| Literature DB >> 24449572 |
Gisela Orozco1, Sebastien Viatte, John Bowes, Paul Martin, Anthony G Wilson, Ann W Morgan, Sophia Steer, Paul Wordsworth, Lynne J Hocking, Anne Barton, Jane Worthington, Stephen Eyre.
Abstract
OBJECTIVE: The number of confirmed rheumatoid arthritis (RA) loci currently stands at 32, but many lines of evidence indicate that expansion of existing genome-wide association studies (GWAS) enhances the power to detect additional loci. This study was undertaken to extend our previous RA GWAS in a UK cohort, adding more independent RA cases and healthy controls, with the aim of detecting novel association signals for susceptibility to RA in a homogeneous UK cohort.Entities:
Mesh:
Year: 2014 PMID: 24449572 PMCID: PMC4285161 DOI: 10.1002/art.38196
Source DB: PubMed Journal: Arthritis Rheumatol ISSN: 2326-5191 Impact factor: 10.995
Previously confirmed rheumatoid arthritis (RA) loci association results in the original WTCCC association analysis and the expanded UK RA GWAS[*]
| Chr. | SNP | Gene | WTCCC study | Expanded UK RA GWAS | ||||
|---|---|---|---|---|---|---|---|---|
| Proxy | OR (95% CI) | Proxy | OR (95% CI) | |||||
| 1 | rs3890745 | 8.47 × 10−6 | 0.82 (0.75–0.89) | 1.43 × 10−6 | 0.85 (0.79–0.91) | |||
| 1 | rs2476601 | rs6679677 | 2.60 × 10−25 | 1.90 (1.68–2.15) | 4.87 × 10−33 | 1.77 (1.61–1.95) | ||
| 1 | rs11586238 | 4.13 × 10−4 | 1.19 (1.08–1.31) | rs4271251 | 6.47 × 10−3 | 1.11 (1.03–1.19) | ||
| 1 | rs12746613 | 0.04 | 1.14 (1.01–1.29) | 0.03 | 1.11 (1.01–1.22) | |||
| 1 | rs10919563 | 0.003 | 0.82 (0.72–0.94) | 7.18 × 10−5 | 0.82 (0.74–0.9) | |||
| 2 | rs13031237 | None | rs13031721 | 0.29 | 1.04 (0.97–1.11) | |||
| 2 | rs934734 | 0.10 | 0.93 (0.86–1.01) | 0.11 | 0.95 (0.89–1.01) | |||
| 2 | rs10865035 | rs9653442 | 5.48 × 10−4 | 1.16 (1.07–1.26) | rs1160542 | 1.37 × 10−5 | 1.15 (1.08–1.23) | |
| 2 | rs7574865 | rs11893432 | 0.02 | 1.13 (1.02–1.25) | rs10181656 | 6.64 × 10−4 | 1.14 (1.06–1.23) | |
| 2 | rs1980422 | 4.80 × 10−3 | 1.15 (1.04–1.26) | 1.75 × 10−4 | 1.15 (1.07–1.24) | |||
| 2 | rs3087243 | 0.09 | 0.93 (0.86–1.01) | 0.02 | 0.92 (0.87–0.99) | |||
| 3 | rs13315591 | 0.20 | 1.10 (0.95–1.26) | None | ||||
| 4 | rs874040 | None | rs6448432 | 3.88 × 10−7 | 1.19 (1.11–1.28) | |||
| 4 | rs6822844 | None | rs62322744 | 6.42 × 10−3 | 1.18 (1.05–1.32) | |||
| 5 | rs6859219 | 5.5 × 10−6 | 0.78 (0.70–0.87) | None | ||||
| 5 | rs26232 | rs556560 | 2.46 × 10−4 | 0.85 (0.78–0.93) | rs556560 | 9.64 × 10−5 | 0.88 (0.82–0.94) | |
| 6 | rs6910071 | rs6457617 | 3.49 × 10−79 | 0.44 (0.40–0.48) | rs3763309 | 1.50 × 10−124 | 2.3 (2.14–2.46) | |
| 6 | rs548234 | 0.01 | 1.12 (1.02–1.22) | 1.24 × 10−3 | 1.12 (1.04–1.19) | |||
| 6 | rs6920220 | 6.11 × 10−6 | 1.25 (1.13–1.37) | 3.11 × 10−8 | 1.23 (1.14–1.32) | |||
| 6 | rs394581 | 5.86 × 10−3 | 0.88 (0.80–0.96) | None | ||||
| 6 | rs3093023 | rs6907666 | 0.05 | 1.09 (1–1.18) | rs3093024 | 1.88 × 10−3 | 1.11 (1.04–1.18) | |
| 7 | rs10488631 | rs12531711 | 0.03 | 1.16 (1.02–1.31) | 3.10 × 10−3 | 1.16 (1.05–1.28) | ||
