Additional file 1: Table S1. of Usefulness of the SF-36 Health Survey in screening for depressive and anxiety disorders in rheumatoid arthritis

Title of data – SF36 Mental Health (MH) and Mental Component Summary (MCS) scores as predictors of pMDD, pGAD or any psycholgical disorder (pMDD or pGAD) according to PHQ9 or GAD7 criteria. Description of data – summary of all potential thresholds identified for indicating presence of pMDD or pGAD, along with relevant sensitivity and specificity data. (DOCX 17 kb

Analysis of association of <i>PTPN22</i> ‘haplotype 6–10’ group (<i>rs12144309</i>: C&gt;T) with rheumatoid arthritis.

<p>1. Cases top line, controls bottom line. The NZ controls deviated mildly from HWE (<i>P</i> = 0.02).</p><p>2. Imputed genotypes were taken from <a href="http://www.wtccc.org.uk" target="_blank">www.wtccc.org.uk</a>.</p><p>3. The Mantel-Haenszel combined OR = 0.90 [0.82–0.98], <i>P</i> = 0.021. The Breslow-Day test for heterogeneity <i>P</i> = 0.90.</p

Haplotype structure of structure of a portion of the <i>PTPN22</i> haplotype block.

<p>The figure was generated by Haploview using Phase 2 CEPH CEU HapMap data downloaded from <a href="http://www.hapmap.org" target="_blank">www.hapmap.org</a>, with the boundaries being <i>rs4145859</i> (114.312 Mb) and <i>rs10745340</i> (114.437 Mb).</p

Analysis of association of <i>PTPN22</i> ‘haplotype 5’ (<i>rs3789607</i>: T&gt;C) with rheumatoid arthritis.

<p>1 Cases top line, controls bottom line. The Carlton Set 2 cases and controls, the combined other cases and total cases deviated mildly from HWE (<i>P</i> = 0.02, 0.03, 0.05 and 0.02, respectively).</p><p>2 Allele 2; number of chromosomes (frequency).</p><p>3 Genotype data from <i>rs17274634</i> were used (r² = 1 with <i>rs3789607</i> in CEPH CEU (<a href="http://www.hapmap.org" target="_blank">www.hapmap.org</a>)).</p><p>4 The Mantel-Haenszel pooled OR = 0.87 [0.82–0.93], <i>P</i> = 7.5×10⁻⁶; Breslow-Day test for heterogeneity <i>P</i> = 0.083. The Mantel-Haenszel pooled OR excluding Carlton et al data was 0.91 [0.85–0.98], <i>P</i> = 0.016; Breslow-Day <i>P</i> = 0.50.</p

Analysis of association of <i>PTPN22</i> ‘haplotype 4’ (<i>rs3811021</i>: A&gt;G) with rheumatoid arthritis.

<p>1 Cases top line, controls bottom line.</p><p>2 Imputed genotypes were taken from <a href="http://www.wtccc.org.uk" target="_blank">www.wtccc.org.uk</a>.</p><p>3 The Mantel-Haenszel combined OR  = 0.85 [0.72–1.01], <i>P</i> = 0.071. The Breslow-Day test for heterogeneity <i>P</i>&lt;0.001.</p

Prediction model receiver operating characteristic curves.

<p>Panel A = WTCCC; Panel B = UKRAGG; ROCs calculated for discriminating between ACPA-positive RA and controls; AUC = area under the curve. WTCCC model AUC comparisons: SNP versus HLA, <i>P</i><0.0001; HLA versus HLA-SNP, <i>P</i> = 0.0118; HLA-SNP versus HLA-Smoking, <i>P</i> = 0.3327; HLA-Smoking versus HLA-SNP-Smoking, <i>P</i> = 0.0001. UKRAGG model AUC comparisons: SNP versus HLA, <i>P</i><0.0001; HLA versus HLA-SNP, <i>P</i> = 0.665; HLA-SNP versus HLA-Smoking, <i>P</i> = 0.0145; HLA-Smoking versus HLA-SNP-Smoking, <i>P</i> = 0.1671.</p

Relationship between modelling components and age of RA onset.

a<p> = HLA and SNP variables represent the summary OR scores generated by the models incorporating HLA and SNP data respectively;</p>b<p> = variables included in UKRAGG multivariate model after variable pruning using backwards selection and model comparison with Akaike's Information Criterion;</p>c<p> = as only one parameter was significant in the WTCCC univariate analysis no multivariate model was fitted.</p

<i>Rs2476601-rs12566340</i> haplotypic analysis.

<p>1. Within each cell in the RA half, NZ data are top, WTCCC data middle and combined bottom.</p

Non-HLA RA susceptibility SNP allele frequencies and their association with seropositive RA in WTCCC and UKRAGG.

<p>SNPs are ordered by significance (most significant by <i>P</i>_GWAS listed first); all alleles attained genome-wide significance in the published meta-analysis; Ca = Cases; Co = Controls; MAF = Minor Allele Frequency;</p>a<p> = MAF in controls.</p

Classical <i>HLA-DRB1</i> allele frequencies and their association with seropositive RA in WTCCC and UKRAGG.

<p>All alleles attained genome-wide significance in the published meta-analysis; MAF = minor allele frequency; Co = controls; Ca = Cases;</p>a<p> = OR incalculable due to no allele copies in the control group.</p