Introduction
Methods
Patients and controls
Genes and SNPs selection
Validation of the SNPs by DNA sequencing
Genotyping
Statistical analysis
Results
Case-control study
SNP | Genotype | Cases N = 763 | (%) | Controls N = 734 | (%) | OR | 95% CI |
P-value |
---|---|---|---|---|---|---|---|---|
CD28 | ||||||||
rs3181098 | GG | 315 | 41 | 331 | 45 | |||
AG | 331 | 43 | 325 | 44 | 1.05 | 0.84–1.31 | ||
AA | 117 | 15 | 78 | 11 | 1.50 | 1.07–2.11 | 0.06 | |
G-allele | 961 | 63 | 987 | 67 | ||||
A-allele | 565 | 37 | 481 | 33 | 1.18 | 1.00–1.38 | 0.05 | |
rs3181100 | CC | 279 | 37 | 229 | 31 | |||
CG | 368 | 48 | 357 | 49 | 0.87 | 0.69–1.10 | ||
GG | 116 | 15 | 145 | 20 | 0.68 | 0.50–0.93 | 0.05 | |
C-allele | 926 | 61 | 815 | 56 | ||||
G-allele | 600 | 39 | 647 | 44 | 0.83 | 0.71–0.97 | 0.02 | |
rs3181101 | CC | 570 | 75 | 559 | 77 | |||
CG | 175 | 23 | 165 | 23 | 0.98 | 0.76–1.26 | ||
GG | 17 | 2 | 7 | 10 | 1.97 | 0.78–4.96 | 0.35 | |
C-allele | 1,315 | 86 | 1,283 | 88 | ||||
G-allele | 209 | 14 | 179 | 12 | 1.06 | 0.85–1.33 | 0.61 | |
rs1181390 | GG | 474 | 62 | 467 | 64 | |||
GT | 257 | 34 | 233 | 32 | 1.14 | 0.91–1.43 | ||
TT | 32 | 4 | 33 | 5 | 0.92 | 0.55–1.55 | 0.47 | |
G-allele | 1,205 | 79 | 1,167 | 80 | ||||
T-allele | 321 | 21 | 299 | 20 | 1.06 | 0.88–1.28 | 0.53 | |
rs1181388 | GG | 575 | 76 | 545 | 74 | |||
AG | 169 | 22 | 170 | 23 | 0.98 | 0.76–1.26 | ||
AA | 17 | 2 | 18 | 3 | 0.90 | 0.45–1.81 | 0.95 | |
G-allele | 1,319 | 87 | 1,260 | 86 | ||||
A-allele | 203 | 13 | 206 | 14 | 0.97 | 0.78–1.20 | 0.76 | |
rs17533594 | AA | 483 | 63 | 474 | 65 | |||
AG | 257 | 34 | 232 | 32 | 1.11 | 0.89–1.40 | ||
GG | 23 | 3 | 24 | 3 | 0.94 | 0.52–1.73 | 0.63 | |
A-allele | 1,223 | 80 | 1,180 | 81 | ||||
G-allele | 303 | 20 | 280 | 19 | 1.06 | 0.88–1.28 | 0.55 | |
rs3116494 | AA | 414 | 54 | 393 | 54 | |||
AG | 307 | 40 | 299 | 41 | 1.01 | 0.81–1.26 | ||
GG | 42 | 6 | 39 | 5 | 1.09 | 0.67–1.75 | 0.94 | |
A-allele | 1,135 | 74 | 1,085 | 74 | ||||
G-allele | 391 | 26 | 377 | 26 | 1.02 | 0.86–1.21 | 0.79 | |
rs3181107 | AA | 659 | 86 | 620 | 85 | |||
AG | 100 | 13 | 106 | 15 | 0.92 | 0.67–1.25 | ||
GG | 4 | 1 | 6 | 1 | 0.74 | 0.20–2.79 | 0.78 | |
A-allele | 1,418 | 93 | 1,346 | 92 | ||||
