Table 3.
Frequency of tumors mutated or hypermethylated in cancer-associated driver gene sets for each cancer type.
| Cancer type | Recurrently mutated genes selected in cancer-associated driver gene set for given cancer typea | Percent tumors mutated (%)b | Beta value hypermethylation cutoffc | Percent tumors hypermethylated (%)d |
|---|---|---|---|---|
| OV | TP53 (73.2%) | 73.2 | 0.313 | 92.4 |
| BRCA | PI3K3CA (31.6%), TP53 (24.8%), CDH1 (7.1%) | 54.2 | 0.190 | 74.4 |
| PAAD | KRAS (90.7%), TP53 (61.3%), SMAD4 (16.7%), CDKN2A (10.7%) | 95.3 | 0.070 | 90.7 |
| LUAD | TP53 (41.1%), KRAS (31.9%), LRP1B (25.4%), PCLO (18.4%), STK11 (8.6%), KEAP1 (15.1%), RELN (14.1%), FAT4 (15.7%), EGFR (9.2%), PTPRD (13.5%), CPS1 (10.3%), GRIN2A (10.8%), NF1 (8.1%), EPHA5 (9.2%), FAT1 (10.8%), MKI67 (8.6%), SETBP1 (8.1%), NOTCH4 (10.3%) | 85.4 | 0.071 | 75.7 |
| LIHC | TP53 (24.1%), CTNNB1 (25.2%), ALB (4.3%) | 46.9 | 0.058 | 90.1 |
| KIRP | MET (7.5%) | 7.5 | 0.025 | 50.6 |
| PRAD | TP53 (9.8%), SPOP (11.0%) | 20.5 | 0.523 | 52.0 |
| HNSC | TP53 (59.8%), FAT1 (15.9%), CDKN2A (17.5%), PIK3CA (18.0%), NOTCH1 (14.5%), LRP1B (17.1%), KMT2D (12.7%), PCLO (15.3%), NSD1 (9.2%), CASP8 (9.2%) | 85.3 | 0.181 | 98.6 |
| STAD | TP53 (39.3%), LRP1B (24.6%), ARID1A (12.0%), FAT4 (18.6%), PCLO (16.0%), KMT2D (10.0%), PIK3CA (16.9%), ACVR2A (1.4%), LRRK2 (13.5%), KMT2C (8.6%), CIC (8.9%), UBR5 (4.3%), PREX2 (11.7%), APC (7.7%), ERBB4 (11.5%), TRRAP (10.6%), RNF213 (9.7%), STK19 (0.3%), KMT2B (4.6%), RPL22 (1.7%), PTPRT (8.9%), PRKDC (7.4%), ZFHX3 (7.2%), RELN (9.7%), EP400 (7.7%) | 82.5 | 0.161 | 96.6 |
| BLCA | TP53 (45.4%), ARID1A (16.9%), KDM6A (15.4%), PIK3CA (20.0%) | 63.8 | 0.316 | 94.6 |
| KIRC | VHL (36.1%), PBRM1 (19.8%), SETD2 (9.5%) | 52.9 | 0.016 | 75.3 |
aPercentages indicate the fraction of tumors from a given cancer type with a non-silent single nucleotide polymorphism in the given gene of the cancer-associated gene set.
bA tumor is considered mutated if it is mutated in any of the genes in the corresponding cancer-associated gene set.
cBeta value cutoff for a given cancer type at methylation array probe cg21790626 that is greater than 95% of the controls.
dHypermethylation for each cancer type based on a beta value cutoff above 95% of the controls for that given cancer type.