Meta-analysis confirms association between TNFA-G238A variant and JIA, and between PTPN22-C1858T variant and oligoarticular, RF-polyarticular and RF-positive polyarticular JIA.

Merlyn J Kaalla,Kelly Rouster-Stevens,April Whiting,Karen N Conneely,Lori Ponder,Milton R Brown,John F Bohnsack,K Alaine Broadaway,Sampath Prahalad,Larry B Vogler,Lynn B Jorde,Sheila Angeles-Han,Mina Rohani-Pichavant,Michael P Epstein,David T Okou

doi:10.1186/1546-0096-11-40

Abstract

BackgroundAlthough more than 100 non-HLA variants have been tested for associations with juvenile idiopathic arthritis (JIA) in candidate gene studies, only a few have been replicated. We sought to replicate reported associations of single nucleotide polymorphisms (SNPs) in the PTPN22, TNFA and MIF genes in a well-characterized cohort of children with JIA.MethodsWe genotyped and analyzed 4 SNPs in 3 genes: PTPN22 C1858T (rs2476601), TNFA G-308A, G-238A (rs1800629, rs361525) and MIF G-173C (rs755622) in 647 JIA cases and 751 healthy controls. We tested for association between each variant and JIA as well as JIA subtypes. We adjusted for multiple testing using permutation procedures. We also performed a meta-analysis that combined our results with published results from JIA association studies.ResultsWhile the PTPN22 variant showed only modest association with JIA (OR = 1.29, p = 0.0309), it demonstrated a stronger association with the RF-positive polyarticular JIA subtype (OR = 2.12, p = 0.0041). The MIF variant was not associated with the JIA as a whole or with any subtype. The TNFA-238A variant was associated with JIA as a whole (OR 0.66, p = 0.0265), and demonstrated a stronger association with oligoarticular JIA (OR 0.33, p = 0.0006) that was significant after correction for multiple testing. TNFA-308A was not associated with JIA, but was nominally associated with systemic JIA (OR = 0.33, p = 0.0089) and enthesitis-related JIA (OR = 0.40, p = 0.0144). Meta-analyses confirmed significant associations between JIA and PTPN22 (OR 1.44, p <0.0001) and TNFA-238A (OR 0.69, p < 0.0086) variants. Subtype meta-analyses of the PTPN22 variant revealed associations between RF-positive, RF-negative, and oligoarticular JIA, that remained significant after multiple hypothesis correction (p < 0.0005, p = 0.0007, and p < 0.0005, respectively).ConclusionsWe have confirmed associations between JIA and PTPN22 and TNFA G-308A. By performing subtype analyses, we discovered a statistically-significant association between the TNFA-238A variant and oligoarticular JIA. Our meta-analyses confirm the associations between TNFA-238A and JIA, and show that PTPN22 C1858T is associated with JIA as well as with RF-positive, RF-negative and oligoarticular JIA.

Highlights

More than 100 non-human leukocyte antigens (HLA) variants have been tested for associations with juvenile idiopathic arthritis (JIA) in candidate gene studies, only a few have been replicated
The PTPN22 variant has been investigated for an association with JIA in seven other case-control comparisons (Table 3) [6,8,10,11,12,25,26]
The pooled meta-analysis confirmed a strong association between JIA and PTPN22 with an odds ratios (OR) of 1.44, p < 0.0001 (Figure 1, Table 4)

Summary

Introduction

More than 100 non-HLA variants have been tested for associations with juvenile idiopathic arthritis (JIA) in candidate gene studies, only a few have been replicated. While associations between JIA and variants in HLA are well established, non-HLA genetic variants play a role in JIA susceptibility, and have increasingly been identified by genome-wide and candidate gene studies [4,5,6]. Of nearly 100 non-HLA polymorphisms tested for associations with JIA by candidate gene studies, only a handful of associations have been replicated in independent cohorts [2,5,7,8]. The International JIA Immunochip consortium has confirmed many of the genetic associations and identified several new loci with genome-wide evidence for association [9]

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