| Literature DB >> 35480322 |
Shiyang Wang1, Xiulin Wen2, Ruimin Zhao1, Yanxia Bai1.
Abstract
Background: Laryngeal cancer is more common in middle-aged and older men. We conducted an association analysis between ZNF208 polymorphisms and laryngeal cancer (LC) risk in the Northwestern Chinese Han male.Entities:
Keywords: Northwestern Chinese Han male; ZNF208 gene; case-control study; genetic variants; laryngeal cancer
Year: 2022 PMID: 35480322 PMCID: PMC9035488 DOI: 10.3389/fgene.2022.813823
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.772
Characteristics of the cases and controls included in the study.
| Characteristics | Case (%) | Control (%) |
| |
|---|---|---|---|---|
| Number | 172 | 180 | ||
| Gender | Male | 172 | 180 | |
| Age (years), mean ± SD | 60.78 ± 10.05 | 60.25 ± 5.48 | 0.538 | |
| Lymph node metastasis | No | 117 (68.02) | ||
| Yes | 55 (31.98) | |||
| Smoking | No | 37 (21.51) | ||
| Yes | 135 (78.49) | |||
Allele frequencies of the four SNPs in ZNF208.
| SNP_ID | Chr. | Position | Allele | HaploReg | MAF | HWE | OR (95%CI) |
| FDR test | |
|---|---|---|---|---|---|---|---|---|---|---|
| Case | Control | |||||||||
| rs2188972 | 19p12 | Intron | A/G | Motifs changed, selected eQTL hits | 0.515 | 0.485 | 0.654 | 1.22 (0.91–1.65) | 0.178 | 0.445 |
| rs2188971 | 19p12 | Intron | T/C | Selected eQTL hits | 0.301 | 0.251 | 1.000 | 1.28 (0.91–1.79) | 0.146 | 0.243 |
| rs8103163 | 19p12 | Intron | A/C | Motifs changed, selected eQTL hits | 0.322 | 0.253 | 1.000 |
|
| 0.108 |
| rs7248488 | 19p12 | Intron | A/C | Motifs changed, selected eQTL hits | 0.329 | 0.253 | 1.000 |
|
| 0.063 |
MAF, Minor allele frequency; HWE, Hardy-Weinberg equilibrium; OR, odds ratio; 95%CI: 95% confidence interval. p < 0.05 indicates statistical significance. Bold values indicate a significant difference.
Genotypic model analysis of the relationship between the ZNF208 SNPs and the risk of LC.
| Model | Genotype | Control | Case | Adjusted by age | ||
|---|---|---|---|---|---|---|
| OR (95%CI) |
| FDR test | ||||
| rs2188972 | — | |||||
| Codominant | G/G | 50 (27.8%) | 37 (21.6%) | 1 | 0.350 | 0.350 |
| G/A | 93 (51.7%) | 92 (53.8%) | 1.33 (0.80–2.23) | |||
| A/A | 37 (20.6%) | 42 (24.6%) | 1.55 (0.84–2.87) | |||
| Dominant | G/G | 50 (27.8%) | 37 (21.6%) | 1 | 0.180 | 0.300 |
| G/A-A/A | 130 (72.2%) | 134 (78.4%) | 1.39 (0.86–2.27) | |||
| Recessive | G/G-G/A | 143 (79.4%) | 129 (75.4%) | 1 | 0.340 | 0.425 |
| A/A | 37 (20.6%) | 42 (24.6%) | 1.28 (0.77–2.11) | |||
| Log-additive | --- | --- | --- | 1.25 (0.92–1.70) | 0.160 | 0.800 |
| rs2188971 | ||||||
| Codominant | C/C | 100 (55.9%) | 81 (50.3%) | 1 | 0.260 | 0.325 |
