Genomic Data Commons (GDC)
The NCI's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine.
The GDC supports several cancer genome programs at the NCI Center for Cancer Genomics (CCG), including The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET).
Navigating the GDC - A Case Study is a workshop which helps users to learn GDC tools and data types available to support cancer genomic study.
Molecular data available in GDC.
| Cancer Types | Primary Site | Program | # Cases | Genotyping Array | WXS | RNA-Seq | miRNA-Seq | Methylation array | Protein expression array | Gene expression array | miRNA expression array | Total RNA-Seq | Bisulfite-Seq |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Acute Myeloid Leukemia[AML] | Blood | TARGET | 923 | 0 | 19 | 179 | 265 | 0 | 0 | 0 | 0 | 0 | 0 |
| Acute Myeloid Leukemia[LAML] | Bone Marrow | TCGA | 200 | 143 | 149 | 151 | 103 | 140 | 0 | 140 | 0 | 0 | 0 |
| Adrenocortical Carcinoma[ACC] | Adrenal Gland | TCGA | 80 | 92 | 92 | 79 | 80 | 80 | 46 | 0 | 0 | 0 | 0 |
| Bladder Urothelial Carcinoma[BLCA] | Bladder | TCGA | 412 | 412 | 412 | 408 | 409 | 417 | 344 | 0 | 0 | 4 | 6 |
| Brain Lower Grade Glioma[LGG] | Brain | TCGA | 516 | 514 | 515 | 512 | 512 | 516 | 430 | 27 | 0 | 0 | 0 |
| Breast Invasive Carcinoma[BRCA] | Breast | TCGA | 1097 | 1096 | 1050 | 1092 | 1079 | 1095 | 885 | 527 | 0 | 11 | 5 |
| Cervical Squamous Cell Carcinoma and endocervical adenocarcinoma[CESC] | Cervix | TCGA | 307 | 302 | 305 | 304 | 307 | 307 | 173 | 0 | 0 | 0 | 0 |
| Cholangiocarcinoma[CHOL] | Bile Duct | TCGA | 36 | 36 | 51 | 36 | 36 | 36 | 30 | 0 | 0 | 0 | 0 |
| Clear Cell Sarcoma of the Kidney[CCSK] | Kidney | TARGET | 13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Colon Adenocarcinoma[COAD] | Colorectal | TCGA | 461 | 458 | 443 | 456 | 444 | 459 | 362 | 162 | 0 | 13 | 2 |
| Esophageal Carcinoma[ESCA] | Esophagus | TCGA | 185 | 185 | 184 | 164 | 184 | 185 | 126 | 0 | 0 | 0 | 0 |
| Glioblastoma Multiforme[GBM] | Brain | TCGA | 528 | 593 | 401 | 166 | 5 | 599 | 238 | 587 | 576 | 0 | 6 |
| Head and Neck Squamous Cell Carcinoma[HNSC] | Head and Neck | TCGA | 528 | 521 | 527 | 501 | 524 | 528 | 357 | 0 | 0 | 0 | 0 |
| High-Risk Wilms Tumor[WT] | Kidney | TARGET | 663 | 0 | 41 | 122 | 127 | 0 | 0 | 0 | 0 | 0 | 0 |
| Kidney Chromophobe[KICH] | Kidney | TCGA | 66 | 66 | 66 | 66 | 66 | 66 | 63 | 0 | 0 | 0 | 0 |
| Kidney Renal Clear Cell Carcinoma[KIRC] | Kidney | TCGA | 536 | 532 | 345 | 530 | 516 | 533 | 476 | 72 | 0 | 4 | 0 |
