New Distance-Based approach for Genome-Wide Association Studies
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Date
2022-09-01Author
Irigoyen Garbizu, Itziar
Cormand, Bru
Soler Artigas, María
Sánchez Mora, Cristina
Ramos Quiroga, Josep Antoni
Arenas Solá, Concepción
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IEEE/ACM Transactions on Computational Biology and Bioinformatics 19(5) : 2938 - 2949 (2022)
Abstract
With the rise of genome-wide association studies (GWAS), the analysis of typical GWAS data sets with thousands of single-nucleotide polymorphisms (SNPs) has become crucial in biomedicine research. Here, we propose a new method to identify SNPs related to disease in case-control studies. The method, based on genetic distances between individuals, takes into account the possible population substructure, and avoids the issues of multiple testing. The method provides two ordered lists of SNPs; one with SNPs which minor alleles can be considered risk alleles for the disease, and another one with SNPs which minor alleles can be considered as protective. These two lists provide a useful tool to help the researcher to decide where to focus attention in a first stage.