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Open AccessArticle

FDHE-IW: A Fast Approach for Detecting High-Order Epistasis in Genome-Wide Case-Control Studies

School of Computer Science & Technology, Xi’an University of Posts & Telecommunications, Xi’an 710121, China
Genes 2018, 9(9), 435; https://doi.org/10.3390/genes9090435
Received: 11 June 2018 / Revised: 16 August 2018 / Accepted: 16 August 2018 / Published: 29 August 2018
Detecting high-order epistasis in genome-wide association studies (GWASs) is of importance when characterizing complex human diseases. However, the enormous numbers of possible single-nucleotide polymorphism (SNP) combinations and the diversity among diseases presents a significant computational challenge. Herein, a fast method for detecting high-order epistasis based on an interaction weight (FDHE-IW) method is evaluated in the detection of SNP combinations associated with disease. First, the symmetrical uncertainty (SU) value for each SNP is calculated. Then, the top-k SNPs are isolated as guiders to identify 2-way SNP combinations with significant interaction weight values. Next, a forward search is employed to detect high-order SNP combinations with significant interaction weight values as candidates. Finally, the findings were statistically evaluated using a G-test to isolate true positives. The developed algorithm was used to evaluate 12 simulated datasets and an age-related macular degeneration (AMD) dataset and was shown to perform robustly in the detection of some high-order disease-causing models. View Full-Text
Keywords: Single-nucleotide polymorphism; high-order epistasis; interaction weight Single-nucleotide polymorphism; high-order epistasis; interaction weight
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Tuo, S. FDHE-IW: A Fast Approach for Detecting High-Order Epistasis in Genome-Wide Case-Control Studies. Genes 2018, 9, 435.

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