TCGA Research Network Publications

A comprehensive list of publications by The Cancer Genome Atlas program. This list is updated as the TCGA Analysis Network continues to study and mine the data. Cancers Selected for Study lists original marker publications by cancer type. Supplemental and associated data files are located in the GDC.

2008

Comprehensive genomic characterization defines human glioblastoma genes and core pathwaysExit Disclaimer
Nature. 2008;455(7216):1061-1068. doi:10.1038/nature07385 

2011

Integrated genomic analyses of ovarian carcinomaExit Disclaimer
Nature. 2011;474(7353):609-615. doi:10.1038/nature10166

2012

Comprehensive molecular characterization of human colon and rectal cancerExit Disclaimer
Nature. 2012;487(7407):330-337. doi:10.1038/nature11252

Comprehensive molecular portraits of human breast tumoursExit Disclaimer
Nature. 2012;490(7418):61-70. doi:10.1038/nature11412

Comprehensive genomic characterization of squamous cell lung cancersExit Disclaimer
Nature. 2012;489(7417):519-525. doi:10.1038/nature11404 

2013

Integrated genomic characterization of endometrial carcinomaExit Disclaimer
Nature. 2013;497(7447):67-73. doi:10.1038/nature12113

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemiaExit Disclaimer
N Engl J Med. 2013;368(22):2059-2074. doi:10.1056/NEJMoa1301689 

Comprehensive molecular characterization of clear cell renal cell carcinomaExit Disclaimer
Nature. 2013;499(7456):43-49. doi:10.1038/nature12222 

The Cancer Genome Atlas Pan-Cancer analysis projectExit Disclaimer
Nat Genet. 2013;45(10):1113-1120. doi:10.1038/ng.2764 

The somatic genomic landscape of glioblastomaExit Disclaimer
Cell. 2013;155(2):462-477. doi:10.1016/j.cell.2013.09.034 

2014

Comprehensive molecular characterization of urothelial bladder carcinomaExit Disclaimer
Nature. 2014;507(7492):315-322. doi:10.1038/nature12965 

Comprehensive molecular profiling of lung adenocarcinomaExit Disclaimer
Nature. 2014;511(7511):543-550. doi:10.1038/nature13385

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of originExit Disclaimer
Cell. 2014;158(4):929-944. doi:10.1016/j.cell.2014.06.049 

The Somatic Genomic Landscape of Chromophobe Renal Cell CarcinomaExit Disclaimer
Cancer Cell. 2014;26(3):319-330. doi:10.1016/j.ccr.2014.07.014

Comprehensive molecular characterization of gastric adenocarcinomaExit Disclaimer
Nature. 2014;513(7517):202-209. doi:10.1038/nature13480 

Integrated genomic characterization of papillary thyroid carcinomaExit Disclaimer
Cell. 2014;159(3):676-690. doi:10.1016/j.cell.2014.09.050 

2015

Comprehensive genomic characterization of head and neck squamous cell carcinomasExit Disclaimer
Nature. 2015;517(7536):576-582. doi:10.1038/nature14129 

Genomic Classification of Cutaneous MelanomaExit Disclaimer
Cell. 2015;161(7):1681-1696. doi:10.1016/j.cell.2015.05.044

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade GliomasExit Disclaimer
N Engl J Med. 2015;372(26):2481-2498. doi:10.1056/NEJMoa1402121 

Comprehensive Molecular Portraits of Invasive Lobular Breast CancerExit Disclaimer
Cell. 2015;163(2):506-519. doi:10.1016/j.cell.2015.09.033 

The Molecular Taxonomy of Primary Prostate CancerExit Disclaimer
Cell. 2015;163(4):1011-1025. doi:10.1016/j.cell.2015.10.025 

2016

Comprehensive Molecular Characterization of Papillary Renal-Cell CarcinomaExit Disclaimer
N Engl J Med. 2016;374(2):135-145. doi:10.1056/NEJMoa1505917 

Comprehensive Pan-Genomic Characterization of Adrenocortical CarcinomaExit Disclaimer
Cancer Cell. 2016;29(5):723-736. doi:10.1016/j.ccell.2016.04.002 

