A nonlinear mixed-effect mixture model for functional mapping of dynamic traits

Heredity

Volumn 101, Issue 4, 2008, Pages 321-328

  Hou, W ^a   Li, H ^a   Zhang, B ^b   Huang, M ^b   Wu, R ^a,b,c  

^a University of Florida ^*  (United States)

^b NANJING FORESTRY UNIVERSITY   (China)

^c UNIVERSITY OF FLORIDA   (United States)

Author keywords

Growth trajectories; Mixture model; Nonlinear mixed effect model; Poplar; QTL mapping

Indexed keywords

DECIDUOUS TREE; ECOLOGICAL MODELING; ESTIMATION METHOD; GENOTYPE; MAPPING METHOD;

ALGORITHM; ARTICLE; ASPEN; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETICS; GENOTYPE; MONTE CARLO METHOD; PHENOTYPE; QUANTITATIVE TRAIT; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; GENOTYPE; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, STATISTICAL; MONTE CARLO METHOD; PHENOTYPE; POPULUS; QUANTITATIVE TRAIT, HERITABLE;

EID: 52549085906     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2008.53     Document Type: Article

References (45)

1. Beal SL, Sheiner LB (1982). Estimating population kinetics. Crit Rev Biomed Eng 8: 195-222.
2. Chen Z (2005). The full EM algorithm for the MLEs of QTL effects and positions and their estimated variances in multiple interval mapping. Biometrics 61: 474-480.
3. Chi EM, Reinsel GC (1989). Models for longitudinal data with random effects and AR (1) errors. J Am Stat Assoc 84: 452-459.
4. Churchill GA, Doerge RW (1994). Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
5. Davidian M, Giltinan D (1995). Nonlinear Models for Repeated Measurement Data. Chapman and Hall: New York.
6. Davidian M, Giltinan DM (2003). Nonlinear models for repeated measurements: an overview and update. J Agric Biol Environ Stat 8: 387-419.
7. Diggle PJ, Heagerty P, Liang KY, Zeger SL (2002). Analysis of Longitudinal Data. Oxford University Press: Oxford, UK.
8. Grattapaglia D, Sederoff RR (1994). Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudotestcross: mapping strategy and RAPD markers. Genetics 137: 1121-1137.
9. Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, Markowitz M (1995). Rapid turnover of plasma virions and CD4 lymphocytes in HIV infection. Nature 373: 123-126.
10. Lagarius JC, Reeds JA, Wright MH, Wright PE (1998). Convergence properties of the Neler-Mead simplex method in low dimensions. SIAM J Optim 9: 112-147.
11. Laird NM, Ware JH (1982). Random effects models for longitudinal data. Biometrics 38: 963-974.
12. Lin M, Wu RL (2005). Theoretical basis for the identification of allelic variants that encode drug efficacy and toxicity. Genetics 170: 919-928.
13. Lindstrom MJ, Bates DM (1990). Nonlinear mixed effects models for repeated measures data. Biometrics 46: 673-687.
14. Liu T, Zhao W, Tian LL, Wu RL (2005). An algorithm for molecular dissection of tumor progression. J Math Biol 50: 336-354.
15. Lynch M, Walsh B (1998). Genetics and Analysis of Quantitative Traits. Sinauer: Sunderland, MA, USA.
16. Ma C-X, Casella G, Wu RL (2002). Functional mapping of quantitative trait loci underlying the character process: a theoretical framework. Genetics 161: 1751-1762.
17. Malosetti M, Visser RGF, Celis-Gamboa C, van Eeuwijk FA (2006). QTL methodology for response curves on the basis of non-linear mixed models, with an illustration to senescence in potato. Theor Appl Genet 113: 288-300.
18. Rodriguez-Zas SL, Southney BR, Heyen DW, Lewin HA (2002). Detection of quantitative trait loci influencing dairy traits using a model for longitudinal data. J Dairy Sci 85: 2681-2691.
19. Schabenberger O (1995). The use of ordinal response methodology in forestry. Forest Sci 41: 321-336.
20. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB et al. (1998). Comprehensive identification of cell-cycle regulated genes in Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 95: 14863-14868.
21. Tierney L, Kadane JB (1986). Accurate approximations for posterior moments and marginal densities. J Am Stat Assoc 81: 82-86.
22. von Bertalanffy L (1957). Quantitative laws in metabolism and growth. Q Rev Biol 32: 217-231.
23. Vonesh EF, Wang H, Nie L, Majumdar D (2002). Conditional second-order generalized estimating equations for generalized linear and nonlinear mixed-effects models. J Am Stat Assoc 97: 271-283.
24. Wang ZH, Hou W, Wu RL (2006). A statistical model to analyze quantitative trait locus interactions for HIV dynamics from the virus and human genomes. Stat Med 25: 495-511.
25. Wang ZH, Wu RL (2004). A statistical model for high-resolution mapping of quantitative trait loci determining human HIV-1 dynamics. Stat Med 23: 3033-3051.
26. Wang H, Zhang Y-M, Li X, Masinde GL, Mohan S, Baylink DJ et al. (2005). Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics 170: 465-480.
27. West GB, Brown JH, Enquist BJ (1997). A general model for the origin of allometric scaling laws in biology. Science 276: 122-126.
28. West GB, Brown JH, Enquist BJ (2001). A general model for ontogenetic growth. Nature 413: 628-631.
29. Wolfinger RD (1993). Laplace's approximation for nonlinear mixed models. Biometrika 80: 791-795.
30. Wu L (2002). A joint model for nonlinear mixed-effects models with censoring and covariates measured with error, with application to AIDS studies. J Am Stat Assoc 97: 955-964.
31. Wu L (2004a). Exact and approximate inferences for nonlinear mixed-effects models with missing covariates. J Am Stat Assoc 32: 700-709.
32. Wu L (2004b). Nonlinear mixed-effects models with nonignorably missing covariates. Can J Stat 32: 27-37.
33. Wu RL, Lin M (2006). Functional mapping? How to map and study the genetic architecture of dynamic complex traits. Nat Rev Genet 7: 229-237.
34. Wu RL, Ma C-X, Lin M, Casella G (2004a). A general framework for analyzing the genetic architecture of developmental characteristics. Genetics 166: 1541-1551.
35. Wu RL, Ma C-X, Lin M, Wang ZH, Casella G (2004b). Functional mapping of quantitative trait loci underlying growth trajectories using a transform-both-sides logistic model. Biometrics 60: 729-738.
36. Wu RL, Ma CX, Lou XY, Casella G (2003a). Molecular dissection of allometry, ontogeny, and plasticity: a genomic view of developmental biology. Bioscience 53: 1041-1047.
37. Wu RL, Ma C-X, Zhao W, Casella G (2003b). Functional mapping of quantitative trait loci underlying growth rates: a parametric model. Physiol Genomics 14: 241-249.
38. Wu RL, Wang ZH, Zhao W, Cheverud JM (2004c). A mechanistic model for genetic machinery of ontogenetic growth. Genetics 168: 2383-2394.
39. Wu W-R, Li W-M, Tang D-Z, Lu H-R, Worland AJ (1999). Time-related mapping of quantitative trait loci underlying tiller number in rice. Genetics 151: 297-303.
40. Xu S (2003). Estimating polygenic effects using markers of the entire genome. Genetics 163: 789-801.
41. Xu S (2007). Derivation of the shrinkage estimates of quantitative trait locus effects. Genetics 177: 1255-1258.
42. Yang RQ, Tian Q, Xu S (2006). Mapping quantitative trait loci for longitudinal traits in line crosses. Genetics 173: 2339-2356.
43. Yang RQ, Xu S (2007). Bayesian shrinkage analysis of quantitative trait loci for dynamic traits. Genetics 176: 1169-1185.
44. Yin TM, Zhang XY, Huang MR, Wang MX, Zhuge Q, Zhu LH et al. (2002). Molecular linkage maps of the Populus genome. Genome 45: 541-555.
45. Zhao W, Chen YQ, Casella G, Cheverud JM, Wu RL (2005). A nonstationary model for functional mapping of complex traits. Bioinformatics 21: 2469-2477.