Bayesian model selection for characterizing genomic imprinting effects and patterns

Bioinformatics

Volumn 26, Issue 2, 2010, Pages 235-241

  Yang, Runqing ^a   Wang, Xin ^a   Wu, Zeyuan ^a   Prows, Daniel R ^b   Lin, Min ^c  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

^c DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; COMPUTER SIMULATION; GENOME IMPRINTING; QUANTITATIVE TRAIT LOCUS;

BAYES THEOREM; COMPUTER SIMULATION; GENOMIC IMPRINTING; QUANTITATIVE TRAIT LOCI;

EID: 75249092988     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp620     Document Type: Article

References (48)

1. Allis, C.D. et al. (2007) Epigenetics. Cold Spring Harbor Laboratory Press, New York.
2. Ball, R.D. (2001) Bayesian methods for quantitative trait loci mapping based on model selection: approximate analysis using the Bayesian information criterion. Genetics, 159, 1351-1364.
3. Cheverud, J.M. et al. (1996) Quantitative trait loci for murine growth. Genetics, 142, 1305-1319.
4. Cheverud, J.M. et al. (2008) Genomic imprinting effects on adult body composition in mice. Proc. Natl Acad. Sci. USA, 105, 4253-4258.
5. 2 design. Genomics, 87, 543-551.
6. de Koning, D.J. et al. (2000) Genome-wide scan for body composition in pigs reveals important role of imprinting. Proc. Natl Acad. Sci. USA, 97, 7947-7950.
7. de Koning, D.J. et al. (2002) On the detection of imprinted quantitative trait loci in experimental crosses of outbred species. Genetics, 161, 931-938.
8. de Vicente, M.C. and Tankslay, S.D. (1991) Genome-wide reduction in recombination of backcross progeny derived from male versus female gametes in an interspecific cross of tomato. Theor. Appl. Genet., 83, 173-178.
9. Diao, G. and Lin, D.Y. (2005) Semiparametric methods for mapping quantitative trait loci with censored data. Biometrics, 61, 789-798.
10. Diao, G. et al. (2004) Mapping quantitative trait loci with censored observations. Genetics, 168, 1689-1698.
11. Dib, C. et al. (1996)Acomprehensive genetic map of the human genome based on 5,264 microsatellites. Nature, 380, 152-154.
12. Dietrich, W.F. et al. (1996)Acomprehensive genetic map of the mouse genome. Nature, 380, 149-152.
13. Falconer, D.S. and Mackay, T.F.C. (1996) Introduction to Quantitative Genetics. Longman, London.
14. George, E.I. and McCulloch, R.E. (1997) Approaches for Bayesian variable selection. Stat. Sin., 7, 339-373.
15. Groover, A.T. et al. (1995) Sexrelated differences in meiotic recombination frequency in Pinus taeda. J. Hered., 86, 157-158.
16. Haghighi, F. and Hodge, S.E. (2002) Likelihood formulation of parent-of-origin effects on segregation analysis, including ascertainment. Am. J. Hum. Genet., 70, 142-156.
17. Haldane, J.B.S. (1922) The part played by recurrent mutation in evolution. Am. Nat., 67, 5-9.
18. Hanson, R.L. et al. (2001) Assessment of parent-of-origin effects in linkage analysis of quantitative traits. Am. J. Hum. Genet., 68, 951-962.
19. Hayashi, T. and Awata, T. (2008) A Bayesian method for simultaneously detecting Mendelian and imprinted quantitative trait loci in experimental crosses of outbred species. Genetics, 178, 527-538.
20. Huxley, J.S. (1928) Sexual difference of linkage Grammarus chereuxi. J. Genet. 20, 145-156.
21. Kalbfleish, J.D. and Prentice, R.L. (2002) The Statistical Analysis of Failure Time Data. Wiley, Hoboken, NJ.
22. Kass, R.E. and Raftery, A.E. (1995) Bayes factors. J. Am. Stat. Assoc., 773-795.
23. Kiefer, J.C. (2007) Epigenetics in development. Dev. Dyn., 236, 1144-1156.
