Table 1.
Comprehensive table of genes aberrantly methylated in BE and EAC
| Genes | Location | Method* | Normal | Metaplastic | Dysplastic | Carcinoma | Source | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| |||||||||||||||
| N | Meth | % | N | Meth | % | N | Meth | % | N | Meth | % | ||||
| 3OST2/HS3ST2 | 16p12 | MSP | 57 | 1 | 1.8 | 60 | 47 | 78.3 | nd | nd | nd | 73 | 28 | 38.4 | [26] |
| AKAP12 | 6q24-25 | MSP | 66 | 0 | 0.0 | 60 | 29 | 48.3 | 40 | 21 | 52.5 | 67 | 35 | 52.2 | [39] |
| APC | 5q21-q22 | MS-SSCA and MS-DBA | 16 | 0 | 0.0 | 25 | 16 | 64.0 | nd | nd | nd | 27 | 25 | 92.6 | [28] |
| APC | 5q21-q22 | MSP | 17 | 0 | 0.0 | 48 | 24 | 50.0 | 46 | 28 | 60.9 | 32 | 20 | 62.5 | [42] |
| APC | 5q21-q22 | MSP | 64 | 9 | 14.1 | 92 | 75 | 81.5 | nd | nd | nd | 77 | 54 | 70.1 | [26] |
| APC | 5q21-q22 | MSP | 41 | 3 | 7.3 | nd | nd | nd | nd | nd | nd | 41 | 28 | 68.3 | [31] |
| APC | 5q21-q22 | Mc-MSP | 56 | 14 | 25.0 | 40 | 38 | 95.0 | 7 | 7 | 100.0 | 37 | 35 | 94.6 | [41] |
| APC | 5q21-q22 | MethyLight | 31 | 3 | 9.7 | 10 | 8 | 80.0 | 9 | 8 | 88.9 | 22 | 15 | 68.2 | [16] |
| CALCA | 11p15.2 | MethyLight | 31 | 4 | 12.9 | 10 | 4 | 40.0 | 9 | 5 | 55.6 | 22 | 11 | 50.0 | [16] |
| CDH13 | 16q24 | MSP | 66 | 0 | 0.0 | 60 | 42 | 70.0 | 40 | 31 | 77.5 | 67 | 51 | 76.1 | [44] |
| CRBP1/RBP1 | 3q23 | MSP | 64 | 1 | 1.6 | 93 | 31 | 33.3 | nd | nd | nd | 77 | 30 | 39.0 | [26] |
| DAPK1 | 9q34.1 | MSP | 20 | 4 | 20.0 | 28 | 14 | 50.0 | 21 | 11 | 52.4 | 35 | 21 | 60.0 | [33] |
| DAPK1 | 9q34.1 | MSP | 41 | 2 | 4.9 | nd | nd | nd | nd | nd | nd | 41 | 8 | 19.5 | [31] |
| ESR1 | 6q25.1 | MSP | 41 | 5 | 12.2 | nd | nd | nd | nd | nd | nd | 41 | 21 | 51.2 | [31] |
| CHD1 / E-Cadherin | 16q22.1 | MSP | 41 | 5 | 12.2 | nd | nd | nd | nd | nd | nd | 41 | 27 | 65.9 | [31] |
| ESR 1 | 6q25.1 | MethyLight | 31 | 0 | 0.0 | 10 | 4 | 40.0 | 9 | 8 | 88.9 | 22 | 19 | 86.4 | [16] |
| GPX3 | 5q23 | MSP | 12 | 2 | 16.7 | 21 | 13 | 61.9 | 11 | 9 | 81.8 | 34 | 30 | 88.2 | [25] |
| GPX3 | 5q23 | Quantitative bisulphite pyrosequencing | 37 | 3 | 8.1 | 10 | 9 | 90.0 | 8 | 7 | 87.5 | 100 | 62 | 62.0 | [46] |
| GPX7 | 1p32 | Quantitative bisulphite pyrosequencing | 37 | 0 | 0.0 | 11 | 2 | 18.2 | 10 | 8 | 80.0 | 100 | 67 | 67.0 | [46] |
