Table 2.
Mutation frequency driver genes.
| Metastatic CRC | Primary CRC—(TCGA, combined studies cBioportal) | Metastatic CRC—(Yaeger et al.) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | dN/dS q-value | Mutations (N) | Mutations (%) | Mutations (N) | Mutations (%) | Fisher p-value | FDR Hochberg | % change in meta | Mutations (N) | Mutations (%) | Fisher p-value | FDR Hochberg |
| TP53 | 0 | 317 | 73.9 | 1123 | 57.6 | 2.04E-10 | 4.7E-09 | 16.3 | 246 | 76.6 | 0.395 | 1 |
| ZFP36L2 | 0 | 42 | 9.8 | 97 | 5.0 | 3.61E-04 | 0.008 | 4.8 | Not present | |||
| KRAS | 0 | 203 | 47.3 | 744 | 38.2 | 5.88E-04 | 0.012 | 9.1 | 127 | 39.6 | 0.037 | 0.487 |
| APC | 0 | 336 | 78.3 | 1372 | 70.4 | 8.86E-04 | 0.018 | 7.9 | 241 | 75.1 | 0.335 | 1 |
| PIK3CA | 0 | 68 | 15.9 | 445 | 22.8 | 0.001 | 0.023 | −7.0 | 49 | 15.3 | 0.840 | 1 |
| B2M | 5.37E-03 | 8 | 1.9 | 91 | 4.7 | 0.007 | 0.128 | −2.8 | 2 | 0.6 | 0.202 | 1 |
| SMAD4 | 0 | 74 | 17.2 | 243 | 12.5 | 0.010 | 0.164 | 4.8 | 47 | 14.6 | 0.367 | 1 |
| ATM | 9.50E-04 | 33 | 7.7 | 227 | 11.6 | 0.017 | 0.266 | −4.0 | 18 | 5.6 | 0.306 | 1 |
| FBXW7 | 0 | 51 | 11.9 | 301 | 15.4 | 0.061 | 0.912 | −3.6 | 25 | 7.8 | 0.068 | 0.814 |
| AMER1 | 0 | 37 | 8.6 | 209 | 10.7 | 0.220 | 0.913 | −2.1 | 11 | 3.4 | 0.004 | 0.067 |
| ARID1A | 1.13E-09 | 39 | 9.1 | 201 | 10.3 | 0.480 | 0.913 | −1.2 | 15 | 4.7 | 0.022 | 0.333 |
| BCL9 | 5.27E-02 | 28 | 6.5 | 107 | 5.5 | 0.419 | 0.913 | 1.0 | Not present | |||
| BCL9L | 2.24E-06 | 27 | 6.3 | 133 | 6.8 | 0.750 | 0.913 | −0.5 | Not present | |||
| BRAF | 0 | 56 | 13.1 | 273 | 14.0 | 0.644 | 0.913 | −1.0 | 38 | 11.8 | 0.657 | 1 |
| ELF3 | 5.37E-03 | 7 | 1.6 | 51 | 2.6 | 0.299 | 0.913 | −1.0 | Not present | |||
| LMTK3 | 1.33E-02 | 15 | 3.5 | 56 | 2.9 | 0.530 | 0.913 | 0.6 | not present | |||
| NRAS | 0 | 26 | 6.1 | 125 | 6.4 | 0.913 | 0.913 | −0.4 | 14 | 4.4 | 0.329 | 1 |
| PTEN | 4.30E-08 | 17 | 4.0 | 123 | 6.3 | 0.069 | 0.913 | −2.3 | 14 | 4.4 | 0.854 | 1 |
| RNF43 | 2.20E-02 | 28 | 6.5 | 162 | 8.3 | 0.239 | 0.913 | −1.8 | 21 | 6.5 | 1.000 | 1 |
| SMAD3 | 5.68E-03 | 11 | 2.6 | 72 | 3.7 | 0.309 | 0.913 | −1.1 | 11 | 3.4 | 0.518 | 1 |
| SOX9 | 0 | 41 | 9.6 | 177 | 9.1 | 0.782 | 0.913 | 0.5 | 16 | 5.0 | 0.025 | 0.352 |
| TCF7L2 | 1.07E-09 | 50 | 11.7 | 177 | 9.1 | 0.103 | 0.913 | 2.6 | 19 | 5.9 | 0.007 | 0.116 |
| TGIF1 | 1.33E-02 | 18 | 4.2 | 62 | 3.2 | 0.300 | 0.913 | 1.0 | Not present | |||
Twenty-three genes identified as putative driver genes using the ratio of nonsynonymous to synonymous substitutions caused by the somatic nucleotide mutations (SNV and InDels; dN/dS analysis). P-values are derived from the Fisher exact test (two-sided) and corrected for multiple testing using the FDR (Hochberg) method.