24. Knott, S.A. et al. (1996) Methods for multiple-marker mapping of quantitative trait loci in half-sib populations. Theor. Appl. Genet., 93, 71-80.
25. Knott, S.A. et al. (1998) Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics, 149, 1069-1080.
26. Kohn, R. et al. (2001) Nonparametric regression using linear combinations of basis functions. Stat. Comput., 11, 313-322.
27. Kuo, L. and Mallick, B. (1998) Variable selection for regression models. Sankhya Ser. B, 60, 65-81.
28. Mantey, C. et al. (2005) Mapping and exclusion mapping of genomic imprinting effects in mouse F2 families. J. Hered., 96, 329-338.
29. Naumova, A. and Croteau, S. (2004) Mechanisms of epigenetic variation: polymorphic imprinting. Curr. Genomics, 84, 417-429.
30. Neff, M.W. et al. (1999) A second-generation genetic linkage map of the domestic dog, Canis familiaris. Genetics, 151, 803-820.
31. Pauler, F.M. and Barlow, D.P. (2006) Imprinting mechanisms-it only takes two. Genes Dev., 20, 1203-1206.
32. Plummer, M. et al. (2004) CODA: output analysis and diagnostics for MCMC, v. 0.9-5. Institute of Mathematical Statistics, Beachwood, OH (http://www-fis.iarc.fr/coda).
33. Prows, D.R. et al. (2007a) A genetic mouse model to investigate hyperoxic acute lung injury survival. Physiol. Genomics, 30, 262-270.
34. Prows, D.R. et al. (2007b) Genetic analysis of hyperoxic acute lung injury survival in reciprocal intercross mice. Physiol. Genomics, 30, 271-281.
35. Raftery, A.E. et al. (1997) Bayesian model averaging for linear regression models. J. Am. Stat. Assoc., 92, 179-191.
36. Rao, S. and Xu, S. (1998) Mapping quantitative trait loci for ordered categorical traits in four-way crosses. Heredity, 81(Pt 2), 214-224.
37. Sandovici, I. et al. (2003) Familial aggregation of abnormal methylation of parental alleles at the IGF2/H19 and IGF2R differentially methylated regions. Hum. Mol. Genet., 12, 1569-1578.
38. Sandovici, I. et al. (2005) Interindividual variability and parent of origin DNA methylation differences at specific human Alu elements. Hum. Mol. Genet., 14, 2135-2143.
39. Shete, S. and Amos, C.I. (2002) Testing for genetic linkage in families by a variance-components approach in the presence of genomic imprinting. Am. J. Hum. Genet., 70, 751-757.
40. Shete, S. et al. (2003) Genomic imprinting and linkage test for quantitative-trait Loci in extended pedigrees. Am. J. Hum. Genet., 73, 933-938.
41. Sillanpaa, M.J. and Corander, J. (2002) Model choice in gene mapping: what and why. Trends Genet., 18, 301-307.
42. Tuiskula-Haavisto, M. et al. (2004) Quantitative trait loci with parent-of-origin effects in chicken. Genet. Res., 84, 57-66.
43. Vaughn, T.T. et al. (1999) Mapping quantitative trait loci for murine growth: a closer look at genetic architecture. Genet. Res., 74, 313-322.
44. Wang, H. et al. (2005) Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics, 170, 465-480.
45. Wood, A.J. and Oakey, R.J. (2006) Genomic imprinting in mammals: emerging themes and established theories. PLoS Genet., 2, e147.
46. Yi, N. et al. (2005) Bayesian model selection for genome-wide epistatic quantitative trait loci analysis. Genetics, 170, 1333-1344.
47. Yi, N. et al. (2007) Bayesian mapping of genomewide interacting quantitative trait loci for ordinal traits. Genetics, 176, 1855-1864.
48. Zhang, Y.M. and Xu, S. (2005) Advanced statistical methods for detecting multiple quantitative trait loci. Recent Res. Devel. Genet. Breeding, 2, 1-23.