Background
Methods
Subjects
SNP Selection and Genotyping
Locus* | Primer sequence | |
---|---|---|
12555 | Forward | 5' ACTCAGTTACTTTCATTTGTTTATTCCTTAAC 3' |
Reverse for A | 5' CCTTTAATTAAATCAAAATTGAGTTCAT 3' | |
Reverse for G | 5' CCTTTAATTAAATCAAAATTGAGTTCAC 3' | |
13789 | Forward | 5' GAATCTCAGATTATGAGTGTTGCATTT 3' |
Reverse for A | 5' CATAGAGAGTGATAGCAACCCAGTCT 3' | |
Reverse for G | 5' CATAGAGAGTGATAGCAACCCAGTCC 3' | |
17023 | Forward for A | 5' GGGATTGCAAGCGTGAGACA 3' |
Forward for C | 5' GGGATTGCAAGCGTGAGACC 3' | |
Reverse | 5' TTTGCAGATTCTACGACTTGAAAAAG 3' | |
24351 | Forward for A | 5' GAGCTCCTGAGCATCACAGAGATA 3' |
Forward for T | 5' GAGCTCCTGAGCATCACAGAGATT 3' | |
Reverse for A | 5' ACTACCTGTCAGGTATGTTTGCTCAT 3' | |
Reverse for T | 5' CTTACCTGTCAGGTATGTTTGCTCAT 3' | |
31598 | Forward for A | 5' CAATAAAGGTCTCTGTTTAAAGTTTCAA 3' |
Forward for G | 5' CAATAAAGGTCTCTGTTTAAAGTTTCAG 3' | |
Reverse for A | 5' CAACACATCAGGGATACTCTGAGAAT 3' | |
Reverse for G | 5' GTACCCAACACATCAGGGATACTCT 3' | |
40240 | Forward | 5' AGGGATGCTCTGACCACCTG 3' |
Reverse for A | 5' GTGTGGATACTTGCGAGGTCTCT 3' | |
Reverse for G | 5' TGTGGATACTTGGGAGGTCTCC 3' | |
111380 | Forward for C | 5' TCTCTTTGGTACAACATAGTAAATCTCACC 3' |
Forward for T | 5' TCTCTTTTTGGTACAACATAGTAAATCTCACT 3' | |
Reverse for C | 5' TTACCAACTGTTTTCCCATAATTGTG 3' | |
Reverse for T | 5' CCAACTGTTTTCCCATAATTGTGAG 3' |
Statistical Analysis
Results
Japanese population | Control (n = 424) | Sarcoidosis (n = 181) |
Pvalue |
---|---|---|---|
Male (%)*
| 65.3 | 30.9 | <0.05 |
Age (median, range)
†
| 38, 18-72 | 45, 10-78 | <0.05 |
Stage (0/I/II/III/IV)
| - | 21/90/59/11/0 | |
Occular lesion (%)
| - | 54.7 | |
Cutaneous lesion (%)
| - | 17.7 | |
Cardiac lesion (%)
| - | 7.2 |
SNP ID | Locus* | Role | AA change | Allele | Controls n (%) | Cases n (%) |
P
†
| Genotype | Controls n (%) | Cases n (%) |
P
‡
|
---|---|---|---|---|---|---|---|---|---|---|---|
rs2477637
| 12555 | intron1 | none | A | 547 (64.5) | 213 (58.8) | 0.062 | AA | 180 (42.5) | 73 (40.3) | 0.016 |
G | 301 (35.5) | 149 (41.2) | AG | 187 (44.1) | 67 (37.0) | ||||||
GG | 57 (13.4) | 41 (22.7) | |||||||||
rs2253120
| 13789 | exon2 | none | G | 638 (75.2) | 253 (69.9) | 0.053 | GG | 250 (59.0) | 86 (47.5) | 0.016 |
A | 210 (24.8) | 109 (30.1) | AG | 138 (32.5) | 81 (44.8) | ||||||
AA | 36 (8.5) | 14 (7.7) | |||||||||
rs2477631
| 17023 | intron2 | none | A | 443 (52.2) | 191 (52.8) | 0.868 | AA | 120 (28.3) | 46 (25.4) | 0.296 |
C | 405 (47.8) | 171 (47.2) | AC | 203 (47.9) | 99 (54.7) | ||||||
CC | 101 (23.8) | 36 (19.9) | |||||||||
