Generalized linear mixed models for mapping multiple quantitative trait loci

Heredity

Volumn 109, Issue 1, 2012, Pages 41-49

  Che, X ^a   Xu, S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

binary trait; binomial trait; mixed model; overdispersion; QTL

Indexed keywords

DISPERSION; ESTIMATION METHOD; FERTILIZATION (REPRODUCTION); GENETIC ANALYSIS; GENOTYPE; NUMERICAL MODEL; PHENOTYPE; QUANTITATIVE ANALYSIS; WHEAT;

ARTICLE; CHROMOSOME MAP; GENETICS; GENOTYPE; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL; WHEAT;

CHROMOSOME MAPPING; GENOTYPE; LINEAR MODELS; PHENOTYPE; QUANTITATIVE TRAIT LOCI; TRITICUM;

TRITICUM AESTIVUM;

EID: 84863718888     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2012.10     Document Type: Article

References (29)

1. Boer MP, Wright D, Feng L, Podlich DW, Luo L, Cooper M et al. (2007). A mixed-model quantitative trait loci (QTL) analysis for multiple-environment trial data using environmental covariables for QTL-by-environment interactions, with an example in maize. Genetics 177: 1801-1813. (Pubitemid 350277072)
2. Breslow NE, Clayton DG (1993). Approximate inference in generalized linear mixed models. J Am Stat Assoc 88: 9-25.
3. DeGroot MH (2004). Optimal Statistical Decision. John Wiley and Sons: Hoboken, New Jersey.
4. Dou B, Hou B, Xu H, Lou X, Chi X, Yang J et al. (2009). Efficient mapping of a female sterile gene in wheat (Triticum aestivum L). Genet Res Camb 91: 337-343.
5. Friedman J, Hastie T, Tibshirani R (2010). Regularization paths for generalized linear models via coordinate descent. J Stat Softw 33: 1-22.
6. Gelman A, Carlin JB, Stern HS, Rubin DB (2004). Bayesian Data Analysis. Chapman and Hall, New York.
7. Henderson CR (1950). Estimation of genetic parameters (Abstract). Ann Math Statist 21: 309-310.
8. Hoerl AE, Kennard RW (1970). Ridge regression: biased estimation for nonorthogonal problems. Technometrics 12: 55-67.
9. Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE et al. (2007). A genomewide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 39: 870-874. (Pubitemid 47014500)
10. Jiang C, Zeng Z-B (1997). Mapping quantitative trait loci with dominance and missing markers in various crosses from two inbred lines. Genetica 101: 47-58. (Pubitemid 28065451)
11. Kidd KK, Ott J (1984). Power and sample size in linkage studies. Human Gene Mapping 7(1984): Seventh International Workshop on Human Gene Mapping. Cytogenet Cell Genet 37: 510-511.
12. McCullagh P, Nelder JA (1989). Generalized Linear Models. Chapman and Hall: New York.
13. McCulloch CE, Neuhaus JM (2005). Generalized Linear Mixed Model. Encyclopedia of Biostatistics. John Wiley and Sons, Ltd: San Francisco.
14. McGilchrist CA (1994). Estimation in generalized mixed models. JR Stat Soc B 56: 61-69.
15. Picard R, Cook D (1984). Cross-validation of regression models. J Am Stat Assoc 79: 575-583.
16. Rao SQ, Xu S (1998). Mapping quantitative trait loci for ordered categorical traits in four-way crosses. Heredity 81: 214-224. (Pubitemid 28403816)
17. Rebai A (1997). Comparison of methods for regression interval mapping in QTL analysis with non-normal traits. Genet Res, Camb 69: 69-74. (Pubitemid 27219962)
18. Risch N (1991). A note on multiple testing procedures in linkage analysis. Am J Hum Genet 48: 1058-1064. (Pubitemid 21903067)
19. Tibshirani R (1996). Regression shrinkage and selection via the lasso. J R Stat Soc B 58: 267-288.
20. Visscher PM, Haley CS, Knott SA (1996). Mapping QTLs for binary traits in backcross and F2 populations. Genet Res Camb 68: 55-63. (Pubitemid 26285474)
21. Vonesh EF (1996). A note on the use of Laplaces approximation for nonlinear mixedeffects models. Biometrika 83: 447-452.
22. Wald A (1943). Tests of statistical hypotheses concerning several parameters when the number of observations is large. Trans Amer Math Soc 54: 426-482.
23. Wedderburn RWM (1974). Quasi-likelihood functions, generalized linear models, and the Gauss-Newton method. Biometrika 61: 439-447.
24. Wolfinger R, OConnell M (1993). Generalized linear mixed models: A pseudo-likelihood approach. J Statist Comput Simul 48: 233-243.
25. Xu S, Hu Z (2010). Generalized linear model for interval mapping of quantitative trait loci. Theor Appl Genet 121: 47-63.
26. Xu S, Yi N (2000). Mixed model analysis of quantitative trait loci. Proc Nat Acad Sci USA 97: 14542-14547. (Pubitemid 32016612)
27. Yi N, Banerjee S (2009). Hierarchical generalized linear models for multiple quantitative trait locus mapping. Genetics 181: 1101-1113.
28. Ypma TJ (1995). Historical development of the Newton-Raphson method. SIAM Review 37: 531-551.
29. Zou H (2006). The adaptive Lasso and its oracle properties. J Am Stat Assoc 101: 1418-1429.