source: http://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinksGUI/inst/doc/data.html
The Cancer Genome Atlas (TCGA) Research Network has reported integrated genome-wide studies of various diseases. We have added some of the subtypes defined by these reports in our package.
| TCGA dataset | Link | Paper | Journal |
|---|---|---|---|
| ACC | doi:10.1016/j.ccell.2016.04.002 | Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. | Cancer cell 2016 |
| BRCA | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465532/ | Comprehensive molecular portraits of human breast tumors | Nature 2013 |
| BLCA | http://www.cell.com/cell/fulltext/S0092-8674(17)31056-5 | Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer Cell 2017 | |
| CHOL | http://www.sciencedirect.com/science/article/pii/S2211124717302140?via%3Dihub | Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles | Cell Reports 2017 |
| COAD | http://www.nature.com/nature/journal/v487/n7407/abs/nature11252.html | Comprehensive molecular characterization of human colon and rectal cancer | Nature 2012 |
| ESCA | https://www.nature.com/articles/nature20805 | Integrated genomic characterization of oesophageal carcinoma | Nature 2017 |
| GBM | http://dx.doi.org/10.1016/j.cell.2015.12.028 | Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma | Cell 2016 |
| HNSC | http://www.nature.com/nature/journal/v517/n7536/abs/nature14129.html | Comprehensive genomic characterization of head and neck squamous cell carcinomas | Nature 2015 |
| KICH | http://www.sciencedirect.com/science/article/pii/S1535610814003043 | The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma | Cancer cell 2014 |
| KIRC | http://www.nature.com/nature/journal/v499/n7456/abs/nature12222.html | Comprehensive molecular characterization of clear cell renal cell carcinoma | Nature 2013 |
| KIRP | http://www.nejm.org/doi/full/10.1056/NEJMoa1505917 | Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma | NEJM 2016 |
| LIHC | http://linkinghub.elsevier.com/retrieve/pii/S0092-8674(17)30639-6 | Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma | Cell 2017 |
| LGG | http://dx.doi.org/10.1016/j.cell.2015.12.028 | Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma | Cell 2016 |
| LUAD | http://www.nature.com/nature/journal/v511/n7511/abs/nature13385.html | Comprehensive molecular profiling of lung adenocarcinoma | Nature 2014 |
| LUSC | http://www.nature.com/nature/journal/v489/n7417/abs/nature11404.html | Comprehensive genomic characterization of squamous cell lung cancers | Nature 2012 |
| PAAD | http://www.cell.com/cancer-cell/fulltext/S1535-6108(17)30299-4 | Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma | Cancer Cell 2017 |
| PCPG | http://dx.doi.org/10.1016/j.ccell.2017.01.001 | Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma | Cancer cell 2017 |
| PRAD | http://www.sciencedirect.com/science/article/pii/S0092867415013392 | The Molecular Taxonomy of Primary Prostate Cancer | Cell 2015 |
| READ | http://www.nature.com/nature/journal/v487/n7407/abs/nature11252.html | Comprehensive molecular characterization of human colon and rectal cancer | Nature 2012 |
| SARC | http://www.cell.com/cell/fulltext/S0092-8674(17)31203-5 | Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas | Cell 2017 |
| SKCM | http://www.sciencedirect.com/science/article/pii/S0092867415006340 | Genomic Classification of Cutaneous Melanoma | Cell 2015 |
| STAD | http://www.nature.com/nature/journal/v511/n7511/abs/nature13385.html | Comprehensive molecular characterization of gastric adenocarcinoma | Nature 2013 |
| THCA | http://www.sciencedirect.com/science/article/pii/S0092867414012380 | Integrated Genomic Characterization of Papillary Thyroid Carcinoma | Cell 2014 |
| UCEC | http://www.nature.com/nature/journal/v497/n7447/abs/nature12113.html | Integrated genomic characterization of endometrial carcinoma | Nature 2013 |
| UCS | http://www.cell.com/cancer-cell/fulltext/S1535-6108(17)30053-3 | Integrated Molecular Characterization of Uterine Carcinosarcoma Cancer | Cell 2017 |
| UVM | http://www.cell.com/cancer-cell/fulltext/S1535-6108(17)30295-7 | Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma | Cancer Cell 2017 |
