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. 2018 Aug 29;9(9):435. doi: 10.3390/genes9090435

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© 2018 by the author.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

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An example of the fast approach for detecting high-order epistasis with interaction weight (FDHE-IW) approach for detecting 3-way single nucleotide polymorphism (SNP) combinations associated with a given phenotype. (1) Using the dataset with N SNPs, the SU value of each SNP was calculated. (2) The top three SNPs with the largest SU values were selected from the N SNPs, and then the three SNPs were employed as seeds to calculate the 2-way interaction weights (IW) with the other SNPs. (3) The top nine 2-way SNP-combinations were selected from the 2-way SNP combinations that pair with the three parent SNPs from (2), based on IW values. (4) The top 9 × 3 = 27 3-way SNP-combinations that are formed from a parent SNP-combination in (3) were selected based on IW. (5) The G-test statistical method was employed to test the 27 3-way SNP combinations, and two 3-way SNP combinations were verified using the G-test.