Bayesian quantitative trait loci mapping for multiple traits

Genetics

Volumn 179, Issue 4, 2008, Pages 2275-2289

  Banerjee, Samprit ^a   Yandell, Brian S ^b   Yi, Neng Jun ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; GENE MAPPING; GENETIC MODEL; GENETIC TRAIT; MONTE CARLO METHOD; PLEIOTROPY; PRIORITY JOURNAL; PROBABILITY; QUANTITATIVE TRAIT LOCUS; SIMULATION; CHROMOSOME MAP; GENETIC LINKAGE; METHODOLOGY;

ALGORITHMS; BAYES THEOREM; CHROMOSOME MAPPING; LINKAGE (GENETICS); MARKOV CHAINS; MONTE CARLO METHOD; QUANTITATIVE TRAIT LOCI;

EID: 55749111897     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.108.088427     Document Type: Article

References (45)

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. BROMAN, K. W., and T. SPEED, 2002 A model selection approach for the identification of quantitative trait loci in experimental crosses. J. R. Stat. Soc. B 64(4): 641-656.
3. BROMAN, K. W., H. WU, Ś. SEN and G. A. CHURCHILL, 2003 R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889-890.
4. BURNHAM, K. P., and D. R. ANDERSON, 2002 Model Selection and Multi-Model Inference. Springer-Verlag, New York.
5. GELMAN, A., J. CARLIN, H. STERN and D. RUBIN, 2004 Bayesian Data Analysis. Chapman & Hall/CRC, London.
6. GILBERT, H., and P. LE ROY, 2003 Comparison of three multitrait methods for QTL detection. Genet. Sel. Evol. 35: 281-304.
7. GILBERT, H., and P. LE ROY, 2004 Power of three multitrait methods for QTL detection in crossbreed populations. Genet Sel. Evol. 36: 347-361.
8. GRIFFITHS, W. E., 2001 Bayesian Inference in the Seemingly Unrelated Regressions Model (Working Series Paper 793). Department of Economics, University of Melbourne, Melbourne, Australia.
9. HACKETT, C. A., R. C. MEYER and W. T. B. THOMAS, 2001 Multi-trait QTL mapping in barley using multivariate regression. Genet. Res. Camb. 77: 95-106.
10. HUANG, J., and Y. JIANG, 2003 Genetic linkage analysis of a dichotomous trait incorporating a tightly linked quantitative trait in affected sib pairs. Am. J. Hum. Genet. 72: 949-960.
11. JACKSON, A. U., A. FORNÉS, A.GALECKI, R. A. MILLER and D. T. BURKE, 1999 Multiple-trait quantitative trait loci analysis using a large mouse sibship. Genetics 151: 785-795.
12. JIANG, C., and Z.-B. ZENG, 1995 Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140: 1111-1127.
13. 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.
14. KAO, C.-H., and Z.-B. ZENG, 2002 Modeling epistasis of quantitative trait loci using Cockerham's model. Genetics 160: 1243-1261.
15. KNOTT, S. A., and C. S. HALEY, 2000 Multitrait least squares for quantitative trait loci detection. Genetics 156: 899-911.
16. LANDER, E. S., and D. BOTSTEIN, 1989 Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
17. LANGE, C., and J. C. WHITTAKER, 2001 Mapping quantitative trait loci using generalized estimating equations. Genetics 159: 1325-1337.
18. LIU, J., Y. LIU, X. LIU and H.-W. DENG, 2007 Bayesian mapping of quantitative trait loci for multiple complex traits with the use of variance components. Am. J. Hum. Genet. 81: 304-320.
19. LUND, M. S., P. SØRENSEN, B. GULDBRANDTSEN and D. A. SORENSEN, 2003 Multitrait fine mapping of quantitative trait loci using combined linkage disequilibria and linkage analysis. Genetics 163: 405-410.
20. MÄHLER, M., C. MOST, S. SCHMIDTKE, J. P. SUNDBERG, R. LI et al., 2002 Genetics of colitis susceptibility in IL-10-deficient mice: backcross versus F2 results contrasted by principal component analysis. Genomics 80: 274-282.
21. MANGIN, B., P. THOQUET and N. GRIMSLEY, 1998 Pleiotropic QTL analysis. Biometrics 54: 88-99.
22. MEUWISSEN, T. H., and M. E. GODDARD, 2004 Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data. Genet. Sel. Evol. 36: 261-279.
