Developments in statistical analysis in quantitative genetics

Genetica

Volumn 136, Issue 2, 2009, Pages 319-332

  Sorensen, Daniel ^a  

^a DANISH INSTITUTE OF AGRICULTURAL SCIENCES   (Denmark)

Author keywords

Genetic models; McMC; Statistical genetics

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; ENVIRONMENT; GENETIC MARKER; GENETIC PROCEDURES; GENETIC VARIABILITY; GENETICS; GENOMICS; HUMAN; STATISTICAL ANALYSIS;

ANIMALS; DATA INTERPRETATION, STATISTICAL; ENVIRONMENT; GENETIC MARKERS; GENETIC TECHNIQUES; GENETIC VARIATION; GENOMICS; HUMANS; MODELS, GENETIC;

EID: 67349285370     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-008-9303-5     Document Type: Article

References (87)

1. JH Albert S Chib 1993 Bayesian analysis of binary and polychotomous response data J Am Stat Assoc 88 669 679
2. DA Anderson M Aitkin 1985 Variance component models with binary response: interviewer variability J R Stat Soc B 47 203 210
3. J Besag 1994 Contribution to the discussion paper by Grenander and Miller J R Stat Soc B 56 591 592
4. A Blasco M Piles L Varona 2003 A Bayesian analysis of the effect of selection for growth rate on growth curves in rabbits Genet Sel Evol 35 21 41
5. GEP Box DR Cox 1964 An analysis of transformations J R Stat Soc B 26 211 252
6. CS Carlson MA Eberle MJ Rieder Q Yi L Kruglyak DA Nickerson 2004 Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium Am J Hum Genet 74 106 120
7. H Chipman E George R McCulloch 1998 Bayesian CART model search (with discussion) J Am Stat Assoc 93 935 960
8. OF Christensen RP Waagepetersen 2002 Bayesian prediction of spatial count data using generalized linear mixed models Biometrics 58 280 286
9. RN Curnow 1961 The estimation of repeatability and heritability from records subject to culling Biometrics 17 553 566
10. LH Damgaard IR Korsgaard 2006 A bivariate quantitative genetic model for a linear Gaussian trait and a survival trait Genet Sel Evol 38 35 64
11. LH Damgaard IR Korsgaard 2006 A bivariate quantitative genetic model for a threshold trait and a survival trait Genet Sel Evol 38 565 581
12. IJM de Boer JAM van Arendonk 1992 Prediction of additive and dominance effects in selected or unselected populations with inbreeding Theor Appl Genet 84 451 459
13. DGT Denison BK Mallik AFM Smith 1998 Automatic Bayesian curve fitting J R Stat Soc B 60 333 350
14. J Detilleux PL Leroy 2000 Application of a mixed normal mixture model to the estimation of mastitis-related parameters J Dairy Sci 83 2341 2349
15. V Ducrocq G Casella 1996 Bayesian analysis of mixed survival models Genet Sel Evol 28 505 529
16. V Ducrocq RL Quaas E Pollak G Casella 1988 Length of productive life of dairy cows. II. Variance component estimation and sire evaluation J Dairy Sci 71 3071 3079
17. DS Falconer 1965 The inheritance of liability to certain diseases, estimated from the incidence among relatives Ann Hum Genet 29 51 76
18. RA Fisher 1918 The correlation between relatives on the supposition of Mendelian inheritance Trans R Soc Edinb 52 399 433
19. JL Foulley D Gianola S Im 1987 Genetic evaluation of traits distibuted as Poisson-binomial with reference to reproductive characters Theor Appl Genet 73 870 877
20. A Gelman XL Meng H Stern 1996 Posterior predictive assessment of model fitness via realized discrepancies (with discussion) Stat Sin 6 733 807
21. Gelman A, Carlin JB, Stern HS, Rubin DB (2004) Bayesian Data Analysis. Chapman and Hall
22. EI George RE McCulloch 1993 Variable selection via Gibbs sampling J Am Stat Assoc 8 881 889
23. CJ Geyer 1992 Practical Markov chain Monte Carlo Stat Sci 7 473 511
24. D Gianola 1982 Theory and analysis of threshold characters J Anim Sci 54 1079 1096
25. D Gianola RL Fernando 1986 Bayesian methods in animal breeding theory J Anim Sci 63 217 244
26. D Gianola JL Foulley 1983 Sire evaluation for ordered categorical data with a threshold model Genet Sel Evol 15 201 223
27. Gianola D, Foulley JL, Fernando RL (1986) Prediction of breeding values when variances are not known. In: proceedings of the third world congress on genetics applied to livestock production, vol XII. University of Nebraska, Lincoln, pp 356-370
28. D Gianola M Perez-Enciso MA Toro 2003 On marker-assisted prediction of genetic value: beyond the ridge Genetics 157 1819 1829
