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.
| Ellrott, Kyle; Bailey, Matthew H; Saksena, Gordon et al. (2018) Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst 6:271-281.e7 |
| Campbell, Joshua D; Yau, Christina; Bowlby, Reanne et al. (2018) Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep 23:194-212.e6 |
| Gao, Qingsong; Liang, Wen-Wei; Foltz, Steven M et al. (2018) Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep 23:227-238.e3 |
| Thorsson, Vésteinn; Gibbs, David L; Brown, Scott D et al. (2018) The Immune Landscape of Cancer. Immunity 48:812-830.e14 |
| Radovich, Milan; Pickering, Curtis R; Felau, Ina et al. (2018) The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell 33:244-258.e10 |
| Shen, Hui; Shih, Juliann; Hollern, Daniel P et al. (2018) Integrated Molecular Characterization of Testicular Germ Cell Tumors. Cell Rep 23:3392-3406 |
| Berger, Ashton C; Korkut, Anil; Kanchi, Rupa S et al. (2018) A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell 33:690-705.e9 |
| Hoadley, Katherine A; Yau, Christina; Hinoue, Toshinori et al. (2018) Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell 173:291-304.e6 |
| Schaub, Franz X; Dhankani, Varsha; Berger, Ashton C et al. (2018) Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Syst 6:282-300.e2 |
| Liu, Jianfang; Lichtenberg, Tara; Hoadley, Katherine A et al. (2018) An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell 173:400-416.e11 |
Showing the most recent 10 out of 75 publications