G-allele | 108 | 7 | 118 | 8 | 0.91 | 0.68–1.20 | 0.49 | |
rs3116496 (IVS3 + 17) | TT | 487 | 64 | 475 | 65 | |||
CT | 254 | 33 | 231 | 32 | 1.10 | 0.88–1.38 | ||
CC | 22 | 3 | 24 | 3 | 0.89 | 0.48–1.64 | 0.63 | |
T-allele | 1,228 | 81 | 1,181 | 81 | ||||
C-allele | 298 | 20 | 279 | 20 | 1.04 | 0.86–1.26 | 0.66 | |
CTLA4 | ||||||||
rs16840252 | CC | 521 | 68 | 489 | 67 | 1.00 | ||
CT | 218 | 29 | 222 | 30 | 0.91 | 0.72–1.15 | ||
TT | 23 | 3 | 21 | 3 | 1.02 | 0.54–1.91 | 0.74 | |
C-allele | 1,260 | 83 | 1,200 | 82 | ||||
T-allele | 264 | 17 | 264 | 18 | 0.95 | 0.78–1.15 | 0.57 | |
rs5742909 (CT44) | CC | 619 | 81 | 596 | 81 | 1.00 | ||
CT | 136 | 18 | 130 | 18 | 0.96 | 0.73–1.27 | ||
TT | 8 | 1 | 8 | 1 | 0.89 | 0.32–2.49 | 0.95 | |
C-allele | 1,374 | 90 | 1,322 | 90 | ||||
T-allele | 152 | 10 | 146 | 10 | 0.96 | 0.75–1.23 | 0.74 | |
rs231775 (CT42) | AA | 289 | 38 | 283 | 39 | 1.00 | ||
AG | 369 | 48 | 345 | 47 | 1.08 | 0.86–1.36 | ||
GG | 104 | 14 | 106 | 14 | 0.97 | 0.70–1.36 | 0.71 | |
A-allele | 947 | 62 | 911 | 62 | ||||
G-allele | 577 | 38 | 557 | 38 | 1.01 | 0.87–1.18 | 0.90 | |
rs231777 | CC | 539 | 71 | 514 | 70 | 1.00 | ||
CT | 208 | 27 | 203 | 28 | 0.97 | 0.76–1.23 | ||
TT | 15 | 2 | 16 | 2 | 0.83 | 0.39–1.77 | 0.87 | |
C-allele | 1,286 | 84 | 1,231 | 84 | ||||
T-allele | 238 | 16 | 235 | 16 | 0.95 | 0.78–1.17 | 0.64 | |
rs3087243 (CT60) | GG | 246 | 32 | 223 | 30 | 1.00 | ||
AG | 355 | 47 | 388 | 53 | 0.81 | 0.63–1.03 | ||
AA | 162 | 21 | 122 | 17 | 1.22 | 0.89–1.65 | 0.01 | |
G-allele | 847 | 56 | 834 | 57 | ||||
A-allele | 679 | 45 | 632 | 43 | 1.06 | 0.91–1.23 | 0.45 | |
rs11571319 (CT61) | GG | 518 | 68 | 488 | 67 | 1.00 | ||
AG | 222 | 29 | 223 | 31 | 0.93 | 0.73–1.17 | ||
AA | 23 | 3 | 21 | 3 | 1.02 | 0.54–1.92 | 0.81 | |
G-allele | 1,258 | 82 | 1,199 | 82 | ||||
A-allele | 268 | 18 | 265 | 18 | 0.96 | 0.79–1.16 | 0.64 | |
rs11571302 (JO31) | GG | 225 | 30 | 210 | 29 | 1.00 | ||
GT | 370 | 49 | 383 | 52 | 0.87 | 0.68–1.12 | ||
TT | 168 | 22 | 140 | 19 | 1.14 | 0.84–1.55 | 0.15 | |
G-allele | 820 | 54 | 803 | 55 | ||||
T-allele | 706 | 46 | 663 | 45 | 1.05 | 0.90–1.22 | 0.53 | |
rs7665213 (JO30) | GG | 228 | 30 | 211 | 29 | 1.00 | ||
AG | 370 | 49 | 383 | 52 | 0.87 | 0.68–1.12 | ||
