Table 1 Association analysis results for those SNPs associated with multiple autoimmune diseases in a cohort of patients with JIA

From: Association of the AFF3 gene and IL2/IL21 gene region with juvenile idiopathic arthritis

Marker

Chr

Gene a

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)

  1. Abbreviations: Chr, chromosome; HWE, P-value statistic for Hardy–Weinberg equilibrium test; JIA, juvenile idiopathic arthritis; MAF, minor allele frequency; SNP, single-nucleotide polymorphism.
  2. 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.
  3. 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.
  4. aThe gene name refers to the nearest gene in the region although SNPs are not necessarily intra-genic.
  5. bUK 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
  6. cHealthy 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.
  7. dGenotype 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.
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