| Literature DB >> 33824876 |
Jingjing Chen1, Yuanfang Xu1, Hongyuan Hu2, Tianbo Jin3,4.
Abstract
BACKGROUND: Cervical cancer (CC) is the second most common tumor in women worldwide. Studies have been accepted that genetic variations play an important role in the development of CC. The aim of this study was to evaluate the impact of TCF7L1 variants on CC risk.Entities:
Mesh:
Substances:
Year: 2021 PMID: 33824876 PMCID: PMC8007361 DOI: 10.1155/2021/6670456
Source DB: PubMed Journal: Biomed Res Int Impact factor: 3.411
Primers used for this study.
| SNP_ID | 2nd-PCRP | 1st-PCRP | UEP DIR | UEP SEQ |
|---|---|---|---|---|
| rs11904127 | ACGTTGGATGTGACTGGCTTCCCCTTGCAT | ACGTTGGATGGTGTGTCCCACAGAGTTCAG | F | TCCCCTTGCATCCCCTG |
| rs2366264 | ACGTTGGATGGCAACAGAGCAAGACAGCAT | ACGTTGGATGGATGGCAATAAATGCTATGG | F | agccAGACAGCATCTCTTTTTTT |
| rs11689667 | ACGTTGGATGGAGGAAGAAATCAATGACCC | ACGTTGGATGAGGAGTACTCACGTAGTCAC | F | aaTTGGAGTTTAATTCAGCGC |
| rs62162674 | ACGTTGGATGTGTTGAACACCTCAACACGG | ACGTTGGATGGGACTAGATGGTCTCCTTTG | F | ccctaAACACGGTCGGCACTCCCA |
SNP: single nucleotide polymorphisms; PCRP: polymerase chain reaction primer; UEP-DIR: unextension primer sequence direction; UEP SEQ: unextended mini-sequencing primer sequence. 1st-PCRP means the first PCR primer. 2nd-PCRP means the second PCR primer.
Characteristic of cervical cancer patients and healthy controls in this study.
| Characteristics | Cases ( | Controls ( |
|
|---|---|---|---|
| Age, years (mean ± SD) | 51.62 ± 9.78 | 51.36 ± 10.30 | 0.684 |
| >51 | 257 (50.6%) | 241 (48.5%) | |
| ≤51 | 251 (49.4%) | 256 (51.5%) | |
| Squamous carcinoma | 230 (40.0%) | ||
| Adenocarcinoma | 44 (8.7%) | ||
| Missing | 234 (51.3%) | ||
| Clinical stage | |||
| I/II | 199 (39.2%) | ||
| III/IV | 61 (12.0%) | ||
| Missing | 164 (48.8%) |
p value was calculated by Student's t-test. p < 0.05 indicates statistical significance.
Basic information and allele frequencies of TCF7L1 SNPs.
| SNP ID | Chromosome position | Role | Alleles (minor/major) | MAF | O (HET) | E (HET) |
| |
|---|---|---|---|---|---|---|---|---|
| Case | Control | |||||||
| rs11904127 | chr2: 85257695 | Intron | A/G | 0.364 | 0.420 | 0.514 | 0.487 | 0.228 |
| rs2366264 | chr2: 85261888 | Intron | T/G | 0.294 | 0.313 | 0.428 | 0.430 | 0.917 |
| rs11689667 | chr2: 85264242 | Intron | C/T | 0.290 | 0.316 | 0.434 | 0.433 | 1.000 |
| rs62162674 | chr2: 85275113 | Intron | C/G | 0.297 | 0.339 | 0.473 | 0.448 | 0.270 |
SNP: single nucleotide polymorphisms; MAF: minor allele frequency; HWE: Hardy–Weinberg equilibrium. p values were calculated by exact test. p < 0.05 indicates statistical significance.
