Document Type

Article

Publication Date

9-22-2009

Publication Title

BioData Mining

Department

Geisel School of Medicine

Abstract

Genome-wide association studies are becoming the de facto standard in the genetic analysis of common human diseases. Given the complexity and robustness of biological networks such diseases are unlikely to be the result of single points of failure but instead likely arise from the joint failure of two or more interacting components. The hope in genome-wide screens is that these points of failure can be linked to single nucleotide polymorphisms (SNPs) which confer disease susceptibility. Detecting interacting variants that lead to disease in the absence of single-gene effects is difficult however, and methods to exhaustively analyze sets of these variants for interactions are combinatorial in nature thus making them computationally infeasible. Efficient algorithms which can detect interacting SNPs are needed. ReliefF is one such promising algorithm, although it has low success rate for noisy datasets when the interaction effect is small. ReliefF has been paired with an iterative approach, Tuned ReliefF (TuRF), which improves the estimation of weights in noisy data but does not fundamentally change the underlying ReliefF algorithm. To improve the sensitivity of studies using these methods to detect small effects we introduce Spatially Uniform ReliefF (SURF).

DOI

10.1186/1756-0381-2-5

Original Citation

Greene CS, Penrod NM, Kiralis J, Moore JH. Spatially uniform relieff (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Min. 2009 Sep 22;2(1):5. doi: 10.1186/1756-0381-2-5. PMID: 19772641; PMCID: PMC2761303.

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