Common variants at CD40 and other loci confer risk of rheumatoid arthritis

Abstract

To identify rheumatoid arthritis risk loci in European populations, we conducted a meta-analysis of two published genome-wide association (GWA) studies totaling 3,393 cases and 12,462 controls. We genotyped 31 top-ranked SNPs not previously associated with rheumatoid arthritis in an independent replication of 3,929 autoantibody-positive rheumatoid arthritis cases and 5,807 matched controls from eight separate collections. We identified a common variant at the CD40 gene locus (rs4810485, P = 0.0032 replication, P = 8.2 x 10(-9) overall, OR = 0.87). Along with other associations near TRAF1 (refs. 2,3) and TNFAIP3 (refs. 4,5), this implies a central role for the CD40 signaling pathway in rheumatoid arthritis pathogenesis. We also identified association at the CCL21 gene locus (rs2812378, P = 0.00097 replication, P = 2.8 x 10(-7) overall), a gene involved in lymphocyte trafficking. Finally, we identified evidence of association at four additional gene loci: MMEL1-TNFRSF14 (rs3890745, P = 0.0035 replication, P = 1.1 x 10(-7) overall), CDK6 (rs42041, P = 0.010 replication, P = 4.0 x 10(-6) overall), PRKCQ (rs4750316, P = 0.0078 replication, P = 4.4 x 10(-6) overall), and KIF5A-PIP4K2C (rs1678542, P = 0.0026 replication, P = 8.8 x 10(-8) overall).

Figure 1

Enrichment of SNPs with z scores >2 in replication samples. For each of the 31 SNPs tested, we calculated a one-sided CMH z-score statistic from our two-staged replication data. Results were calculated using either stage 1 replication samples only (n = 14 SNPs) or using both stage 1 and 2 replication samples (n = 17 SNPs). A z score of 0 corresponds to a P value of 0.5, and a z score of 1.65 corresponds to a P value of 0.05. For a random collection of unassociated SNPs, this histogram should approximate a normal distribution (dotted line).

Figure 2

CD40 region and association with rheumatoid arthritis. (a) Observed association within a 400-kb region surrounding the CD40 locus in meta-analysis of three GWA datasets. We plot the meta-analysis P value on the y axis versus genomic position on chromosome 20 on the x axis. Best associated SNP was rs4810485 (large red diamond). Other data points are shaded with increasing red intensity to suggest LD to rs4810485: dark red signifies r² ≥ 0.8, orange 0.8 > r² ≥ 0.5, gray 0.5 > r² ≥ 0.2, and white r² < 0.2. In two-tailed joint analysis including all 11 collections, the SNP was strongly associated with risk of rheumatoid arthritis (P = 8.2 × 10⁻⁹, large blue diamond). Along the bottom of the figure we plot the recombination rate with the CEU HapMap (light blue line) and have indicated known human genes (black arrows). (b) The LD structure for a 200-kb region (indicated by dark blue bar along the x axis in a) surrounding the rs4810485 SNP (red arrow). The rs4810485 SNP is located in the second intron of CD40. LD between SNPs is indicated by the redness of individual spots in the triangular graphic, the most intense red spots have a D′ = 1. (c) Forest plot for rs4810485 association across 11 collections. For each sample collection we plot the odds ratio (small diamond) and the 95% CI. A light dashed line indicates the final odds ratio across all collections. The top three bars (green) represent GWA data and the diamond below them summarizes their meta-analyzed effect. The next eight bars (red) represent replication data and the diamond below them summarizes their meta-analyzed effect. The final diamond at the bottom of the page (clear) represents the final meta-analysis odds ratio and the 95% CI for all 11 collections.

Figure 3

CCL21 region and association with rheumatoid arthritis. (a) Observed association in the 400-kb region surrounding the CCL21 locus in meta-analysis of three GWA datasets; plot characteristics are similar to those in Figure 2. Best associated SNP was rs2812378 (large red diamond). In two-tailed joint analysis including all 11 collections this SNP was associated with rheumatoid arthritis at P = 2.8 × 10⁻⁷ (large blue diamond). (b) The LD structure for a 200-kb region surrounding the rs2812378 SNP (red arrow). The rs2812378 SNP is located close to the 5′end of the CCL21. (c) Forest plot for rs2812378 association across 11 collections.