Table 3. Comparative analysis of DNA methylation in cancer-related genes of patient-derived xenografts.
| Gene/No. of methylation site | Group No.1 | Group No.7 | Group No.16 | Group No.23 | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PDOX/human | PDHX/human | PDOX/human | PDHX/human | PDOX/human | PDHX/human | PDOX/human | PDHX/human | |||||||||
| X | O | X | O | X | O | X | O | X | O | X | O | X | O | X | O | |
| +/− | +/− | +/− | +/− | +/− | +/− | +/− | +/− | |||||||||
| ACVR2A/19 | 17 | 2/0 | 19 | - | 19 | - | 19 | - | 19 | - | 19 | - | 19 | - | 19 | - |
| APC/40 | 40 | - | 33 | 1/6 | 33 | 1/6 | 35 | 0/5 | 34 | 0/6 | 33 | 0/7 | 24 | 10/6 | 24 | 12/4 |
| ARID1A/29 | 29 | - | 25 | 2/2 | 27 | 2/0 | 27 | 2/0 | 26 | 2/1 | 27 | 1/1 | 26 | 3/0 | 27 | 2/0 |
| ATM/59 | 52 | 7/0 | 59 | - | 58 | 1/0 | 59 | - | 59 | - | 59 | - | 59 | - | 59 | - |
| BCORL1/20 | 19 | 0/1 | 20 | - | 19 | 0/1 | 19 | 0/1 | 20 | - | 20 | - | 20 | - | 16 | 3/1 |
| BRCA1/52 | 51 | 1/0 | 45 | 0/7 | 36 | 0/16 | 37 | 0/15 | 48 | 0/4 | 45 | 0/7 | 51 | 1/0 | 50 | 0/2 |
| BRCA2/19 | 19 | - | 18 | 1/0 | 18 | 0/1 | 18 | 0/1 | 19 | - | 19 | - | 19 | - | 19 | - |
| CALD1/57 | 53 | 3/0 | 51 | 0/6 | 51 | 0/6 | 51 | 0/6 | 55 | 0/2 | 54 | 0/3 | 54 | 1/2 | 53 | 2/2 |
| CDKN2A/7 | 7 | - | 7 | - | 1 | 6/0 | 1 | 6/0 | 0 | 7/0 | 0 | 7/0 | 1 | 6/0 | 0 | 7/0 |
| DISP2/18 | 18 | - | 16 | 1/1 | 17 | 0/1 | 17 | 0/1 | 16 | 0/2 | 16 | 0/2 | 16 | 2/0 | 16 | 0/2 |
| FBLN2/50 | 45 | 1/4 | 38 | 3/9 | 40 | 2/8 | 39 | 4/7 | 38 | 1/11 | 37 | 1/12 | 42 | 8/0 | 42 | 4/4 |
| FBXW7/22 | 22 | - | 21 | 0/1 | 22 | - | 22 | - | 22 | - | 22 | - | 20 | 2/0 | 21 | 0/1 |
| HIVEP1/27 | 27 | - | 27 | - | 27 | - | 27 | - | 27 | - | 27 | - | 25 | 2/0 | 26 | 0/1 |
| ITPR3/50 | 49 | 0/1 | 44 | 0/6 | 47 | 0/3 | 46 | 0/4 | 47 | 0/3 | 47 | 0/3 | 50 | - | 48 | 0/2 |
| JAG1/24 | 23 | 1/0 | 24 | - | 24 | - | 24 | - | 24 | - | 24 | - | 23 | 1/0 | 23 | 0/1 |
| KALRN/67 | 65 | 1/1 | 62 | 0/5 | 61 | 0/6 | 53 | 0/14 | 60 | 0/7 | 54 | 0/13 | 59 | 8/0 | 63 | 0/4 |
| KDM6A/15 | 15 | - | 14 | 0/1 | 15 | - | 15 | - | 14 | 0/1 | 14 | 0/1 | 14 | 1/0 | 14 | 0/1 |
| KRAS/34 | 33 | 0/1 | 31 | 0/3 | 33 | 0/1 | 33 | 0/1 | 33 | 0/1 | 33 | 0/1 | 33 | 1/0 | 33 | 0/1 |
| MACF1/87 | 81 | 2/4 | 75 | 2/10 | 79 | 0/8 | 80 | 1/6 | 82 | 0/5 | 81 | 0/6 | 77 | 8/2 | 77 | 0/10 |
| MAP2K4/25 | 24 | 1/0 | 25 | - | 25 | - | 25 | - | 25 | - | 25 | - | 20 | 4/1 | 21 | 4/0 |
