Integrated analysis of genetic data with R

Human Genomics

Volumn 2, Issue 4, 2006, Pages 258-265

  Zhao, Jing Hua ^a   Tan, Qihua ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b ODENSE UNIVERSITY HOSPITAL   (Denmark)

Author keywords

Complex traits; Linkage and association analysis; Software

Indexed keywords

ALCOHOLISM; BAYES THEOREM; BIOINFORMATICS; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COVARIANCE; FEASIBILITY STUDY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ALGORITHM; GENETIC ANALYSIS; HUMAN; INFORMATION PROCESSING; INTERMETHOD COMPARISON; INTERNET; MICROSATELLITE MARKER; MOLECULAR PHYLOGENY; POPULATION GENETICS; REVIEW; STATISTICAL ANALYSIS; STATISTICAL MODEL;

EID: 32044468293     PISSN: 14797364     EISSN: 14797364     Source Type: Journal    
DOI: 10.1186/1479-7364-2-4-258     Document Type: Review

References (52)

1. Collins, F.S., Morgan, M. and Patrinos, A. (2003), 'The Human Genome Project: Lessons from large-scale biology', Science Vol. 300, pp. 286-290.
2. Weale, M.E. (2004), 'A survey of current software for haplotype phase inference', Hum. Genomics Vol. 1, pp. 141-144.
3. Salem, R.M., Wessel, J. and Schork, N.J. (2005), 'A comprehensive literature review of haplotyping software and methods for use with unrelated individuals', Hum. Genomics Vol. 2, pp. 39-66.
4. Lander, E.S. and Schork, N.J. (1994), 'Genetic dissection of complex traits', Science Vol. 265, pp. 2037-2048.
5. Dudbridge, F. (2003), 'A survey of current software for linkage analysis', Hum. Genomics Vol. 1, pp. 63-65.
6. Ott, J. (1976), 'A computer program for linkage analysis of general human pedigrees', Am. J. Hum. Genet. Vol. 28, pp. 528-529.
7. Ott, J. (1974), 'Estimation of the recombination fraction in human pedigrees: Efficient computation of the likelihood for human linkage studies', Am. J. Hum. Genet. Vol. 26, pp. 588-597.
8. Morton, N.E., Rao, D.C. and Lalouel, J.-M. (1983), 'Methods in Genetic Epidemiology', Karger, New York, NY.
9. Guo, S.W. and Lange, K. (2000), 'Genetic mapping of complex traits: Promises, problems, and prospects', Theor Popul. Biol. Vol. 57, pp. 1-11.
10. Venables, W.N. and Ripley, B.D. (2002), 'Modern Applied Statistics with S', Springer, New York, NY.
11. Chambers, J.M. (1998), 'Programming with Data', Springer, New York.
12. Chambers, J.M. and Hastie, T.J. (1992), 'Statistical Models in S', Chapman & Hall, London, UK.
13. Satagopan, J.M., Yandell, B.S., Newton, M.A. et al. (1996), 'A Bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo', Genetics Vol. 144, pp. 805-816.
14. Burkett, K., McNeney, B. and Graham, J. (2004), 'A note on inference of trait associations with SNP haplotypes and other attributes in generalized linear models', Hum. Hered. Vol. 57, pp. 200-206.
15. Schaid, D.J., Rowland, C.M., Tines, D.E. et al. (2002), 'Score tests for association between traits and haplotypes when linkage phase is ambiguous', Am. J. Hum. Genet. Vol. 70, pp. 425-434.
16. Lake, S.L., Lyon, H., Tantisira, K. et al. (2003), 'Estimation and tests of haplotype - environment interaction when linkage phase is ambiguous', Hum. Hered. Vol. 55, pp. 56-65.
17. Goudet, J. (2005), 'Hierfstat, a package for R to compute and test variance components and F statistics', Mol. Ecol. Notes Vol. 5, pp. 184-186.
18. Weir, B.S. and Wilson, S.R. (1986), 'Log-linear models for linked loci', Biometrics Vol. 42, pp. 665-670.
19. Huttley, G.A. and Wilson, S.R. (2000), 'Testing for concordant equilibria between population samples', Genetics Vol. 156, pp. 2127-2135.
20. Luo, Z.W. (1998), 'Detecting linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations', Heredity Vol. 80, pp. 198-208.
21. Sen, S., Satagopan, J. and Churchill, J. (2005), 'QTL study design from an information perspective', Genetics Vol. 170, pp. 447-464.
22. Devlin, B. and Roeder, K. (1999), 'Genomic control for association studies', Biometrics Vol. 55, pp. 997-1004.
23. Hirotsu, C., Aoki, S., Inada, T. et al. (2001), 'An exact test for the association between the disease and alleles at highly polymorphic loci with particular interest in the haplotype analysis', Biometrics Vol. 57, pp. 769-778.
24. Zhao, J.H. (2004), '2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis', Bioinformatics Vol. 20, pp. 1325-1326.