| C/T | 68 (38%) | 63 (39.1%) | 1.15 (0.73–1.80) | |||
| T/T | 11 (6.2%) | 17 (10.6%) | 1.95 (0.86–4.40) | |||
| Dominant | C/C | 100 (55.9%) | 81 (50.3%) | 1 | 0.290 | 0.290 |
| C/T-T/T | 79 (44.1%) | 80 (49.7%) | 1.26 (0.82–1.93) | |||
| Recessive | C/C-C/T | 168 (93.8%) | 144 (89.4%) | 1 | 0.130 | 0.650 |
| T/T | 11 (6.2%) | 17 (10.6%) | 1.83 (0.83–4.05) | |||
| Log-additive | --- | --- | --- | 1.28 (0.92–1.79) | 0.140 | 0.350 |
| rs8103163 | ||||||
| Codominant | C/C | 100 (55.6%) | 81 (47.4%) | 1 | 0.097 | 0.121 |
| C/A | 69 (38.3%) | 70 (40.9%) | 1.25 (0.81–1.96) | |||
| A/A | 11 (6.1%) | 20 (11.7%) | 2.30 (1.04–5.10) | |||
| Dominant | C/C | 100 (55.6%) | 81 (47.4%) | 1 | 0.120 | 0.120 |
| C/A-A/A | 80 (44.4%) | 90 (52.6%) | 1.40 (0.92–2.13) | |||
| Recessive | C/C-C/A | 169 (93.9%) | 151 (88.3%) | 1 | 0.056 | 0.093 |
| A/A | 11 (6.1%) | 20 (11.7%) | 2.09 (0.97–4.51) | |||
| Log-additive | --- | --- | --- |
|
| 0.210 |
| rs7248488 | ||||||
| Codominant | C/C | 100 (55.6%) | 80 (47.1%) | 1 | 0.052 | 0.065 |
| C/A | 69 (38.3%) | 68 (40%) | 1.24 (0.79–1.94) | |||
| A/A | 11 (6.1%) | 22 (12.9%) | 2.56 (1.17–5.60) | |||
| Dominant | C/C | 100 (55.6%) | 80 (47.1%) | 1 | 0.100 | 0.100 |
| C/A-A/A | 80 (44.4%) | 90 (52.9%) | 1.42 (0.93–2.16) | |||
| Recessive | C/C-C/A | 169 (93.9%) | 148 (87.1%) | 1 |
| 0.063 |
| A/A | 11 (6.1%) | 22 (12.9%) |
| |||
| Log-additive | --- | --- | --- |
|
|
|
OR, odds ratio; CI, confidence interval. p values were calculated by Wald test by unconditional logistic regression adjusted by age. Bold values indicate a significant difference (p < 0.05).
Association analysis result between the ZNF208 SNPs and the risk of LC based on the smoking stratification.
| Model | Genotype | Smoking = no | Smoking = yes | OR (95%CI) |
| FDR test |
|---|---|---|---|---|---|---|
| rs2188972 | ||||||
| Codominant | G/G | 24 (26.1%) | 45 (23.7%) | 1 | 0.310 | 0.413 |
| G/A | 53 (57.6%) | 99 (52.1%) | 1.00 (0.55–1.81) | |||
| A/A | 15 (16.3%) | 46 (24.2%) | 1.64 (0.76–3.51) | |||
| Dominant | G/G | 24 (26.1%) | 45 (23.7%) | 1 | 0.660 | 0.660 |
| G/A-A/A | 68 (73.9%) | 145 (76.3%) | 1.14 (0.64–2.02) | |||
| Recessive | G/G-G/A | 77 (83.7%) | 144 (75.8%) | 1 | 0.120 | 0.480 |
| A/A | 15 (16.3%) | 46 (24.2%) | 1.64 (0.86–3.13) | |||
| Log-additive | --- | --- | --- | 1.25 (0.87–1.81) | 0.230 | 0.460 |
| rs2188971 | ||||||
| Codominant | C/C | 49 (56.3%) | 96 (51.9%) | 1 | 0.150 | 0.300 |
| T/C | 35 (40.2%) | 71 (38.4%) | 1.04 (0.61–1.76) | |||
| T/T | 3 (3.5%) | 18 (9.7%) | 3.06 (0.86–10.90) | |||
| Dominant | C/C | 49 (56.3%) | 96 (51.9%) | 1 | 0.490 | 0.490 |
| T/C-T/T | 38 (43.7%) | 89 (48.1%) | 1.20 (0.72–2.00) | |||
| Recessive | C/C-T/C | 84 (96.5%) | 167 (90.3%) | 1 | 0.053 | 0.212 |
