Background
Methods
Study population
SNP selection and genotyping
SNP | First-PCRP | Second-PCRP | UEP_DIR | UEP_SEQ |
---|---|---|---|---|
rs6907943 | ACGTTGGATGACCAGGTGTTGGAGTTCAGC | ACGTTGGATGGGTGTTTGTTTGCAGCTCGT | F | tgtgTGCAGCTCGTTAGCAT |
rs2077681 | ACGTTGGATGGTGAATTTAACTGCACTGGG | ACGTTGGATGAACCTCGAGGACATCATGCC | R | ggggtACATCATGCCAAGTGGA |
rs9503400 | ACGTTGGATGAGTAAGTGCTCAGTAAACGG | ACGTTGGATGTGCTCAAGGCTGTCTAGGTG | R | ggagGGCTGTCTAGGTGTTCTTTG |
rs17548629 | ACGTTGGATGTCAACAGTATCAGCCCTGAG | ACGTTGGATGTGGCATTCTGGTACCTTCAC | F | ccccTCACCCAGCCTGAGTG |
Statistical analysis
Results
Characteristics | Cervical cancer cases (N = 342) | Healthy controls (N = 498) | P Value |
---|---|---|---|
Age (year, mean ± SD) | 43.27 ± 11.78 | 43.46 ± 13.03 | 0.832 |
> 43 | 176 (51%) | 263 (53%) | |
≤ 43 | 166 (49%) | 235 (47%) | |
Stage (%) | |||
I II | 132 (39%) | ||
III IV | 80 (23%) | ||
Absence | 130 (38%) |
SNP | Chromosome | BP | Alleles | Group | Genotype | Allele | MAF | HWE p | HaploReg | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|
rs6907943 | 6 | 3,078,032 | A/C | CC | CA | AA | C | A | Enhancer histone marks, Motifs changed, Selected eQTL hits | |||
Control | 13 (2.62%) | 129 (25.96%) | 355 (71.42%) | 155 (15.59%) | 839 (84.41%) | 0.156 | 0.734 | |||||
Case | 15 (4.40%) | 77 (22.58%) | 249 (73.02%) | 107 (15.69%) | 575 (84.31%) | 0.157 | ||||||
rs2077681 | 6 | 3,085,866 | A/G | CC | CT | TT | C | T | Motifs changed, Selected eQTL hits | |||
Control | 9 (1.82%) | 140 (28.28%) | 346 (69.90%) | 158 (15.96%) | 832 (84.04%) | 0.160 | 0.313 | |||||
Case | 19 (5.57%) | 89 (26.10%) | 233 (68.33%) | 127 (18.62%) | 555 (81.38%) | 0.186 | ||||||
rs9503400 | 6 | 3,108,673 | A/G | AA | AG | GG | A | G | Enhancer histone marks, Motifs changed | |||
Control | 1 (0.20%) | 47 (9.44%) | 450 (90.36%) | 49 (4.92%) | 947 (95.08%) | 0.051 | 1.000 | |||||
Case | 3 (0.88%) | 39 (11.40%) | 300 (87.72%) | 45 (6.58%) | 639 (93.42%) | 0.066 | ||||||
rs17548629 | 6 | 3,114,223 | C/T | TT | TC | CC | T | C | Motifs changed | |||
Control | 9 (1.81%) | 122 (24.50%) | 367 (73.69%) | 140 (14.06%) | 856 (85.94%) | 0.141 | 0.855 | |||||
Case | 10 (2.92%) | 72 (21.05%) | 260 (76.03%) | 92 (13.45%) | 592 (86.55%) | 0.134 |
SNP | Model | Allele/Genotype | Frequency (Control/Case) | OR (95%CI) | P Value | FDR-p Value |
---|---|---|---|---|---|---|
rs6907943 | Allele | C | 15.59%/15.69% | 1.01 (0.77–1.32) | 0.958 | 0.958 |
A | 84.41%/84.31% | 1.00 | ||||
Codominant | CC | 2.62%/4.40% | 1.65 (0.77–3.52) | 0.199 | 0.597 | |
