Table 3. RAS-RAF codon and other key alterations by TC-6 subgroup.
| Gene | Total Mutations | Total Deletions | Most Common Subgroups | Count (Percentage) | Least Common Subgroups | Count (Percentage) | Fisher Exact Testp-value |
|---|---|---|---|---|---|---|---|
| RAS-RAF | 311 (38.6%) | D1-HRD, CCND1 | 192/414 (46.4%) | D2, MMSET, MAF | 115/381 (30.2%) | < 0.001 | |
| KRAS | 134 (16.6%) | D1-HRD, MAF | 55/261 (21.1%) | D2, MMSET, CCND1 | 77/534 (14.4%) | 0.020 | |
| G12/13 | 66 (8.2%) | MAF | 7/48(14.6%) | D1-HRD, D2, CCND1, MMSET | 58/747 (7.8%) | 0.162 | |
| Q61 | 68 (8.4%) | D1-HRD, D2, CCND1 | 59/658 (9.0%) | MMSET, MAF | 8/137(5.8%) | 0.309 | |
| NRAS | 151 (18.8%) | D1-HRD, D2, CCND1 | 140/658 (21.3%) | MMSET, MAF | 11/137 (8.0%) | < 0.001 | |
| G12/13 | 26 (3.2%) | MMSET, MAF | 8/137(5.8%) | D1-HRD, D2, CCND1 | 18/658 (2.7%) | 0.107 | |
| Q61 | 125 (15.5%) | D1-HRD, D2, CCND1 | 122/658 (18.5%) | MMSET, MAF | 3/137(2.2%) | < 0.001 | |
| BRAF V600E | 26 (3.2%) | MMSET, MAF | 7/137(5.1%) | D1-HRD, D2, CCND1 | 17/658 (2.6%) | 0.163 | |
| TP53 | 91 (11.3%) | 3 (0.4%) | D1-HRD, CCND1, MAF | 62/462 (13.4%) | D2, MMSET | 31/333 (9.3%) | 0.093 |
| TRAF3 | 27 (3.4%) | 14 (1.7%) | D2, MMSET, MAF | 35/381 (9.2%) | D1-HRD, CCND1 | 6/414(1.4%) | < 0.001 |
| FGFR3 | 25 (3.1%) | MMSET | 25/89 (28.1%) | D1-HRD, D2, CCND1, MAF | 0/706(0.0%) | < 0.001 | |
| RB1 | 23 (2.9%) | 15 (1.9%) | D2, MMSET | 23/333 (6.9%) | D1-HRD, CCND1, MAF | 15/462 (3.2%) | 0.019 |
| CDKN2C | 6 (0.7%) | 23 (2.9%) | D2, MMSET | 22/333 (6.6%) | D1-HRD, CCND1, MAF | 7/462(1.5%) | < 0.001 |
| DNMT3A | 26 (3.2%) | D2, CCND1, MMSET | 21/534 (3.9%) | D1, MAF | 3/261(1.1%) | 0.044 | |
| ATM/ATR | 32 (4.0%) | MMSET, MAF | 12/137 (8.8%) | D1-HRD, D2, CCND1 | 20/658 (3.0%) | 0.006 | |
| TET2 | 23 (2.9%) | 1 (0.1%) | D2, MAF | 12/292 (4.1%) | D1-HRD, CCND1, MMSET | 11/503 (2.2%) | 0.129 |
| BIRC3 | 2 (0.2%) | 21 (2.6%) | MMSET | 13/89 (14.6%) | D1-HRD, D2, CCND1, MAF | 10/706 (1.4%) | < 0.001 |
RAS-RAF and other key alterations are not distributed evenly across TC-6 subgroups. We have reported the most significant difference in distribution for each specific gene. A full breakdown of mutation and deletion by subgroup can be found in Supplementary Table 2.
All rows with p-values < 0.01 are bolded. Mutations and deletions are reported in first two columns, and their combined sum (alterations) is divided across the TC-6 subgroups. CCND3-6p21 subgroup is not included in this subgroup analysis due to sample size restraints. For cases with co-occurrence of RAS-RAF mutations, the mutation with highest variant allele frequency is reported here.