SNP selection for predicting a quantitative trait

References

• Banos , G. , Woolliams , J. A. , Woodward , B. W. , Forbes , A. B. and Coffey , M. P. 2008 . Impact of single nucleotide polymorphisms in leptin, leptin receptor, growth hormone receptor, and diacylglycerol acyltransferase (dgat1) gene loci on milk production, feed, and body energy traits of UK dairy cows . J. Dairy Sci. , 91 : 3190 – 3200 . (doi:10.3168/jds.2007-0930)
   PubMed Web of Science ®Google Scholar
• Chun , H. and Keles , S. 2010 . Sparse partial least squares regression for simultaneous dimension reduction and variable selection . J. R. Statist. Soc. B , 72 ( 1 ) : 3 – 25 . (doi:10.1111/j.1467-9868.2009.00723.x)
   Google Scholar
• Daetwyler , H. D. , Schenkel , F. S. , Sargolzaei , M. and Robinson , J. A.B. 2008 . A genome scan to detect quantative trait loci for economically important traits in holstein cattle using two methods and a dense single nucleotide polymorphism map . J. Dairy Sci. , 91 : 3225 – 3236 . (doi:10.3168/jds.2007-0333)
   PubMed Web of Science ®Google Scholar
• Efron , B. , Hastie , T. , Johnstone , I. and Tibshirani , R. 2004 . Least angle regression . Ann. Statist. , 32 ( 2 ) : 407 – 499 . (doi:10.1214/009053604000000067)
   Web of Science ®Google Scholar
• Efron , B. and Tibshirani , R. 1993 . An Introduction to the Bootstrap , New York : Chapman and Hall .
   Google Scholar
• Feng , Z. , Wong , W. , Gao , X. and Schenkel , F. 2011 . Generalized genetic association study with samples of related subjects . Ann. Appl. Stat. , Available at http://www.imstat.org/aoas/next_issue.html.
   Web of Science ®Google Scholar
• Hoerl , A. E. 1962 . Application of ridge analysis to regression problems . Chem. Eng. Prog. , 58 : 54 – 59 .
   Google Scholar
• Johnson , B. A. 2009 . On LASSO for censored data . EJS , 3 : 485 – 506 .
   Google Scholar
• Jolliffe , I. T. , Trendafilov , N. T. and Uddin , M. 2003 . A modified principal component technique based on the lass . J. Comput. Graph. Stat. , 12 ( 3 ) : 531 – 547 . (doi:10.1198/1061860032148)
   Web of Science ®Google Scholar
• Lee , S. H. , van der Werf , J. H.J. , Hayes , B. J. , Goddard , M. E. and Visscher , P. M. 2008 . Predicting unobserved phenotypes for complex traits from whole-genome SNP data . PloS Genet. , 4 ( 10 ) p. e1000231, doi:10.1371/journal. pgen.1000231.
   Web of Science ®Google Scholar
• Ma , S. , Song , S. and Huang , J. 2007 . Supervised group Lasso with applications to microarray data analysis . BMC Bioinf. , 8 p. 60, doi:10.1186/1471-2105-8-60.
   Web of Science ®Google Scholar
• R Development Core Team . R: A Language and Environment for Statistical Computing software available at http://www.R-project.org.
   Google Scholar
• Schenkel , F. S. , Sargolzaei , M. , Kistemaker , G. , Jansen , G. B. , Sullivan , P. , Van Doormaal , B. J. , VanRaden , P. M. and Wiggans , G. R. Reliability of genomic evaluation of holstein cattle in Canada . Proceedings of the Interbull International Workshop – Genomic Information in Genetic Evaluations . Sweden. pp. 26 – 29 .
   Google Scholar
• Smaragdov , M. G. 2009 . Genomic selection as a possible accelerator of traditional selection . Genetika , 45 ( 2 ) : 633 – 636 .
   Google Scholar
• Tibshirani , R. 1996 . Regression shrinkage and selection via the lasso . J. R. Statist. Soc. B , 58 : 267 – 288 .
   Google Scholar
• Weisberg , S. 1980 . Applied Linear Regression , New York : Wiley .
   Google Scholar
• Wold , H. 1996 . Estimation of Principal Components and Related Models by Iterative Least Squares , New York : Academic Press .
   Google Scholar
• Xu , S. 2007 . An empirical Bayes method for estimating epistatic effects of quantitative trait loci . Biometrics , 63 ( 2 ) : 513 – 521 . (doi:10.1111/j.1541-0420.2006.00711.x)
   PubMed Web of Science ®Google Scholar
• Zou , H. , Hastie , T. and Tibshirani , R. 2006 . Sparse principal component analysis . J. Comput. Graph. Statist. , 15 : 265 – 286 . (doi:10.1198/106186006X113430)
   Web of Science ®Google Scholar