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This article is part of the supplement: Selected articles from the 9th International Workshop on Data Mining in Bioinformatics (BIOKDD)

Open Access Introduction

FEPI-MB: identifying SNPs-disease association using a Markov Blanket-based approach

Bing Han1, Xue-wen Chen1* and Zohreh Talebizadeh2

Author affiliations

1 Bioinformatics and Computational Life Sciences Laboratory, Information and Telecommunication Technology Center, Department of Electrical Engineering and Computer Science, The University of Kansas, 1520 West 15th Street, Lawrence, KS 66045, USA

2 Children’s Mercy Hospital and University of Missouri - Kansas City, Kansas City, MO 64108, USA

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Citation and License

BMC Bioinformatics 2011, 12(Suppl 12):S3  doi:10.1186/1471-2105-12-S12-S3

Published: 24 November 2011



The interactions among genetic factors related to diseases are called epistasis. With the availability of genotyped data from genome-wide association studies, it is now possible to computationally unravel epistasis related to the susceptibility to common complex human diseases such as asthma, diabetes, and hypertension. However, the difficulties of detecting epistatic interaction arose from the large number of genetic factors and the enormous size of possible combinations of genetic factors. Most computational methods to detect epistatic interactions are predictor-based methods and can not find true causal factor elements. Moreover, they are both time-consuming and sample-consuming.


We propose a new and fast Markov Blanket-based method, FEPI-MB (Fast EPistatic Interactions detection using Markov Blanket), for epistatic interactions detection. The Markov Blanket is a minimal set of variables that can completely shield the target variable from all other variables. Learning of Markov blankets can be used to detect epistatic interactions by a heuristic search for a minimal set of SNPs, which may cause the disease. Experimental results on both simulated data sets and a real data set demonstrate that FEPI-MB significantly outperforms other existing methods and is capable of finding SNPs that have a strong association with common diseases.


FEPI-MB algorithm outperforms other computational methods for detection of epistatic interactions in terms of both the power and sample-efficiency. Moreover, compared to other Markov Blanket learning methods, FEPI-MB is more time-efficient and achieves a better performance.