PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models

BMC Bioinformatics. 2022 Apr 2;23(1):117. doi: 10.1186/s12859-022-04645-7.

Abstract

Background: Epistasis is the interaction between different genes when expressing a certain phenotype. If epistasis involves more than two loci it is called high-order epistasis. High-order epistasis is an area under active research because it could be the cause of many complex traits. The most common way to specify an epistasis interaction is through a penetrance table.

Results: This paper presents PyToxo, a Python tool for generating penetrance tables from any-order epistasis models. Unlike other tools available in the bibliography, PyToxo is able to work with high-order models and realistic penetrance and heritability values, achieving high-precision results in a short time. In addition, PyToxo is distributed as open-source software and includes several interfaces to ease its use.

Conclusions: PyToxo provides the scientific community with a useful tool to evaluate algorithms and methods that can detect high-order epistasis to continue advancing in the discovery of the causes behind complex diseases.

Keywords: Epistasis model; Gene interaction; Heritability; Penetrance; Prevalence; Python; Simulation; SymPy.

MeSH terms

  • Epistasis, Genetic*
  • Models, Genetic*
  • Penetrance
  • Phenotype
  • Software