Table 1.
Cancer genes with 3D HotMAPS regions identified in TCGA tumor types and in Landscapes Benchmark or Cancer Gene Census.
| Gene | Landscapes Benchmark | Cancer Gene Census (CGC) | TCGA Tumor Type(s) |
|---|---|---|---|
| FGFR3 | OG | Dom | BLCA |
| SF3B1 | OG | Dom | BRCA, BLCA |
| FGFR2 | OG | Dom | BRCA, UCEC |
| KRAS | OG | Dom | CESC, UCS, PAAD, STAD, BLCA, UCEC, LUAD, BRCA |
| PIK3CA | OG | Dom | ESCA, CESC, UCS, LUSC, GBM, STAD, LGG*, BLCA, UCEC, PRAD, LUAD, KIRC, BRCA, HNSC |
| NFE2L2 | OG | Dom | ESCA, HNSC, BLCA, UCEC, LUSC |
| IDH1 | OG | Dom | GBM, LGG, SKCM |
| IDH2 | OG | Dom | LGG |
| PTPN11 | OG | Dom | LGG |
| MAP2K1 | OG | Dom | LUAD*, SKCM |
| GNAS | OG | Dom | PAAD |
| BRAF | OG | Dom | THCA, GBM, LUAD, SKCM, PRAD* |
| HRAS | OG | Dom | THCA, PCPG, BLCA, HNSC, LUSC* |
| NRAS | OG | Dom | THCA, SKCM |
| PPP2R1A | OG | Dom? | UCS, UCEC |
| SPOP | OG | Rec | PRAD |
| ERBB2 | OG | ESCA*, BRCA, BLCA | |
| EGFR | OG | GBM, LGG, LUAD | |
| RET | OG | PCPG | |
| PIK3R1 | TSG | Rec | BRCA*, GBM, UCEC*, LGG* |
| FBXW7 | TSG | Rec | CESC*, UCS, LUSC*, STAD, BLCA, UCEC, HNSC |
| TP53 | TSG | Rec | ESCA, UCS, PAAD, LUSC, GBM, STAD, LGG, BLCA, UCEC, PRAD, LUAD, OV, BRCA, HNSC |
| CIC | TSG | Rec | LGG |
| SMARCA4 | TSG | Rec | LGG* |
| BCOR | TSG | Rec | UCEC |
| PTEN | TSG | BRCA, GBM*, UCEC | |
| CDKN2A | TSG | ESCA* | |
| VHL | TSG | KIRC* | |
| NOTCH1 | TSG | LGG* | |
| SMAD4 | TSG | STAD* | |
| RHOA | Dom | BLCA*, HNSC, STAD | |
| RAC1 | Dom | HNSC, SKCM | |
| ERBB3 | Dom | STAD |
OG=oncogene. TSG=tumor suppressor gene (Landscapes benchmark). Cancer Gene Census Dom=dominant. Rec=recessive. Dom?=probably dominant. TCGA tumor types = tumor types in which the gene had a significant 3D mutation hotspot region (q=0.01). ACC=Adrenocortical carcinoma, BLCA=Bladder Urothelial Carcinoma, BRCA=Breast Invasive Carcinoma, CESC=Cervical squamous cell carcinoma and endocervical adenocarcinoma, ESCA=Esophagael Carcinoma, GBM=Glioblastoma Multiforme, HNSC=Head and Neck squamous cell carcinoma, KICH=Kidney chromophobe, KIRC=Kidney renal clear cell carcinoma, KIRP= Kidney Renal Papillary Cell Carcinoma, LGG=low-grade glima, LIHC=Liver hepatocellular carcinoma, LUAD=Lung adenocarcinoma, LUSC=Lung squamous cell carcinoma, OV=Ovarian serous cystadenocarcinom, PAAD=Pancreatic adenocarcinoma, PCPG=Pheochromocytoma and Paraganglioma, PRAD=Prostate adenocarcinoma, SKCM=Skin Cutaneous Melanoma, STAD=Stomach adenocarcinoma, THCA=Thyroid carcinoma, UCEC=Uterine Corpus Endometrial Carcinoma and UCS=Uterine Carcinosarcoma.
At least one 3D hotspot region in the gene/tumor type was not detected with the 1D-only version of the algorithm.