Association analysis between TCF7L1 SNPs and cervical cancer risk.
| SNP ID | Model | Genotype | Case | Control | Without adjusted | With adjusted | ||
|---|---|---|---|---|---|---|---|---|
| OR (95% CI) |
| OR (95% CI) |
| |||||
| rs11904127 | Allele | G | 644 | 564 | 1 | |||
| A | 368 | 408 | 0.79 (0.66-0.95) | 0.010 | ||||
| Codominant | GG | 209 | 157 | 1 | 1 | |||
| GA | 226 | 250 | 0.68 (0.52-0.89) | 0.006 | 0.68 (0.52-0.89) | 0.006 | ||
| AA | 71 | 79 | 0.68 (0.46-0.99) | 0.044 | 0.67 (0.46-0.99) | 0.043 | ||
| Dominant | GG | 209 | 157 | 1 | 1 | |||
| AG-AA | 297 | 329 | 0.68 (0.52-0.88) | 0.003 | 0.68 (0.52-0.88) | 0.003 | ||
| Recessive | GG-AG | 435 | 407 | 1 | 1 | |||
| AA | 71 | 79 | 0.84 (0.59-1.19) | 0.329 | 0.84 (0.59-1.19) | 0.323 | ||
| Log-additive | — | — | — | 0.79 (0.66-0.95) | 0.010 | 0.79 (0.66-0.94) | 0.010 | |
| rs2366264 | Allele | G | 716 | 677 | 1 | |||
| T | 298 | 309 | 0.91 (0.75-1.10) | 0.343 | ||||
| Codominant | GG | 249 | 233 | 1 | 1 | |||
| GT | 218 | 211 | 0.97 (0.75-1.25) | 0.799 | 0.97 (0.74-1.25) | 0.797 | ||
| TT | 40 | 49 | 0.76 (0.49-1.20) | 0.245 | 0.76 (0.48-1.20) | 0.244 | ||
| Dominant | GG | 249 | 233 | 1 | 1 | |||
| TG-TT | 258 | 260 | 0.93 (0.72-1.19) | 0.558 | 0.93 (0.72-1.19) | 0.556 | ||
| Recessive | GG-TG | 467 | 444 | 1 | 1 | |||
| TT | 40 | 49 | 0.78 (0.50-1.20) | 0.256 | 0.78 (0.50-1.20) | 0.256 | ||
| Log-additive | — | — | — | 0.91 (0.75-1.10) | 0.340 | 0.91 (0.75-1.10) | 0.338 | |
| rs11689667 | Allele | T | 719 | 674 | 1 | |||
| C | 293 | 312 | 0.88 (0.73-1.07) | 0.191 | ||||
| Codominant | TT | 253 | 230 | 1 | 1 | |||
| TC | 213 | 214 | 0.90 (0.70-1.17) | 0.452 | 0.90 (0.70-1.17) | 0.447 | ||
| CC | 40 | 49 | 0.74 (0.47-1.17) | 0.198 | 0.74 (0.47-1.17) | 0.198 | ||
| Dominant | TT | 253 | 230 | 1 | 1 | |||
| TC-CC | 253 | 263 | 0.87 (0.68-1.12) | 0.290 | 0.87 (0.68-1.12) | 0.287 | ||
| Recessive | TT-TC | 466 | 444 | 1 | 1 | |||
| CC | 40 | 49 | 0.78 (0.50-1.21) | 0.260 | 0.78 (0.50-1.21) | 0.261 | ||
| Log-additive | — | — | — | 0.88 (0.73-1.07) | 0.188 | 0.88 (0.72-1.07) | 0.187 | |
| rs62162674 | Allele | G | 711 | 654 | 1 | |||
| C | 301 | 336 | 0.82 (0.68-0.99) | 0.044 | ||||
| Codominant | GG | 245 | 210 | 1 | 1 | |||
| GC | 221 | 234 | 0.81 (0.62-1.05) | 0.112 | 0.81 (0.62-1.05) | 0.107 | ||
| CC | 40 | 51 | 0.67 (0.43-1.06) | 0.086 | 0.67 (0.43-1.06) | 0.085 | ||
| Dominant | GG | 245 | 210 | 1 | 1 | |||
| CG-CC | 261 | 285 | 0.79 (0.61-1.01) | 0.057 | 0.78 (0.61-1.01) | 0.054 | ||
| Recessive | GG-CG | 466 | 444 | 1 | 1 | |||
| CC | 40 | 51 | 0.75 (0.48-1.15) | 0.188 | 0.75 (0.48-1.15) | 0.189 | ||
| Log-additive | — | — | — | 0.82 (0.67-0.99) | 0.039 | 0.81 (0.67-0.99) | 0.038 | |
CI: confidence interval; OR: odds ratio; SNP: single nucleotide polymorphism. p values were calculated by logistic regression analysis without adjustment. p values were calculated by logistic regression analysis with adjustment for age. p < 0.05 indicates statistical significance.
