A large-scale rheumatoid arthritis genetic study identifies association at chromosome 9q33.2

Abstract

Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease affecting both joints and extra-articular tissues. Although some genetic risk factors for RA are well-established, most notably HLA-DRB1 and PTPN22, these markers do not fully account for the observed heritability. To identify additional susceptibility loci, we carried out a multi-tiered, case-control association study, genotyping 25,966 putative functional SNPs in 475 white North American RA patients and 475 matched controls. Significant markers were genotyped in two additional, independent, white case-control sample sets (661 cases/1322 controls from North America and 596 cases/705 controls from The Netherlands) identifying a SNP, rs1953126, on chromosome 9q33.2 that was significantly associated with RA (OR(common) = 1.28, trend P(comb) = 1.45E-06). Through a comprehensive fine-scale-mapping SNP-selection procedure, 137 additional SNPs in a 668 kb region from MEGF9 to STOM on 9q33.2 were chosen for follow-up genotyping in a staged-approach. Significant single marker results (P(comb)<0.01) spanned a large 525 kb region from FBXW2 to GSN. However, a variety of analyses identified SNPs in a 70 kb region extending from the third intron of PHF19 across TRAF1 into the TRAF1-C5 intergenic region, but excluding the C5 coding region, as the most interesting (trend P(comb): 1.45E-06 --> 5.41E-09). The observed association patterns for these SNPs had heightened statistical significance and a higher degree of consistency across sample sets. In addition, the allele frequencies for these SNPs displayed reduced variability between control groups when compared to other SNPs. Lastly, in combination with the other two known genetic risk factors, HLA-DRB1 and PTPN22, the variants reported here generate more than a 45-fold RA-risk differential.

Figure 1. Case-control association results and linkage disequilibrium structure of the 9q33.2 region.

A physical map of the 668 kb surrounding the original associated SNP, rs1953126, with the location of all 138 markers genotyped in sample set 1 noted. The markers in red indicate the 43 SNPs genotyped in all three sample sets. The locations of LD Block 1 and LD Block 2 are indicated. Above the physical map, the trend P-values are displayed for the SNPs genotyped in each of the three sample sets. The red line indicates trend P = 0.01. The LD structure across the 668 kb region from MEGF9 to STOM, based on pairwise D' values from the CEU HapMap, is displayed below the physical map.

Figure 2. The LD architecture of the 9q33.2 region.

(A) Pairwise linkage disequilibrium values (r²) for all 138 SNPs genotyped in Sample Set 1. Cases and controls are shown separately. (B) Pairwise LD values between rs1953126 and each of the 137 other SNPs genotyped in Sample Set 1. Locations of the two main LD blocks are shown in bold. (C) SNPs within each of the two LD groups in Block 1. SNPs in black were genotyped in this study and are listed according to their position. SNPs in grey were not genotyped but highly correlated (r²>0.93) with either Group 1 or Group 2 SNPs in the CEU HapMap data. Note that all of the SNPs in grey lie in LD Block 1 between rs10985070 and rs2900180.

Figure 3. A five-SNP sliding window haplotype analysis of the 9q33.2 region.

Each sample set is shown separately with the combined analysis in bolded black. The approximate location of the PHF19, TRAF1, RAB14 and GSN genes are listed above.

Figure 4. Relative risk plotted as a function of the genetic load of three validated RA risk variants in HLA-DRB1, PTPN22 and TRAF1.

Individuals are classified according to the number of copies of the HLA-DRB1 shared epitope (0, 1 and 2) (SE-positive HLA-DRB1 alleles found in this sample set were: 0101, 0102, 0401, 0404, 0405, 0408 and 1001), carriage of the W620 PTPN22 missense SNP (TT + CT vs CC) and diplotypes at the TRAF1 SNPs, rs2239657, rs7021880 and rs7021049. The frequency of each combination of markers in cases and controls is highlighted in white (case/control).