25. Yu, C. and Zelterman, D. (2002), 'Statistical inference for familial disease clusters', Biometrics Vol. 58, pp. 481-491.
26. Strand, A. (2002), 'Metasim 1.0: An individual-based environment for simulating population genetics of complex population dynamics', Mol. Ecol. Notes Vol. 2, p. 376.
27. Broman, K.W, Wu, H., Sen, S. et al. (2003), 'R/qtl: QTL mapping in experimental crosses', Bioinformatics Vol. 19, pp. 889-890.
28. Mott, R., Talbot, C.J., Turri, M.G. et al. (2000), 'A method for fine mapping quantitative trait loci in outbred animal stocks', Proc. Natl. Acad. Sci. USA Vol. 97, pp. 12649-12654.
29. Clayton, D. and Jones, H. (1999), 'Transmission/disequilibrium tests for extended marker haplotypes', Am. J. Hum. Genet. Vol. 65, pp. 1161-1169.
30. Nicholson, G., Smith, A.V, Jónsson, F. et al. (2002), 'Assessing population differentiation and isolation from single-nucleotide polymorphism data', J.R. Star. Soc. B Vol. 64, pp. 695-715.
31. Espeland, M.A. (1986), 'A general class of models for discrete multivariate data', Commun. Stat.-Simul. Vol. 15, pp. 405-424.
32. Friendly, M. (2000), 'Visualizing Categorical Data', SAS Institute, Cary NC.
33. Efron, B. (2004), 'Large-scale simultaneous hypothesis testing', J. Am. Stat. Assoc. Vol. 99, pp. 96-104.
34. Tritchlern, D., Liu, Y and Fallah, S. (2003), 'A test of linkage for complex discrete and continuous traits in nuclear families', Biometrics Vol. 59, pp. 382-392.
35. Liu, Y., Tritchler, D. and Bull, S.B. (2002), 'A unified framework for transmission-disequilibrium test analysis of discrete and continuous traits', Genet. Epidemiol. Vol. 22, pp. 26-40.
36. Yang, Y., Zhang, J., Hoh, J. et al. (2003), 'Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA', Proc. Natl. Acad. Sci. USA Vol. 100, pp. 7225-7230.
37. Betensky, R.A. and Rabinowitz, D. (2000), 'Simple approximations for the maximal transmission/disequilibrium test with a multi-allelic marker', Ann. Hum. Genet. Vol. 64, pp. 567-574.
38. Chapman, J.M., Cooper, J.D., Todd, J.A. et al. (2003), 'Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power', Hum. Hered. Vol. 56, pp. 18-31.
39. Lowe, C.E., Cooper, J.D., Chapman, J.M. et al. (2004), 'Cost-effective analysis of candidate genes using htSNPs: A staged approach', Genes Immun. Vol. 5, pp. 301-305.
40. Zapata, C., Carollo, C. and Rodriguez, S. (2001), 'Sampling variance and distribution of the D measure of overall gametic disequilibrium between multiallelic loci', Ann. Hum. Genet. Vol. 65, pp. 395-406.
41. Zhao, J.H., Curtis, D. and Sham, P.C. (2000), 'Model-free analysis and permutation tests for allelic associations', Hum. Hered. Vol. 50, pp. 133-139,
42. Zhao, J.H. and Sham, P.C. (2002), 'Faster haplotype frequency estimation using unrelated subjects', Hum. Hered. Vol. 53, pp. 36-41.
43. Zhao, J.H., Lissarrague, S., Essioux, L. et al. (2002), 'GENECOUNTING: Haplotype analysis with missing genotypes', Bioinformatics Vol. 18, pp. 1694-1695.
44. Excoffier, L. and Slatkin, M. (1995), 'Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population', Mol. Biol. Evol. Vol. 12, pp. 921-927.
45. Noonan, J.P., Li, J., Nguyen, L. et al. (2003), 'Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster', Am. J. Hum. Genet. Vol. 72, pp. 621-635.
46. Zaykin, D.V., Westfall, P.H., Young, S.S. et al. (2002), 'Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals', Hum. Hered. Vol. 53, pp. 79-91.
47. Kerem, B.S., Rommens, J.M., Buchanan, J.A. et al. (1989), 'Identification of the cystic fibrosis gene: Genetic analysis', Science Vol. 245. pp. 1073-1080.
48. Daly, M.J., Rioux, J.D., Schaffner, S.E. et al. (2001), 'High-resolution haplotype structure in the human genome', Nat. Genet. Vol. 29, pp. 229-232.
49. Curtis, D., Zhao, J.H. and Sham, P.C. (1999), 'Comparison of GENEHUNTER and MFLINK for analysis of COGA linkage data', Genet. Epidemiol. Vol. 17(Suppl. 1), pp. S115-S120.
50. Zhao, J.H. (2005), 'Mixed-effects Cox models of alcohol dependence in extended families', BMC Genet., In press.
51. Merikangas, K.R. and Risch, N. (2003), 'Will the genomics revolution revolutionize psychiatry, Am. J. Psychiatry Vol. 160, pp. 625-635.
52. Banfield, J. (1999), 'Rweb: Web-based statistical analysis', J. Stat. Soft., Vol. 4, pp. 1-15.