A New Algorithm for Multivariate Genome Wide Association Studies Based on Differential Evolution and Extreme Learning Machines

David Álvarez Gutiérrez, Fernando Sánchez Lasheras, Vicente Martín Sánchez, Sergio Luis Suárez Gómez, Víctor Moreno, Ferrán Moratalla-Navarro and Antonio José Molina de la Torre
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David Álvarez Gutiérrez: SERGAS, UAP CS, 27720 A Pontenova, Spain
Fernando Sánchez Lasheras: Department of Mathematics, University of Oviedo, 33007 Oviedo, Spain
Vicente Martín Sánchez: CIBERESP, University of Leon, Vegazana Campus, 24400 Leon, Spain
Sergio Luis Suárez Gómez: Department of Mathematics, University of Oviedo, 33007 Oviedo, Spain
Víctor Moreno: Oncology Data Analytics Programme, Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, 08907 Barcelona, Spain
Ferrán Moratalla-Navarro: Oncology Data Analytics Programme, Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, 08907 Barcelona, Spain
Antonio José Molina de la Torre: IBIOMED, University of Leon, Vegazana Campus, 24400 Leon, Spain

Mathematics, 2022, vol. 10, issue 7, 1-21

Abstract: Genome-wide association studies (GWAS) are observational studies of a large set of genetic variants, whose aim is to find those that are linked to a certain trait or illness. Due to the multivariate nature of these kinds of studies, machine learning methodologies have been already applied in them, showing good performance. This work presents a new methodology for GWAS that makes use of extreme learning machines and differential evolution. The proposed methodology was tested with the help of the genetic information (370,750 single-nucleotide polymorphisms) of 2049 individuals, 1076 of whom suffer from colorectal cancer. The possible relationship of 10 different pathways with this illness was tested. The results achieved showed that the proposed methodology is suitable for detecting relevant pathways for the trait under analysis with a lower computational cost than other machine learning methodologies previously proposed.

Keywords: machine learning; differential evolution; extreme learning machines; genome-wide association studies; single nucleotide polymorphism; pathways analysis (search for similar items in EconPapers)
JEL-codes: C (search for similar items in EconPapers)
Date: 2022
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