AA | 165 | 22 | 137 | 19 | 1.13 | 0.83–1.53 | 0.17 | |
G-allele | 826 | 54 | 805 | 55 | ||||
A-allele | 700 | 46 | 657 | 45 | 1.04 | 0.90–1.21 | 0.59 | |
rs11571297 (JO27) | TT | 214 | 28 | 193 | 26 | 1.00 | ||
CT | 376 | 49 | 393 | 54 | 0.84 | 0.65–1.08 | ||
CC | 173 | 23 | 148 | 20 | 1.07 | 0.79–1.45 | 0.15 | |
T-allele | 804 | 53 | 779 | 53 | ||||
C-allele | 722 | 47 | 689 | 47 | 1.02 | 0.88–1.18 | 0.81 | |
ICOS | ||||||||
rs10932029 (+173) | TT | 538 | 71 | 488 | 67 | 1.00 | ||
CT | 204 | 27 | 228 | 31 | 0.82 | 0.65–1.03 | ||
CC | 21 | 3 | 15 | 2 | 1.14 | 0.57–2.27 | 0.20 | |
T-allele | 1,280 | 84 | 1,204 | 82 | ||||
C-allele | 246 | 16 | 258 | 18 | 0.89 | 0.73–1.08 | 0.23 | |
rs4335928 | TT | 579 | 76 | 559 | 76 | 1.00 | ||
CT | 170 | 22 | 162 | 22 | 0.99 | 0.77–1.28 | ||
CC | 14 | 2 | 12 | 2 | 1.11 | 0.50–2.47 | 0.96 | |
T-allele | 1,328 | 87 | 1,280 | 87 | ||||
C-allele | 198 | 13 | 186 | 13 | 1.01 | 0.80–1.26 | 0.96 | |
rs4675374 | CC | 457 | 60 | 436 | 60 | 1.00 | ||
CT | 272 | 36 | 258 | 35 | 0.98 | 0.78–1.23 | ||
TT | 34 | 5 | 38 | 5 | 0.85 | 0.52–1.40 | 0.82 | |
C-allele | 1,186 | 78 | 1,130 | 77 | ||||
T-allele | 340 | 22 | 334 | 23 | 0.96 | 0.80–1.14 | 0.62 | |
rs7602383 | AA | 550 | 72 | 533 | 73 | 1.00 | ||
AG | 197 | 26 | 183 | 25 | 1.01 | 0.79–1.29 | ||
GG | 16 | 2 | 17 | 2 | 0.93 | 0.46–1.90 | 0.98 | |
A-allele | 1,297 | 85 | 1,249 | 85 | ||||
G-allele | 229 | 15 | 217 | 15 | 0.99 | 0.81–1.23 | 0.95 | |
rs4521021 | TT | 450 | 59 | 451 | 61 | 1.00 | ||
CT | 276 | 36 | 260 | 35 | 1.00 | 0.80–1.25 | ||
CC | 37 | 5 | 23 | 3 | 1.47 | 0.83–2.60 | 0.41 | |
T-allele | 1,176 | 77 | 1,162 | 80 | ||||
C-allele | 350 | 23 | 306 | 21 | 1.07 | 0.89–1.28 | 0.45 | |
rs11571323 | GG | 587 | 77 | 534 | 73 | 1.00 | ||
AG | 161 | 21 | 184 | 25 | 0.81 | 0.63–1.04 | ||
AA | 15 | 2 | 13 | 2 | 1.30 | 0.60–2.84 | 0.18 | |
G-allele | 1,335 | 88 | 1,252 | 86 | ||||
A-allele | 191 | 13 | 210 | 14 | 0.89 | 0.71–1.10 | 0.29 | |
rs12466129 | TT | 448 | 59 | 451 | 62 | 1.00 | ||
AT | 273 | 36 | 239 | 33 | 1.14 | 0.91–1.43 | ||
AA | 42 | 6 | 42 | 6 | 0,94 | 0.59–1.51 | 0.47 | |
T-allele | 1,169 | 77 | 1,141 | 78 | ||||
A-allele | 357 | 23 | 323 | 22 | 1.06 | 0.89–1.27 | 0.54 | |
