title: An adaptive threshold determination method of feature screening for genomic selection.
abstract: BACKGROUND
  Although the dimension of the entire genome can be extremely large, only a parsimonious set of influential SNPs are correlated with a particular complex trait and are important to the prediction of the trait. Efficiently and accurately selecting these influential SNPs from millions of candidates is in high demand, but poses challenges. We propose a backward elimination iterative distance correlation (BE-IDC) procedure to select the smallest subset of SNPs that guarantees sufficient prediction accuracy, while also solving the unclear threshold issue for traditional feature screening approaches.
  
  
  RESULTS
  Verified through six simulations, the adaptive threshold estimated by the BE-IDC performed uniformly better than fixed threshold methods that have been used in the current literature. We also applied BE-IDC to an Arabidopsis thaliana genome-wide data. Out of 216,130 SNPs, BE-IDC selected four influential SNPs, and confirmed the same FRIGIDA gene that was reported by two other traditional methods.
  
  
  CONCLUSIONS
  BE-IDC accommodates both the prediction accuracy and the computational speed that are highly demanded in the genomic selection.
authors.affiliation: Department of Mathematics and Statistics, Utah State University, Logan, 84322, UT, USA. guifang.fu@usu.edu.
authors.forename: Guifang
authors.initials: G
authors.lastname: Fu
authors.affiliation: Department of Mathematics and Statistics, Utah State University, Logan, 84322, UT, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Wang
authors.affiliation: Department of Mathematics and Statistics, Utah State University, Logan, 84322, UT, USA.
authors.forename: Xiaotian
authors.initials: X
authors.lastname: Dai
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D003198:Computer Simulation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D008957:Models, Genetic; D010641:Phenotype; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide
chemical_list: D029681:Arabidopsis Proteins; C414613:FRI protein, Arabidopsis
keywords: Backward elimination; FRIGIDA expression; Feature screening; Genomic selection