title: Application of high-dimensional feature selection: evaluation for genomic prediction in man.
abstract: In this study, we investigated the effect of five feature selection approaches on the performance of a mixed model (G-BLUP) and a Bayesian (Bayes C) prediction method. We predicted height, high density lipoprotein cholesterol (HDL) and body mass index (BMI) within 2,186 Croatian and into 810 UK individuals using genome-wide SNP data. Using all SNP information Bayes C and G-BLUP had similar predictive performance across all traits within the Croatian data, and for the highly polygenic traits height and BMI when predicting into the UK data. Bayes C outperformed G-BLUP in the prediction of HDL, which is influenced by loci of moderate size, in the UK data. Supervised feature selection of a SNP subset in the G-BLUP framework provided a flexible, generalisable and computationally efficient alternative to Bayes C; but careful evaluation of predictive performance is required when supervised feature selection has been used.
authors.affiliation: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh.
authors.forename: M L
authors.initials: ML
authors.lastname: Bermingham
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh.
authors.forename: R
authors.initials: R
authors.lastname: Pong-Wong
authors.affiliation: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh.
authors.forename: A
authors.initials: A
authors.lastname: Spiliopoulou
authors.affiliation: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh.
authors.forename: C
authors.initials: C
authors.lastname: Hayward
authors.affiliation: Centre for Population Health Sciences, University of Edinburgh.
authors.forename: I
authors.initials: I
authors.lastname: Rudan
authors.affiliation: Centre for Population Health Sciences, University of Edinburgh.
authors.forename: H
authors.initials: H
authors.lastname: Campbell
authors.affiliation: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh.
authors.forename: A F
authors.initials: AF
authors.lastname: Wright
authors.affiliation: Centre for Population Health Sciences, University of Edinburgh.
authors.forename: J F
authors.initials: JF
authors.lastname: Wilson
authors.affiliation: Pharmatics Limited, UK.
authors.forename: F
authors.initials: F
authors.lastname: Agakov
authors.affiliation: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh.
authors.forename: P
authors.initials: P
authors.lastname: Navarro
authors.affiliation: 1] MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh [2] The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh.
authors.forename: C S
authors.initials: CS
authors.lastname: Haley
mesh_terms: D001499:Bayes Theorem; D001827:Body Height / Q000235:genetics*; D015992:Body Mass Index; D008076:Cholesterol, HDL / Q000097:blood / Q000235:genetics*; D023281:Genomics / Q000379:methods; D006801:Humans; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D019655:Quantitative Trait, Heritable
chemical_list: D008076:Cholesterol, HDL