Bayesian Model Choice and Search Strategies for Mapping Interacting Quantitative Trait Loci

Genetics

Volumn 165, Issue 2, 2003, Pages 867-883

  Yi, Nengjun ^a   Xu, Shizhong ^b   Allison, David B ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; ENVIRONMENTAL FACTOR; GENE MAPPING; GENETIC MODEL; GENETIC REGULATION; GENETIC TRAIT; GENOTYPE; MONTE CARLO METHOD; PRIORITY JOURNAL; PROBABILITY; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL;

BAYES THEOREM; CHROMOSOME MAPPING; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; EPISTASIS, GENETIC; GENETIC MARKERS; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI;

ANIMALIA;

EID: 0242381258     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (63)

1. 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.
2. BINK, M. C. A. M., P. UIMARI, M. J. SILLANPÄÄ, L. L. G. JANSS and R. C. JANSEN, 2002 Multiple QTL mapping in related plant populations via a pedigree-analysis approach. Theor. Appl. Genet. 104: 751-762.
3. BOER, M. P., C. J. F. TER BRAAK and R. C. JANSEN, 2002 A penalized likelihood method for mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 162: 951-960.
4. BROOKS, S. P., and P. GIUDICI, 2000 Markov chain Monte Carlo convergence assessment via two-way analysis of variance. J. Comput. Graph. Stat. 9: 266-276.
5. CARLBORG, O., L. ANDERSSON and B. KINGHORN, 2000 The use of a genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci. Genetics 155: 2003-2010.
6. CHEVERUND, J. M., and E. J. ROUTMAN, 1995 Epistasis and its contribution to genetic variance components. Genetics 139: 1455-1461.
7. CORANDER, J., and M. J. SILLANPÄÄ, 2002 A unified approach to joint modeling of multiple quantitative and qualitative traits in gene mapping. J. Theor. Biol. 218: 435-446.
8. CULVERHOUSE, R., B. K. SUAREZ, J. LIN and T. REICH, 2002 A perspective on epistasis: limits of models displaying no main effect. Am. J. Hum. Genet. 70 (2): 461-471.
9. DAW, E. W., S. C. HEATH and E. M. WIJSMAN, 1999 Multiple oligogenic analysis of age-at-onset data with applications to Alzheimer disease pedigrees. Am. J. Hum. Genet. 64: 839-851.
10. DELLAPORTAS, P., and J. J. FORSTER, 1999 Markov chain Monte Carlo model determination for hierarchical and graphical log-linear models. Biometrika 86: 615-633.
11. DELLAPORTAS, P., J. J. FORSTER and I. NTZOUFRAS, 2002 On Bayesian model and variable selection using MCMC. Stat. Comput. 12: 27-36.
12. DONG, C., S. WANG, W.-D. LI, D. LI, H. ZHAO et al., 2003 Interacting genetic loci on chromosomes 20 and 10 influence extreme human obesity. Am. J. Hum. Genet. 72: 115-124.
13. FERNANDEZ, J. R., L. M. TARANTINO, S. M. HOFER, G. P. VOGLER and G. E. MCCLEARN, 2000 Epistatic quantitative trait loci for alcohol preference in mice. Behav. Genet. 30 (6): 431-437.
14. FIJNEMAN, R. J. A., S. S. DE VRIES, R. C. JANSEN and P. DEMANT, 1996 Complex interactions of new quantitative trait loci, Sluc1, Sluc2, Sluc3, and Sluc4 that influence the susceptibility to lung cancer in mouse. Nat. Genet. 14: 465-467.
15. FRANKEL, W. N., and N. J. SCHORK, 1996 Who's afraid of epistasis. Nat. Genet. 14: 371-373.
16. GAFFNEY, P. J., 2001 An efficient reversible jump Markov chain Monte Carlo approach to detect multiple loci and their effects in inbred crosses. Ph.D. Dissertation, Department of Statistics, University of Wisconsin, Madison, WI.
