CCG Updates and Insights
Featuring current topics in cancer genomics research and news and updates from CCG.
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An Introduction to Proteogenomics Part 2: Wielding the Proteomic ToolsIn the second guest post from the Office of Cancer Clinical Proteomics Research, our colleagues describe how proteogenomic research is done and some of the findings made so far about tumor subtypes, immune microenvironment, and other aspects of tumor biology. Many of the new insights were enabled by combining genomic and proteomic data.
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Brain Tumors Hack the Neuronal Microenvironment in Multiple Ways to Drive Tumor GrowthA glioblastoma genetic screen done in mice shows how very different pathways can be altered by different variants of the same key gene—in this case PIK3CA. Tumor cells may even act on neighboring, wild type cells to promote tumorigenesis. The work was led by Drs. Benjamin Deneen, Kenneth Scott, and Gordon Mills, researchers from NCI’s Cancer Target Discovery and Development (CTD^2) Network.
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An Introduction to Proteogenomics: Appreciating the Complexity of the Central DogmaMany layers of regulation affect the flow of information from DNA to RNA to protein. In a guest post from the Office of Cancer Clinical Proteomics Research, our colleagues describe the importance of incorporating proteomics to better understand—and potentially treat—the complexities of cancer.
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Visualizing Single-Cell RNA-Seq Data with t-SNE: Researcher Interview with Dmitry Kobak and Philipp BerensTo visualize and interpret single-cell RNA-seq data, researchers must select from endless combinations of computational methods and parameters. Dr. Dmitry Kobak and Dr. Philipp Berens discuss the pros and cons of one popular method in “The art of using t-SNE for single-cell transcriptomics.”
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Cervical Tumors from Ugandan Patients, Immunoprofiler Consortium, and Clinical Trials Stemming from CTD^2 Network: August OCG e-NewsletterA genomic study of Ugandan cervical cancer patients, the UCSF Immunoprofiler Consortium, clinical trials informed by the Cancer Target Discovery and Development Network’s research, and other highlights from the August 2020 edition of the Office of Cancer Genomics (OCG) e-Newsletter.
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Continuing Our Work in the Time of Two PandemicsCCG Director Lou Staudt reflects on two pandemics—COVID-19 and racial injustice—and resolves to use the scientific method to address health care disparities.
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Single-Cell Metabolic Analyses of the Tumor Microenvironment: Researcher Interview with Jason LocasaleDr. Jason Locasale discusses new insights into the metabolic programs of different cell types in the tumor microenvironment—something enabled by the single-cell RNA sequencing revolution. Looking at metabolism helps us understand the activity of specific immune cells and how a patient might respond to different treatments.
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Introducing the Personal Genomics PodcastPersonal Genomics is NCI’s premier podcast about people in cancer genomics research. On this narrative podcast, researchers will share their stories about what happens behind the scenes of research.
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DREAM Challenges, Precision Medicine Algorithms, and Perspectives on Cancer Genomics Research: December OCG e-NewsletterComputational challenges, a suite of algorithms for identifying effective cancer treatments, a scientist interview on translating genomics for precision medicine for cancer, and other highlights from the December 2019 edition of the Office of Cancer Genomics (OCG) e-Newsletter.
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Over 44,000 AACR Project GENIE Cases Available in the GDCNCI’s Genomic Data Commons (GDC) has released data for 44,756 cancer cases from AACR Project GENIE. By making this massive data set available through the GDC, AACR and their partners hope to expand the reach and potential impact of the project and accelerate precision oncology research.