| Literature DB >> 17665434 |
I Marinou1, J Healy, D Mewar, D J Moore, M C Dickson, M H Binks, D S Montgomery, K Walters, A G Wilson.
Abstract
OBJECTIVE: Recent evidence has highlighted a major genetic contribution to radiographic damage in rheumatoid arthritis (RA). The objective of this study was to determine whether genetic variants in the loci for interleukin-1 (IL-1), IL-6, IL-10, protein tyrosine phosphatase N22 (PTPN22), and selenoprotein S are associated with radiographic damage.Entities:
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Year: 2007 PMID: 17665434 PMCID: PMC2435416 DOI: 10.1002/art.22814
Source DB: PubMed Journal: Arthritis Rheum ISSN: 0004-3591
Details of individual single-nucleotide polymorphisms (SNPs)
| SNP number | Gene | Description |
|---|---|---|
| rs17561 | Ser114Ala | |
| rs16944 | Promoter (−511) | |
| rs1143634 | Synonymous coding, Phe105Phe | |
| rs419598 | Synonymous coding, Ala39Ala | |
| rs1800872 | Promoter (−592) | |
| rs1800896 | Promoter (−1082) | |
| rs1800795 | Promoter (−174) | |
| rs2476601 | Arg620Trp | |
| Not applicable | 5′-untranslated region | |
| rs4965814 | Intron 5 | |
| rs4965373 | 3′-untranslated region |
Sequences and concentrations of oligonucleotide primers and probes, and annealing temperatures used in polymerase chain reactions for TaqMan-based genotyping*
| SNP | Forward primer, 5′→3′ | μ | Reverse primer, 5′→3′ | μ | Probe, 5′→3′ | μ | Temp. |
|---|---|---|---|---|---|---|---|
| CCAGCTTCCTCAACCACAATAAATG | 36 | CAACTGCTCCAAGGATAGATGATGA | 36 | VIC–TCAGGTGTCCATACAGG | 8 | 60°C | |
| FAM–TCAGGTGTCCGTACAGG | 8 | ||||||
| GTCTCTACCTTGGGTGCTGTTC | 36 | GAGGCTCCTGCAATTGACAGA | 36 | VIC–TCTGCCTCAGGAGCT | 8 | 60°C | |
| FAM–CTGCCTCGGGAGCT | 8 | ||||||
| ACCTAAACAACATGTGCTCCACA | 36 | ATCGTGCACATAAGCCTCGTTA | 36 | VIC–CATGTGTCGAAGAAGA | 8 | 60°C | |
| FAM–CATGTGTCAAAGAAGA | 8 | ||||||
| TCTGCACTTGTGATCATGGTTTTAGA | 36 | TGTATTTCACATTGCTCAGGAAGCT | 36 | VIC–CTAGGTCAGCACCTTT | 8 | 60°C | |
| FAM–CCTAGGTCATCACCTTT | 8 | ||||||
| GGGATGTTAACCAGAAGACCTTCTATCT | 25 | CAACCACTCACCTTCTAAATTGACATT | 25 | TET–ACAACCAACTAGTTGCCGGATACTTGC | 17.5 | 64°C | |
| FAM–AACAACCAACTAGTTGCTGGATACTTGCAA | 5 | ||||||
| GGTAAAGGAGCCTGGAACACATC | 36 | GCCCTTCCATTTTACTTTCCAGAGA | 36 | VIC–CCCGCCTGTACTGTAG | 85 | 60°C | |
| FAM–CCGCCTGTCCTGTAG | 8 | ||||||
| GATAGGAGGTCCCTTACTTTCCTCTTA | 5 | CACACACAAATCCAAGACAACACTAC | 30 | TET–CCTACTTCCCCTTCCCAAAGAAGCC | 15 | 63°C | |
| FAM–CTACTTCCCCCTCCCAAAGAAGCCT | 5 | ||||||
| GACGACCTAAGCTGCACTTTTC | 36 | GGGCTGATTGGAAACCTTATTAAGATTG | 36 | VIC–CTTTAGCATGGCAAGAC | 8 | 60°C | |
| FAM–CTTTAGCATCGCAAGAC | 8 | ||||||
| GCCAGGTTTAGTCTTCTGACACAAA | 36 | AGCAGGGCCACAGACTTG | 36 | VIC–CTGACCTTAAACGCTGAGC | 8 | 60°C | |
| FAM–CTGACCTTAAACACTGAGC | 8 | ||||||
| TTGCCAGACTTATTTTGGGTGAGT | 36 | TTCAAGGAGATTTATGGACTTCAATTTGTCT | 36 | VIC–TTTTTATTACAACCTCTAACTATT | 8 | 60°C | |
| FAM–TTACAACCTCCAACTATT | 8 |
SNP = single-nucleotide polymorphism; temp. = temperature.
Baseline clinical characteristics of the patients with rheumatoid arthritis*
| No. of patients | 964 |
| Age, mean ± SD years | 61.3 ± 12.3 |
| Disease duration, mean ± SD years | 15.6 ± 10.7 |
| Female sex, no. (%) | 695 (72.1) |
| Male sex, no. (%) | 269 (27.9) |
| Rheumatoid factor positive, no. (%) | 604 (68.4) |
| Rheumatoid factor negative, no. (%) | 279 (31.6) |
| Anti–cyclic citrullinated peptide positive, no. (%) | 697 (76.3) |
| Anti–cyclic citrullinated peptide negative, no. (%) | 217 (23.7) |
Rheumatoid factor status was determined in 883 patients, while antibody status was determined in 914 patients.