| Kidney Renal Papillary Cell Carcinoma[KIRP] | Kidney | TCGA | 291 | 290 | 290 | 289 | 291 | 291 | 215 | 16 | 0 | 0 | 0 |
| Liver Hepatocellular Carcinoma[LIHC] | Liver | TCGA | 377 | 376 | 376 | 371 | 373 | 377 | 184 | 0 | 0 | 0 | 0 |
| Lung Adenocarcinoma[LUAD] | Lung | TCGA | 521 | 518 | 582 | 515 | 513 | 579 | 365 | 32 | 0 | 12 | 5 |
| Lung Squamous Cell Carcinoma[LUSC] | Lung | TCGA | 504 | 504 | 502 | 501 | 478 | 503 | 328 | 154 | 0 | 0 | 4 |
| Lymphoid Neoplasm Diffuse Large B-cell Lymphoma[DLBC] | Lymph Nodes | TCGA | 48 | 48 | 48 | 48 | 47 | 48 | 33 | 0 | 0 | 0 | 0 |
| Mesothelioma[MESO] | Pleura | TCGA | 87 | 87 | 83 | 86 | 87 | 87 | 63 | 0 | 0 | 0 | 0 |
| Neuroblastoma[NBL] | Nervous System | TARGET | 1120 | 0 | 221 | 151 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Osteosarcoma[OS] | Bone | TARGET | 384 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Ovarian Serous Cystadenocarcinoma[OV] | Ovary | TCGA | 586 | 573 | 460 | 376 | 489 | 602 | 426 | 582 | 578 | 0 | 0 |
| Pancreatic Adenocarcinoma[PAAD] | Pancreas | TCGA | 185 | 185 | 185 | 177 | 178 | 184 | 123 | 0 | 0 | 0 | 0 |
| Pheochromocytoma and Paraganglioma[PCPG] | Adrenal Gland | TCGA | 179 | 179 | 179 | 179 | 179 | 179 | 80 | 0 | 0 | 0 | 0 |
| Prostate Adenocarcinoma[PRAD] | Prostate | TCGA | 498 | 498 | 498 | 496 | 494 | 498 | 352 | 0 | 0 | 4 | 0 |
| Rectum Adenocarcinoma[READ] | Colorectal | TCGA | 171 | 166 | 168 | 167 | 161 | 165 | 131 | 69 | 0 | 0 | 2 |
| Rhabdoid Tumor[RT] | Kidney | TARGET | 75 | 0 | 0 | 5 | 44 | 0 | 0 | 0 | 0 | 0 | 72 |
| Sarcoma[SARC] | Soft Tissue | TCGA | 261 | 261 | 255 | 259 | 259 | 261 | 223 | 0 | 0 | 0 | 0 |
| Skin Cutaneous Melanoma[SKCM] | Skin | TCGA | 470 | 470 | 470 | 468 | 448 | 470 | 353 | 0 | 0 | 0 | 0 |
| Stomach Adenocarcinoma[STAD] | Stomach | TCGA | 443 | 443 | 443 | 380 | 436 | 478 | 392 | 0 | 0 | 0 | 4 |
| Testicular Germ Cell Tumors[TGCT] | Testis | TCGA | 150 | 134 | 150 | 150 | 50 | 140 | 118 | 0 | 0 | 0 | 0 |
| Thymoma[THYM] | Thymus | TCGA | 127 | 124 | 123 | 119 | 124 | 124 | 90 | 0 | 0 | 0 | 0 |
| Thyroid Carcinoma[THCA] | Thyroid | TCGA | 507 | 505 | 502 | 502 | 506 | 507 | 372 | 0 | 0 | 0 | 0 |
| Uterine Carcinosarcoma[UCS] | Uterus | TCGA | 54 | 57 | 57 | 56 | 57 | 57 | 47 | 0 | 0 | 0 | 0 |
| Uterine Corpus Endometrial Carcinoma[UCEC] | Uterus | TCGA | 548 | 547 | 553 | 555 | 550 | 559 | 440 | 69 | 0 | 4 | 5 |
| Uveal Melanoma[UVM] | Eye | TCGA | 80 | 80 | 80 | 80 | 80 | 80 | 12 | 0 | 0 | 0 | 0 |