Table 9. .
Diplotype Analysis for the IL23R SNPs rs7530511 and rs11209026
| Discovery Sample SetGlobala P=.033 |
Replication 1 Sample SetGlobala P=8.47×10-6 |
Replication 2 Sample SetGlobala P=.009 |
Combined AnalysisGlobalb P=5.45×-7 |
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| No. (%) of |
No. (%) of |
No. (%) of |
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| Diplotypec | Cases | Controls | OR | Pd | Cases | Controls | OR | Pd | Cases | Controls | OR | Pd | ORcommon(95% CI)e | Pcombf |
| C-G/C-G | 340 (.728) | 288 (.626) | 1.60 | 9.58×10−4 | 357 (.717) | 316 (.635) | 1.46 | 6.73×10−3 | 350 (.728) | 279 (.658) | 1.39 | .025 | 1.48 (1.26–1.74) | 2.24×10−5 |
| C-G/T-G | 84 (.180) | 112 (.243) | .68 | .020 | 81 (.163) | 90 (.181) | .88 | .502 | 94 (.195) | 81 (.191) | 1.03 | .933 | .85 (.70–1.02) | … |
| C-G/C-A | 33 (.071) | 43 (.093) | .74 | .232 | 45 (.090) | 72 (.145) | .59 | .010 | 30 (.062) | 43 (.101) | .59 | .037 | .63 (.49–.82) | .005 |
| C-G/T-A | 0 | 0 | … | … | 0 | 0 | … | … | 0 | 0 | … | … | … | … |
| C-A/C-A | 2 (.004) | 2 (.004) | .98 | 1 | 1 (.002) | 5 (.010) | .20 | .217 | 1 (.002) | 2 (.005) | .44 | .602 | .43 (.08–1.38) | .667 |
| C-A/T-G | 4 (.009) | 8 (.017) | .47 | .260 | 7 (.014) | 7 (.014) | 1.00 | 1.000 | 2 (.004) | 9 (.021) | .19 | .029 | .52 (.24–1.00) | .136 |
| C-A/T-A | 0 | 0 | … | … | 2 (.004) | 0 | … | .499 | 0 | 0 | … | … | … | … |
| T-G/T-G | 4 (.009) | 7 (.015) | .56 | .382 | 5 (.010) | 8 (.016) | .62 | .579 | 4 (.008) | 10 (.024) | .35 | .102 | .49 (.23–.95) | .270 |
| T-G/T-A | 0 | 0 | … | … | 0 | 0 | … | … | 0 | 0 | … | … | … | … |
| T-A/T-A | 0 | 0 | … | … | 0 | 0 | … | … | 0 | 0 | … | … | … | … |
Because of small counts in some of the cells, as well as the distribution of these counts, global P values were obtained by performing a permutation procedure on the data and generating a log-likelihood ratio homogeneity statistic for each permutation. The convergence of the statistic to its limiting distribution was measured by plotting the first two central moments as a function of the number of replicates. When the number of replicates reached a number in which the error of the P value estimates from a subsequent modeling procedure was negligible (<1%), a gamma distribution was fit using maximum-likelihood estimates for the parameters. Integration of the resulting gamma distribution yielded the global P values.
Calculated using Fisher’s combined test.
Allele 1 rs7530511-allele 1 rs11209026/allele 2 rs7530511-allele 2 rs11209026.
Calculated using Fisher’s exact test.
Calculated using a Mantel-Haenszel common OR.
Calculated for diplotypes with the same effect (risk or protection) in all three sample sets, with use of Fisher’s combined test.