rs2477664
| 24351 | exon4 | none | A | 455 (53.7) | 191 (52.8) | 0.776 | AA | 131 (30.9) | 49 (27.1) | 0.412 |
T | 393 (46.3) | 171 (47.2) | AT | 193 (45.5) | 93 (51.4) | ||||||
TT | 100 (23.6) | 39 (21.5) | |||||||||
rs692527
| 31598 | intron5 | none | A | 474 (55.9) | 184 (50.8) | 0.105 | AA | 130 (30.7) | 50 (27.6) | 0.145 |
G | 374 (44.1) | 178 (49.2) | AG | 214 (50.5) | 84 (46.4) | ||||||
GG | 80 (18.9) | 47 (26.0) | |||||||||
rs1926736
| 40240 | exon7 | Gly/Ser | G | 443 (52.2) | 198 (54.7) | 0.433 | GG | 111 (26.2) | 56 (30.9) | 0.455 |
A | 405 (47.8) | 164 (45.3) | AG | 221 (52.1) | 86 (47.5) | ||||||
AA | 92 (21.7) | 39 (21.5) | |||||||||
rs544995
| 111041 | 3'-UTR | none | G | 598 (70.5) | 254 (70.2) | 0.957 | GG | 200 (47.2) | 88 (48.6) | 0.526 |
A | 250 (29.5) | 108 (29.8) | AG | 198 (46.7) | 78 (43.1) | ||||||
AA | 26 (6.1) | 15 (8.3) | |||||||||
rs544995
| 111065 | 3'-UTR | none | G | 522 (63.4) | 239 (66.0) | 0.159 | GG | 163 (38.4) | 75 (41.4) | 0.148 |
A | 326 (39.6) | 123 (34.0) | AG | 196 (46.2) | 89 (49.2) | ||||||
AA | 65 (15.3) | 17 (9.4) | |||||||||
rs691005
| 111380 | 3'-UTR | none | T | 576 (67.9) | 226 (62.4) | 0.064 | TT | 191 (45.0) | 79 (43.6) | 0.003 |
C | 272 (32.1) | 136 (37.6) | TC | 194 (45.8) | 68 (37.6) | ||||||
CC | 39 (9.2) | 34 (18.8) |
Dominant model | Recessive model | |||
---|---|---|---|---|
OR [95% CI]* |
Pvalue* | OR [95% CI]* |
Pvalue* | |
rs2477637
| 1.04 [0.71-1.52] | 0.843 | 1.76 [1.09-2.84] | 0.02 |
rs2253120
| 1.62 [1.12-2.36] | 0.011 | 0.83 [0.42-1.65] | 0.593 |
rs2477631
| 1.08 [0.70-1.64] | 0.739 | 0.79 [0.50-1.24] | 0.298 |
rs2477664
| 1.18 [0.78-1.78] | 0.433 | 0.87 [0.56-1.36] | 0.535 |
rs692527
| 1.15 [0.76-1.74] | 0.496 | 1.58 [1.02-2.46] | 0.042 |
rs1926736
| 0.78 [0.52-1.17] | 0.222 | 0.97 [0.62-1.53] | 0.906 |
rs554995
| 0.90 [0.62-1.31] | 0.588 | 1.43 [0.70-2.95] | 0.326 |
rs554313
| 0.83 [0.57-1..21] | 0.336 | 0.65 [0.36-1.18] | 0.159 |
rs691005
| 1.00 [0.69-1.46] | 0.987 | 2.53 [1.47-4.37] | 0.001 |
Haplotype | controls (%)* | cases (%)* | total (%)* | haplotype-specific score | simulated P
†
|
---|---|---|---|---|---|
rs2477631-rs2477664 | |||||
A-A | 48.6 | 48.4 | 48.6 | -0.171 | 0.863 |
C-T | 42.7 | 42.9 | 42.8 | 0.089 | 0.929 |
rs692527-rs1926736
| |||||
A-A | 46.0 | 41.4 | 44.6 | -1.601 | 0.111 |
A-G | 9.8 | 9.5 | 9.7 | -0.428 | 0.667 |
G-G | 42.4 | 45.2 | 43.2 | 1.074 | 0.279 |
rs554995-rs554313-rs691005
| |||||
G-G-T | 30.6 | 30.6 | 30.6 | 0.098 | 0.916 |
A-G-C | 27.7 | 29.4 | 28.1 | 0.741 | 0.452 |
G-A-T | 29.3 | 36.2 | 34.7 | 2.220 | 0.028 |