title: A novel approach to simulate gene-environment interactions in complex diseases.
abstract: BACKGROUND
  Complex diseases are multifactorial traits caused by both genetic and environmental factors. They represent the major part of human diseases and include those with largest prevalence and mortality (cancer, heart disease, obesity, etc.). Despite a large amount of information that has been collected about both genetic and environmental risk factors, there are few examples of studies on their interactions in epidemiological literature. One reason can be the incomplete knowledge of the power of statistical methods designed to search for risk factors and their interactions in these data sets. An improvement in this direction would lead to a better understanding and description of gene-environment interactions. To this aim, a possible strategy is to challenge the different statistical methods against data sets where the underlying phenomenon is completely known and fully controllable, for example simulated ones.
  
  
  RESULTS
  We present a mathematical approach that models gene-environment interactions. By this method it is possible to generate simulated populations having gene-environment interactions of any form, involving any number of genetic and environmental factors and also allowing non-linear interactions as epistasis. In particular, we implemented a simple version of this model in a Gene-Environment iNteraction Simulator (GENS), a tool designed to simulate case-control data sets where a one gene-one environment interaction influences the disease risk. The main aim has been to allow the input of population characteristics by using standard epidemiological measures and to implement constraints to make the simulator behaviour biologically meaningful.
  
  
  CONCLUSIONS
  By the multi-logistic model implemented in GENS it is possible to simulate case-control samples of complex disease where gene-environment interactions influence the disease risk. The user has full control of the main characteristics of the simulated population and a Monte Carlo process allows random variability. A knowledge-based approach reduces the complexity of the mathematical model by using reasonable biological constraints and makes the simulation more understandable in biological terms. Simulated data sets can be used for the assessment of novel statistical methods or for the evaluation of the statistical power when designing a study.
authors.affiliation: Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli "Federico II"-Università di Salerno, Italy. roamato@na.infn.it
authors.forename: Roberto
authors.initials: R
authors.lastname: Amato
authors.forename: Michele
authors.initials: M
authors.lastname: Pinelli
authors.forename: Daniel
authors.initials: D
authors.lastname: D'Andrea
authors.forename: Gennaro
authors.initials: G
authors.lastname: Miele
authors.forename: Mario
authors.initials: M
authors.lastname: Nicodemi
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Raiconi
authors.forename: Sergio
authors.initials: S
authors.lastname: Cocozza
mesh_terms: D004194:Disease / Q000209:etiology* / Q000235:genetics; D004777:Environment; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D006801:Humans; D015233:Models, Statistical; D009010:Monte Carlo Method; D012307:Risk Factors