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomasExit Disclaimer
Nat Genet. 2016;48(6):607-616. doi:10.1038/ng.3564 

2017

Integrated genomic characterization of oesophageal carcinomaExit Disclaimer
Nature. 2017;541(7636):169-175. doi:10.1038/nature20805 

Comprehensive Molecular Characterization of Pheochromocytoma and ParagangliomaExit Disclaimer
Cancer Cell. 2017;31(2):181-193. doi:10.1016/j.ccell.2017.01.001 

Integrated Molecular Characterization of Uterine CarcinosarcomaExit Disclaimer
Cancer Cell. 2017;31(3):411-423. doi:10.1016/j.ccell.2017.02.010 

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular ProfilesExit Disclaimer
Cell Rep. 2017;18(11):2780-2794. doi:10.1016/j.celrep.2017.02.033

Integrated genomic and molecular characterization of cervical cancerExit Disclaimer
Nature. 2017;543(7645):378-384. doi:10.1038/nature21386 

Comprehensive and Integrative Genomic Characterization of Hepatocellular CarcinomaExit Disclaimer
Cell. 2017;169(7):1327-1341.e23. doi:10.1016/j.cell.2017.05.046 

Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal MelanomaExit Disclaimer
Cancer Cell. 2017;32(2):204-220.e15. doi:10.1016/j.ccell.2017.07.003 

Integrated Genomic Characterization of Pancreatic Ductal AdenocarcinomaExit Disclaimer
Cancer Cell. 2017;32(2):185-203.e13. doi:10.1016/j.ccell.2017.07.007 

Comprehensive Molecular Characterization of Muscle-Invasive Bladder CancerExit Disclaimer
Cell. 2017;171(3):540-556.e25. doi:10.1016/j.cell.2017.09.007 

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue SarcomasExit Disclaimer
Cell. 2017;171(4):950-965.e28. doi:10.1016/j.cell.2017.10.014 

2018

The Integrated Genomic Landscape of Thymic Epithelial TumorsExit Disclaimer
Cancer Cell. 2018;33(2):244-258.e10. doi:10.1016/j.ccell.2018.01.003 

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome AtlasExit Disclaimer
Cell Syst. 2018;6(3):282-300.e2. doi:10.1016/j.cels.2018.03.003 

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic PipelinesExit Disclaimer
Cell Syst. 2018;6(3):271-281.e7. doi:10.1016/j.cels.2018.03.002 

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human CancersExit Disclaimer 
Cell Rep. 2018;23(1):255-269.e4. doi:10.1016/j.celrep.2018.03.077 

Systematic Analysis of Splice-Site-Creating Mutations in CancerExit Disclaimer
Cell Rep. 2018;23(1):270-281.e3. doi:10.1016/j.celrep.2018.03.052 

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer TypesExit Disclaimer
Cell Rep. 2018;23(1):282-296.e4. doi:10.1016/j.celrep.2018.01.088 

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell CarcinomaExit Disclaimer
Cell Rep. 2018;23(1):313-326.e5. doi:10.1016/j.celrep.2018.03.075 

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor ContextExit Disclaimer
Cell Rep. 2018;23(1):297-312.e12. doi:10.1016/j.celrep.2018.03.064 

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology ImagesExit Disclaimer
Cell Rep. 2018;23(1):181-193.e7. doi:10.1016/j.celrep.2018.03.086 

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome AtlasExit Disclaimer
Cell Rep. 2018;23(1):172-180.e3. doi:10.1016/j.celrep.2018.03.046 

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome AtlasExit Disclaimer
Cell Rep. 2018;23(1):239-254.e6. doi:10.1016/j.celrep.2018.03.076 

Driver Fusions and Their Implications in the Development and Treatment of Human CancersExit Disclaimer
Cell Rep. 2018;23(1):227-238.e3. doi:10.1016/j.celrep.2018.03.050 

