Table 2 Genetic and clinical features of all samples from TCGA and samples from TCGA belonging to each of the four methylation-based clusters
CIMP-H (n = 59) n (%) | CIMP-L (n = 104) n (%) | Cluster 3 (n = 124) n (%) | Cluster 4 (n = 94) n (%) | ALL (n = 381) n (%) | |
|---|---|---|---|---|---|
APC/WT | 19/40 (32.2/67.8) | 43/61 (41.3/58.7) | 49/75 (39.5/60.5) | 42/52 (44.7/55.3) | 153/228 (40.2/59.8) |
KRAS/WT | 12/47 (20.3/79.7) | 28/76 (26.9/73.1) | 20/104 (16.1/83.9) | 9/85 (9.6/90.4) | 69/312 (18.1/81.9) |
TP53/WT | 15/44 (25.4/74.6) | 23/81 (22.1/77.9) | 43/81 (34.7/65.3) | 37/57 (39.4/60.6) | 118/263 (31.0/69.0) |
BRAF/WT | 21/38 (35.6/64.4) | 5/99 (4.8/95.2) | 4/120 (3.2/96.8) | 0/94 (0.0/100.0) | 30/351 (7.9/92.1) |
MLH1 Methylated/Unmethylated | 29/30 (49.2/50.8) | 8/96 (7.7/92.3) | 2/122 (1.6/98.4) | 3/91 (3.2/96.8) | 42/339 (11.0/89.0) |
Gender Female/Male | 30/29 (50.8/49.2) | 46/58 (44.2/55.8) | 51/73 (41.1/58.9) | 47/47 (50.0/50.0) | 174/207 (45.7/54.3) |
Location | |||||
Ascending colon | 39 (73.6) | 53 (52.5) | 23 (18.7) | 10 (11.0) | 125 (34.2) |
Transverse colon | 8 (15.1) | 16 (15.8) | 18 (14.6) | 6 (6.6) | 48 (13.2) |
Descending colon | 2 (3.8) | 5 (5.0) | 2 (1.6) | 5 (5.5) | 14 (3.8) |
Sigmoid colon | 3 (5.7) | 13 (12.9) | 34 (27.6) | 36 (39.6) | 86 (23.6) |
Rectum | 1 (1.9) | 14 (13.9) | 46 (37.4) | 31 (34.1) | 92 (25.2) |
No data | 6 | 3 | 1 | 3 | 16 |
T | |||||
T1 | 2 (3.4) | 2 (1.9) | 4 (3.3) | 3 (3.2) | 11 (2.9) |
T2 | 12 (20.3) | 18 (17.3) | 7 (5.7) | 15 (16.1) | 52 (13.7) |
T3 | 37 (62.7) | 71 (68.3) | 91 (74.0) | 67 (72.0) | 266 (70.2) |
T4 | 7 (11.9) | 13 (12.5) | 21 (17.1) | 8 (8.6) | 49 (12.9) |
Tis | 1 (1.7) | 1 (0.3) | |||
No data | 1 | 1 | 2 | ||
N | |||||
N0 | 38 (64.4) | 63 (60.6) | 60 (48.8) | 43 (46.2) | 204 (53.8) |
N1 | 12 (20.3) | 22 (21.2) | 40 (32.5) | 29 (31.2) | 103 (27.2) |
N2 | 9 (15.3) | 19 (18.3) | 21 (17.1) | 21 (22.6) | 70 (18.5) |
Nx | 2 (1.6) | 2 (0.5) | |||
No data | 1 | 1 | 2 | ||
M | |||||
M0 | 46 (79.3) | 71 (69.6) | 83 (68.0) | 58 (63.7) | 258 (69.2) |
M1 | 3 (5.2) | 11 (10.8) | 23 (18.9) | 16 (17.6) | 53 (14.2) |
Mx | 9 (15.5) | 20 (19.2) | 16 (13.1) | 17 (18.7) | 62 (16.6) |
No data | 1 | 2 | 2 | 3 | 8 |
MSI | |||||
MSI-H | 28 (47.5) | 12 (11.5) | 6 (4.8) | 7 (7.5) | 53 (14.0) |
MSI-L | 9 (15.3) | 23 (22.1) | 16 (12.9) | 14 (15.1) | 62 (16.4) |
MSS | 22 (37.3) | 68 (65.4) | 102 (82.3) | 72 (77.4) | 264 (69.7) |
Indeterminate | 1 | 1 | 2 | ||
Stage | |||||
Stage I | 14 (24.1) | 17 (17.0) | 6 (5.2) | 15 (17.0) | 52 (14.5) |
Stage II | 24 (41.4) | 43 (43.0) | 48 (41.4) | 23 (26.1) | 138 (38.1) |
Stage III | 17 (29.3) | 29 (29.0) | 40 (34.5) | 32 (36.4) | 118 (32.6) |
Stage IV | 3 (5.2) | 11 (11.0) | 22 (19.0) | 18 (20.5) | 54 (14.9) |
No data | 1 | 4 | 8 | 6 | 19 |