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Open Access Research article

Survival dimensionality reduction (SDR): development and clinical application of an innovative approach to detect epistasis in presence of right-censored data

Lorenzo Beretta1*, Alessandro Santaniello1, Piet LCM van Riel24, Marieke JH Coenen3 and Raffaella Scorza1

Author Affiliations

1 Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico and University of Milan, Milan, Italy

2 Department of Rheumatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands

3 Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands

4 On behalf of the Dutch Rheumatoid Arthritis Monitoring (DREAM) registry

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BMC Bioinformatics 2010, 11:416  doi:10.1186/1471-2105-11-416

Published: 6 August 2010

Abstract

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.

Availability: http://sourceforge.net/projects/sdrproject/ webcite