rs10172036 | GG | 301 | 40 | 283 | 39 | 1.00 | ||
GT | 353 | 46 | 352 | 48 | 0.92 | 0.73–1.15 | ||
TT | 109 | 14 | 97 | 13 | 1.04 | 0.75–1.45 | 0.63 | |
G-allele | 955 | 63 | 918 | 63 | ||||
T-allele | 571 | 37 | 546 | 37 | 0.99 | 0.85–1.16 | 0.93 | |
rs10183087 | AA | 461 | 61 | 418 | 57 | 1.00 | ||
AC | 263 | 35 | 277 | 38 | 0.85 | 0.68–1.06 | ||
CC | 38 | 5 | 37 | 5 | 1.04 | 0.63–1.70 | 0.32 | |
A-allele | 1,185 | 78 | 1,113 | 76 | ||||
C-allele | 339 | 22 | 351 | 24 | 0.92 | 0.77–1.10 | 0.36 | |
rs10932036 | AA | 611 | 80 | 594 | 81 | 1.00 | ||
AT | 144 | 19 | 129 | 18 | 1.09 | 0.83–1.44 | ||
TT | 7 | 1 | 7 | 1 | 1.12 | 0.37–3.35 | 0.81 | |
A-allele | 1,366 | 90 | 1,317 | 90 | ||||
T-allele | 158 | 10 | 143 | 10 | 1.08 | 0.85–1.39 | 0.53 |
Association between polymorphisms and prognosis
SNP | Genotype | Cases (%) N = 587 | Metastases free survival | Overall survival | ||||
---|---|---|---|---|---|---|---|---|
OR | 95% CI |
P-value | OR | 95% CI |
P-value | |||
rs3181098 | GG | 247 (42) | ||||||
AG/AA | 340 (58) | 1.34 | 1.02–1.77 | 0.04 | 1.18 | 0.81–1.72 | 0.38 | |
rs3181100 | CC | 212 (36) | ||||||
CG/GG | 375 (64) | 0.82 | 0.62–1.08 | 0.16 | 0.82 | 0.56–1.20 | 0.31 | |
rs3181101 | CC | 440 (75) | ||||||
CG/GG | 146 (25) | 1.28 | 0.94–1.74 | 0.12 | 1.21 | 0.80–1.83 | 0.38 | |
rs1181390 | GG | 360 (61) | ||||||
GT/TT | 227 (39) | 0.92 | 0.70–1.21 | 0.56 | 1.16 | 0.80–1.67 | 0.45 | |
rs1181388 | GG | 440 (75) | ||||||
AG/AA | 146 (25) | 0.86 | 0.63–1.17 | 0.32 | 0.82 | 0.53–1.25 | 0.35 | |
rs17533594 | AA | 372 (63) | ||||||
AG/GG | 215 (37) | 1.03 | 0.78–1.35 | 0.84 | 1.23 | 0.85–1.79 | 0.28 | |
rs3116494 | AA | 319 (54) | ||||||
AG/GG | 268 (46) | 0.99 | 0.76–1.30 | 0.96 | 1.13 | 0.79–1.62 | 0.52 | |
rs3181107 | AA | 506 (86) | ||||||
AG/GG | 81 (14) | 0.81 | 0.54–1.21 | 0.30 | 0.73 | 0.41–1.29 | 0.28 | |
rs3116496 (IVS3 +17) | TT | 378 (64) | ||||||
CT/CC | 209 (36) | 1.16 | 0.88–1.53 | 0.29 | 1.39 | 0.96–2.02 | 0.08 |
SNP | Genotype | Cases (%) N = 587 | Metastases free survival | Overall survival | ||||
---|---|---|---|---|---|---|---|---|
OR | 95% CI |
P-value | OR | 95% CI |
P-value | |||
rs16840252 | CC | 399 (68) | ||||||