29. D Gianola RL Fernando A Stella 2006 Genomic-assisted prediction of genetic value with semiparametric procedures Genetics 173 1761 1776
30. P Gustafson YC MacNab S Wen 2004 On the value of derivative evaluations and random walk suppression in Markov chain Monte Carlo algorithms Stat Comput 14 23 38
31. JP Gutierrez B Nieto P Piqueras N Ibáñez C Salgado 2006 Genetic parameters for canalisation analysis of litter size and litter weight at birth in mice Genet Sel Evol 38 445 462
32. Hartl DL, Jones EW (2005) Genetics. Analysis of Genes and Genomes. Jones and Bartlett Publishers, Sudbury, Massachusetts
33. DA Harville RW Mee 1984 A mixed model procedure for analyzing ordered categorical data Biometrics 40 393 408
34. Hastie T, Tibshirani R (1990) Generalized additive models. Chapman and Hall
35. Henderson CR (1950) Specific and general combining ability. In: Gowen JW (eds) Heterosis. Iowa State College Press, Ames, Iowa, pp 352-370
36. Henderson CR (1963) Selection index and expected selection advance. In: Hanson WD, Robinson HF (eds) Statistical genetics and plant breeding, National Academy of Sciences. National Research Council Publication No. 982, Washington, DC, pp 141-163
37. Henderson CR (1973) Sire evaluation and genetic trends. In: proceedings of the animal breeding and genetics symposium in honor of Dr. J. L. Lush. American Society of Animal Science, Champaign, pp 10-41
38. CR Henderson 1975 Best linear unbiased estimation and prediction under a selection model Biometrics 31 423 447
39. CR Henderson 1976 A simple method for the inverse of a numerator relationship matrix used in prediction of breeding values Biometrics 32 69 83
40. WG Hill XS Zhang 2004 Effects on phenotypic variability of directional selection arising through genetic differences in residual variability Genet Res 83 121 132
41. JA Hoeting D Madigan AE Raftery CT Volinsky 1999 Bayesian model averaging: a tutorial Stat Sci 14 382 417
42. N Ibáñez L Varona D Sorensen JL Noguera 2007 A study of heterogeneity of environmental variance for slaughter weight in pigs Animal 2 19 26
43. Ibáñez N, Sorensen D, Waagepetersen R, Blasco A (2008) Selection for environmental variation: a statistical analysis and power calculations. Genetics (in press)
44. Im S, Fernando R, Gianola D (1989) Likelihood inferences in animal breeding: a missing-data theory view point. Genet Sel Evol 21:399-414
45. Johnson NL, Kotz S (1969) Distributions in statistics: discrete distributions. Wiley, New York
46. Kennedy BW (1990) The use of mixed model methods in the analysis of designed experiments. In: Gianola D, Hammond K (eds) Advances in statistical methods for genetic improvement of livestock. Springer-Verlag, New York, pp 77-97
47. D Lambert 1992 Zero-inflated Poisson regression, with an application to defects in manufacturing Technometrics 34 1 14
48. Lee HKH (2004) Bayesian nonparametrics via neural networks. ASA-SIAM Series
49. DY Lin D Zen 2006 Likelihood-based inference on haplotype effects in genetic association studies J Am Stat Assoc 101 89 104
50. TFC Mackay RF Lyman 2005 Drosophila bristles and the nature of quantitative genetic variation Philos Trans R Soc B 360 1513 1527
51. D Madigan AE Raftery 1994 Model selection and accounting for model uncertainty in graphical models using Occam's window J Am Stat Assoc 89 1535 1546
52. Mäki-Tanila A, Kennedy BW (1986) Mixed model methodology under genetic models with a small number of additive and non-additive loci. In: Proceedings of the 3rd world congress on genetics applied to livestock production, vol 12. University of Nebraska, pp 443-447
53. V Martinez L Bünger WG Hill 2000 Analysis of response to 20 generations of selection for body composition in mice: fit to infinitesimal model assumptions Genet Sel Evol 32 3 21
54. CE McCulloch 1994 Maximum likelihood variance components estimation for binary data J Am Stat Assoc 89 330 335
55. THE Meuwissen BJ Hayes ME Goddard 2001 Prediction of total genetic value using genome-wide dense marker maps Genetics 157 1819 1829
56. K Meyer WG Hill 1991 Mixed model analysis of a selection experiment for food intake in mice Genet Res 57 71 81
57. HA Mulder P Bijma WG Hill 2007 Prediction of breeding values and selection responses with genetic heterogeneity of environmental variance Genetics 175 1895 1910
