EpiGEN: an epistasis simulation pipeline.

Computer Simulation Epigen Epistasis, Genetic Genome-Wide Association Study Polymorphism, Single Nucleotide Software

Journal

Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944

Informations de publication

Date de publication:
08 12 2020
Historique:
received: 14 11 2019
revised: 03 04 2020
accepted: 08 04 2020
pubmed: 15 4 2020
medline: 4 3 2021
entrez: 15 4 2020
Statut: ppublish

Résumé

Simulated data are crucial for evaluating epistasis detection tools in genome-wide association studies. Existing simulators are limited, as they do not account for linkage disequilibrium (LD), support limited interaction models of single nucleotide polymorphisms (SNPs) and only dichotomous phenotypes or depend on proprietary software. In contrast, EpiGEN supports SNP interactions of arbitrary order, produces realistic LD patterns and generates both categorical and quantitative phenotypes. EpiGEN is implemented in Python 3 and is freely available at https://github.com/baumbachlab/epigen. Supplementary data are available at Bioinformatics online.

Identifiants

DOI: 10.1093/bioinformatics/btaa245 PMID: 32289146
pubmed: 32289146
pii: 5820008
doi: 10.1093/bioinformatics/btaa245
doi:

Substances chimiques

Epigen 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

4957-4959

Informations de copyright

© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Auteurs

David B Blumenthal (DB)

Technical University of Munich, School of Life Sciences Weihenstephan, Chair of Experimental Bioinformatics, 85354 Freising, Germany.

Lorenzo Viola (L)

Technical University of Munich, School of Life Sciences Weihenstephan, Chair of Experimental Bioinformatics, 85354 Freising, Germany.

Markus List (M)

Technical University of Munich, School of Life Sciences Weihenstephan, Chair of Experimental Bioinformatics, 85354 Freising, Germany.

Jan Baumbach (J)

Technical University of Munich, School of Life Sciences Weihenstephan, Chair of Experimental Bioinformatics, 85354 Freising, Germany.

Paolo Tieri (P)

CNR National Research Council, IAC Institute for Applied Computing, 00185 Rome, Italy.

Tim Kacprowski (T)

Technical University of Munich, School of Life Sciences Weihenstephan, Chair of Experimental Bioinformatics, 85354 Freising, Germany.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Simulation numérique › EpiGEN: an epistasis simulation pipeline.
questionsmedicales.fr › Facteurs biologiques › Protéines et peptides de signalisation intercellulaire › Protéines de la famille de l'EGF › Épigène › EpiGEN: an epistasis simulation pipeline.
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Épistasie › EpiGEN: an epistasis simulation pipeline.
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Épidémiologie moléculaire › Étude d'association pangénomique › EpiGEN: an epistasis simulation pipeline.
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › EpiGEN: an epistasis simulation pipeline.
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › EpiGEN: an epistasis simulation pipeline.