The LASSO and sparse least squares regression methods for SNP selection in predicting quantitative traits

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 2, 2012, Pages 629-636

  Feng, Zeny Z ^a   Yang, Xiaojian ^a   Subedi, Sanjeena ^a   McNicholas, Paul D ^a  

^a UNIVERSITY OF GUELPH   (Canada)

Author keywords

Bioinformatics; regression analysis; statistical computing.

Indexed keywords

CLOSE PROXIMITY; COVARIATES; DIMENSION REDUCTION; HOLSTEIN CATTLE; LEAST ABSOLUTE SHRINKAGE AND SELECTION OPERATORS; LEAST-SQUARES REGRESSION METHOD; PARTIAL LEAST SQUARES; PHENOTYPIC VARIATIONS; QUANTITATIVE TRAITS; REGRESSION COEFFICIENT; SIMULATION STUDIES; SINGLE NUCLEOTIDE POLYMORPHISMS; STATISTICAL COMPUTING; SUBSET SELECTION; VARIABLE SELECTION;

BIOINFORMATICS; FEATURE EXTRACTION; FORECASTING; REGRESSION ANALYSIS; SHRINKAGE;

LEAST SQUARES APPROXIMATIONS;

BOS;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CATTLE; COMPUTER SIMULATION; GENETICS; METHODOLOGY; QUANTITATIVE TRAIT LOCUS; REGRESSION ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; BOVINAE; PROCEDURES;

ALGORITHMS; ANIMALS; CATTLE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; LEAST-SQUARES ANALYSIS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84863068606     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.139     Document Type: Article

References (16)

1. D. Gianola, R.L. Fernando, and A. Stella, "Genomic-Assisted Prediction of Genetic Value with Semiparametric Procedures," Genetics, vol. 173, pp. 1761-1776, 2006. (Pubitemid 44127674)
2. E.L. Heffner, M.E. Sorrells, and J.L. Jannink, "Genomic Selection for Crop Improvement," Crop Science, vol. 49, pp. 1-12, 2009.
3. S.H. Lee, J.H.J. van der Werf, B.J. Hayes, M.E. Goddard, and P.M. Visscher, "Predicting Unobserved Phenotypes for Complex Traits from Whole Genome SNP Data," PLoS Genetics, vol. 4, no. 10, e10000231, doi:10.1371/journal.pgen.1000231, 2008.
4. O. Gonzĺez-Recio, A. Gianola, G.J.M. Rosa, K.A. Weigel, and A. Kranis, "Genome-Assisted Prediction of a Quantitative Trait Measured in Parents and Progeny: Application to Food Conversion Rate in Chickens," Genetics Selection Evolution, vol. 41, p. 3, 2009.
5. R. Tibshirani, "Regression Shrinkage and Selection via the Lasso," J. Royal Statistical Soc. B., vol. 58, pp. 267-288, 1996.
6. S. Chun and S. Keles, "Sparse Partial Least Squares Regression for Simultaneous Dimension Reduction and Variable Selection," J. Royal Statistical Soc. B., vol. 72, pp. 3-25, 2010.
7. T.H.E. Meuwissen, B.J. Hayes, and M.E. Goddard, "Prediction of Total Genetic Value Using Genomic-Wide Dense Marker Maps," Genetics, vol. 157, pp. 1819-1829, 2001. (Pubitemid 32298846)
8. D. Gianola, M. Perez-Enciso, and M.A. Toro, "On Marker-Assisted Prediction of Genetic Value: Beyond the Ridge," Genetics, vol. 163, pp. 347-365, 2003. (Pubitemid 36222678)
9. G. de los Campos, H. Naya, D. Gianola, J. Crossa, A. Legarra, E. Manfredi, K. Weigel, and J.M. Cotes, "Predicting Quantitative Traits with Regression Models for Dense Molecular Markers and Pedigree," Genetics, vol. 182, pp. 375-385, 2009.
10. M.G. Usai, M.E. Goddard, and B.J. Hayes, "LASSO with Crossvalidation for Genomic Selection," Genetics Research, vol. 91, pp. 427-436, 2009.
11. T. Park and G. Casella, "The Baysian LASSO," J. Am. Statistical Assoc., vol. 103, pp. 681-686, 2008.
12. C. Colombani, A. Legarra, P. Croiseau, F. Guillaume, S. Fritz, V. Ducrocq, and C. Robert-Granié, "Application of PLS and Sparse PLS Regression in Genome Selection," Proc. Ninth World Congress Genetics Applied to Livestock Production, Aug. 2010.
13. N. Long, D. Gianola, G.J.M. Rosa, and K.A. Weigel, "Dimension Reduction and Variable Selection for Genomic Selection: Application to Predicting Milk Yield in Holsteins," J. Animal Breeding and Genetics, vol. 128, pp. 1-11, 2011.
14. J.S. Preisser, K.K. Lohman, and P.J. Rathouz, "Performance of Weighted Estimating Equations for Longitudinal Binary Data with Drop-Outs Missing at Random," Statistics in Medicine, vol. 21, pp. 3035-3054, 2002. (Pubitemid 35189826)
15. Z. Feng, W. Wong, X. Gao, and F. Shenkel, "Generalized Genetic Association Study with Samples of Related Individuals," Annals of Applied Statistics, To Appear, 2011.
16. H. Wold, "Estimation of Principal Components and Related Models by Iterative Least Squares," Multivariate Analysis, pp. 391-442, 1966.