Kass RE, Raftery AE (1995) Bayes factors and model uncertainty. J Am Stat Assoc 90:773-795
32. Farrall M, Morris AP (2005) Gearing up for genome-wide gene-association studies. Hum Mol Genet 14:R157-R162
33. Evans WE, Relling MV (1999) Pharmacogenomics: translating functional genomics into rational therapeutics. Science 286:487-491
34. Sachse C, Brockmoller J, Bauer S, Roots I (1997) Cytochrome P450 2D6 variants in a Caucasian population: allele frequencies and phenotype consequences. Am J Hum Genet 60:284-295
35. Hartigan JA (1975) Clustering algorithms. Wiley, New York
36. Morris AP, Whittaker JC, Xu C-F, Hosking L, Balding DJ (2003) Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity. Proc Natl Acad Sci USA 100:13442-13446
37. Griffiths RD, Marjoram P (1997) An ancestral recombination graph. In: Donnelly P, Tavare S (eds) Progress in population genetics and human evolution. Springer-Verlag, New York, pp 257-270
38. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18:337-338
39. Nordborg M (2001) Coalescent theory. In: Balding DJ, Bishop M, Cannings C (eds) Handbook of statistical genetics. Wiley, Chichester, pp 179-212
40. Lin DY, Zeng D, Millikan R (2005) Maximum likelihood estimation of haplotype effects and haplotype-environment interactions in association studies. Genet Epidemiol 29:299-312
41. Weale ME, Depondt C, Macdonald SJ, Smith A, Lai PS, Shorvon SD, Wood NW, Goldstein DB (2003) Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: implications for linkage-disequilibrium gene mapping. Am J Hum Genet 73:551-565
42. de Bakker PIW, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, Altshuler D (2005) Efficiency and power in genetic association studies. Nat Genet 37:1217-1223