The association of TCF7L1 SNPs with the risk of cervical cancer stratified by age.
| SNP | Model | Allele/genotype | Case | Control | OR (95% CI) |
| Case | Control | OR (95% CI) |
|
|---|---|---|---|---|---|---|---|---|---|---|
| Age | > 51 | ≤ 51 | ||||||||
| rs11904127 | Allele | G | 327 | 268 | 1 | 317 | 296 | 1 | ||
| A | 185 | 206 | 0.74 (0.57-0.95) | 0.019 | 183 | 202 | 0.85 (0.66-1.09) | 0.199 | ||
| Codominant | GG | 108 | 76 | 1 | 101 | 81 | 1 | |||
| GA | 111 | 116 | 0.67 (0.46-0.99) | 0.049 | 115 | 134 | 0.69 (0.47-1.01) | 0.056 | ||
| AA | 37 | 45 | 0.58 (0.34-0.98) | 0.040 | 34 | 34 | 0.80 (0.46-1.40) | 0.435 | ||
| Dominant | GG | 108 | 76 | 1 | 101 | 81 | 1 | |||
| AG-AA | 148 | 161 | 0.65 (0.45-0.94) | 0.021 | 149 | 168 | 0.71 (0.49-1.03) | 0.068 | ||
| Recessive | GG-AG | 219 | 192 | 1 | 216 | 215 | 1 | |||
| AA | 37 | 45 | 0.72 (0.45-1.16) | 0.173 | 34 | 34 | 0.99 (0.60-1.66) | 0.982 | ||
| Log-additive | — | — | — | 0.74 (0.58-0.96) | 0.021 | — | — | 0.84 (0.64-1.09) | 0.186 | |
| rs2366264 | Allele | G | 365 | 317 | 1 | 351 | 360 | 1 | ||
| T | 147 | 159 | 0.80 (0.61-1.05) | 0.111 | 151 | 150 | 1.03 (0.79-1.35) | 0.816 | ||
| Codominant | GG | 129 | 108 | 1 | 120 | 125 | 1 | |||
| GT | 107 | 101 | 0.89 (0.61-1.29) | 0.531 | 111 | 110 | 1.05 (0.73-1.51) | 0.793 | ||
| TT | 20 | 29 | 0.58 (0.31-1.08) | 0.083 | 20 | 20 | 1.05 (0.54-2.04) | 0.898 | ||
| Dominant | GG | 129 | 108 | 1 | 120 | 125 | 1 | |||
| TG-TT | 127 | 130 | 0.82 (0.57-1.17) | 0.265 | 131 | 130 | 1.05 (0.74-1.49) | 0.787 | ||
| Recessive | GG-TG | 236 | 209 | 1 | 231 | 235 | 1 | |||
| TT | 20 | 29 | 0.61 (0.33-1.11) | 0.104 | 20 | 20 | 1.02 (0.53-1.95) | 0.950 | ||
| Log-additive | — | — | — | 0.80 (0.61-1.05) | 0.113 | — | — | 1.03 (0.79-1.36) | 0.810 | |
| rs11689667 | Allele | T | 366 | 315 | 1 | 353 | 359 | 1 | ||
| C | 146 | 161 | 0.78 (0.60-1.02) | 0.072 | 147 | 151 | 0.99 (0.76-1.30) | 0.942 | ||
| Codominant | TT | 130 | 106 | 1 | 123 | 124 | 1 | |||
| TC | 106 | 103 | 0.84 (0.58-1.22) | 0.360 | 107 | 111 | 0.97 (0.67-1.40) | 0.873 | ||
| CC | 20 | 29 | 0.56 (0.30-1.05) | 0.069 | 20 | 20 | 1.01 (0.52-1.97) | 0.975 | ||
| Dominant | TT | 130 | 106 | 1 | 230 | 235 | 1 | |||
| TC-CC | 126 | 132 | 0.78 (0.55-1.11) | 0.165 | 123 | 124 | 0.98 (0.69-1.39) | 0.895 | ||
| Recessive | TT-TC | 236 | 209 | 1 | 127 | 131 | 1 | |||
| CC | 20 | 29 | 0.61 (0.33-1.11) | 0.103 | 20 | 20 | 1.03 (0.54-1.96) | 0.941 | ||
