Background: Epistasis is recognized as a fundamental part of the genetic architecture of individuals. Several computational approaches have been developed to model gene-gene interactions in case-control studies, however, none of them is suitable for time-dependent analysis. Herein we introduce the Survival Dimensionality Reduction (SDR) algorithm, a non-parametric method specifically designed to detect epistasis in lifetime datasets.Results: The algorithm requires neither specification about the underlying survival distribution nor about the underlying interaction model and proved satisfactorily powerful to detect a set of causative genes in synthetic epistatic lifetime datasets with a limited number of samples and high degree of right-censorship (up to 70%). The SDR method was then applied to a series of 386 Dutch patients with active rheumatoid arthritis that were treated with anti-TNF biological agents. Among a set of 39 candidate genes, none of which showed a detectable marginal effect on anti-TNF responses, the SDR algorithm did find that the rs1801274 SNP in the FcγRIIa gene and the rs10954213 SNP in the IRF5 gene non-linearly interact to predict clinical remission after anti-TNF biologicals.Conclusions: Simulation studies and application in a real-world setting support the capability of the SDR algorithm to model epistatic interactions in candidate-genes studies in presence of right-censored data.
Survival dimensionality reduction (SDR) : development and clinical application of an innovative approach to detect epistasis in presence of right-censored data / L. Beretta, A. Santaniello, P. L. van Riel, M. J. Coenen, R. Scorza. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - 11(2010 Aug), pp. 416.416-416.416.
|Titolo:||Survival dimensionality reduction (SDR) : development and clinical application of an innovative approach to detect epistasis in presence of right-censored data|
SANTANIELLO, ALESSANDRO (Secondo)
SCORZA, RAFFAELLA (Ultimo)
|Settore Scientifico Disciplinare:||Settore MED/09 - Medicina Interna|
|Data di pubblicazione:||ago-2010|
|Digital Object Identifier (DOI):||http://dx.doi.org/10.1186/1471-2105-11-416|
|Appare nelle tipologie:||01 - Articolo su periodico|