title: Comparison of classification methods for detecting associations between SNPs and chick mortality.
abstract: Multi-category classification methods were used to detect SNP-mortality associations in broilers. The objective was to select a subset of whole genome SNPs associated with chick mortality. This was done by categorizing mortality rates and using a filter-wrapper feature selection procedure in each of the classification methods evaluated. Different numbers of categories (2, 3, 4, 5 and 10) and three classification algorithms (naïve Bayes classifiers, Bayesian networks and neural networks) were compared, using early and late chick mortality rates in low and high hygiene environments. Evaluation of SNPs selected by each classification method was done by predicted residual sum of squares and a significance test-related metric. A naïve Bayes classifier, coupled with discretization into two or three categories generated the SNP subset with greatest predictive ability. Further, an alternative categorization scheme, which used only two extreme portions of the empirical distribution of mortality rates, was considered. This scheme selected SNPs with greater predictive ability than those chosen by the methods described previously. Use of extreme samples seems to enhance the ability of feature selection procedures to select influential SNPs in genetic association studies.
authors.affiliation: Department of Animal Sciences, University of Wisconsin, Madison, WI 53706, USA. nlong@wisc.edu
authors.forename: Nanye
authors.initials: N
authors.lastname: Long
authors.forename: Daniel
authors.initials: D
authors.lastname: Gianola
authors.forename: Guilherme J M
authors.initials: GJ
authors.lastname: Rosa
authors.forename: Kent A
authors.initials: KA
authors.lastname: Weigel
authors.forename: Santiago
authors.initials: S
authors.lastname: Avendaño
mesh_terms: D000465:Algorithms; D000818:Animals; D002645:Chickens / Q000235:genetics*; D005260:Female; D005821:Genetic Techniques; D008297:Male; D008957:Models, Genetic; D009026:Mortality; D020641:Polymorphism, Single Nucleotide; D011201:Poultry Diseases / Q000235:genetics* / Q000401:mortality*