Modeling associations between genetic markers using Bayesian networks

Bioinformatics

Volumn 26, Issue 18, 2010, Pages

  Villanueva, Edwin ^a   Maciel, Carlos Dias ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CHROMOSOME MAP; EVALUATION; GENE LINKAGE DISEQUILIBRIUM; GENETIC MARKER; HAPLOTYPE; HUMAN; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; BAYES THEOREM; CHROMOSOME MAPPING; GENETIC MARKERS; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77956545115     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq392     Document Type: Article

References (33)

1. Barrett,J. et al. (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263-265.
2. Browning,S.R. and Browning,B.L. (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet., 81, 1084-1097.
3. Chickering,D. (2002) Learning equivalence classes of Bayesian-network structures. J. Mach. Learn. Res., 2, 445-498.
4. Chickering,D. et al. (2004) Large-sample learning of Bayesian networks is NP-Hard. J. Mach. Learn. Res., 5, 1287-1330.
5. Cooper,G.F. and Herskovits,E.A. (1992) A Bayesian method for the induction of probabilistic networks from data. Mach. Learn., 9, 309-347.
6. ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia of DNAelements) Project. Science, 306, 636-640.
7. Hao,K. et al. (2007) LdCompare: rapid computation of single-and multiple-marker r(2) and genetic coverage. Bioinformatics, 23, 252-254.
8. Heckerman,D. and Chickering,D.M. (1995) Learning Bayesian networks: the combination of knowledge and statistical data. Mach. Learn., 20, 197-243.
9. Heckerman,D. et al. (1995) Real-world applications of Bayesian networks. Commun. ACM, 38, 24-26.
10. Hedrick,P. (1987) Gametic disequilibrium measures-proceed with caution. Genetics, 117, 331-341.
11. Hudson,R. (2001) Two-locus sampling distributions and their application. Genetics, 159, 1805-1817.
12. Kingman,J. (2000) Origins of the coalescent: 1974-1982. Genetics, 156, 1461-1463.
13. Larranaga,P. et al. (1996) Learning Bayesian network structures by searching for the best ordering with genetic algorithms. IEEE Trans. Syst. Man Cybernet. A Syst. Hum., 26, 487-493.
14. Li,N. and Stephens,M. (2003) Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics, 165, 2213-2233.
15. Liu,Z. and Lin,S. (2005) Multilocus LD measure and tagging SNP selection with generalized mutual information. Genet. Epidemiol., 29, 353-364.
16. Maniatis,N. et al. (2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proc. Natl Acad. Sci. USA, 99, 2228-2233.
17. McVean,G. et al. (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics, 160, 1231-1241.
18. Mueller,J. (2004) Linkage disequilibrium for different scales and applications. Brief. Bioinform., 5, 355-364.
19. Neapolitan,R.E. (2003) Learning Bayesian Networks. Prentice-Hall, Inc., Upper Saddle River, NJ.
20. Nicolas,P. et al. (2006) A model-based approach to selection of tag SNPs. BMC Bioinformatics, 7, Article 303.
21. Nothnagel,M. et al. (2002) Entropy as a measure for linkage disequilibrium over multilocus haplotype blocks. Hum. Hered., 54, 186-198.
22. Pearl,J. (1988) Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference. Morgan Kaufmann Publishers Inc., San Francisco, CA.
23. Pettersson,F. et al. (2004) GOLDsurfer: three dimensional display of linkage disequilibrium. Bioinformatics, 20, 3241-3243.
24. Pritchard,J. and Przeworski,M. (2001) Linkage disequilibrium in humans: Models and data. Am. J. Hum. Genet., 69, 1-14.
25. Sabatti,C. and Risch,N. (2002) Homozygosity and linkage disequilibrium. Genetics, 160, 1707-1719.
26. Scheet,P. and Stephens,M. (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet., 78, 629-644.
27. The International HapMap Consortium (2003) The International HapMap Project. Nature, 426, 789-796.
28. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.
29. Thomas,A. (2005) Characterizing allelic associations from unphased diploid data by graphical modeling. Genet. Epidemiol., 29, 23-35.
30. Thomas,A. and Camp,N. (2004) Graphical modeling of the joint distribution of alleles at associated loci. Am. J. Hum. Genet., 74, 1088-1101.
31. Tishkoff,S. et al. (1996) Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science, 271, 1380-1387.
32. Zhang,W. et al. (2004) Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps. Proc. Natl Acad. Sci. USA, 101, 18075-18080.
33. Zhang,L. et al. (2009) A multilocus linkage disequilibrium measure based on mutual information theory and its applications. Genetica, 137, 355-364.