| GSTM2 | 1p13.3 | Quantitative bisulphite pyrosequencing | 37 | 2 | 5.4 | 10 | 5 | 50.0 | 9 | 5 | 55.6 | 97 | 67 | 69.1 | [46] |
| GSTM3 | 1p13.3 | Quantitative bisulphite pyrosequencing | 36 | 0 | 0.0 | 8 | 1 | 12.5 | 8 | 3 | 37.5 | 100 | 15 | 15.0 | [46] |
| HPP1/TMEF2 | 2q32.3 | MSP | 64 | 2 | 3.1 | 93 | 41 | 44.1 | 20 | 15 | 75.0 | 77 | 55 | 71.4 | [26] |
| ID4 | 6p22.3 | Mc-MSP | 56 | 12 | 21.4 | 40 | 31 | 77.5 | 7 | 6 | 85.7 | 37 | 28 | 75.7 | [41] |
| MGMT | 10q26 | MSP | 28 | 6 | 21.4 | 27 | 24 | 88.9 | 13 | 13 | 100.0 | 47 | 37 | 78.7 | [48] |
| MGMT | 10q26 | MethyLight | 10 | 2 | 20.0 | 13 | 8 | 61.5 | nd | nd | nd | 132 | 84 | 63.6 | [47] |
| MGMT | 10q26 | MSP | 63 | 11 | 17.5 | 60 | 15 | 25.0 | nd | nd | nd | 77 | 18 | 23.4 | [26] |
| MGMT | 10q26 | MethyLight | 31 | 17 | 54.8 | 10 | 6 | 60.0 | 9 | 8 | 88.9 | 22 | 16 | 72.7 | [16] |
| MGMT | 10q26 | Mc-MSP | 56 | 1 | 1.8 | 40 | 19 | 47.5 | 7 | 5 | 71.4 | 37 | 21 | 56.8 | [41] |
| MGMT | 10q26 | MSP | 41 | 10 | 24.4 | nd | nd | nd | nd | nd | nd | 41 | 24 | 58.5 | [31] |
| MYOD1 | 11p15.4 | MethyLight | 31 | 0 | 0.0 | 10 | 4 | 40.0 | 9 | 6 | 66.7 | 22 | 10 | 45.5 | [16] |
| NELL1 | 11p15.1 | MSP | 66 | 0 | 0.0 | 60 | 28 | 46.7 | 40 | 21 | 52.5 | 67 | 32 | 47.8 | [36] |
| p16/CDKN2A | 9p21 | MSP | 17 | 0 | 0.0 | 47 | 14 | 29.8 | 45 | 19 | 42.2 | 41 | 22 | 53.7 | [42] |
| p16/CDKN2A | 9p21 | MSP | 41 | 10 | 24.4 | nd | nd | nd | nd | nd | nd | 41 | 16 | 39.0 | [31] |
| p16/CDKN2A | 9p21 | MSP | 64 | 2 | 3.1 | 93 | 14 | 15.1 | 20 | 11 | 55.0 | 76 | 34 | 44.7 | [26] |
| p16/CDKN2A | 9p21 | MS-SSCA and MS-DBA | 16 | 0 | 0.0 | 27 | 2 | 7.4 | nd | nd | nd | 27 | 13 | 48.1 | [28] |
| p16/CDKN2A | 9p21 | MethyLight | 31 | 0 | 0.0 | 10 | 2 | 20.0 | 9 | 2 | 22.2 | 22 | 9 | 40.9 | [16] |
| p16/CDKN2A | 9p21 | Mc-MSP | 56 | 5 | 8.9 | 40 | 11 | 27.5 | 7 | 3 | 42.9 | 37 | 22 | 59.5 | [41] |
| CRBP1/RBP1 | 3q23 | Mc-MSP | 56 | 10 | 17.9 | 40 | 23 | 57.5 | 7 | 4 | 57.1 | 37 | 26 | 70.3 | [41] |
| RPRM reprimo | 2q23 | MSP | 19 | 0 | 0.0 | 25 | 9 | 36.0 | 11 | 7 | 63.6 | 75 | 47 | 62.7 | [35] |
| RIZ1/PRDM2 | 1p36.21 | MSP | 63 | 2 | 3.2 | 69 | 41 | 59.4 | nd | nd | nd | 77 | 45 | 58.4 | [26] |
| RUNX3 | 1p36 | Mc-MSP | 56 | 3 | 5.4 | 40 | 19 | 47.5 | 7 | 4 | 57.1 | 37 | 27 | 73.0 | [41] |
| RUNX3 | 1p36 | MSP | 63 | 1 | 1.6 | 93 | 23 | 24.7 | 20 | 12 | 60.0 | 77 | 37 | 48.1 | [26] |
