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

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

Borja González-Seoane  1 , Christian Ponte-Fernández  2 , Jorge González-Domínguez  3 , María J Martín  3
Affiliations

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

Borja González-Seoane et al. BMC Bioinformatics. .

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.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Generation of a penetrance table. Flowchart of the program
Fig. 2
Fig. 2
Use of PyToxo as a library in a Python program
Fig. 3
Fig. 3
PyToxo GUI initial screen
See this image and copyright information in PMC

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