23. MILLER, A. J., 1984 Selection of subsets of regression variables. J. R. Stat. Soc. A 147: 389-425.
24. PLUMMER, M., N. BEST, K. COWLES and K. VINES, 2004 Output Analysis and Diagnostics for MCMC, v. 0.9-5. Institute of Mathematical Statistics, Beachwood, OH.
25. RAFTERY, A. E., D. MADIGAN and J. A. HOETING, 1997 Bayesian model averaging for linear regression models. J. Am. Stat. Assoc. 92: 179-191.
26. SATAGOPAN, J. M., and B. S. YANDELL, 1996 Estimating the number of quantitative trait loci via model determination. Special Contributed Paper Session on Genetic Analysis of Quantitative Traits and Complex Diseases. Biometric Section, Joint Statistical Meeting, Chicago.
27. SEN, Ś., and G. A. CHURCHILL, 2001 A statistical framework for quantitative trait mapping. Genetics 159: 371-387.
28. SILLANPÄÄ,M. J., and J. CORANDER, 2002 Model choice in gene mapping: what and why. Trends Genet. 18: 301-307.
29. SMITH, M., and R. KOHN, 2000 Nonparametric seemingly unrelated regression. J. Econometrics 98: 257-281.
30. VERZILLI, C. J., N. STALLARD and J. C. WHITTAKER, 2005 Bayesian modeling of multivariate quantitative traits using seemingly unrelated regression. Genetic Epidemiol. 28: 313-325.
31. VIEIRA, C., E. G. PASYUKOVA, Z.-B. ZENG, J. B. HACKETT, R. F. LYMAN et al., 2000 Genotype-environment interaction for quantitative trait loci affecting life span in Drosophila melanogaster. Genetics 154: 213-227.
32. WANG, H., Y. C. M. ZHANG, X. LI, G. L. MASINDE, S. MOHAN et al., 2005 Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics 170: 465-480.
33. WILLIAMS, J. T., H. BEGLEITER, B. PORJESZ, H. J. EDENBERG, T. FOROUD et al., 1999a Joint multipoint linkage analysis of multivariate qualitative and quantitative traits. II. Alcoholism and event-related potentials. Am. J. Hum. Genet. 65: 1148-1160.
34. WILLIAMS, J. T., P. VAN EERDEWEGH, L. ALMASY and J. BLANGERO, 1999b Joint multipoint linkage analysis of multivariate qualitative and quantitative traits. I. Likelihood formulation and simulation results. Am. J. Hum. Genet. 65: 1134-1147.
35. XU, C., Z. LI and S. XU, 2005 Joint mapping of quantitative trait loci for multiple binary characters. Genetics 169: 1045-1059.
36. YANG, R., and S. XU, 2007 Bayesian shrinkage analysis of quantitative trait loci for dynamic traits. Genetics 176: 1169-1185.
37. YANDELL, B. S., T. MEHTA, S. BANERJEE, D. SHRINER, R. VENKATARAMAN et al., 2007 R/qtlbim: QTL with Bayesian interval mapping in experimental crosses. Bioinformatics 23(5): 641-643.
38. YI, N., 2004 A unified Markov chain Monte Carlo framework for mapping multiple quantitative trait loci. Genetics 167: 967-975.
39. YI, N., and D. SHRINER, 2008 Advances in Bayesian multiple QTL mapping in experimental designs. Heredity 100: 240-252.
40. YI, N., and S. XU, 2002 Mapping quantitative trait loci with epistatic effects. Genet. Res. Camb. 79: 185-198.
41. YI, N., S. XU and D. B. ALLISON, 2003 Bayesian model choice and search strategies for mapping interacting quantitative trait loci. Genetics 165: 867-883.
42. YI, N., B. S. YANDELL, G.A. CHURCHILL, D.B. ALLISON, E. J. Eisen et al., 2005 Bayesian model selection for genomewide epistatic quantitative trait loci analysis. Genetics 170: 1333-1344.
43. YI, N., D. SHRINER, S. BANERJEE, T. MEHTA, D. POMP et al., 2007 An efficient Bayesian model selection approach for interacting QTL models with many effects. Genetics 176: 1865-1877.
44. ZELLNER, A., 1962 An efficient method of estimating seemingly unrelated regressions and tests for aggregation bias. J. Am. Stat. Assoc. 57: 348-368.
45. ZENG, Z.-B., T. WANG and W. ZOU, 2005 Modeling quantitative trait loci and interpretation of models. Genetics 169: 1711-1725.