| 8 | rs2736340 | 8.01 × 10−3 | 1.14 (1.03–1.25) | 0.05 | 1.07 (1–1.15) | |||
| 9 | rs2812378 | 1.14 × 10−3 | 1.15 (1.06-1.26) | None | ||||
| 9 | rs3761847 | 0.80 | 0.99 (0.91–1.07) | 0.19 | 1.04 (0.98–1.11) | |||
| 10 | rs2104286 | 7.06 × 10−6 | 0.81 (0.73–0.89) | 1.46 × 10−6 | 0.84 (0.78–0.9) | |||
| 10 | rs4750316 | 5.22 × 10−5 | 0.80 (0.72–0.89) | 1.55 × 10−4 | 0.85 (0.78–0.93) | |||
| 11 | rs540386 | 0.04 | 0.88 (0.77–0.99) | rs1046864 | 0.01 | 0.89 (0.8–0.98) | ||
| 12 | rs1678542 | 2.81 × 10−5 | 0.83 (0.76–0.91) | 9.75 × 10−8 | 0.83 (0.78–0.89) | |||
| 20 | rs4810485 | 0.07 | 0.91 (0.83–1.01) | rs1569723 | 0.22 | 0.95 (0.89–1.03) | ||
| 22 | rs3218253 | 1.88 × 10−4 | 1.19 (1.09–1.31) | 2.51 × 10−4 | 1.15 (1.07–1.23) | |||
WTCCC = Wellcome Trust Case Control Consortium; GWAS = genome-wide association study; Chr. = chromosome; SNP = single-nucleotide polymorphism; OR = odds ratio; 95% CI = 95% confidence interval.
Figure 1Manhattan plots showing P values for genetic association with rheumatoid arthritis (RA) in the original Wellcome Trust Case Control Consortium genome-wide association study (GWAS) (a) and the expanded UK GWAS (b). Panels are truncated at a −log10P value of 35. Single-nucleotide polymorphisms having an association with RA at genome-wide levels of significance are shown above the horizontal red line.
Candidate rheumatoid arthritis (RA) susceptibility loci previously associated with other autoimmune diseases and showing suggestive evidence of association with RA in the expanded UK RA GWAS[*]
| Chr. | SNP | Locus | Assoicated autoimmune disease | Expanded UK RA GWAS | Validation study | Combined analysis | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MAF | OR (95% CI)[ | Proxy/comment | MAF | OR (95% CI) | ||||||||||
| RA | Controls | RA | Controls | OR (95% CI) | ||||||||||
| 7 | rs1047022 | T1D, IBD | 0.15 | 0.19 | 6.4 × 10−7 | 0.80 (0.74–0.88) | Failed QC | |||||||
| 11 | rs6421571 | PBC | 0.17 | 0.19 | 6.3 × 10−5 | 0.84 (0.78–0.92) | 0.18 | 0.19 | 0.02 | 0.90 (0.82–0.98) | 1.8 × 10−5 | 0.88 (0.83–0.93) | ||
| 12 | rs11181399 | MS | 0.40 | 0.45 | 2.5 × 10−7 | 0.8 (0.79–0.90) | rs7954523 | 0.39 | 0.39 | 0.96 | 0.99 (0.93–1.08) | 7.01 × 10−5 | 0.91 (0.87–0.95) | |
| 16 | rs7187962 | T1D | 0.27 | 0.31 | 8.6 × 10−6 | 0.85 (0.79–0.91) | rs6564350[ | 0.30 | 0.31 | 0.40 | 0.97 (0.89–1.05) | |||
| 19 | rs6417247 | IBD | 0.30 | 0.33 | 9.1 × 10−5 | 0.87 (0.82–0.93) | rs8112449 | 0.32 | 0.33 | 0.20 | 0.95 (0.88–1.03) | 1.5 × 10−3 | 0.93 (0.88–0.97) | |
| 22 | rs1043099 | CD, T1D | 0.18 | 0.21 | 7.8 × 10−6 | 0.83 (0.77–0.90) | 0.19 | 0.21 | 2.70 × 10−3 | 0.87 (0.80–0.95) | 6.9 × 10−9 | 0.84 (0.79–0.89) | ||
Associations were identified at the significance level of P < 0.0001. Chr. = chromosome; MAF = minor allele frequency; T1D = type 1 diabetes; IBD = inflammatory bowel disease; QC = quality control; PBC = primary biliary cirrhosis; MS = multiple sclerosis; CD = celiac disease.
