Work

HiSSI: high-order SNP-SNP interactions detection based on efficient significant pattern and differential evolution

Year: 2019

Type: article

Abstract: Background Detecting single nucleotide polymorphism (SNP) interactions is an important and challenging task in genome-wide association studies (GWAS). Various efforts have been devoted to detect SNP interactions. However, the large volume of SNP datasets results in such a big number of high-order SNP combinations that restrict the power of detecting interactions. Methods In this paper, to combat with this challenge, we propose a two-stage approach (called HiSSI) to detect high-order SNP-SNP interactions. In the screening stage, HiSSI employs a statistically significant pattern that takes into account family wise error rate, to control false positives and to effectively screen two-locus combinations candidate set. In the searching stage, HiSSI applies two different search strategies (exhaustive search and heuristic search based on differential evolution along with χ2-test) on candidate pairwise SNP combinations to detect high-order SNP interactions. Results Extensive experiments on simulated datasets are conducted to evaluate HiSSI and recently proposed and related approaches on both two-locus and three-locus disease models. A real genome-wide dataset: breast cancer dataset collected from the Wellcome Trust Case Control Consortium (WTCCC) is also used to test HiSSI. Conclusions Simulated experiments on both two-locus and three-locus disease models show that HiSSI is more powerful than other related approaches. Real experiment on breast cancer dataset, in which HiSSI detects some significantly two-locus and three-locus interactions associated with breast cancer, again corroborate the effectiveness of HiSSI in high-order SNP-SNP interaction identification.

Source: BMC Medical Genomics

DOI: 10.1186/s12920-019-0584-6

Authors: Xia Cao, Jie Liu, Maozu Guo, Jun Wang

Institutions: Southwest University, Beijing University of Civil Engineering and Architecture

Language: English

Topic: Genetic Associations and Epidemiology

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $2,145