Journal Article

Toxo: a library for calculating penetrance tables of high-order epistasis models

Martín, María J., González-Domínguez, Jorge, Ponte-Fernández, Christian, Carvajal-Rodríguez, Antonio

2020

Overview

Background Epistasis is defined as the interaction between different genes when expressing a specific phenotype. The most common way to characterize an epistatic relationship is using a penetrance table, which contains the probability of expressing the phenotype under study given a particular allele combination. Available simulators can only create penetrance tables for well-known epistasis models involving a small number of genes and under a large number of limitations. Results Toxo is a MATLAB library designed to calculate penetrance tables of epistasis models of any interaction order which resemble real data more closely. The user specifies the desired heritability (or prevalence) and the program maximizes the table’s prevalence (or heritability) according to the input epistatic model boundaries. Conclusions Toxo extends the capabilities of existing simulators that define epistasis using penetrance tables. These tables can be directly used as input for software simulators such as GAMETES so that they are able to generate data samples with larger interactions and more realistic prevalences/heritabilities.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Analysis and modelling of complex systems / Bioinformatics / Biomedical and Life Sciences / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Computer simulation / Epistasis / Epistasis model / Epistasis, Genetic / Gametes / Gene interaction / Genes / Genotype / Genotype & phenotype / Heritability / Libraries / Life Sciences / Microarrays / Models, Genetic / Penetrance / Phenotype / Phenotypes / Population / Prevalence / Restrictions / Simulation / Simulators / Software / User-Computer Interface