CT/TT | 187 (32) | 1.11 | 0.84–1.48 | 0.46 | 1.25 | 0.85–1.82 | 0.26 | |
rs5742909 (CT44) | CC | 476 (81) | ||||||
CT/TT | 111 (19) | 1.24 | 0.88–1.72 | 0.22 | 1.40 | 0.90–2.18 | 0.14 | |
rs231775 (CT42) | AA | 219 (37) | ||||||
AG/GG | 367 (63) | 0.99 | 0.75–1.30 | 0.93 | 0.92 | 0.63–1.33 | 0.64 | |
rs231777 | CC | 414 (71) | ||||||
CT/TT | 172 (29) | 1.04 | 0.78–1.39 | 0.79 | 1.23 | 0.83–1.80 | 0.30 | |
rs3087243 (CT60) | GG | 195 (33) | ||||||
AG/AA | 392 (67) | 0.99 | 0.74–1.31 | 0.92 | 0.93 | 0.63–1.36 | 0.69 | |
rs11571319 (CT61) | GG | 397 (68) | ||||||
AG/AA | 190 (32) | 1.10 | 0.83–1.45 | 0.51 | 1.19 | 0.81–1.73 | 0.38 | |
rs11571302 (JO31) | GG | 173 (30) | ||||||
GT/TT | 414 (71) | 0.95 | 0.71–1.27 | 0.72 | 0.80 | 0.55–1.17 | 0.26 | |
rs7665213 (JO30) | GG | 176 (30) | ||||||
AG/AA | 411 (70) | 0.95 | 0.72–1.27 | 0.74 | 0.83 | 0.57–1.21 | 0.32 | |
rs11571297 (JO27) | TT | 163 (28) | ||||||
CT/CC | 424 (72) | 0.87 | 0.65–1.16 | 0.33 | 0.76 | 0.52–1.11 | 0.16 |
SNP | Genotype | Cases (%) N = 587 | Metastases free survival | Overall survival | ||||
---|---|---|---|---|---|---|---|---|
OR | 95% CI |
P-value | OR | 95% CI |
P-value | |||
rs10932029 (+173) | TT | 412 (70) | ||||||
CT/CC | 175 (30) | 0.87 | 0.65–1.17 | 0.36 | 0.79 | 0.53–1.18 | 0.25 | |
rs4335928 | TT | 446 (76) | ||||||
CT/CC | 141 (24) | 1.17 | 0.86–1.60 | 0.32 | 1.26 | 0.82–1.92 | 0.29 | |
rs4675374 | CC | 352 (60) | ||||||
CT/TT | 235 (40) | 1.08 | 0.82–1.42 | 0.58 | 1.31 | 0.91–1.88 | 0.15 | |
rs7602383 | AA | 421 (72) | ||||||
AG/GG | 166 (28) | 1.02 | 0.76–1.37 | 0.88 | 1.12 | 0.75–1.66 | 0.59 | |
rs4521021 | TT | 345 (59) | ||||||
CT/CC | 242 (41) | 0.96 | 0.73–1.26 | 0.77 | 1.19 | 0.83–1.71 | 0.35 | |
rs11571323 | GG | 452 (77) | ||||||
AG/AA | 135 (23) | 1.07 | 0.78–1.46 | 0.70 | 1.27 | 0.83–1.94 | 0.28 | |
rs12466129 | TT | 340 (58) | ||||||
AT/AA | 247 (42) | 0.86 | 0.66–1.13 | 0.28 | 1.03 | 0.72–1.48 | 0.88 | |
rs10172036 | GG | 232 (40) | ||||||
GT/TT | 355 (61) | 1.12 | 0.85–1.50 | 0.42 | 0.86 | 0.58–1.26 | 0.43 | |
rs10183087 | AA | 352 (60) | ||||||
AC/CC | 234 (40) | 0.87 | 0.66–1.15 | 0.33 | 0.93 | 0.64–1.35 | 0.70 | |
rs10932036 | AA | 467 (80) | ||||||
AT/TT | 119 (20) | 0.76 | 0.54–1.06 | 0.11 | 0.76 | 0.48–1.19 | 0.23 |