17. GAUDERMAN, W. J., and D. C. THOMAS, 2000 The role of interacting determinants in the localization of genes. Adv. Genet. 42: 393-412.
18. GELMAN, A., J. CARLIN, H. STERN and D. RUBIN, 1995 Bayesian data analysis. Chapman & Hall, London.
19. GREEN, P. J., 1995 Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711-732.
20. HALEY, C. S., and S. A. KNOTT, 1992 A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315-324.
21. HEATH, S. C., 1997 Markov chain Monte Carlo segregation and linkage analysis for oligogenic models. Am. J. Hum. Genet. 61: 748-760.
22. HOESCHELLE, I., 2001 Mapping quantitative trait loci in outbred pedigrees, pp. 599-644 in Handbook of Statistical Genetics, edited by D. J. BALDING, M. BISHOP and C. CANNINGS. John Wiley & Sons, New York.
23. HOESCHELE, I., P. UIMARI, F. E. GRIGNOLA, Q. ZHANG and K. M. GAGE, 1997 Advances in statistical methods to map quantitative trait loci in outbred populations. Genetics 147: 1445-1457.
24. HOTI, F. J., M. J. SILLANPÄÄ and L. HOLMSTROM, 2002 A note on estimating the posterior density of a quantitative trait locus from a Markov chain Monte Carlo sample. Genet. Epidemiol. 22: 369-376.
25. HURME, P., M. J. SILLANPÄÄ, E. ARJAS, T. REPO and O. SAVOLAINEN, 2000 Genetic basis of climatic adaption in Scots pine by Bayesian quantitative trait locus analysis. Genetics 156: 1309-1322.
26. JANNINK, J., and R. JANSEN, 2001 Mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 157: 445-454.
27. JANSEN, R. C., and P. STAM, 1994 High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447-1455.
28. JIANG, C., and Z-B. ZENG, 1997 Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101: 47-58.
29. KAO, C. H., and Z-B. ZENG, 2002 Modeling epistasis of quantitative trait loci using Cockerham's model. Genetics 160: 1243-1261.
30. KAO, C. H., Z-B. ZENG and R. D. TEASDALE, 1999 Multiple interval mapping for quantitative trait loci. Genetics 152: 1203-1216.
31. LANDER, E. S., and D. BOTSTEIN, 1989 Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
32. LARK, K. G., K. CHASE, F. R. ADLER, L. M. MANSUR and J. J. ORF, 1995 Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another. Proc. Natl. Acad. Sci. USA 92: 4656-4660.
33. LEE, J. K., and D. C. THOMAS, 2000 Performance of Markov chain Monte Carlo approaches for mapping genes in oligogenic models with an unknown number of loci. Am. J. Hum. Genet. 67: 1232-1250.
34. Liu, J. S., F. LIANG and W. H. WONG, 2000 The multiple-try method and local optimization in Metropolis sampling. J. Am. Stat. Assoc. 95: 121-134.
35. LYNCH, M., and B. WALSH, 1998 Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.
36. NTZOUFRAS, I., 1999 Aspects of Bayesian model and variable selection using MCMC. Ph.D. Dissertation, Department of Statistics, Athens University, of Economics and Business, Athens, Greece.
37. POPE, P. T., and J. T. WEBSTER, 1972 The use of an F-statistic in stepwise regression procedures. Technometrics 14: 327-340.
38. ROUTMAN, E. J., and J. M. CHEVERUD, 1997 Gene effects on a quantitative trait: two-locus epistatic effects measured at microsatellite markers and at estimated QTL. Evolution 5: 1654-1662.
39. SATAGOPAN, J. M., and B. S. YANDELL, 1996 Estimating the number of quantitative trait loci via Bayesian model determination. Joint Statistical Meeting, October 1996, Chicago.
40. SATAGOPAN, J. M., B. S. YANDELL, M. A. NEWTON and T. C. OSBORN, 1996 A Bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. Genetics 144: 805-816.