Genotypes and modified Larsen scores of radiographic damage
| Gene | Genotype | Patients, no. (%) | Median modified Larsen score | |
|---|---|---|---|---|
| TT | 31 (3.4) | 50.0 | ||
| TC | 238 (26.4) | 33.0 | 0.04 | |
| CC | 632 (70.1) | 25.5 | ||
| AA | 32 (3.4) | 27.5 | ||
| AC | 309 (33.3) | 22.0 | 0.006 | |
| CC | 587 (63.3) | 32.0 | ||
| AA | 186 (21.6) | 24.0 | ||
| AG | 415 (48.3) | 27.0 | 0.01 | |
| GG | 259 (30.1) | 31.0 | ||
| CC | 39 (4.7) | 36.0 | ||
| TC | 334 (40.2) | 29.0 | 0.4 | |
| TT | 458 (55.1) | 27.5 | ||
| CC | 166 (17.8) | 25.0 | ||
| CG | 482 (51.8) | 27.0 | 0.005 | |
| GG | 282 (30.3) | 33.5 | ||
| GG | 89 (9.5) | 33.0 | ||
| GA | 421 (45.2) | 27.0 | 0.8 | |
| AA | 422 (45.3) | 28.0 | ||
| TT | 37 (4.2) | 49.0 | ||
| TC | 332 (37.7) | 22.0 | 0.1 | |
| CC | 511 (58.1) | 29.0 | ||
| TT | 64 (7.0) | 31.0 | ||
| GT | 398 (43.4) | 27.0 | 0.8 | |
| GG | 454 (49.6) | 28.0 | ||
| TT | 8 (1.6) | 49.5 | ||
| CT | 128 (25.1) | 31.0 | 0.6 | |
| CC | 373 (73.3) | 33.0 | ||
| TT | 24 (2.6) | 44.5 | ||
| CT | 282 (30.2) | 28.0 | 0.2 | |
| CC | 628 (67.2) | 28.0 | ||
| GG | 99 (11.1) | 27.0 | ||
| GA | 398 (44.8) | 30.5 | 0.4 | |
| AA | 391 (44.0) | 26.0 |
Maximum possible score is 160.
By Cuzick's test for trend.
Genotype frequencies and autoantibody status*
| Gene | Genotype | Anti-CCP positive | Anti-CCP negative | OR (95% CI) | RF positive | RF negative | OR (95% CI) | ||
|---|---|---|---|---|---|---|---|---|---|
| TT | 29 | 2 | 5.2 (1.3–45.7) | 0.01 | 23 | 5 | 2.2 (0.8–7.4) | 0.1 | |
| TC | 177 | 50 | 1.3 (0.9–1.9) | 138 | 76 | 0.9 (0.6–1.2) | 0.3 | ||
| CC | 446 | 161 | 404 | 190 | |||||
| AA | 28 | 6 | 1.5 (0.6–4.5) | 0.5 | 25 | 8 | 1.4 (0.6–3.7) | 0.6 | |
| AC | 222 | 72 | 1.0 (0.7–1.4) | 0.9 | 191 | 96 | 0.9 (0.7–1.2) | 0.5 | |
| CC | 432 | 138 | 375 | 169 | |||||
| AA | 138 | 36 | 1.1 (0.7–1.9) | 0.6 | 120 | 52 | 1.1 (0.7–1.8) | 0.6 | |
| AG | 291 | 113 | 0.8 (0.5–1.1) | 0.2 | 253 | 129 | 1.0 (0.7–1.4) | 0.8 | |
| GG | 191 | 57 | 159 | 78 | |||||
| CC | 120 | 40 | 0.9 (0.6–1.5) | 0.7 | 98 | 56 | 0.7 (0.5–1.1) | 0.1 | |
| CG | 351 | 112 | 1.0 (0.7–1.4) | 0.9 | 304 | 140 | 0.9 (0.6–1.3) | 0.6 | |
| GG | 207 | 64 | 184 | 77 |
The presence of anti–cyclic citrullinated peptide (anti-CCP) and rheumatoid factor (RF) was compared for each single-nucleotide polymorphism with reference to the commonest genotype. OR = odds ratio; 95% CI = 95% confidence interval.
By Fisher's exact test for association.
Modified Larsen scores across genotypes, according to anti-CCP and RF status*
| Anti-CCP positive | Anti-CCP negative | RF positive | RF negative | |
|---|---|---|---|---|
| TT/TC | 31.0 (206) | 20.0 (50) | 42.0 (161) | 19.0 (81) |
| CC | 37.5 (445) | 8.5 (158) | 33.5 (404) | 13.0 (188) |
| | 0.5 | 0.04 | 0.2 | 0.07 |
| AA/AC | 29.0 (250) | 6.0 (76) | 31.0 (216) | 11.0 (103) |
| CC | 37.0 (431) | 16.0 (135) | 40.0 (375) | 18.5 (168) |
| | 0.06 | 0.002 | 0.05 | 0.002 |
| AA | 27.5 (138) | 6.0 (36) | 29.5 (120) | 8.0 (52) |
| AG | 33.5 (290) | 15.5 (110) | 37.0 (253) | 16.0 (127) |
| GG | 38.0 (191) | 10.0 (55) | 38.0 (159) | 17.5 (78) |
| | 0.02 | 0.2 | 0.1 | 0.03 |
| CC | 29.0 (120) | 13.0 (39) | 30.00 (98) | 13.00 (56) |
| GC | 32.0 (350) | 13.0 (109) | 34.00 (304) | 13.00 (139) |
| GG | 41.0 (207) | 10.0 (63) | 44.00 (184) | 10.00 (76) |
| | 0.004 | 0.9 | 0.01 | 0.9 |
Values are the median Larsen scores (number of carriers). Anti-CCP = anti–cyclic citrullinated peptide; RF = rheumatoid factor; IL-10 = interleukin-10.
By Cuzick's test for trend.