Table 2.
Location, minor allele frequencies (MAF), odds ratios (OR), 95% confidence intervals (95% CI), and P-values from allelic tests in stage 1.
| Location (bp) | Marker | Allele | SLE MAF | Controls MAF | OR (95% CI) | P |
|---|---|---|---|---|---|---|
| 10871619 | rs6498114 | G | 0.223 | 0.254 | 0.85 (0.72–0.99) | 0.04 |
| 10879381 | rs12932187 | G | 0.056 | 0.066 | 0.85 (0.64–1.12) | 0.24 |
| 10889846 | rs8043545 | C | 0.242 | 0.280 | 0.82 (0.71–0.96) | 0.01 |
| 10899453 | rs4781015 | A | 0.184 | 0.219 | 0.81 (0.68–0.95) | 0.01 |
| 10900989 | rs7189406 | G | 0.062 | 0.069 | 0.90 (0.69–1.17) | 0.46 |
| 10903900 | rs4781016 | A | 0.289 | 0.270 | 1.10 (0.95–1.27) | 0.20 |
| 10908349 | rs4774 | C | 0.313 | 0.268 | 1.24 (1.07–1.44) | 4.2×10−3 |
| 10911864 | rs6498126 | G | 0.204 | 0.207 | 0.98 (0.84–1.16) | 0.81 |
| 10924559 | rs4781024 | A | 0.429 | 0.413 | 1.07 (0.93–1.22) | 0.34 |
We tested allelic association by creating 2x2 contingency tables and estimating odds ratios (OR) with Fisher’s exact test (PLINK). A significance threshold was set in stage 1 (P = 5.56×10−3) using a Bonferroni correction for the number of independent tests. Analyses were stratified by DRB1*03:01. P-values reported for the allelic association tests were empirically based on 10,000 permutations and were two-tailed. Empirical P-values were estimated by permuting tests, counting the number of times the permuted test was greater than the observed test, and dividing by the total number of simulations (10,000). Interaction between DRB1*03:01 risk alleles and CIITA variants were assessed in PLINK using logistic regression. The predictor was the CIITA variant and the outcome was presence of the DRB1*03:01 allele. The case-only gene x gene interaction test was applied to improve power, and the assumption of linkage equilibrium between DRB1*03:01 and CIITA was fulfilled.40,41 PLINK (maxT permutation procedure) was used to permute the ordering of the outcome status. In stage 1 of this study in the overall sample there was 80% power to detect an OR ranging from 1.4 to 1.5, based on power estimations in PGA v2.0 (Bethesda, MD, USA; minor allele frequency 0.1–0.5, two-sided α = 5.56×10−3).
In the current study, genotypes for the-168A/G promoter polymorphism (rs3087456) were not available. However, strong LD (r2 > 0.90) exists between rs3087456 and nearby rs12928665, as reported for a sample of independent healthy controls.4 Genotypes for rs12928665 were available for all cases and the stage 1 controls, and did not provide evidence of association.