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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 pathways
Nature. 2008;455(7216):1061-1068. doi:10.1038/nature07385 

2011

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

2012

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

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

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

2013

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

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

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

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

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

2014

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

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

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

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

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

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

2015

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

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

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

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

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

2016

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

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma
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 carcinomas
Nat Genet. 2016;48(6):607-616. doi:10.1038/ng.3564 

2017

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

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

Integrated Molecular Characterization of Uterine Carcinosarcoma
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 Profiles
Cell Rep. 2017;18(11):2780-2794. doi:10.1016/j.celrep.2017.02.033

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

Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma
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 Melanoma
Cancer Cell. 2017;32(2):204-220.e15. doi:10.1016/j.ccell.2017.07.003 

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

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

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

2018

The Integrated Genomic Landscape of Thymic Epithelial Tumors
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 Atlas
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 Pipelines
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 Cancers 
Cell Rep. 2018;23(1):255-269.e4. doi:10.1016/j.celrep.2018.03.077 

Systematic Analysis of Splice-Site-Creating Mutations in Cancer
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 Types
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 Carcinoma
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 Context
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 Images
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 Atlas
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 Atlas
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 Cancers
Cell Rep. 2018;23(1):227-238.e3. doi:10.1016/j.celrep.2018.03.050 

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
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 Types
Cell Rep. 2018;23(1):213-226.e3. doi:10.1016/j.celrep.2018.03.047 

SnapShot: TCGA-Analyzed Tumors
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 Cancer
Cell. 2018;173(2):291-304.e6. doi:10.1016/j.cell.2018.03.022 

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

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

Oncogenic Signaling Pathways in The Cancer Genome Atlas
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 Genomics
Cell. 2018;173(2):305-320.e10. doi:10.1016/j.cell.2018.03.033 

Comprehensive Characterization of Cancer Driver Genes and Mutations
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 Analytics
Cell. 2018;173(2):400-416.e11. doi:10.1016/j.cell.2018.02.052 

Pathogenic Germline Variants in 10,389 Adult Cancers
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 Samples
Cell. 2018;173(2):386-399.e12. doi:10.1016/j.cell.2018.03.027 

Genomic and Functional Approaches to Understanding Cancer Aneuploidy
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 Cancers
Cancer Cell. 2018;33(4):690-705.e9. doi:10.1016/j.ccell.2018.03.014 

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas
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 Cancer
Cancer Cell. 2018;33(4):706-720.e9. doi:10.1016/j.ccell.2018.03.006 

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

Integrated Molecular Characterization of Testicular Germ Cell Tumors
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 Patients
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 Superfamily
Cell Systems. 2018;7(4);422-437.e7 doi: 10.1016/j.cels.2018.08.010

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

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

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

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