Bayesian graphical models for genomewide association studies

American Journal of Human Genetics

Volumn 79, Issue 1, 2006, Pages 100-112

  Verzilli, Claudio J ^a   Stallard, Nigel ^b   Whittaker, John C ^a  

^a LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^b UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450 2D6;

ARTICLE; BAYES THEOREM; COMPUTER GRAPHICS; COMPUTER MODEL; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HERITABILITY; MATHEMATICAL COMPUTING; MONTE CARLO METHOD; PHENOTYPE; PRIORITY JOURNAL; PROBABILITY; SINGLE NUCLEOTIDE POLYMORPHISM; TASK PERFORMANCE;

EID: 33745276855     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/505313     Document Type: Article

References (43)

1. Cheung VG, Spielman RS, Ewens KG, Weber TM, Morley M, Burdick JT (2005) Mapping determinants of human gene expression by regional and genomewide association. Nature 437:1365-1369
2. Farrall M, Morris AP (2005) Gearing up for genomewide gene-association studies. Hum Mol Genet 14:R157-R162
3. Maraganore DM, de Andrade M, Lesnick TG, Strain KJ, Farrer MJ, Rocca WA, Pant PVK, Frazer KA, Cox DR, Ballinger DG (2005) High-resolution whole-genome association study of Parkinson disease. Am J Hum Genet 77:685-693
4. Lawrence RW, Evans DM, Cardon LR (2005) Prospects and pitfalls in whole genome association studies. Philos Trans R Soc Lond B Biol Sci 360:1589-1595
5. 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
6. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516-1517
7. Gibbs RA, Belmont JW, Hardenbol P, Willis TD, Yu F, Yang H, Ch'ang LY, et al (2003) The International HapMap Project. Nature 426:789-796
8. Gibbs RA, Belmont JW, Boudreau A, Leal SM, Hardenbol P, Pasternak S, Wheeler DA, et al (2005) A haplotype map of the human genome. Nature 437:1299-1320
9. International Map Working Group (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933
10. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR (2005) Whole-genome patterns of common DNA variation in three human populations. Science 307:1072-1079
11. Wang WYS, Barratt BJ, Clayton DG, Todd JA (2005) Genomewide association studies: theoretical and practical considerations. Nat Rev Genet 6:109-118
12. Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, et al (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature 418:544-548
13. McVean GA, Myers SR, Hunt S, Deloukas P, Bentley DR, Donnelly P (2004) The fine-scale structure of recombination rate variation in the human genome. Science 304:581-584
14. Evans DM, Cardon LR (2005) A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations. Am J Hum Genet 76:681-687
15. Mueller JC, Lohmussaar E, Magi R, Remm M, Bettecken T, Lichtner P, Biskup S, Illig T, Pfeufer A, Luedemann J, Schreiber S, Pramstaller P, Pichler I, Romeo G, Gaddi A, Testa A, Wichmann HE, Metspalu A, Meitinger T (2005) Linkage disequilibrium patterns and tagSNP transferability among European populations. Am J Hum Genet 76:387-398
16. Zondervan KT, Cardon LR (2004) The complex interplay among factors that influence allelic association. Nat Rev Genet 5:89-100
17. Morris AP, Whittaker JC, Xu CF, Hosking LK, Balding DJ (2003) Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity. Proc Natl Acad Sci USA 100:13442-13446
18. 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
19. Thomas DC, Stram DO, Conti D, Molitor J, Marjoram P (2003) Bayesian spatial modeling of haplotype associations. Hum Hered 56:32-40
20. 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
21. Zöllner S, Pritchard JK (2005) Coalescent-based association mapping of complex trait loci. Genetics 169:1071-1092
22. Hosking LK, Boyd PR, Xu CF, Nissum M, Cantone K, Purvis IJ, Khakhar R, Barnes MR, Liberwirth U, Hagen-Mann K, Ehm MG, Riley JH (2002) Linkage disequilibrium mapping identifies a 390 kb region associated with CYP2D6 poor drug metabolising activity. Pharmacogenomics J 2:165-175
23. Dawid A, Lauritzen S (1993) Hyper-Markov laws in the statistical analysis of decomposable graphical models. Ann Stat 21:1272-1317
24. Madigan D, York J (1995) Bayesian graphical models for discrete data. Int Stat Rev 63:215-232
25. Giudici P, Green P, Tarantola C (1999) Efficient model determination for discrete graphical models, technical report. University of Pavia, Pavia, Italy
26. Cowell RG, Dawid AP, Lauritzen SL, Spiegelhalter DJ (1999) Probabilistic networks and expert systems. Springer-Verlag, New York
27. Borgelt C, Kruse R (2002) Graphical models: methods for data analysis and mining. John Wiley, Chichester, United Kingdom
28. Dellaportas P, Forster JJ (1999) Markov chain Monte Carlo model determination for hierarchical and graphical log-linear models. Biometrika 86:615-633
29. Viallefont V, Raftery AE, Richardson S (2001) Variable selection and Bayesian model averaging in case-control studies. Stat Med 20:3215-3230
30. Denison DGT, Holmes CC, Mallick BK, Smith AFM (2002) Bayesian methods for nonlinear classification and regression. John Wiley, Chicester, United Kingdom
31. Verzilli CJ, Stallard N, Whittaker JC (2005) Bayesian modelling of multivariate quantitative traits using seemingly unrelated regressions. Genet Epidemiol 28:313-325
32. Murray I, Ghahramani Z (2004) Bayesian learning in undirected graphical models: approximate MCMC algorithms. In: Chickering M, Halpern J (eds) Proceedings of the 20th Annual Conference on Uncertainty in Artificial Intelligence, Banff, Canada. AUAI Press, Arlington, VA
33. O'Hagan A, Forster J (2004) Kendall's advanced theory of statistics, volume 2B: Bayesian inference. Arnold, London
34. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18:337-338
35. R Development Core Team (2004) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna (http://www.r-project.org/)
36. Maniatis N, Morton NE, Gibson J, Xu CF, Hosking LK, Collins A (2005) The optimal measure of linkage disequilibrium reduces error in association mapping of affection status. Hum Mol Genet 14:145-153
37. Thomas A, Camp NJ (2004) Graphical modeling of the joint distribution of alleles at associated loci. Am J Hum Genet 74:1088-1101
38. Thomas A (2005) Characterizing allelic associations from unphased diploid data by graphical modeling. Genet Epidemiol 29:23-35
39. Rodin AS, Boerwinkle E (2005) Mining genetic epidemiology data with Bayesian networks I: Bayesian networks and example application (plasma apoE levels). Bioinformatics 21:3273-3278
40. Sebastiani P, Ramoni MF, Nolan V, Baldwin CT, Steinberg MH (2005) Genetic dissection and prognostic modeling of over stroke in sickle cell anemia. Nat Genet 37:435-440
41. Little RJA, Rubin DB (1987). Statistical analysis with missing data. John Wiley, New York
42. Monti S, Cooper GF (1999) Learning hybrid Bayesian networks from data. In: Jordan MI (ed) Learning in graphical models. MIT Press, Cambridge, MA
43. Tarantola C (2004) MCMC model determination for discrete graphical models. Stat Modelling 4:39-61