Table 5.
Two-locus GxG interactions among 7 SNPs assessed by A-MDR
| 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 |
(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).