Table 2.
DNA methylation diagnostics for the early recurrence (ER) group based on pyrosequencing data
| Probe IDa | Positionb | DNA methylation statusc | AUC | Cut-off value (%) |
Initial cohort | Validation cohort | ||
|---|---|---|---|---|---|---|---|---|
| Sensitivity (%)d | Specificity (%)e | Sensitivity (%)d | Specificity (%)e | |||||
| cg00945409 | 1 | ER < non-ER | 0.778 | 58.6 | 90.9 | 60.0 | 66.7 | 44.4 |
| 2 | 0.764 | 71.6 | 86.4 | 68.3 | 22.2 | 88.9 | ||
| cg07846168 | 1 | ER < non-ER | 0.791 | 61.3 | 95.5 | 56.7 | NA | NA |
| cg17206555 | 1 | ER < non-ER | 0.811 | 23.5 | 86.4 | 71.7 | 66.7 | 77.8 |
| 2 | 0.760 | 18.7 | 86.4 | 65.0 | 55.6 | 74.1 | ||
| cg02046247 | 1 | ER < non-ER | 0.775 | 79.0 | 90.9 | 60.0 | 88.9 | 63.0 |
| 2 | 0.739 | 92.0 | 86.4 | 53.3 | 88.9 | 7.41 | ||
| cg18289710 | 1 | ER < non-ER | 0.759 | 61.6 | 72.7 | 70.0 | 77.8 | 22.2 |
| cg09229620 | 2 | ER < non-ER | 0.708 | 41.7 | 77.3 | 56.7 | NA | NA |
| 3 | 0.715 | 62.8 | 77.3 | 56.7 | NA | NA | ||
| cg15930703 | 1 | ER < non-ER | 0.753 | 42.9 | 100 | 40.0 | 88.9 | 14.8 |
| 2 | 0.730 | 28.9 | 63.6 | 80.0 | 55.6 | 40.7 | ||
| cg21873275 | 1 | ER < non-ER | 0.744 | 77.7 | 72.7 | 68.3 | 44.4 | 74.1 |
| cg02192855 | 1 | ER > non-ER | 0.720 | 13.1 | 50.0 | 93.3 | 22.2 | 63.0 |
| 3 | 0.773 | 7.32 | 81.8 | 60.0 | 44.4 | 37.0 | ||
| cg19918599 | 1 | ER < non-ER | 0.759 | 77.9 | 86.4 | 58.3 | 77.8 | 55.6 |
| 2 | 0.721 | 70.2 | 77.3 | 60.0 | 77.8 | 59.3 | ||
| cg20549290 | 1 | ER < non-ER | 0.777 | 84.1 | 72.7 | 75.0 | NA | NA |
| 2 | 0.739 | 82.0 | 77.3 | 61.7 | NA | NA | ||
| cg14064694 | 2 | ER > non-ER | 0.714 | 19.0 | 54.6 | 81.7 | 33.3 | 51.9 |
| 3 | 0.759 | 9.99 | 95.5 | 45.0 | 77.8 | 29.6 | ||
| 4 | 0.710 | 34.4 | 40.9 | 95.0 | 11.1 | 77.8 | ||
AUC area under the curve value obtained by receiver-operating characteristic curve analysis, NA not analyzed due to PCR failure
aProbe IDs for the Infinium HumanMethylation450 BeadChip (Illumina)
bInfinium probe CpG sites and their neighboring CpG sites which were analyzed using pyrosequencing and numbered as shown in Table S2. Exact Infinium probe CpG sites are underlined
c“ER < non-ER”, when the DNA methylation level of the sample was lower than the cut-off value, the sample was diagnosed as belonging to the ER group; “ER > non-ER”, when the DNA methylation level of the sample was higher than the cut-off value, the sample was diagnosed as belonging to the ER group
dSensitivity is defined as the ratio of the number of tissue samples diagnosed as belonging to the ER group based on the criteria relative to the exact number of the patients belonging to the ER group
eSpecificity is defined as the ratio of the number of tissue samples not diagnosed as belonging to the ER group using the criteria employed, relative to the exact number of patients belonging to the non-ER group