HiSeeker: Detecting High-Order SNP Interactions Based on Pairwise SNP Combinations.

ABSTRACT: Detecting single nucleotide polymorphisms' (SNPs) interaction is one of the most popular approaches for explaining the missing heritability of common complex diseases in genome-wide association studies. Many methods have been proposed for SNP interaction detection, but most of them only focus on pairwise interactions and ignore high-order ones, which may also contribute to complex traits. Existing methods for high-order interaction detection can hardly handle genome-wide data and suffer from low detection power, due to the exponential growth of search space. In this paper, we proposed a flexible two-stage approach (called HiSeeker) to detect high-order interactions. In the screening stage, HiSeeker employs the chi-squared test and logistic regression model to efficiently obtain candidate p

SUBMITTER: Liu J 

PROVIDER: S-EPMC5485517 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature