Table 2.
Genetic variants associated with anti-TNF response in patients with IBD and their effect size.
| Genetic variants [minor/ major allele] | Discovery cohort MAF [NR vs R] | Replicate cohort MAF [NR vs R] | Combined cohort MAF [NR vs R] | OR [95% CI] | Adjusted OR [95% CI] |
|---|---|---|---|---|---|
| Position | Allelic OR [95% CI] | Allelic OR [95% CI] | Allelic OR [95% CI] | [Additive mode] | |
| Candidate gene | p-Value | p-Value | p-Value | p-Value | p-Value |
| rs116724455 [C/T] | 0.07 vs 0.005 | 0.06 vs 0.002 | 0.06 vs 0.003 | ||
| chr01:173,191,085 | 13.8 [2.26–85.4] | 27.3 [2.42–309] | 18.6 [4.38–79.6] | 19.9 [4.57–86.7] | 43.1 [6.98–266] |
| TNFSF4, TNFSF18 | p = 2.43E-04 | p = 6.28E-06 | p = 5.37E-08 | p = 4.79E-08 | p = 1.14E-04 |
| rs2228416 [T/C] | 0.11 vs 0.02 | 0.14 vs 0.03 | 0.12 vs 0.03 | ||
| chr09: 19,126,281 | 5.97 [1.87–19.1] | 5.21 [1.76–15.4] | 5.33 [2.43–11.7] | 5.25 [2.33–11.8] | 5.42 [2.05–14.3] |
| PLIN2,HAUS6 | p = 7.17E-04 | p = 9.87E-04 | p = 3.76E-06 | p = 5.24E-06 | p = 1.62E-03 |
| rs762787 [T/C] | 0.17 vs 0.04 | 0.19 vs 0.07 | 0.18 vs 0.06 | ||
| chr03: 46,488,936 | 4.74 [1.92–11.7] | 3.39 [1.37–8.35] | 3.82 [2.03–7.17] | 4.27 [2.16–8.48] | 5.04 [2.23–11.4] |
| LTF, CCR5, CCRL2 | p = 2.46E-04 | p = 5.22E-03 | p = 9.51E-06 | p = 6.47E-06 | p = 1.95E-04 |
| rs9572250 [G/A] | 0.45 vs 0.19 | 0.39 vs 0.21 | 0.43 vs 0.20 | ||
| chr13: 70,302,178 | 3.52 [1.87–6.63] | 2.39 [1.18–4.84] | 2.94 [1.84–4.70] | 3.00 [1.84–4.89] | 3.24 [1.80–5.85] |
| KLHL1 | p = 4.30E-05 | p = 0.01 | p = 2.84E-06 | p = 3.19E-06 | p = 7.71E-05 |
| rs144256942 [G/A] | 0.07 vs 0.003 | 0.06 vs 0.01 | 0.06 vs 0.007 | ||
| chr01: 213,732,082 | 27.8 [2.83–273] | 5.42 [1.01–28.9] | 9.30 [2.77–31.2] | 9.88 [2.88–33.9] | 10.2 [2.26–46.4] |
| PROX1,RPS6KC1 | p = 1.97E-05 | p = 0.02 | p= 1.27E-05 | p = 1.14E-05 | p = 4.41E-03 |
| rs523781 [G/C] | 0.20 vs 0.06 | 0.14 vs 0.06 | 0.17 vs 0.06 | ||
| chr09: | 3.81 [1.65- | 2.73 [0.98- | 3.36 [1.77- | 3.97 | 4.90 [2.02- |
| 77,323,239 | 8.80] | 7.60] | 6.39] | [1.95–8.07] | 11.9] |
| RORB,TRPM6 | p = 8.84E-04 | p = 0.04 | p = 9.79E-05 | p = 5.28E-05 | p = 7.81E-04 |
Abbreviations: A, adenine; C, cytosine; chr, chromosome; G, guanine; MAF, minor allele frequency; NR, no response; OR, odds ratio; R, response; T, thymine; TNF, tumour necrosis factor; CI, confidence interval,IBD, inflammatory bowel disease.