| MLL3/24 | 24 | - | 22 | 1/1 | 22 | 1/1 | 24 | - | 23 | 1/0 | 23 | 0/1 | 22 | 2/0 | 22 | 2/0 |
| MYCBP2/19 | 17 | 2/0 | 18 | 1/0 | 19 | - | 19 | - | 19 | - | 19 | - | 18 | 0/1 | 18 | 1/0 |
| NBEA/58 | 57 | 1/0 | 51 | 3/4 | 48 | 2/8 | 48 | 0/10 | 51 | 2/5 | 53 | 2/3 | 53 | 4/1 | 52 | 6/0 |
| NF2/19 | 19 | - | 19 | - | 19 | - | 19 | - | 19 | - | 19 | - | 19 | - | 19 | - |
| PBRM1/18 | 16 | 2/0 | 18 | - | 18 | - | 18 | - | 18 | - | 18 | - | 18 | - | 15 | 2/1 |
| PLXNB2/45 | 45 | - | 33 | 1/11 | 36 | 0/9 | 36 | 0/9 | 33 | 0/12 | 33 | 0/12 | 32 | 11/2 | 33 | 2/10 |
| PTEN/63 | 63 | - | 62 | 0/1 | 63 | - | 63 | - | 61 | 1/1 | 61 | 1/1 | 61 | 2/0 | 61 | 1/1 |
| RBM10/29 | 28 | 0/1 | 12 | 0/17 | 29 | - | 29 | - | 29 | - | 27 | 2/0 | 27 | 2/0 | 29 | - |
| RNF43/11 | 10 | 1/0 | 8 | 0/3 | 7 | 0/4 | 7 | 0/4 | 7 | 0/4 | 7 | 0/4 | 8 | 3/0 | 8 | 0/3 |
| SDK2/68 | 63 | 0/5 | 44 | 5/19 | 53 | 5/10 | 57 | 3/8 | 63 | 0/5 | 61 | 0/7 | 53 | 12/3 | 55 | 6/7 |
| SETD2/24 | 24 | - | 24 | - | 24 | - | 24 | - | 24 | - | 24 | - | 24 | - | 24 | - |
| SF3B1/17 | 17 | - | 17 | - | 17 | - | 17 | - | 17 | - | 17 | - | 17 | - | 17 | - |
| SIN3B/18 | 17 | 0/1 | 17 | 0/1 | 17 | 0/1 | 17 | 0/1 | 17 | 0/1 | 16 | 0/2 | 17 | 1/0 | 17 | 0/1 |
| SMAD3/58 | 58 | - | 49 | 0/9 | 53 | 0/5 | 53 | 0/5 | 51 | 0/7 | 47 | 0/11 | 53 | 5/0 | 51 | 3/4 |
| SMAD4/15 | 11 | 1/3 | 14 | 0/1 | 14 | 0/1 | 14 | 0/1 | 15 | 14 | 1/0 | 14 | 1/0 | 14 | 0/1 | |
| SMARCA4/44 | 43 | 0/1 | 42 | 0/2 | 43 | 0/1 | 43 | 0/1 | 40 | 0/4 | 40 | 0/4 | 42 | 2/0 | 42 | 0/2 |
| SPTB/33 | 32 | 0/1 | 30 | 0/3 | 29 | 0/4 | 31 | 0/2 | 30 | 0/3 | 30 | 0/3 | 30 | 2/1 | 30 | 0/3 |
| TGFBR1/10 | 8 | 2/0 | 9 | 0/1 | 9 | 0/1 | 9 | 0/1 | 9 | 0/1 | 9 | 1/0 | 8 | 2/0 | 8 | 0/2 |
| TGFBR2/37 | 36 | 1/0 | 32 | 0/5 | 34 | 0/3 | 34 | 0/3 | 33 | 0/4 | 33 | 0/4 | 31 | 6/0 | 33 | 2/2 |
| TLE4/16 | 15 | 0/1 | 15 | 0/1 | 16 | - | 16 | - | 16 | - | 16 | - | 15 | 0/1 | 15 | 0/1 |
| TP53/38 | 38 | - | 37 | 0/1 | 38 | - | 38 | - | 38 | - | 37 | 0/1 | 38 | - | 38 | - |
| TP53BP2/20 | 20 | - | 20 | - | 20 | - | 20 | - | 20 | - | 20 | - | 20 | - | 20 | - |
| U2AF1/20 | 20 | - | 18 | 1/1 | 19 | 1/0 | 19 | 1/0 | 20 | - | 20 | - | 18 | 2/0 | 19 | 1/0 |
| Total / 1425 | 13 70 |
29/26 | 12 65 |
22/138 | 12 99 |
21/105 | 13 02 |
17/106 | 13 21 |
14/90 | 13 00 |
16/109 | 12 90 |
115/20 | 12 91 |
60/74 |