Corrected P values (corrected for genetic inflation factor lambda) were as follows: for rs1047022, P = 1.42 × 10−6; for rs6421571, P = 1.07 × 10−4; for rs11181399, P = 5.86 × 10−7; for rs7187962, P = 1.628 × 10−5; for rs6417247, P = 1.50 × 10−4; for rs1043099, P = 1.49 × 10−5.
Association results in the original Wellcome Trust Case Control Consortium study were as follows: for rs1047022, P = 1.106 × 10−6, odds ratio (OR) 0.74 (95% confidence interval [95% CI] 0.66–0.84); for rs6421571, P = 0.02, OR 0.88 (95% CI 0.79–0.98); for rs11181399, P = 3.98 × 10−5, OR 0.83 (95% CI 0.76–0.91); for rs7187962, P = 7.07 × 10−6, OR 0.80 (95% CI 0.73–0.88); for rs6417247, P = 2.31 × 10−3, OR 0.87 (95% CI 0.79–0.95); for rs1043099, P = 1.65 × 10−4, OR 0.81 (95% CI 0.72–0.90).
Single-nucleotide polymorphism (SNP) rs6564350 was not present in the expanded UK RA genome-wide association study (GWAS) data set, and therefore combined analysis of this SNP could not be performed.
Figure 2Regional plot of association with rheumatoid arthritis (RA) at chromosome 22q12. The P values for association (−log10 values) of each single-nucleotide polymorphism (SNP) are plotted against their physical position on chromosome 22 (top panel). Estimated recombination rates from the 1000 Genomes Project population show the local linkage disequilibrium (LD) structure (middle panel). Different colors indicate the LD of each SNP with rs1043099, based on pairwise r2 values from the 1000 Genomes Project. Gene annotations are shown in the lower panel.
Potential regulatory role of the rheumatoid arthritis–associated single-nucleotide polymorphism (SNP) rs1043099 and its proxies[*]
| SNP | Relative location | Gene | Transcribed region | Histone modifications | TFBS | DNase I HS | FAIRE | CTCF binding | eQTL |
|---|---|---|---|---|---|---|---|---|---|
| rs2108093 | 3′ | Yes | Yes | Yes | Yes | Yes | |||
| rs1043099 | Exonic, 3′-UTR | Yes | Yes | Yes | Yes | Yes | |||
| rs4823085 | 5′ | Yes | Yes | Yes | Yes | Yes | Yes | Yes | |
| rs929454 | Intronic | Yes | Yes | Yes | Yes | Yes | |||
| rs4820831 | Intronic | Yes | Yes | Yes | Yes | Yes | Yes | ||
| rs740219 | Intronic | Yes | Yes | Yes | Yes | Yes | |||
| rs5753071 | 3′ | Yes | Yes | Yes | Yes | Yes | |||
| rs10376 | Exonic, 3′-UTR | Yes | Yes | Yes | Yes | Yes | |||
| rs2041199 | Intronic | Yes | Yes | Yes | Yes | ||||
| rs4339043 | Intronic | Yes | Yes | Yes | Yes | Yes | |||
| rs5749066 | Intronic | Yes | Yes | Yes | Yes | Yes | |||
| rs5753080 | Intronic | Yes | Yes | Yes | |||||
| rs10427610 | Intronic | Yes | Yes | Yes | Yes | Yes | Yes | ||
| rs4820008 | Intronic | Yes | Yes | Yes | |||||
| rs737950 | Intronic | Yes | Yes | Yes | |||||
| rs5749078 | Intronic | Yes | Yes | Yes | Yes | ||||
| rs9619104 | 3′ | Yes | Yes | Yes | Yes |
Proxies of rs1043099 were correlated at r2 > 0.8. Results are the summary output from the Assimilator bioinformatics analysis. TFBS = transcription factor binding site; HS = hypersensitive sites; FAIRE = open chromatin by formaldehyde-assisted isolation of regulatory elements; CTCF = CCCTC binding factor; eQTL = expression quantitative trait loci; 3′-UTR = 3′-untranslated region.