The proposal titled """"""""TCGA Data Analysis Center at Berkeley"""""""" focuses on integrating data from The Cancer Genome Atlas (TCGA) and providing that integrated analysis to the community by timely computation and redistribution through the TCGA Data Coordinating Center. The proposal includes six key elements (1) quality control of TCGA data, (2) systematic classification of tumors by molecular data, (3) analysis and integration of histopathology images (H&E), (4) interpretation of gene expression data in the context of other molecular data, (5) identification of interacting genetic loci by aberration co-occurrence, and (6) creation of genetic influence diagrams. These analyses will be performed on the mutation, copy number, genotype, expression, methylation and miRNA analyses that are likely to be key components of TCGA. Data analyses will begin after a cohesive analytical strategy is developed in a design document that clearly lays out the process by which our group will receive, analyze, and redistribute information. Our proposal includes collaborators who are pathologists, cancer biologists, geneticists, genomicists, computer scientists, and statisticians who have a proven track record of working together on large projects.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Resource-Related Research Projects--Cooperative Agreements (U24)
Project #
5U24CA143799-04
Application #
8325456
Study Section
Special Emphasis Panel (ZCA1-SRLB-U (O1))
Program Officer
Yang, Liming
Project Start
2009-09-28
Project End
2014-07-31
Budget Start
2012-08-01
Budget End
2013-07-31
Support Year
4
Fiscal Year
2012
Total Cost
$646,044
Indirect Cost
$112,063
Name
Oregon Health and Science University
Department
Genetics
Type
Schools of Medicine
DUNS #
096997515
City
Portland
State
OR
Country
United States
Zip Code
97239
Cherniack, Andrew D; Shen, Hui; Walter, Vonn et al. (2017) Integrated Molecular Characterization of Uterine Carcinosarcoma. Cancer Cell 31:411-423
Cancer Genome Atlas Research Network. Electronic address: elizabeth.demicco@sinaihealthsystem.ca; Cancer Genome Atlas Research Network (2017) Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell 171:950-965.e28
Robertson, A Gordon; Kim, Jaegil; Al-Ahmadie, Hikmat et al. (2017) Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell 171:540-556.e25
Cancer Genome Atlas Research Network; Albert Einstein College of Medicine; Analytical Biological Services et al. (2017) Integrated genomic and molecular characterization of cervical cancer. Nature 543:378-384
Van Hook, Kathryn; Wang, Zhiping; Chen, Dexi et al. (2017) ?N-ASPP2, a novel isoform of the ASPP2 tumor suppressor, promotes cellular survival. Biochem Biophys Res Commun 482:1271-1277
Farshidfar, Farshad; Zheng, Siyuan; Gingras, Marie-Claude et al. (2017) Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep 18:2780-2794
Fishbein, Lauren; Leshchiner, Ignaty; Walter, Vonn et al. (2017) Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma. Cancer Cell 31:181-193
Cancer Genome Atlas Research Network; Analysis Working Group: Asan University; BC Cancer Agency et al. (2017) Integrated genomic characterization of oesophageal carcinoma. Nature 541:169-175
Huo, Dezheng; Hu, Hai; Rhie, Suhn K et al. (2017) Comparison of Breast Cancer Molecular Features and Survival by African and European Ancestry in The Cancer Genome Atlas. JAMA Oncol 3:1654-1662
Robertson, A Gordon; Shih, Juliann; Yau, Christina et al. (2017) Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell 32:204-220.e15

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