Table 1.
Association analysis results for those SNPs associated with multiple autoimmune diseases in a cohort of patients with JIA
| Marker | Chr | Genea | HWE controls | Major allele/minor allele (1/2) | MAF cases | MAF controls | Genotype frequency cases (%)b | Genotype frequency controls (%)c | Trend test P-valued | Allelic OR (95% CI) | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 12 | 11 | 22 | 12 | 11 | |||||||||
| rs1160542 | 2 | AFF3 | 0.32 | A/G | 0.5 | 0.45 | 217 (23.7) | 483 (52.8) | 215 (23.5) | 574 (19.3) | 1493 (50.3) | 900 (30.3) | 2.05 × 10−5 | 1.25 (1.13–1.39) |
| rs3087243 | 2 | CTLA4 | 0.74 | G/A | 0.43 | 0.46 | 180 (19.7) | 428 (46.8) | 306 (33.5) | 634 (20.8) | 1523 (50.0) | 892 (29.3) | 0.05 | 0.9 (0.81–1.0) |
| rs6822844 | 4 | IL2/IL21 | 0.19 | G/T | 0.15 | 0.18 | 22 (2.3) | 232 (24.8) | 683 (72.9) | 125 (3.6) | 1003 (29.0) | 2326 (67.3) | 0.0006 | 0.78 (0.67–0.9) |
| rs6897932 | 5 | IL7R | 0.06 | C/T | 0.27 | 0.29 | 62 (6.6) | 377 (40.0) | 504 (53.4) | 267 (7.6) | 1482 (42.3) | 1756 (50.1) | 0.06 | 0.9 (0.8–1.01) |
| rs763361 | 18 | CD226 | 0.84 | C/T | 0.48 | 0.46 | 222 (23.5) | 464 (49.2) | 257 (27.3) | 745 (21.2) | 1750 (49.9) | 1012 (28.9) | 0.13 | 1.08 (0.98–1.2) |
Abbreviations: Chr, chromosome; HWE, P-value statistic for Hardy–Weinberg equilibrium test; JIA, juvenile idiopathic arthritis; MAF, minor allele frequency; SNP, single-nucleotide polymorphism.
A Bonferroni correction of five was applied to correct for the number of loci studied, resulting in a P-value threshold of 0.01 for claims of significance.
Genotyping was performed using the Sequenom iPLEX platform. A 90% sample quality control rate and 90% SNP genotyping success rate was imposed on the analysis.
The gene name refers to the nearest gene in the region although SNPs are not necessarily intra-genic.
UK Caucasian JIA patients (n=1054) from three sources. The British Society for Paediatric and Adolescent Rheumatology (BSPAR) National Repository of JIA (n=654), a cohort of UK Caucasian patients with long-standing JIA (n=201), described previously29 and a third cohort collected as part of the Childhood Arthritis prospective Study (CAPS), a prospective inception cohort study of JIA cases from five centres across United Kingdom (n=199).30
Healthy Caucasian control DNA samples were available from five centres in the United Kingdom as described previously31: Manchester, 924 controls (including 228 in 1958 birth cohort controls); Sheffield, 995 controls; Leeds 532 controls; Aberdeen 862 controls; Oxford 536 controls, total control sample size=3531.
Genotype and allele frequencies were compared between cases with JIA and controls using the Cochrane–Armitage trend test implemented in PLINK32 and allelic odds ratios (ORs) and their 95% confidence intervals (CIs) calculated.