CA | 25.96%/22.58% | 0.85 (0.61–1.18) | 0.333 | 0.666 | ||
AA | 71.42%/73.02% | 1.00 | ||||
Dominant | CC-CA | 28.58%/26.98% | 0.92 (0.68–1.26) | 0.616 | 0.924 | |
AA | 71.42%/73.02% | 1.00 | ||||
Recessive | CC | 2.62%/4.40% | 1.72 (0.81–3.65) | 0.162 | 0.597 | |
CA-AA | 97.38%/95.60% | 1.00 | ||||
Log-additive | 1.01 (0.78–1.31) | 0.956 | 0.958 | |||
rs2077681 | Allele | C | 15.96%/18.62% | 1.21 (0.93–1.56) | 0.155 | 0.245 |
T | 84.04%/81.38% | 1.00 | ||||
Codominant | CC | 1.82%/5.57% | 3.14 (1.40–7.07) | 0.006 | 0.018 | |
CT | 28.28%/26.10% | 0.94 (0.69–1.29) | 0.711 | 0.711 | ||
TT | 69.90%/68.33% | 1.00 | ||||
Dominant | CC-CT | 30.10%/31.67% | 1.08 (0.80–1.45) | 0.634 | 0.711 | |
TT | 69.90%/68.33% | 1.00 | ||||
Recessive | CC | 1.82%/5.57% | 3.20 (1.43–7.16) | 0.005 | 0.018 | |
CT-TT | 98.18%/94.43% | 1.00 | ||||
Log-additive | 1.20 (0.93–1.54) | 0.163 | 0.245 | |||
rs9503400 | Allele | A | 4.92%/6.58% | 1.36 (0.90–2.07) | 0.146 | 0.271 |
G | 95.08%/93.42% | 1.00 | ||||
Codominant | AA | 0.20%/0.88% | 4.46 (0.46–43.25) | 0.197 | 0.271 | |
GA | 9.44%/11.40% | 1.25 (0.79–1.95) | 0.339 | 0.339 | ||
GG | 90.36%/87.72% | 1.00 | ||||
Dominant | AA-GA | 9.64%/12.28% | 1.31 (0.85–2.04) | 0.226 | 0.271 | |
GG | 90.36%/87.72% | 1.00 | ||||
Recessive | AA | 0.20%/0.88% | 4.36 (0.45–42.26) | 0.203 | 0.271 | |
GA-GG | 99.8%/99.12% | 1.00 | ||||
Log-additive | 1.35 (0.89–2.03) | 0.155 | 0.271 | |||
rs17548629 | Allele | T | 14.06%/13.45% | 0.95 (0.72–1.26) | 0.724 | 0.724 |
C | 85.94%/86.55% | 1.00 | ||||
Codominant | TT | 1.81%/2.92% | 1.57 (0.63–3.92) | 0.334 | 0.663 | |
TC | 24.50%/21.05% | 0.83 (0.60–1.16) | 0.277 | 0.663 | ||
CC | 73.69%/76.03% | 1.00 | ||||
Dominant | TT-TC | 26.31%/23.97% | 0.88 (0.64–1.21) | 0.442 | 0.663 | |
CC | 73.69%/76.03% | 1.00 | ||||
Recessive | TT | 1.81%/2.92% | 1.64 (0.66–4.07) | 0.289 | 0.663 | |
TC-CC | 98.19%/97.08% | 1.00 | ||||
Log-additive | 0.95 (0.72–1.26) | 0.724 | 0.724 |
SNP | Model | Age (Cases Vs. Controls) | Stage (III/IV Vs. I/II) | |||||||
---|---|---|---|---|---|---|---|---|---|---|
> 43 (176 Vs. 263) | ≤ 43 (166 Vs. 235) | 80 Vs. 132 | ||||||||
OR (95%CI) | p Value | FDR-p Value | OR (95%CI) | p Value | FDR-p Value | OR (95%CI) | p Value | FDR-p Value | ||
rs6907943 | Allele (15.91–14.83%/84.09–85.17%) | 1.09 (0.75–1.58) | 0.663 | 0.796 | 0.93 (0.63–1.37) | 0.705 | 0.705 | 0.47 (0.24–0.90) | 0.021 | 0.041 |
Codominant | 1.91 (0.69–5.26) | 0.211 | 0.633 | 1.35 (0.42–4.29) | 0.614 | 0.705 | – | – | – | |
