Extended report Previous studies of the PTPN22*C1858T SNP have revealed stronger associations in patients with a family history of disease and in patients with a younger age at onset suggesting that this polymorphism, too, may be associated more with severity than susceptibility.3 10 However, these studies were cross-sectional in nature and subject to the methodological biases outlined. Only one study has examined an inception cohort followed prospec- tively.11 They reported no association with remission or rates of RA joint destruction but an association between PTPN22*1858T risk allele and autoantibody production was noted. We have used the opportunity afforded by the NOAR cohort to address the question of firstly, whether other variants spanning the PTPN22 gene are associated with susceptibility to IP and, secondly, whether any is associated with outcome of disease. MATERIALS AND METHODS Study design SNP variants spanning the PTPN22 gene were tested firstly for their association with susceptibility to IP by comparing genotype and allele frequencies between new onset IP cases with population controls. Secondly, a within-cohort analysis was performed testing each variant for association with a number of clinical outcome measures reflecting disease severity including presence of radiological erosions, physical function as measured using the Health Assessment Questionnaire (HAQ) score and disease activity at defined time-points following disease presentation.12 Study population Cases were recruited from NOAR, a primary care-based cohort of subjects with new onset IP.13 In brief, NOAR aims to recruit all new adult attendees at primary care with IP, defined as swelling of two or more joints, lasting .4 weeks, after exclusion of diagnoses other than undifferentiated IP, post-viral IP, RA or psoriatic arthritis. Subjects are assessed by trained metrologists, within 2 weeks of referral, using a standardised approach. Data gathered included joint counts for swelling and tenderness. Blood was taken for serum analysis (rheumatoid factor (RF), C-reactive protein (CRP) and anti-cyclic citrinulated peptide (CCP) testing) and DNA extraction. Subjects were followed up annually thereafter.13 The 1987 criteria for RA were applied at every visit and subjects classified as having RA if they had cumulatively satisfied the criteria by that time point.14 At baseline and annually thereafter the subjects completed the eight-domain HAQ. Radiographs of the hands and feet were obtained at 1 and/or 5 years. The criteria for requesting radiographs and the scoring process have been published previously.15 The radiographs were read by two readers (with arbitration by a third where necessary) using the Larsen method.16 For the purposes of this study, consecutive patients recruited between 1990 and 1994 who had a DNA sample available were selected. Data for unmatched control individuals recruited from Norfolk general practitioners’ records or from blood donors were available and have been reported previously.7 All subjects were of UK Caucasoid origin. The study was conducted with ethical approval (LREC 2003-075, MREC 99/8/84) and all patients gave their informed consent. Serological tests Baseline serum samples were assayed for RF was using a latex method and a titre of >1:40 was regarded as positive. CRP was 252 measured using nephelometry (http://www.bmglabtech.com/ templates/applications). Anti-CCP testing was performed using the Axis-ShieldH DIASTATTM kit according to manufacturer’s instructions and a result of .5 U/ml was regarded as positive (Axis-Shield, Dundee, UK). Genotyping Thirteen SNPs spanning the PTPN22 gene were selected for investigation. These included the PTPN22*C1858T polymorph- ism, seven tagging SNPs and two of three potentially functional polymorphisms identified by Carlton et al.6 The third SNP, rs3789604 (SNP 37), was not selected for genotyping because of the strong LD exhibited between this and another of the selected SNPs, rs3811021 (SNP 36). Genotyping was undertaken using the SequenomH iPLEX platformTM, according to the manufacturer’s instructions17 (http://www.sequenom.com). Samples were plated onto 26384-well plates. Duplicate samples and negative controls were included to check genotyping quality. For the PTPN22*C1858T (rs2476601, R620W) SNP, additional samples from the cohort had been genotyped in- house previously and that data was included in the current analysis. Only SNPs that were successfully genotyped in .90% samples were included in the analysis. Statistical analysis Genotype and allele carriage frequencies for each SNP were compared between cases and controls using the x2 test for trend and odds ratios (OR) with 95% confidence interval (CI), respectively. Given the linkage disequilibrium known to exist across the gene, logistic regression was undertaken conditioned on the effect of the associated SNP, rs2476601 (R620W). Estimated haplotypes were constructed in Haploview v3.218 and frequencies compared between cases and controls. For the within-cohort analysis of association with disease severity, a number of measures were assessed reflecting disease activity (CRP at baseline, swollen joint count at baseline and at 5 years following presentation), severity (presence of erosions by 1 and 5 years, Larsen score by 1 and 5 years, presence of anti- CCP antibodies and RF at baseline) and disability (HAQ score). Categorical data (erosions by 1 and 5 years, anti-CCP and RF) were analysed using the x2 test while continuous variables were analysed using the Mann–Whitney U test. All analyses were performed in the cohort as a whole and in the subset of patients fulfilling American College of Rheumatology (ACR) criteria for RA by 5 years using STATAH (StataCorp LP, College Station, Texas, USA). For the PTPN22*C1858T SNP, there was a clear a priori hypothesis for testing for association with IP and so no correction was made for multiple testing. However, for the other SNPs tested, the prior probability of detecting association was small and a Bonferroni correction of 12 was applied to correct for number of SNPs tested. RESULTS Subjects In total, 1098 patients were recruited to NOAR between 1990 and 1994 and a DNA sample was available from 843 of them. However, for the majority of SNPs, only 750 samples were tested. Clinical characteristics of the cases are detailed in table 1 and are similar to those reported previously from the NOAR cohort.14 The median age at onset of IP was 53 (interquartile range (IQR) 40–65), 539 (64%) were female and 79.4% had been referred to hospital (secondary care) following onset of their Ann Rheum Dis 2008;67:251–255. doi:10.1136/ard.2007.071894