Data/hora: 03/06/2024 03:38:54

Biblioteca(s): | Embrapa Gado de Leite.
Tipo da produção científica: | Artigo em Periódico Indexado
Circulação/Nível: | A - 1
Data corrente: | 04/12/2014
Data da última atualização: | 05/02/2024
Autoria: | OLIVEIRA, F. C. de; BORGES, C. C. H.; ALMEIDA, F. N.; SILVA, F. F. e; VERNEQUE, R. da S.; SILVA, M. V. G. B.; ARBEX, W. A.
Afiliação: | FABRÍZZIO CONDÉ DE OLIVEIRA, UFJF; CARLOS CRISTIANO HASENCLEVER BORGES, UFJF; FERNANDA NASCIMENTO ALMEIDA, FAPEMIG; FABYANO FONSECA E SILVA, UFV; RUI DA SILVA VERNEQUE, CNPGL; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL; WAGNER ANTONIO ARBEX, CNPGL.
Título: | SNPs selection using support vector regression and genetic algorithms in GWAS
Ano de publicação: | 2014
Fonte/Imprenta: | BMC Genomics, v. 15, article S4, 2014.
Páginas: | 15 p.
Idioma: | Inglês
Notas: | Suppl. 7.
Conteúdo: | Introduction - This paper proposes a new methodology to simultaneously select the most relevant SNPs markers for the characterization of any measurable phenotype described by a continuous variable using Support Vector Regression with Pearson Universal kernel as fitness function of a binary genetic algorithm. The proposed methodology is multi-attribute towards considering several markers simultaneously to explain the phenotype and is based jointly on statistical tools, machine learning and computational intelligence. Results- The suggested method has shown potential in the simulated database 1, with additive effects only, and real database. In this simulated database, with a total of 1,000 markers, and 7 with major effect on the phenotype and the other 993 SNPs representing the noise, the method identified 21 markers. Of this total, 5 are relevant SNPs between the 7 but 16 are false positives. In real database, initially with 50,752 SNPs, we have reduced to 3,073 markers, increasing the accuracy of the model. In the simulated database 2, with additive effects and interactions (epistasis), the proposed method matched to the methodology most commonly used in GWAS. Conclusions- The method suggested in this paper demonstrates the effectiveness in explaining the real phenotype (PTA for milk), because with the application of the wrapper based on genetic algorithm and Support Vector Regression with Pearson Universal, many redundant markers were eliminated, increasing the prediction and accuracy of the model on the real database without quality control filters. The PUK demonstrated that it can replicate the performance of linear and RBF kernels.
Palavras-Chave: | Single nucleotide polymorphisms (SNPs); SNPs markers; Support Vector Regression with Pearson Universal.
Categoria do assunto: | G Melhoramento Genético
Registro original: | Embrapa Gado de Leite (CNPGL)
Exemplares: | CNPGL - (21552-1) - UPC - AP - DD -  -  -  - DIS