| T/T | 3 (3.5%) | 18 (9.7%) | 3.02 (0.86–10.53) | |||
| Log-additive | --- | --- | --- | 1.32 (0.87–1.99) | 0.190 | 0.253 |
| rs8103163 | ||||||
| Codominant | C/C | 49 (53.9%) | 96 (50.3%) | 1 | 0.420 | 0.560 |
| C/A | 37 (40.7%) | 76 (39.8%) | 1.05 (0.62–1.77) | |||
| A/A | 5 (5.5%) | 19 (9.9%) | 1.94 (0.68–5.51) | |||
| Dominant | C/C | 49 (53.9%) | 96 (50.3%) | 1 | 0.570 | 0.570 |
| C/A-A/A | 42 (46.1%) | 95 (49.7%) | 1.15 (0.70–1.90) | |||
| Recessive | C/C-C/A | 86 (94.5%) | 172 (90%) | 1 | 0.190 | 0.760 |
| A/A | 5 (5.5%) | 19 (9.9%) | 1.90 (0.69–5.26) | |||
| Log-additive | --- | --- | --- | 1.22 (0.82–1.81) | 0.320 | 0.640 |
| rs7248488 | ||||||
| Codominant | C/C | 49 (54.4%) | 95 (49.7%) | 1 | 0.300 | 0.400 |
| C/A | 36 (40%) | 75 (39.3%) | 1.07 (0.63–1.82) | |||
| A/A | 5 (5.6%) | 21 (11%) | 2.17 (0.77–6.10) | |||
| Dominant | C/C | 49 (54.4%) | 95 (49.7%) | 1 | 0.460 | 0.460 |
| C/A-A/A | 41 (45.6%) | 96 (50.3%) | 1.21 (0.73–2.00) | |||
| Recessive | C/C-C/A | 85 (94.4%) | 170 (89%) | 1 | 0.130 | 0.520 |
| A/A | 5 (5.6%) | 21 (11%) | 2.10 (0.77–5.76) | |||
| Log-additive | --- | --- | --- | 1.27 (0.86–1.89) | 0.220 | 0.440 |
FIGURE 1Haplotype block map for SNPs of the ZNF208 gene. Linkage disequilibrium plots containing 4 SNPs from ZNF208. Red squares display statistically significant associations between a pair of SNPs, as measured by D’; darker shades of red indicate higher D’.
MDR analysis for impact of ZNF208 variants on risk of LC.
| Model | Training bal. acc. | Testing bal. acc. | CV consistency | Accuracy | Sensitivity | Specificity | OR (95%CI) |
|
|---|---|---|---|---|---|---|---|---|
| rs2188971 | 0.555 | 0.506 | 6/10 | 0.552 | 0.163 | 0.942 | 3.15 (1.48–6.71) |
|
| rs2188972, rs2188971 | 0.583 | 0.555 | 9/10 | 0.581 | 0.488 | 0.674 | 1.98 (1.28–3.06) |
|
| rs2188972, rs2188971, rs8103163 | 0.591 | 0.567 | 9/10 | 0.590 | 0.506 | 0.674 | 2.12 (1.37–3.28) |
|
| rs2188972, rs2188971, rs8103163, rs7248488 | 0.594 | 0.573 | 10/10 | 0.593 | 0.512 | 0.674 | 2.17 (1.40–3.36) |
|
MDR, multifactor dimensionality reduction; bal. acc., balanced accuracy; CV, cross-validation; OR, odds ratio; CI, confidence interval. All p values in this study were two-tailed. Bold values indicate a significant difference (p < 0.05).
FIGURE 2SNP-SNP interaction of four SNPs on ZNF208 gene. (A) Dendrogram of SNP-SNP Interaction. The shorter the line connecting the 2 SNPs, the stronger the interaction. (B) Fruchterman-Reingold of interactions between the four genetic variants. Green and blue represent redundancy or correlation. Contrarily, the redder the color, the more the synergy effect between those four SNPs.