SNPInterForest: a new method for detecting epistatic interactions

Multiple genetic factors and their interactive effects are speculated to contribute to complex diseases. Detecting such genetic interactive effects, i.e., epistatic interactions, however, remains a significant challenge in large-scale association studies.

We have developed a new method, named SNPInterForest, for identifying epistatic interactions by extending an ensemble learning technique called random forest. Random forest is a predictive method that has been proposed for use in discovering single-nucleotide polymorphisms (SNPs), which are most predictive of the disease status in association studies. However, it is less sensitive to SNPs with little marginal effect. Furthermore, it does not natively exhibit information on interaction patterns of susceptibility SNPs. We extended the random forest framework to overcome the above limitations by means of (i) modifying the construction of the random forest and (ii) implementing a procedure for extracting interaction patterns from the constructed random forest. The performance of the proposed method was evaluated by simulated data under a wide spectrum of disease models. SNPInterForest performed very well in successfully identifying pure epistatic interactions with high precision and was still more than capable of concurrently identifying multiple interactions under the existence of genetic heterogeneity. It was also performed on real GWAS data of rheumatoid arthritis from the Wellcome Trust Case Control Consortium (WTCCC), and novel potential interactions were reported.

SNPInterForest, offering an efficient means to detect epistatic interactions without statistical analyses, is promising for practical use as a way to reveal the epistatic interactions involved in common complex diseases.