| High-level chromosomal loss (n = 20) | Low-level chromosomal loss (n = 19) | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
 | Mean level of methylation |  | Methylation alterations (%) | Mean level of methylation |  | Methylation alterations (%) | ||||
CpG sites* | Normal | Tumor | p†| Hypo- | Hyper- | Normal | Tumor | p†| Hypo- | Hyper- |
CpG islands | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
   CDH1, 0 kb | 1.2 | 1.0 | 0.083 | 3 (15) | 0 (0) | 1.1 | 1.1 | 0.560 | 0 (0) | 1 (5) |
   RABGEF1, -0.2 kb | 1.1 | 1.0 | 0.163 | 2 (10) | 0 (0) | 1.0 | 1.0 | 1 | 0 (0) | 0 (0) |
   STAG1, -0.4 kb | 1.1 | 1.0 | 0.330 | 1 (5) | 0 (0) | 1.0 | 1.0 | 1 | 0 (0) | 0 (0) |
   MYBPC2, -0.6 kb | 1.6 | 1.6 | 0.757 | 2 (10) | 1 (5) | 2.0 | 2.3 | 0.090 | 0 (0) | 4 (21) |
   MLH1, -0.6 kb | 1.4 | 1.4 | 1 | 5 (25) | 2 (10) | 1.3 | 1.7 | 0.153 | 0 (0) | 4 (21) |
   PTEN, -0.9 kb | 1.3 | 1.2 | 0.442 | 2 (10) | 0 (0) | 1.1 | 1.1 | 0.560 | 1 (5) | 2 (11) |
   CDKN2A, 0kb | 1.1 | 1.0 | 0.330 | 1 (5) | 0 (0) | 1.0 | 1.4 | 0.072 | 0 (0) | 4 (21) |
   PAX5, -1.0 kb | 2.0 | 1.7 | 0.115 | 7 (35) | 0 (0) | 1.9 | 2.1 | 0.505 | 4 (21) | 5 (26) |
   RUNX2, -3.8 kb | 4.2 | 3.8 | 0.054 | 7 (35) | 0 (0) | 4.2 | 4.3 | 0.376 | 1 (5) | 4 (21) |
-3.0 kb | 1.8 | 1.8 | 1 | 5 (25) | 5 (25) | 2.0 | 2.0 | 1 | 3 (16) | 4 (21) |
-0.7 kb | 2.1 | 2.0 | 0.575 | 5 (25) | 4 (20) | 1.7 | 1.9 | 0.266 | 4 (21) | 6 (32) |
+1.6 kb | 2.0 | 2.2 | 0.295 | 3 (15) | 5 (25) | 2.1 | 2.5 | 0.066 | 2 (11) | 7 (37) |
   RUNX3, -1.7 kb | 2.0 | 3.3 | <0.0001 | 0 (0) | 14 (70) | 2.5 | 3.3 | 0.012 | 0 (0) | 12 (63) |
-0.5 kb | 1.3 | 1.1 | 0.121 | 6 (30) | 2 (10) | 1.8 | 2.4 | 0.035 | 2 (11) | 9 (47) |
-0.1 kb | 1.2 | 1.0 | 0.042 | 4 (20) | 0 (0) | 1.0 | 1.2 | 0.042 | 0 (0) | 4 (21) |
+1.0 kb | 4.0 | 3.8 | 0.519 | 6 (30) | 5 (25) | 3.4 | 3.8 | 0.012 | 0 (0) | 7 (37) |
   VDR, +0.1 kb | 1.0 | 1.0 | 1 | 0 (0) | 0 (0) | 1.0 | 1.0 | 1 | 0 (0) | 0 (0) |
   KIAA1752, +0.4 kb | 2.8 | 2.6 | 0.096 | 8 (40) | 0 (0) | 2.1 | 2.5 | 0.084 | 0 (0) | 7 (37) |
Transitional CpGs | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
   MYBPC2, -1.2 kb | 4.3 | 4.1 | 0.083 | 4 (20) | 0 (0) | 4.3 | 4.2 | 0.546 | 5 (26) | 2 (11) |
   VDR, -0.7 kb | 1.8 | 1.3 | 0.003 | 10 (50) | 0 (0) | 1.5 | 2.1 | 0.056 | 3 (16) | 8 (42) |
   ESR2, -0.9 kb | 1.7 | 1.4 | 0.114 | 6 (30) | 0 (0) | 1.3 | 1.5 | 0.141 | 0 (0) | 4 (22) |
   MLH1, -1.0 kb | 3.1 | 2.5 | 0.050 | 9 (45) | 2 (10) | 2.8 | 3.5 | 0.035 | 1 (5) | 11 (58) |
   FLJ43855, -1.1 kb | 4.0 | 3.5 | 0.043 | 10 (50) | 2 (10) | 3.7 | 4.1 | 0.072 | 2 (11) | 8 (42) |
   PTEN, -1.4 kb | 1.4 | 1.1 | 0.062 | 5 (25) | 0 (0) | 1.1 | 1.3 | 0.119 | 1 (5) | 5 (26) |
   CDKN2A, -1.5 kb | 2.0 | 1.6 | 0.012 | 10 (50) | 2 (10) | 2.0 | 2.8 | 0.025 | 3 (16) | 10 (53) |
+0.8 kb | 4.4 | 3.6 | 0.002 | 12 (60) | 0 (0) | 4.1 | 4.4 | 0.173 | 3 (16) | 7 (37) |
   MUC8, +2.0 kb | 4.4 | 3.7 | 0.001 | 9 (45) | 0 (0) | 4.4 | 4.2 | 0.149 | 6 (32) | 2 (11) |
   MAGEA2, 0 kb | 4.8 | 3.4 | <0.0001 | 11 (55) | 0 (0) | 4.8 | 4.6 | 0.336 | 2 (11) | 0 (0) |
   DDX53, 0 kb | 4.2 | 3.7 | 0.051 | 9 (45) | 2 (10) | 4.5 | 3.9 | 0.096 | 6 (32) | 2 (11) |
   TFF2, -0.2 kb | 2.4 | 2.1 | 0.174 | 7 (35) | 2 (10) | 2.2 | 2.0 | 0.324 | 6 (32) | 2 (11) |
   SERPINB5, -0.3 kb | 2.7 | 2.2 | 0.080 | 10 (50) | 3 (15) | 2.4 | 2.5 | 0.598 | 2 (11) | 4 (21) |
   MSLN, -0.8 kb | 4.3 | 3.6 | 0.005 | 11 (55) | 2 (10) | 3.5 | 3.7 | 0.591 | 1 (5) | 5 (26) |