Table 3 The density of methylation estimated by semiquantitative methylation-specific PCR analysis and sequencing of common PCR DNA
| Â | Â | Â | Methylation-specific PCR | Â | |
|---|---|---|---|---|---|
CpG sites* | Case no. | Â | 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%) |
| Â | Â | Tumor | Level 4 | Level 4 | 48/70 (69%) |
| Â | 26 | Normal | Level 4 | Level 4 | 47/70 (67%) |
| Â | Â | Tumor | Level 3 | No band | 32/70 (46%) |
VDR, -0.7 kb | 1 | Normal | Level 1 | Level 1 | 4/130 (3%) |
| Â | Â | Tumor | Level 1 | Level 1 | 12/130 (9%) |
| Â | 26 | Normal | Level 2 | Level 2 | 44/130 (34%) |
| Â | Â | 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%) |
| Â | 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%) |
| Â | Â | Tumor | Level 1 | Level 1 | 0/200 (0%) |
| Â | 26 | Normal | Level 1 | Level 1 | 4/200 (2%) |
| Â | Â | Tumor | Level 1 | Level 1 | 4/200 (2%) |
CDKN2A, -1.5 kb | 1 | Normal | Level 2 | Level 2 | 19/60 (32%) |
| Â | Â | Tumor | Level 1 | Level 1 | 5/60 (8%) |
| Â | 26 | Normal | Level 2 | Level 2 | 13/60 (22%) |
| Â | Â | Tumor | Level 5 | No band | 54/60 (90%) |
CDKN2A, 0 kb | 1 | Normal | Level 1 | Level 1 | 0/110 (0%) |
| Â | Â | Tumor | Level 1 | Level 1 | 0/110 (0%) |
| Â | 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%) |
| Â | Â | 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%) |
| Â | Â | 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%) |
| Â | Â | Tumor | Level 2 | Level 2 | 41/110 (37%) |
| Â | 26 | Normal | Level 5 | Level 5 | 104/110 (95%) |
| Â | Â | 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%) |
| Â | 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%) |
| Â | Â | 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%) |
| Â | 26 | Normal | Level 4 | Level 4 | 51/70 (73%) |
| Â | Â | Tumor | Level 5 | Level 5 | 61/70 (87%) |