41. SEN, S., and G. CHURCHILL, 2001 A statistical framework for quantitative trait mapping. Genetics 159: 371-387.
42. SILLANPÄÄ, M. J., and E. ARJAS, 1998 Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373-1388.
43. SILLANPÄÄ, M. J., and E. ARJAS, 1999 Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. Genetics 151: 1605-1619.
44. SILLANPÄÄ, M. J., and J. CORANDER, 2002 Model choice in gene mapping: what and why. Trends Genet. 18: 301-307.
45. STEPHENS, D. A., and R. D. FISCH, 1998 Bayesian analysis of quantitative trait locus data using reversible jump Markov chain Monte Carlo. Biometrics 54: 1334-1347.
46. STEPHENS, D., and A. SMITH, 1993 Bayesian inference in multipoint gene mapping. Ann. Hum. Genet. 57: 65-82.
47. SUGIYAMA, F., G. A. CHURCHILL, D. C. HIGGINS, C. JOHNS, K. P. MAKARITSIS et al., 2001 Concordance of murine quantitative trait loci for salt-induced hypertension with rat and human loci. Genomics 71: 70-77.
48. THOMAS, D. C., S. RICHARDSON, J. GAUDERMAN and J. PITKANIEMI, 1997 A Bayesian approach to multipoint mapping in nuclear families. Genet. Epidemiol. 14: 903-908.
49. TINKER, N. A., D. E. MATHER, B. G. ROSSNAGEL, K. J. KASHA and A. KLEINHOFS, 1996 Regions of the genome that affect agronomic performance in two-row barley. Crop Sci. 36: 1053-1062.
50. UIMARI, P., and I. HOESCHELE, 1997 Mapping linked quantitative trait loci using Bayesian method analysis and Markov chain Monte Carlo algorithms. Genetics 146: 735-743.
51. UIMARI, P., and M. J. SILLANPÄÄ, 2001 Bayesian oligogenic analysis of quantitative and qualitative traits in general pedigrees. Genet. Epidemiol. 21: 224-242.
52. UIMARI, P., G. THALLER and I. HOESCHELE, 1996 The use of multiple markers in a Bayesian method for mapping quantitative trait loci. Genetics 143: 1831-1842.
53. WADE, M. J., 2001 Epistasis, complex traits, and mapping genes. Genetica 112/113: 59-69.
54. WANG, D. L., J. ZHU, Z. K. LI and A. H. PATERSON, 1999 Mapping QTLs with epistatic effects and QTLXenvironment interactions by mixed linear model approaches. Theor. Appl. Genet. 99:1255-1264.
55. WU, R. L., 1996 Detecting epistatic genetic variance with a clonally replicated design: model for low- vs. high-order nonallelic interactions. Theor. Appl. Genet. 93: 109-119.
56. XU, S., and N. YI, 2000 Mixed model analysis of quantitative trait loci. Proc. Natl. Acad. Sci. USA 97: 14542-14547.
57. YI, N., and S. XU, 2000 Bayesian mapping of quantitative trait loci for complex binary traits. Genetics 155: 1391-1403.
58. YI, N., and S. XU, 2001 Bayesian mapping of quantitative trait loci under complicated mating designs. Genetics 157: 1759-1771.
59. YI, N., and S. XU, 2002 Mapping quantitative trait loci with epistatic effects. Genet. Res. 79: 185-198.
60. Yu, S. B., J. X. LI, C. G. XU, Y. F. TAN, Y. J. GAO et al., 1997 Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc. Natl. Acad. Sci. USA 94: 9226-9231.
61. YUAN, B., R. NEUMAN, S. H. DUAN, J. L. WEBER, P. Y. KWOK et al., 2000 Linkage of a gene for familial hypobetaliproteinemia to chromosome 3p21.1-22. Am. J. Hum. Genet. 66: 1699-1704.
62. ZENG, Z-B., 1994 Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
63. ZENG, Z-B., C.-H. KAO and C. J. BASTEN, 1999 Estimating the genetic architecture of quantitative traits. Genet. Res. 74: 279-289.