| SFRP1 | 8p11.21 | Mc-MSP | 56 | 7 | 12.5 | 40 | 37 | 92.5 | 7 | 7 | 100.0 | 37 | 35 | 94.6 | [41] |
| SFRP1 | 8p11.21 | MS-SSCA and MS-DBA | 12 | 2 | 16.7 | 21 | 21 | 100.0 | nd | nd | nd | 23 | 21 | 91.3 | [28] |
| SFRP1 | 8p11.21 | MSP | 58 | 10 | 17.2 | 37 | 30 | 81.1 | nd | nd | nd | 40 | 37 | 92.5 | [27] |
| SFRP2 | 4q31.3 | MSP | 58 | 38 | 65.5 | 37 | 33 | 89.2 | nd | nd | nd | 40 | 33 | 82.5 | [27] |
| SFRP4 | 7p14.1 | MSP | 58 | 9 | 15.5 | 37 | 29 | 78.4 | nd | nd | nd | 40 | 29 | 72.5. | [27] |
| SFRP5 | 10q24.1 | MSP | 58 | 10 | 17.2 | 37 | 27 | 73.0 | nd | nd | nd | 40 | 34 | 85 | [27] |
| SOCS1 | 16p13.13 | MSP | 20 | 0 | 0.0 | 30 | nd | nd | 56 | 7 | 12.5 | 19 | 8 | 42.1 | [58] |
| SOCS3 | 17q25.3 | MSP | 20 | 0 | 0.0 | 30 | 4 | 13.3 | 56 | 26 | 46.4 | 19 | 14 | 73.7 | [58] |
| SST | 3q28 | MSP | 67 | 6 | 9.0 | 60 | 44 | 73.3 | 40 | 27 | 67.5 | 67 | 48 | 71.6 | [60] |
| TAC1 | 7q21-22 | MSP | 67 | 5 | 7.5 | 60 | 38 | 63.3 | 40 | 23 | 57.5 | 67 | 41 | 61.2 | [63] |
| TERT | 5p15.33 | MS-SSCA and MS-DBA | 16 | 0 | 0.0 | 24 | 13 | 54.2 | nd | nd | nd | 25 | 16 | 64.0 | [28] |
| TIMP3 | 22q12.1-q13.2; 22q12.33 | MethyLight | 31 | 6 | 19.4 | 10 | 6 | 60.0 | 9 | 7 | 77.8 | 22 | 19 | 86.4 | [16] |
| TIMP3 | 22q12.1-q13.2; 22q12.33 | MSP | 64 | 3 | 4.7 | 93 | 55 | 59.1 | nd | nd | nd | 77 | 43 | 55.8 | [26] |
| TIMP3 | 22q12.1-q13.2; 22q12.33 | MS-SSCA and MS-DBA | 16 | 0 | 0.0 | 24 | 13 | 54.2 | nd | nd | nd | 26 | 17 | 65.4 | [28] |
| TIMP3 | 22q12.1-q13.2; 22q12.33 | Mc-MSP | 56 | 1 | 1.8 | 40 | 35 | 87.5 | 7 | 5 | 71.4 | 35 | 26 | 74.3 | [41] |
| TIMP3 | 22q12.1-q13.2; 22q12.33 | MSP | 41 | 0 | 0.0 | nd | nd | nd | nd | nd | nd | 41 | 8 | 19.5 | [31] |
| HPP1/TMEFF2 | 2q32.3 | Mc-MSP | 56 | 2 | 3.6 | 40 | 30 | 75.0 | 7 | 7 | 100.0 | 36 | 30 | 83.3 | [41] |
| WIF-1 | 12q14.3 | MS-SSCA | 4 | 0 | 0.0 | 31 | 16 | 51.6 | nd | nd | nd | 12 | 10 | 83.3 | [29] |
| WIF-1 | 12q14.3 | MSP | 17 | 4 | 23.5 | nd | nd | nd | nd | nd | nd | 18 | 11 | 61.1 | [29] |
*
MSP = Methylation-specific PCR; Mc-MSP = Melt curve Methylation-specific PCR; MS-SSCA = Methylation sensitive single strand conformation analysis; MS-DBA = Methylation sensitive dot blot assay.
Note: In the metaplastic, dysplastic and carcinoma columns, nd = tissues not studied for methylation.