Incorporating LASSO effects into a mixed model for quantitative trait loci detection
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The identification of quantitative trait loci (QTL) can be viewed as a subset selection problem. In a simulation study the least absolute selection and shrinkage operator (LASSO) is shown to be a useful and powerful tool for QTL identification. LASSO effects are embedded into a mixed model allowing simultaneous modeling of genetic and experimental effects. This provides the flexibility to model the experiment in conjunction with the power of LASSO QTL identification. Estimation is performed using an approximation to the restricted likelihood and modified Gaussian elimination. The extended mixed model is used to analyze a cattle gene mapping dataset.
- Afolayan, R. A., Pitchford, W. S., Weatherly, A. W., and Bottema, C. D. K. (2002), “Genetic Variation in Growth and Body Dimensions of Jersey and Limousin Cross Cattle. 1. Pre-Weaning Performance,”, Asian-Australian Journal of Animal Sciences, 15, 1371–1377.
- Broman, K. W., and Speed, T. R. (2002), “A Model Selection Approach for the Identification of Quantitative Trait Loci in Experimental Crosses,”, Journal of the Royal Statistical Society, Series B, 64, 641–656. CrossRef
- Foster, S. D. (2006), “The LASSO Linear Mixed Model for Mapping Quantitative Trait Loci,” unpublished PhD thesis, University of Adelaide.
- Foster, S. D., Verbyla, A. P., and Pitchford, W. S. (2007), “A Random Model Approach for the LASSO,” Computational Statistics, accepted.
- Gianola, D., Perez-Enciso, M., and Toro, M. A. (2003), “On Marker-Assisted Prediction of Genetic Value: Beyond the Ridge,”, Genetics, 163, 347–365.
- Gilmour, A. R., Thompson, R., and Cullis, B. R. (1995), “Average Information REML: An Efficient Algorithm for Variance Parameter Estimation in Linear Mixed Models,”, Biometrics, 51, 1440–1450. CrossRef
- Haley, C. S., and Knott, S. A. (1992), “A Simple Regression Method for Mapping Quantitative Trail Loci in Line Crosses Using Flanking Markers,”, Heredity, 69, 315–324.
- Henderson, C. R. (1950), “Estimation of Genetic Parameters,”, (abstract), Annals of Mathematical Statistics, 21, 309–310.
- Jansen, R. C. (1993), “Interval Mapping of Multiple Quantitative Trait Loci,”, Genetics, 135, 205–211.
- Kao, C. H. (2000), “On the Differences Between Maximum Likelihood and Regression Interval Mapping in the Analysis of Quantitative Trait Loci,”, Genetics, 156, 855–865.
- Kao, C. H., Zeng, Z. B., and Teasdale, R. D. (1999), “Multiple Interval Mapping for Quantitative Trait Loci,”, Genetics, 152, 1203–1216.
- Knott, S. A., Elsen, J. M., and Haley, C. S. (1996,”, Methods for Multiple-Marker Mapping of Quantitative Trait Loci in Half-Sib Populations,”, Theoretical and Applied Genetics, 93, 71–80. CrossRef
- Lander, E. S., and Botstein, D. (1989), “Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps,”, Genetics, 121, 185–199.
- McCullagh, P., and Tibshirani, R. (1990), “A Simple Method for the Adjustment of Profile Likelihoods,”, Journal of the Royal Statistical Society, Series B, 52, 325–344.
- Miller, A. (2002), Subset Selection in Regression, Vol. 95 of Monographs on Statistics and Applied Probability (2nd ed.), London: Chapman & Hall/CRC.
- Morris, C. A., Cullen, N. G., Pitchford, W. S., Hickey, S. M., Hyndman, D. L., Crawford, A. M., and Bottema, C. D. K. (2003), “QTL for Birth Weight in Bos Taurus Cattle,”, in Proceedings of the Association for the Advancement of Animal Breeding and Genetics, Melbourne, vol. 15, pp. 400–403.
- Osborne, M. R. (1985), Finite Algorithms in Optimization and Data Analysis, Wiley Series in Probability and Mathematical Statistics, Chichester: Wiley.
- Osborne, M. R., Presnell, B., and Turlach, B. A. (2000), “On the LASSO and its Dual,”, Journal of Computational and Graphical Statistics, 9, 319–337. CrossRef
- Patterson, H. D., and Thompson, R. (1971), “Recovery of Interblock Information when Block Sizes are Unequal,” Biometrika, 31, 100–109.
- Satagopan, J. M., Yandell, Y. S., Newton, M. A., and Osborn, T. C. (1996), “A Bayesian Approach to Detect Quantitative Trait Loci using Markov Chain Monte Carlo,”, Genetics, 144, 805–816.
- Seaton, G., Haley, C. S., Knott, S. A., Kearsey, M., and Visscher, P. M. (2002), “QTL Express: Mapping Quantitative Trait Loci in Simple and Complex Pedigrees,”, Bioinformatics, 18, 339–340. CrossRef
- Sen, S., and Churchill, G. A. (2001), “A Statistical Framework for Quantitative Trait Mapping,”, Genetics, 159, 371–387.
- Taylor, J. D., and Verbyla, A. P. (2006), “Asymptotic Likelihood Approximations Using a Partial Laplace Approximation,”, Australian and New Zealand Journal of Statistics, 48, 465–476. CrossRef
- Tibshirani, R. (1996), “Regression Shrinkage and Selection via the Lasso,”, Journal of the Royal Statistical Society, Series B, 48, 267–288.
- Verbyla, A. P. (1990), “A Conditional Derivation of Residual Maximum Likelihood,”, Australian Journal of Statistics, 32, 227–230. CrossRef
- Wang, H., Zhang, Y. M., Li, X. M., Masinde, G. L., Mohan, S., Baylink, D. J., and Xu, S. Z. (2005), “Bayesian Shrinkage Estimation of Quantitative Trait Loci Parameters,”, Genetics, 170, 465–480. CrossRef
- Whittaker, J. C., Thompson, R., and Denham, M. C. (2000), “Marker-Assisted Selection Using Ridge Regression,”, Genetical Research, 75, 249–252. CrossRef
- Xu, S. Z. (2003), “Estimating Polygenic Effects Using Markers of the Entire Genome,”, Genetics 163, 789–801.
- Yi, N. J., Yandell, B. S., Churchill, G. A., Allison, D. B., Eisen, E. J., and Pomp, D. (2005), “Bayesian Model Selection for Genome-Wide Epistatic Quantitative Trait Loci Analysis,”, Genetics, 170, 1333–1344. CrossRef
- Zeng, Z. B. (1994), “Precision Mapping of Quantitative Trait Loci,”, Genetics, 136, 1457–1468.
- Incorporating LASSO effects into a mixed model for quantitative trait loci detection
Journal of Agricultural, Biological, and Environmental Statistics
Volume 12, Issue 2 , pp 300-314
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- Adjusted scores
- Partial Laplace approximation
- Quantitative trial loci
- Restricted likelihood
- Subset selection