Table 2.
Candidate driver genes with significantly recurrent somatic mutations in mucinous ovarian tumors
| Exome cohort | SMG prediction | Validation cohort | Overall | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Mutated samples | Nonsense, frameshift indel, splice | Inframe indel, missense | OncodriveFM | MuSiC q-value | Mutated samples | Nonsense, frameshift indel, splice | Inframe indel, missense | Mutated samples | ||
| q-value | FCPT | LRT | CT | ||||||||
| KRAS | 12 | 0 | 12 | 1.34 × 10−13 | 0 | 0 | 0 | 32 | 0 | 33 | 44/82 |
| TP53 | 7 | 1 | 6 | 3.66 × 10−11 | 2.86 × 10−7 | 1.41 × 10−9 | 1.17 × 10−12 | 15 | 0 | 15 | 22/82 |
| BRAF | 6 | 0 | 6 | 2.45 × 10−8 | 7.77 × 10−7 | 0 | 6.18 × 10−12 | 4 | 0 | 5 | 10/82 |
| CDKN2A | 5 | 5 | 2 | 0.0043 | 1.20 × 10−10 | 0 | 7.93 × 10−17 | 5 | 5 | 0 | 10/63 |
| RNF43 | 5 | 5 | 0 | 4.65 × 10−6 | – | 0.0009 | 0.0004 | 3 | 2 | 1 | 8/65b |
| ELF3 | 3 | 2 | 1 | 0.0079 | – | 0.0003 | 0.0004 | 1 | 1 | 0 | 4/65 |
| ARID1A | 2 | 2 | 0 | 0.0164 | – | 0.0933 | – | – | – | – | 2/24 |
| DCLK1 | 2 | 0 | 2 | – | – | 0.0569 | – | – | – | – | 2/24 |
| ERBB3 | 2 | 0 | 3 | – | – | 0.0014 | 0.0374 | 0 | 0 | 0 | 2/43 |
| FBXW7 | 2 | 1 | 1 | 0.0207 | – | – | – | – | – | – | 2/24 |
| GNAS a | 2 | 0 | 2 | 9.05 × 10−8 | – | – | – | 3 | 0 | 3 | 5/81 |
| KLF5 | 2 | 2 | 0 | 0.0164 | – | 0.0056 | 0.0536 | 0 | 0 | 0 | 2/43 |
| LPHN3 | 2 | 0 | 2 | 0.0493 | – | – | – | – | – | – | 2/24 |
| LRRK2 | 2 | 1 | 1 | 0.0997 | – | – | – | – | – | – | 2/24 |
| TTF1 | 2 | 0 | 2 | – | – | 0.0569 | – | – | – | – | 2/24 |
All non-synonymous mutations in listed genes were validated by Sanger sequencing
CT convolution test, FCPT Fisher’s combined P-value test, LRT likelihood ratio test, SMG significantly mutated gene
aOnly mutations involving the hotspot codon 201 are reported
bIncludes samples from Ryland et al. [8] plus 16 additional samples