Table 3.
The density of methylation estimated by semiquantitative methylation-specific PCR analysis and sequencing of common PCR DNA
| Methylation-specific PCR | |||||
| CpG sites* | Case no. | 32-cycle amplicons using radioisope | 37-cycle amplicons using ethidium bromide | % Methylation in 10 common PCR clones | |
| MYBPC2, -1.2 kb | 1 | Normal | Level 4 | Level 4 | 53/70‡ (76%) |
| Tumor | Level 4 | Level 4 | 48/70 (69%) | ||
| 26 | Normal | Level 4 | Level 4 | 47/70 (67%) | |
| Tumor | Level 3 | No band | 32/70 (46%) | ||
| VDR, -0.7 kb | 1 | Normal | Level 1 | Level 1 | 4/130 (3%) |
| Tumor | Level 1 | Level 1 | 12/130 (9%) | ||
| 26 | Normal | Level 2 | Level 2 | 44/130 (34%) | |
| Tumor | Level 3 | Level 3 | 64/130 (49%) | ||
| MLH1, -1.0 kb | 1 | Normal | Level 3 | Level 3 | 14/30 (47%) |
| Tumor | Level 2 | Level 3† | 10/30 (33%) | ||
| 26 | Normal | Level 2 | No band | 9/30 (30%) | |
| Tumor | Level 4† | Level 3 | 17/30 (57%) | ||
| MLH1, -0.6 kb | 1 | Normal | Level 1 | Level 1 | 0/200 (0%) |
| Tumor | Level 1 | Level 1 | 0/200 (0%) | ||
| 26 | Normal | Level 1 | Level 1 | 4/200 (2%) | |
| Tumor | Level 1 | Level 1 | 4/200 (2%) | ||
| CDKN2A, -1.5 kb | 1 | Normal | Level 2 | Level 2 | 19/60 (32%) |
| Tumor | Level 1 | Level 1 | 5/60 (8%) | ||
| 26 | Normal | Level 2 | Level 2 | 13/60 (22%) | |
| Tumor | Level 5 | No band | 54/60 (90%) | ||
| CDKN2A, 0 kb | 1 | Normal | Level 1 | Level 1 | 0/110 (0%) |
| Tumor | Level 1 | Level 1 | 0/110 (0%) | ||
| 26 | Normal | Level 1 | Level 1 | 0/110 (0%) | |
| Tumor | Level 4 | Level 3† | 76/110 (69%) | ||
| RUNX2, -3.0 kb | 1 | Normal | Level 1 | Level 1 | 8/60 (13%) |
| Tumor | Level 1 | Level 1 | 8/60 (13%) | ||
| 26 | Normal | Level 2† | No band | 11/60 (18%) | |
| Tumor | Level 2† | Level 1 | 9/60 (15%) | ||
| RUNX3, -1.7 kb | 1 | Normal | Level 1 | Level 1 | 6/70 (10%) |
| Tumor | Level 3 | Level 3 | 38/70 (54%) | ||
| 26 | Normal | Level 2 | Level 3† | 27/70 (39%) | |
| Tumor | Level 4 | Level 3† | 45/70 (64%) | ||
| MAGEA2, 0 kb | 1 | Normal | Level 5 | Level 5 | 106/110 (96%) |
| Tumor | Level 2 | Level 2 | 41/110 (37%) | ||
| 26 | Normal | Level 5 | Level 5 | 104/110 (95%) | |
| Tumor | Level 5 | Level 5 | 103/110 (94%) | ||
| TFF2, -0.2 kb | 1 | Normal | Level 2 | Level 3† | 21/60 (35%) |
| Tumor | Level 2 | Level 3† | 19/60 (32%) | ||
| 26 | Normal | Level 3 | Level 3 | 32/60 (53%) | |
| Tumor | Level 2† | Level 3 | 25/60 (42%) | ||
| SERPINB5, -0.3 kb | 1 | Normal | Level 3 | Level 3 | 36/70 (51%) |
| Tumor | Level 2† | No band | 31/70 (44%) | ||
| 26 | Normal | Level 2 | Level 3† | 26/70 (37%) | |
| Tumor | Level 2 | No band | 27/70 (39%) | ||
| MSLN, -0.8 kb | 1 | Normal | Level 5 | Level 5 | 66/70 (94%) |
| Tumor | Level 3 | Level 4† | 38/70 (54%) | ||
| 26 | Normal | Level 4 | Level 4 | 51/70 (73%) | |
| Tumor | Level 5 | Level 5 | 61/70 (87%) | ||
*CpG sites are indicated by the name of the gene and the distance from the transcription start site.
†Different results between methylation-specific PCR and common PCR DNA.
‡'/' separates the number of the methylated CpGs and the total CpGs.