0.89 (0.56–1.42) | 0.629 | 0.796 | 0.80 (0.50–1.27) | 0.335 | 0.705 | 0.50 (0.25–1.02) | 0.056 | 0.056 | ||
Dominant | 0.99 (0.65–1.53) | 0.979 | 0.979 | 0.84 (0.54–1.31) | 0.449 | 0.705 | 0.46 (0.23–0.93) | 0.031 | 0.041 | |
Recessive | 1.96 (0.72–5.37) | 0.190 | 0.633 | 1.43 (0.45–4.53) | 0.542 | 0.705 | – | – | – | |
Log-additive | 1.08 (0.76–1.55) | 0.656 | 0.796 | 0.92 (0.63–1.34) | 0.650 | 0.705 | 0.46 (0.23–0.89) | 0.022 | 0.041 | |
rs2077681 | Allele (18.57–15.46%/81.43–84.54%) | 1.25 (0.87–1.79) | 0.227 | 0.387 | 1.16 (0.80–1.68) | 0.430 | 0.698 | 0.69 (0.40–1.20) | 0.187 | 0.306 |
Codominant | 3.38 (1.15–9.99) | 0.027 | 0.081 | 2.83 (0.83–9.66) | 0.096 | 0.288 | 1.39 (0.33–5.77) | 0.652 | 0.652 | |
0.92 (0.59–1.43) | 0.708 | 0.717 | 0.94 (0.60–1.47) | 0.779 | 0.851 | 0.47 (0.24–0.94) | 0.034 | 0.204 | ||
Dominant | 1.08 (0.71–1.64) | 0.717 | 0.717 | 1.04 (0.68–1.6) | 0.851 | 0.851 | 0.55 (0.29–1.05) | 0.070 | 0.210 | |
Recessive | 3.46 (1.18–10.15) | 0.024 | 0.081 | 2.89 (0.85–9.77) | 0.088 | 0.288 | 1.67 (0.41–6.89) | 0.478 | 0.574 | |
Log-additive | 1.22 (0.86–1.73) | 0.258 | 0.387 | 1.15 (0.79–1.66) | 0.465 | 0.698 | 0.71 (0.42–1.21) | 0.204 | 0.306 | |
rs9503400 | Allele (6.25–4.94%/93.75–95.06%) | 1.28 (0.71–2.30) | 0.404 | 0.404 | 1.45 (0.80–2.63) | 0.222 | 0.347 | 3.42 (1.55–7.56) | 0.001 | 0.004 |
Codominant | – | – | – | 4.41 (0.45–42.80) | 0.201 | 0.347 | – | – | – | |
– | – | – | 1.21 (0.61–2.37) | 0.585 | 0.585 | 3.37 (1.45–7.82) | 0.005 | 0.005 | ||
Dominant | 1.30 (0.71–2.38) | 0.392 | 0.404 | 1.36 (0.71–2.58) | 0.355 | 0.426 | 3.57 (1.55–8.22) | 0.003 | 0.004 | |
Recessive | – | – | – | 4.33 (0.45–41.98) | 0.207 | 0.347 | – | – | – | |
Log-additive | 1.30 (0.71–2.38) | 0.392 | 0.404 | 1.41 (0.80–2.49) | 0.231 | 0.347 | 3.53 (1.56–7.98) | 0.002 | 0.004 | |
rs17548629 | Allele (14.49–12.36%/85.51–87.64%) | 1.20 (0.81–1.78) | 0.361 | 0.579 | 0.74 (0.49–1.12) | 0.153 | 0.355 | 0.41 (0.21–0.83) | 0.011 | 0.036 |
Codominant | 3.99 (1.04–15.32) | 0.044 | 0.132 | 0.44 (0.09–2.20) | 0.315 | 0.355 | – | – | – | |
0.89 (0.56–1.44) | 0.645 | 0.774 | 0.76 (0.48–1.22) | 0.256 | 0.355 | 0.52 (0.24–1.10) | 0.086 | 0.086 | ||
Dominant | 1.05 (0.67–1.63) | 0.846 | 0.846 | 0.73 (0.47–1.16) | 0.185 | 0.355 | 0.44 (0.21–0.93) | 0.031 | 0.041 | |
Recessive | 4.09 (1.07–15.63) | 0.040 | 0.132 | 0.47 (0.09–2.34) | 0.355 | 0.355 | – | – | – | |
Log-additive | 1.19 (0.81–1.74) | 0.386 | 0.579 | 0.74 (0.49–1.11) | 0.147 | 0.355 | 0.43 (0.22–0.87) | 0.018 | 0.036 |