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

Lorenzo Beretta, Alessandro Santaniello, Piet L C M van Riel, Marieke J H Coenen, Raffaella Scorza

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number416
JournalBMC Bioinformatics
Volume11
DOIs
Publication statusPublished - Aug 6 2010

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Structural Biology
  • Applied Mathematics

Fingerprint

Dive into the research topics of 'Survival dimensionality reduction (SDR): Development and clinical application of an innovative approach to detect epistasis in presence of right-censored data'. Together they form a unique fingerprint.

Cite this