Subtype, tumor mutation burden (TMB), aneuploidy score (AS), and fraction genome altered (FGA) in colorectal cancers with or without APC and other WNT/β-catenin pathway alterations from the Cancer Genome Atlas (TCGA)
| Characteristic | Entire cohort (n = 594) | Quadruple altered (n = 95) | APC only altered (n = 300) | Triple altered (n = 44) | Quadruple wild type (n = 95) | P |
|---|---|---|---|---|---|---|
| Subtype | ||||||
| GS | 58 (12.7) | 11 (12.7) | 39 (13.8) | 2 (5) | 6 (12) | GS versus CIN versus MSI: < 0.00001 |
| CIN | 328 (71.4) | 46 (53.5) | 235 (83) | 14 (35) | 33 (66) | |
| MSI | 63 (13.7) | 19 (22.1) | 9 (3.2) | 24 (60) | 11 (22) | |
| POLE | 10 (2.2) | 10 (11.7) | 0 | 0 | 0 | - |
| NA | 135 | 9 | 17 | 4 | 45 | - |
| TMB | ||||||
| ≤ 10 mutations/Mb | 451 (84.5) | 63 (66.3) | 288 (96) | 17 (38.6) | 83 (87.4) | < 0.00001 |
| > 10 mutations/Mb | 83 (15.5) | 32 (33.7) | 12 (4) | 27 (61.4) | 12 (12.6) | |
| NA | 60 | 0 | 0 | 0 | 0 | - |
| AS | ||||||
| < 4 | 108 (18.4) | 30 (32.3) | 39 (13.1) | 29 (65.9) | 15 (15.8) | < 0.00001 |
| 4–24 | 427 (72.9) | 58 (62.4) | 226 (76.1) | 15 (34.1) | 70 (73.7) | |
| > 24 | 51 (8.7) | 5 (5.3) | 32 (10.8) | 0 | 10 (10.5) | |
| NA | 8 | 2 | 3 | 0 | 0 | - |
| FGA | ||||||
| < 0.075 | 115 (19.7) | 28 (30.1) | 32 (10.9) | 24 (55.8) | 16 (17) | < 0.00001 |
| 0.075–0.35 | 319 (54.7) | 49 (52.7) | 179 (61.1) | 15 (34.9) | 54 (57.5) | |
| > 0.35 | 149 (25.6) | 16 (17.2) | 82 (28) | 4 (9.3) | 24 (25.5) | |
| NA | 11 | 2 | 7 | 1 | 1 | - |
Percentages are shown in parentheses. GS: genomically stable; CIN: chromosomal instability, MSI: microsatellite instability; NA: not available; POLE: polymerase epsilon. -: no data