Generating penetrance tables of high-order epistasis models with PyToxo

4 pages•Published: February 16, 2023

Borja González-Seoane, Christian Ponte-Fernández, Jorge González-Domínguez and María J. Martín

Abstract

The interaction among different genes when expressing a particular phenotype is known as epistasis. High-order epistasis, when more than two loci are involved, is an active research area because it could be the cause of many complex traits. The most common abstraction for specifying an epistasis interaction is through a penetrance table, which captures the probability of expressing the studied phenotype given a particular genotype.
Although it is very common for simulators to use penetrance tables, most of them do not allow the user to generate them directly, or present limitations for high-order interac- tions and/or realistic prevalence and heritability values. In this work, we present PyToxo, a Python tool for generating penetrance tables from any-order epistasis models. PyToxo allows to work with more appropriate scenarios than other state-of-the-art tools. Addi- tionally, it also improves in terms of accuracy, speed and ease of use, being available as a library, through a CLI or through a cross-platform GUI.

Keyphrases: epistasis model, gene interaction, heritability, penetrance, prevalence, python, simulation, sympy

In: Alvaro Leitao and Lucía Ramos (editors). Proceedings of V XoveTIC Conference. XoveTIC 2022, vol 14, pages 46-49.

Links:	https://easychair.org/publications/paper/wh8g
	https://doi.org/10.29007/p41g

BibTeX entry

@inproceedings{XoveTIC2022:Generating_penetrance_tables_high,
  author    = {Borja González-Seoane and Christian Ponte-Fernández and Jorge González-Domínguez and María J. Martín},
  title     = {Generating penetrance tables of high-order epistasis models with PyToxo},
  booktitle = {Proceedings of V XoveTIC Conference. XoveTIC 2022},
  editor    = {Alvaro Leitao and Lucía Ramos},
  series    = {Kalpa Publications in Computing},
  volume    = {14},
  publisher = {EasyChair},
  bibsource = {EasyChair, https://easychair.org},
  issn      = {2515-1762},
  url       = {/publications/paper/wh8g},
  doi       = {10.29007/p41g},
  pages     = {46-49},
  year      = {2023}}

Download PDF Open PDF in browser