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Open Access Software

Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2

Michele Pinelli12*, Giovanni Scala13, Roberto Amato134, Sergio Cocozza12 and Gennaro Miele134

Author Affiliations

1 Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli “Federico II” - Università di Salerno, Italy

2 Dipartimento di Biologia e Patologia Cellulare e Molecolare “L. Califano”, Università di Napoli “Federico II”, Napoli, Italy

3 Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S.Angelo, Napoli, Italy

4 INFN Sezione di Napoli, Napoli, Italy

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BMC Bioinformatics 2012, 13:132  doi:10.1186/1471-2105-13-132

Published: 14 June 2012

Abstract

Background

The analysis of complex diseases is an important problem in human genetics. Because multifactoriality is expected to play a pivotal role, many studies are currently focused on collecting information on the genetic and environmental factors that potentially influence these diseases. However, there is still a lack of efficient and thoroughly tested statistical models that can be used to identify implicated features and their interactions. Simulations using large biologically realistic data sets with known gene-gene and gene-environment interactions that influence the risk of a complex disease are a convenient and useful way to assess the performance of statistical methods.

Results

The Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered. The GENS2 tool is able to simulate gene-environment and gene-gene interactions. To make the Simulator more intuitive, the input parameters are expressed as standard epidemiological quantities. GENS2 is written in Python language and takes advantage of operators and modules provided by the simuPOP simulation environment. It can be used through a graphical or a command-line interface and is freely available from http://sourceforge.net/projects/gensim webcite. The software is released under the GNU General Public License version 3.0.

Conclusions

Data produced by GENS2 can be used as a benchmark for evaluating statistical tools designed for the identification of gene-gene and gene-environment interactions.

Keywords:
Gene-environment interaction; Computer simulation; Complex disease; Epistasis; Genetic; Genome-wide association study; Genetics; Population; SimuPOP; Linkage disequilibrium; Genomics