A combinatorial searching method for detecting a set of interacting loci associated with complex traits.

Complex diseases are presumed to be the results of the interaction of several genes and environmental factors, with each gene only having a small effect on the disease. Mapping complex disease genes therefore becomes one of the greatest challenges facing geneticists. Most current approaches of association studies essentially evaluate one marker or one gene (haplotype approach) at a time. These approaches ignore the possibility that effects of multilocus functional genetic units may play a larger role than a single-locus effect in determining trait variability. In this article, we propose a Combinatorial Searching Method (CSM) to detect a set of interacting loci (may be unlinked) that predicts the complex trait. In the application of the CSM, a simple filter is used to filter all the possible locus-sets and retain the candidate locus-sets, then a new objective function based on the cross-validation and partitions of the multi-locus genotypes is proposed to evaluate the retained locus-sets. The locus-set with the largest value of the objective function is the final locus-set and a permutation procedure is performed to evaluate the overall p-value of the test for association between the final locus-set and the trait. The performance of the method is evaluated by simulation studies as well as by being applied to a real data set. The simulation studies show that the CSM has reasonable power to detect high-order interactions. When the CSM is applied to a real data set to detect the locus-set (among the 13 loci in the ACE gene) that predicts systolic blood pressure (SBP) or diastolic blood pressure (DBP), we found that a four-locus gene-gene interaction model best predicts SBP with an overall p-value = 0.033, and similarly a two-locus gene-gene interaction model best predicts DBP with an overall p-value = 0.045.