Table 1.
Summary of TCGA cancer type and number of samples used in each analysis.
| Cancer type | Abbreviation | GI, LOH, WGD | SCNAs | Mutations (hypermutated and MSI-H removed) | Pathway alterations | Gene expression | DNA methylation |
|---|---|---|---|---|---|---|---|
| Adrenocortical carcinoma | ACC | 89 | 89 | 89 (88) | 76 | 77 | 78 |
| Bladder urothelial carcinoma | BLCA | 370 | 369 | 369 (364) | 361 | 366 | 370 |
| Breast invasive carcinoma | BRCA | 1015 | 1011 | 954 (946) | 922 | 1011 | 719 |
| Cervical squamous cell carcinoma and endocervical adenocarcinoma | CESC | 287 | 287 | 271 (263) | 264 | 284 | 287 |
| Cholangiocarcinoma | CHOL | 35 | 35 | 35 (35) | 35 | 35 | 35 |
| Colon adenocarcinoma | COAD | 411 | 411 | 374 (303) | 323 | 410 | 278 |
| Lymphoid neoplasm diffuse large B-cell lymphoma | DLBC | 42 | 42 | 32 (32) | 32 | 42 | 42 |
| Oesophageal carcinoma | ESCA | 176 | 176 | 176 (174) | 165 | 175 | 176 |
| Glioblastoma multiforme | GBM | 489 | 489 | 356 (354) | 116 | 137 | 259 |
| Head and neck squamous cell carcinoma | HNSC | 489 | 489 | 472 (469) | 459 | 481 | 489 |
| Kidney chromophobe | KICH | 66 | 66 | 66 (66) | 65 | 66 | 66 |
| Kidney renal clear cell carcinoma | KIRC | 496 | 496 | 343 (343) | 331 | 493 | 296 |
| Kidney renal papillary cell carcinoma | KIRP | 228 | 228 | 222 (222) | 215 | 228 | 213 |
| Acute myeloid leukaemia | LAML | 126 | 121 | 55 (54) | 101 | 102 | 121 |
| Brain lower grade glioma | LGG | 488 | 488 | 484 (484) | 482 | 488 | 488 |
| Liver hepatocellular carcinoma | LIHC | 355 | 355 | 342 (340) | 334 | 349 | 355 |
| Lung adenocarcinoma | LUAD | 460 | 460 | 456 (438) | 446 | 456 | 402 |
| Lung squamous cell carcinoma | LUSC | 460 | 460 | 444 (437) | 426 | 457 | 336 |
| Mesothelioma | MESO | 82 | 82 | 77 (77) | 77 | 82 | 82 |
| Ovarian serous cystadenocarcinoma | OV | 556 | 556 | 397 (395) | 173 | 288 | 545 |
| Pancreatic adenocarcinoma | PAAD | 133 | 133 | 130 (129) | 113 | 127 | 132 |
| Pheochromocytoma and Paraganglioma | PCPG | 165 | 157 | 165 (164) | 154 | 165 | 165 |
| Prostate adenocarcinoma | PRAD | 434 | 434 | 434 (432) | 425 | 434 | 434 |
| Rectum adenocarcinoma | READ | 152 | 152 | 132 (125) | 109 | 151 | 95 |
| Sarcoma | SARC | 229 | 229 | 213 (211) | 209 | 227 | 229 |
| Skin cutaneous melanoma | SKCM | 434 | 434 | 432 (340) | 332 | 433 | 434 |
| Stomach adenocarcinoma | STAD | 388 | 388 | 385 (345) | 340 | 365 | 341 |
| Testicular germ cell tumours | TGCT | 129 | 129 | 124 (124) | 123 | 129 | 129 |
| Thyroid carcinoma | THCA | 260 | 260 | 249 (248) | 244 | 259 | 258 |
| Thymoma | THYM | 76 | 76 | 76 (76) | 73 | 73 | 76 |
| Uterine corpus endometrial carcinoma | UCEC | 434 | 434 | 421 (282) | 406 | 432 | 360 |
| Uterine carcinosarcoma | UCS | 52 | 52 | 52 (51) | 52 | 52 | 52 |
| Uveal melanoma | UVM | 72 | 72 | 72 (72) | 72 | 72 | 72 |
| Total | 9678 | 9660 | 8899 (8448) | 8055 | 8946 | 8414 |