| Log-additive | — | — | — | 0.78 (0.60-1.02) | 0.073 | — | — | 0.99 (0.75-1.30) | 0.942 | |
| rs62162674 | Allele | G | 362 | 303 | 1 | 349 | 351 | 1 | ||
| C | 150 | 175 | 0.72 (0.55-0.94) | 0.014 | 151 | 161 | 0.94 (0.72-1.23) | 0.668 | ||
| Codominant | GG | 126 | 94 | 1 | 119 | 116 | 1 | |||
| GC | 110 | 115 | 0.72 (0.49-1.04) | 0.081 | 111 | 119 | 0.91 (0.63-1.31) | 0.600 | ||
| CC | 20 | 30 | 0.50 (0.27-0.93) | 0.028 | 20 | 21 | 0.93 (0.48-1.81) | 0.839 | ||
| Dominant | GG | 126 | 94 | 1 | 119 | 116 | 1 | |||
| CG-CC | 130 | 145 | 0.67 (0.47-0.96) | 0.028 | 131 | 140 | 0.91 (0.64-1.29) | 0.602 | ||
| Recessive | GG-CG | 236 | 209 | 1 | 230 | 235 | 1 | |||
| CC | 20 | 30 | 0.59 (0.32-1.07) | 0.080 | 20 | 21 | 0.98 (0.52-1.86) | 0.947 | ||
| Log-additive | — | — | — | 0.71 (0.54-0.93) | 0.014 | — | — | 0.94 (0.71-1.24) | 0.659 | |
p values were calculated by logistic regression adjusted by age. p < 0.05 indicates statistical significance.
Figure 1Haplotype block map for SNPs in the TCF7L1 gene. The numbers inside the diamonds indicate the D′ for pairwise analyses.
The haplotype frequencies of TCF7L1 SNPs and their associations with cervical cancer susceptibility.
| SNP | Haplotype | Frequency | Without adjusted | With adjusted | |||
|---|---|---|---|---|---|---|---|
| Case | Control | OR (95% CI) |
| OR (95% CI) |
| ||
| rs2366264|rs11689667|rs62162674 | TCC | 0.285 | 0.309 | 0.89 (0.73-1.08) | 0.237 | 0.89 (0.73-1.08) | 0.238 |
| rs2366264|rs11689667|rs62162674 | GTC | 0.012 | 0.026 | 0.44 (0.22-0.88) | 0.020 | 0.43 (0.21-0.86) | 0.018 |
| rs2366264|rs11689667|rs62162674 | GTG | 0.308 | 0.343 | 0.84 (0.69-1.02) | 0.079 | 0.84 (0.69-1.02) | 0.076 |
p value calculated by Wald test with and without adjusted by age.
Figure 2SNP-SNP interaction dendrogram. Yellow and blue represent redundancy or correlation.
The analysis of SNP-SNP interaction models with the MDR method.
| Model | Training Bal. Acc. | Testing Bal. Acc. | CVC | OR (95% CI) |
|
|---|---|---|---|---|---|
| rs11904127 | 0.549 | 0.540 | 10/10 | 1.53 (1.18-1.99) | 0.001 |
| rs11904127, rs2366264 | 0.556 | 0.507 | 7/10 | 1.57 (1.21-2.04) | <0.001 |
| rs11904127, rs2366264, rs62162674 | 0.564 | 0.507 | 10/10 | 1.70 (1.31-2.22) | <0.0001 |
| rs11904127, rs2366264, rs11689667, rs62162674 | 0.565 | 0.499 | 10/10 | 1.70 (1.31-2.20) | <0.0001 |
Bal. Acc.: balanced accuracy; CVC: cross-validation consistently. p values were calculated by χ2 test. p < 0.05 indicates statistical significance.