58. Y Ochi RL Prentice 1984 Likelihood inference in a correlated probit regression model Biometrika 71 531 543
59. Stergård J, Jensen J, Madsen P, Gianola D, Klemetsdal G, Heringstad B (2003) Detection of mastitis in dairy cattle by use of mixture models for repeated somatic cell scores: a Bayesian approach via Gibbs sampling. J Dairy Sci 86:3694-3703
60. Stergård J, Madsen P, Gianola D, Klemetsdal G, Jensen J, Heringstad B, Korsgaard IR (2005) A Bayesian threshold-normal mixture model for analysis of a continuous mastitis-related trait. J Dairy Sci 88:2652-2659
61. K Pearson 1904 Contributions to the mathematical theory of evolution Philos Trans R Soc Lond A 185 71 110
62. AE Raftery D Madigan JA Hoeting 1997 Model selection and accounting for model uncertainty in linear regression models J Am Stat Assoc 92 179 191
63. GO Roberts RL Tweedie 1997 Exponential convergence of Langevin diffusions and their approximations Bernoulli 2 314 363
64. A Robertson IM Lerner 1949 The heritability of all-or-none traits: viability of poultry Genetics 34 395 411
65. M Ros D Sorensen R Waagepetersen M Dupont-Nivet M SanCristobal J-C Bonnet J Mallard 2004 Evidence for genetic control of adult weight plasticity in the snail Helix aspersa Genetics 168 2089 2097
66. SI Rowe S White S Avendano WG Hill 2006 Genetic heterogeneity of residual variance in broiler chickens Genet Sel Evol 38 617 635
67. DB Rubin 1976 Inference and missing data Biometrika 63 581 592
68. DB Rubin 1984 Bayesianly justifiable and relevant frequency calculations for the applied statistician Ann Stat 12 1151 1172
69. Ruppert D, Wand MP, Carroll RJ (2003) Semiparametric regression. Cambridge University Press
70. M San Cristobal-Gaudy JM Elsen L Bodin C Chevalet 1998 Prediction of the response to a selection for canalisation of a continuous trait in animal breeding Genet Sel Evol 30 423 451
71. P Sheet M Stephens 2006 A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase Am J Hum Genet 78 629 644
72. Sorensen D, Gianola D (2002) Likelihood, Bayesian, and Markov chain Monte Carlo methods in quantitative genetics. Springer-Verlag, New York
73. D Sorensen R Waagepetersen 2003 Normal linear models with genetically structured residual variance heterogeneity: a case study Genet Res 82 207 222
74. D Sorensen S Andersen D Gianola IR Korsgaard 1995 Bayesian inference in threshold models using Gibbs sampling Genet Sel Evol 27 229 249
75. D Sorensen RL Fernando D Gianola 2001 Inferring the trajectory of genetic variance in the course of artificial selection Genet Res 77 83 94
76. D Sorensen B Guldbrandtsen J Jensen 2003 On the need for a control line in selection experiments: a likelihood analysis Genet Sel Evol 35 3 20
77. D Sorensen A Vernersen S Andersen 2000 Bayesian analysis of response to selection: a case study using litter size in Danish Yorkshire pigs Genetics 156 283 295
78. D Sorensen CS Wang J Jensen D Gianola 1994 Bayesian analysis of genetic change due to selection using Gibbs sampling Genet Sel Evol 26 333 360
79. RJ Tempelman D Gianola 1996 A mixed effects model for overdispersed count data in animal breeding Biometrics 52 265 279
80. R Thompson 1973 The estimation of variance and covariance components with an application when records are subject to culling Biometrics 29 527 550
81. Thompson R (1976) Estimation of quantitative genetic parameters. In: Pollak E, Kempthorne O, Bailey TB (eds) In: proceedings of the international conference on quantitative genetics. Iowa State University, pp 639-657
82. R Thompson 1986 Estimation of realized heritability in a selected population using mixed-model methods Genet Sel Evol 18 475 483
83. Varona L, Sorensen D (2008) Genetic analysis of mortality in pigs using zero-inflated models. (in Preparation)
84. R Waagepetersen N Ibáñez D Sorensen 2008 A comparison of strategies for Markov chain Monte Carlo computation in quantitative genetics Genet Sel Evol 40 161 176
85. S Wright 1934 An analysis of variability in number of digits in an inbred strain of guinea pigs Genetics 19 506 536
86. S Xu 2003 Estimating polygenic effects using markers of the entire genome Genetics 163 789 801
87. XS Zhang WG Hill 2005 Evolution of the environmental component of phenotypic variance: stabilizing selection in changing environments and the cost of homogeneity Evolution 59 1237 1244