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Table 5 Two-locus GxG interactions among 7 SNPs assessed by A-MDR

From: Risk score modeling of multiple gene to gene interactions using aggregated-multifactor dimensionality reduction

Two-locus GxG Interactions pOR p-value FDR pRR p-value FDR pChi p-value FDR
ATIC rs4673990+ MTHFD2 rs12196 3.9 (1.6–13.1) 0.001* 0.013* 1.9 (1.2-4.1) 0.001* 0.027* 6.1 (1.8-21.1) <.001* 0.002*
ATIC rs4673990 + MTHFD2 5nt ins/16nt del 3.7 (1.5-12.8) 0.001* 0.013* 1.8 (1.1-3.6) 0.003* 0.032* 6.0 (1.6-22.0) <.001* 0.002*
MTHFD2 rs12196 + GART rs8971 2.8 (1.1-8.8) 0.013* 0.069 1.6 (0.9-3.4) 0.016* 0.050 5.5 (1.3-20.7) 0.001* 0.009*
MTHFD2 5nt ins/16nt del + GART rs8971 2.6 (1.0-7.9) 0.017* 0.069 1.5 (0.9-2.7) 0.017* 0.050 5.0 (1.1-20.6) 0.002* 0.011*
ATIC rs4673990 + GART rs8971 2.5 (1.1-8.8) 0.027* 0.071 1.4 (0.9-2.4) 0.038* 0.088 4.7 (1.1-19.2) 0.009* 0.019*
ATIC rs2372536 + MTHFD2 5nt ins/16nt del 2.5 (1.0-8.3) 0.017* 0.069 1.6 (1.0-3.6) 0.006* 0.041* 5.0 (1.1-17.6) 0.011* 0.020*
ATIC rs2372536 + MTHFD2 rs12196 2.4 (0.9-8.0) 0.021* 0.069 1.4 (1.0-3.0) 0.033* 0.088 5.6 (1.2-18.3) 0.008* 0.019*
ATIC rs2372536 + GART rs8971 2.2 (0.8-6.5) 0.032* 0.074 1.5 (0.9-2.8) 0.015* 0.050 4.5 (0.8-28.2) 0.012* 0.020*
SLC25A32 rs17803441 +ITPA rs2295553 2.4 (0.8-7.5) 0.023* 0.069 1.6 (1.0-2.8) 0.013* 0.050 4.2 (0.8-17.9) 0.005* 0.019*
ATIC rs4673990 + SLC25A32 rs17803441 2.3 (0.8-8.2) 0.039* 0.081 1.4 (0.8-2.2) 0.061 0.106 4.9 (0.9-30.9) 0.009* 0.019*
MTHFD2 rs12196 + ITPA rs2295553 2.1 (0.9-7.1) 0.047* 0.090 1.4 (0.8-2.1) 0.065 0.106 4.2 (1.0-16.0) 0.025* 0.034*
ATIC rs4673990 + ITPA rs2295553 2.3 (0.7-7.1) 0.074 0.101 1.4 (0.7-2.2) 0.076 0.106 3.7 (0.9-13.2) 0.045* 0.059
MTHFD2 rs12196 + SLC25A32 rs17803441 2.2 (0.7-6.9) 0.060 0.097 1.4 (0.8-2.3) 0.067 0.106 5.2 (0.9-27.2) 0.012* 0.020*
ATIC rs2372536 + SLC25A32 rs17803441 2.2 (0.7-6.1) 0.056 0.097 1.3 (0.9-2.7) 0.062 0.106 6.6 (0.9-37.9) 0.008* 0.019*
MTHFD2 5nt ins/16nt del + MTHFD2 rs12196 2.0 (0.9-7.0) 0.074 0.101 1.3 (0.9-2.2) 0.088 0.115 5.2 (0.8-33.1) 0.008* 0.019*
MTHFD2 5nt ins/16nt del +LC25A32 rs17803441 2.0 (0.6-5.9) 0.077 0.101 1.3 (0.9-3.3) 0.073 0.106 4.2 (0.7-25.5) 0.015* 0.023*
MTHFD2 5nt ins/16nt del + ITPA rs2295553 1.9 (0.8-6.4) 0.114 0.139 1.3 (0.9-2.6) 0.129 0.160 3.9 (0.8-14.6) 0.076 0.094
ATIC rs2372536 + ITPA rs2295553 1.9 (0.8-6.9) 0.119 0.139 1.3 (0.9-2.2) 0.182 0.201 3.9 (0.8-13.3) 0.091 0.101
GART rs8971 + ITPA rs2295553 1.9 (0.8-8.9) 0.186 0.195 1.3 (0.9-3.6) 0.217 0.228 4.7 (0.8-16.1) 0.124 0.130
ATIC rs2372536 + ATIC rs4673990 1.8 (0.7-5.3) 0.131 0.145 1.2 (0.8-2.0) 0.161 0.188 4.0 (0.7-23.3) 0.089 0.101
GART rs8971 + SLC25A32 rs17803441 1.7 (0.4-9.9) 0.227 0.227 1.2 (0.7-5.7) 0.296 0.296 3.5 (0.4-19.1) 0.156 0.156
  1. (Three measures of GxG interactions [pOR, pRR, and pChi] along with 95% confidence intervals [CI] were obtained for each two-locus GxG interaction. The p-value columns list unadjusted p-values, while the FDR columns list p-values after adjustment for multiple comparisons. Significant GxG interactions, as judged by p-value or FDR less than 0.05, are labeled with asterisks. The first GxG interaction in the table was the optimal two-locus GxG interactions identified by the original MDR method with significant testing accuracy but insignificant CVC).
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