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Table 3 The density of methylation estimated by semiquantitative methylation-specific PCR analysis and sequencing of common PCR DNA

From: The 5'-end transitional CpGs between the CpG islands and retroelements are hypomethylated in association with loss of heterozygosity in gastric cancers

    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%)
  1. *CpG sites are indicated by the name of the gene and the distance from the transcription start site.
  2. †Different results between methylation-specific PCR and common PCR DNA.
  3. ‡'/' separates the number of the methylated CpGs and the total CpGs.