Table 1.
DNA methylation levels obtained by Infinium assay for tissue samples of normal control urothelium (C), non-cancerous urothelium (N) from patients with upper urinary tract urothelial carcinoma (UTUC), and the corresponding UTUCs in the initial cohort and urinary bladder urothelial carcinoma (BUC)
| DNA methylation levels (mean ± SD) |
UTUC vs C |
UTUC vs N |
N vs C |
UTUC vs BUC |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Probe IDa | CpG typeb | C (n = 26) | N (n = 31) | UTUC (n = 31) | BUC (n = 14) | P | AUC | P | AUC | P | P |
| cg01227537 | Island | 0.116 ± 0.050 | 0.147 ± 0.080 | 0.424 ± 0.304 | 0.499 ± 0.198 | 4.51 × 10−16 | 1.00 | 1.10 × 10−16 | 1.00 | 1.00 | 2.75 × 10−3 |
| cg01921432 | Island | 0.151 ± 0.032 | 0.180 ± 0.053 | 0.455 ± 0.303 | 0.579 ± 0.161 | 1.57 × 10−13 | 1.00 | 1.50 × 10−13 | 1.00 | 1.00 | 7.63 × 10−3 |
| cg05492975 | Island | 0.859 ± 0.038 | 0.830 ± 0.044 | 0.538 ± 0.310 | 0.382 ± 0.137 | 1.27 × 10−17 | 1.00 | 3.80 × 10−17 | 1.00 | 1.00 | 5.37 × 10−3 |
| cg07197785 | Island | 0.230 ± 0.087 | 0.185 ± 0.083 | 0.479 ± 0.316 | 0.626 ± 0.183 | 2.85 × 10−18 | 1.00 | 5.03 × 10−20 | 1.00 | 1.00 | 1.51 × 10−2 |
| cg07418387 | Shelf | 0.779 ± 0.045 | 0.710 ± 0.072 | 0.440 ± 0.287 | 0.283 ± 0.127 | 4.43 × 10−23 | 1.00 | 2.86 × 10−23 | 1.00 | 1.00 | 7.91 × 10−3 |
| cg08070771 | Shore | 0.128 ± 0.041 | 0.189 ± 0.081 | 0.489 ± 0.314 | 0.487 ± 0.268 | 7.45 × 10−23 | 1.00 | 1.55 × 10−24 | 1.00 | 1.00 | 1.28 × 10−3 |
| cg08364561 | Shore | 0.092 ± 0.046 | 0.122 ± 0.075 | 0.444 ± 0.344 | 0.662 ± 0.143 | 8.12 × 10−19 | 1.00 | 4.34 × 10−20 | 1.00 | 1.00 | 3.33 × 10−2 |
| cg10216717 | Shore | 0.806 ± 0.034 | 0.782 ± 0.055 | 0.501 ± 0.303 | 0.338 ± 0.132 | 3.52 × 10−16 | 1.00 | 9.28 × 10−17 | 1.00 | 1.00 | 1.14 × 10−2 |
| cg10256242 | Shore | 0.864 ± 0.032 | 0.856 ± 0.046 | 0.558 ± 0.321 | 0.443 ± 0.150 | 7.27 × 10−15 | 1.00 | 3.23 × 10−15 | 1.00 | 1.00 | 9.87 × 10−4 |
| cg10874111 | Shore | 0.772 ± 0.046 | 0.803 ± 0.059 | 0.529 ± 0.296 | 0.415 ± 0.162 | 5.85 × 10−15 | 1.00 | 2.10 × 10−16 | 1.00 | 1.00 | 4.40 × 10−3 |
| cg14302471 | Shore | 0.783 ± 0.072 | 0.814 ± 0.075 | 0.501 ± 0.335 | 0.370 ± 0.210 | 2.06 × 10−18 | 1.00 | 2.73 × 10−19 | 1.00 | 1.00 | 9.18 × 10−3 |
| cg14851578 | Shore | 0.768 ± 0.055 | 0.781 ± 0.060 | 0.482 ± 0.319 | 0.335 ± 0.208 | 6.56 × 10−18 | 1.00 | 2.21 × 10−18 | 1.00 | 1.00 | 2.33 × 10−2 |
| cg15822765 | Island | 0.120 ± 0.038 | 0.185 ± 0.082 | 0.493 ± 0.330 | 0.692 ± 0.128 | 9.32 × 10−19 | 1.00 | 2.81 × 10−20 | 1.00 | 1.00 | 1.66 × 10−2 |
| cg16529477 | Shore | 0.128 ± 0.043 | 0.155 ± 0.056 | 0.428 ± 0.303 | 0.513 ± 0.195 | 3.85 × 10−13 | 1.00 | 8.16 × 10−13 | 1.00 | 1.00 | 5.42 × 10−3 |
| cg16705627 | Island | 0.198 ± 0.072 | 0.247 ± 0.104 | 0.519 ± 0.297 | 0.695 ± 0.112 | 2.63 × 10−21 | 1.00 | 4.41 × 10−20 | 1.00 | 1.00 | 1.79 × 10−2 |
| cg18077971 | Shore | 0.137 ± 0.060 | 0.165 ± 0.079 | 0.475 ± 0.335 | 0.583 ± 0.192 | 2.46 × 10−18 | 1.00 | 1.62 × 10−18 | 1.00 | 1.00 | 2.23 × 10−3 |
| cg24035245 | Island | 0.186 ± 0.070 | 0.225 ± 0.094 | 0.500 ± 0.296 | 0.653 ± 0.161 | 1.01 × 10−22 | 1.00 | 5.05 × 10−22 | 1.00 | 1.00 | 2.12 × 10−2 |
| cg26132774 | Island | 0.085 ± 0.040 | 0.104 ± 0.046 | 0.428 ± 0.348 | 0.646 ± 0.141 | 9.09 × 10−16 | 1.00 | 1.94 × 10−15 | 1.00 | 1.00 | 3.80 × 10−2 |
AUC: area under the curve for receiver operating characteristic curve analysis. aProbe IDs for the Infinium HumanMethylation450 BeadChip (Illumina). bCpG islands, island shores (2000-bp region adjacent to a CpG island) and island shelves (2000-bp region adjacent to island shores) are identified based on the University of California, Santa Cruz (UCSC) genome browser (https://genome.ucsc.edu/).