Zeitschrift für genetische Syndrome und Gentherapie
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SNP-SNP Interactions: Focusing on Variable Coding

Fernando Pires Hartwig

Genetic epidemiology is a promising field to identify patterns of disease susceptibility that can be explored in personalized medicine. However, especially for complex traits, the genetic component is likely to be composed of several loci and/or of interactions between them. The last is addressed in this manuscript, which aims to provide an overview of the advantages and disadvantages of statistically-oriented and biologically-oriented approaches for twoSNP interactions. Eight biologically-oriented models of epistasis are discussed, focusing on their implementation, which is exemplified with real data. Additionally, some key technical points (such as reducing statistical power due to multiple testing and use of conceptual considerations) are discussed, and an exploratory step prior to the analysis is proposed to pre-select the models of epistasis to be actually tested. A function (written in R) is provided (under request) to facilitate the implementation of such models (and can be easily modified to implement others). It is stressed that, regardless of the method choice, the biological meaning of the model being tested is critical for correct interpretation of the results.