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous CarcinomasExit Disclaimer
Cell Rep. 2018;23(1):194-212.e6. doi:10.1016/j.celrep.2018.03.063 

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer TypesExit Disclaimer
Cell Rep. 2018;23(1):213-226.e3. doi:10.1016/j.celrep.2018.03.047 

SnapShot: TCGA-Analyzed TumorsExit Disclaimer
Cell. 2018;173(2):530. doi:10.1016/j.cell.2018.03.059 

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of CancerExit Disclaimer
Cell. 2018;173(2):291-304.e6. doi:10.1016/j.cell.2018.03.022 

The Cancer Genome Atlas: Creating Lasting Value beyond Its DataExit Disclaimer
Cell. 2018;173(2):283-285. doi:10.1016/j.cell.2018.03.042 

Machine Learning Identifies Stemness Features Associated with Oncogenic DedifferentiationExit Disclaimer
Cell. 2018;173(2):338-354.e15. doi:10.1016/j.cell.2018.03.034 

Oncogenic Signaling Pathways in The Cancer Genome AtlasExit Disclaimer
Cell. 2018;173(2):321-337.e10. doi:10.1016/j.cell.2018.03.035

Perspective on Oncogenic Processes at the End of the Beginning of Cancer GenomicsExit Disclaimer
Cell. 2018;173(2):305-320.e10. doi:10.1016/j.cell.2018.03.033 

Comprehensive Characterization of Cancer Driver Genes and MutationsExit Disclaimer
Cell. 2018;173(2):371-385.e18. doi:10.1016/j.cell.2018.02.060 

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome AnalyticsExit Disclaimer
Cell. 2018;173(2):400-416.e11. doi:10.1016/j.cell.2018.02.052 

Pathogenic Germline Variants in 10,389 Adult CancersExit Disclaimer
Cell. 2018;173(2):355-370.e14. doi:10.1016/j.cell.2018.03.039 

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient SamplesExit Disclaimer
Cell. 2018;173(2):386-399.e12. doi:10.1016/j.cell.2018.03.027 

Genomic and Functional Approaches to Understanding Cancer AneuploidyExit Disclaimer
Cancer Cell. 2018;33(4):676-689.e3. doi:10.1016/j.ccell.2018.03.007 

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast CancersExit Disclaimer
Cancer Cell. 2018;33(4):690-705.e9. doi:10.1016/j.ccell.2018.03.014 

Comparative Molecular Analysis of Gastrointestinal AdenocarcinomasExit Disclaimer
Cancer Cell. 2018;33(4):721-735.e8. doi:10.1016/j.ccell.2018.03.010 

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in CancerExit Disclaimer
Cancer Cell. 2018;33(4):706-720.e9. doi:10.1016/j.ccell.2018.03.006 

The Immune Landscape of CancerExit Disclaimer
Immunity. 2018;48(4):812-830.e14. doi:10.1016/j.immuni.2018.03.023 

Integrated Molecular Characterization of Testicular Germ Cell TumorsExit Disclaimer
Cell Rep. 2018;23(11):3392-3406. doi:10.1016/j.celrep.2018.05.039 

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 PatientsExit Disclaimer
Cancer Cell. 2018;34(2):211-224.e6. doi:10.1016/j.ccell.2018.07.001

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β SuperfamilyExit Disclaimer
Cell Systems. 2018;7(4);422-437.e7. doi: 10.1016/j.cels.2018.08.010

Integrative Molecular Characterization of Malignant Pleural MesotheliomaExit Disclaimer
Cancer Discovery. 2018;8(12):1548-1565. doi: 10.1158/2159-8290.CD-18-0804

The chromatin accessibility landscape of primary human cancersExit Disclaimer
Science. 2018;362(6413). pii: eaav1898. doi: 10.1126/science.aav1898

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in CancerExit Disclaimer
Cell Reports. 2018;25(5):1304-1317.e5. doi: 10.1016/j.celrep.2018.10.001

2019

Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ DataExit Disclaimer
Cell Systems. 2019;9(1):24-34.e10. doi: 10.1016/j.cels.2019.06.006