Evolutionary Algorithm for Pathways Detection in GWAS Studies

• Published in: Hybrid Artificial Intelligent Systems pp. 111 - 122
• Main Authors: Díez Díaz, Fidel, Sánchez Lasheras, Fernando, de Cos Juez, Francisco Javier, Martín Sánchez, Vicente
• Format: Book Chapter
• Language: English
• Published: Cham Springer International Publishing
• Series: Lecture Notes in Computer Science
• Subjects: Genetic algorithms; Genome wide association studies (GWAS); Genomic data simulator; Pathway analysis; Single nucleotide polymorphism (SNP)
• ISBN: 3030298582; 9783030298586
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/978-3-030-29859-3_10

In genetics, a genome-wide association study (GWAs) involves an analysis of the single-nucleotide polymorphisms (SNPs) that constitute the genome. This analysis is performed on a large set of individuals usually classified as cases and controls. The study of differences in the SNP chains of both groups is known as pathway analysis. The analysis alluded to allows the researcher to go beyond univariate results like those offered by the p-value analysis and its representation by Manhattan plots. Pathway analysis makes it possible to detect weaker single-variant signals and is also helpful in order to understand molecular mechanisms linked to certain diseases and phenotypes. The present research proposes a new algorithm based on evolutionary computation, capable of finding significant pathways in GWA studies. Its performance has been tested with the help of synthetic data sets created with an ad hoc developed genomic data simulator.