AI Article Synopsis
- The analysis of complex diseases in human genetics involves understanding the interactions of genetic and environmental factors, but there is a need for better statistical models to analyze these relationships.
- The Gene-Environment iNteraction Simulator 2 (GENS2) can simulate interactions between genetic and environmental factors, allowing researchers to study epistatic interactions without limitations on sample size or additional factors.
- GENS2 can be used to generate data as benchmarks for evaluating statistical tools aimed at identifying interactions, and it is freely available for use in both graphical and command-line interfaces.
Article 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. 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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538511 | PMC |
| http://dx.doi.org/10.1186/1471-2105-13-132 | DOI Listing |
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