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Blog from February, 2016
SYNOPSIS: One of the most striking outcomes of the cancer genome projects is that tumors of similar types and clinical responses can have patterns of mutations that are strikingly different. Despite these differences, it is becoming very clear that tumor alterations hijack the same hallmark molecular pathways and networks. Thus, a complete vision for cancer precision medicine requires not only genome sequencing, but interpretation of these genomes against a comprehensive map of cancer molecular networks. We have recently started The Cancer Cell Map Initiative (CCMI), aimed at systematically detailing the physical and genetic interactions among cancer genes and how these connections differ between diseased and healthy states. I will describe recent progress in technology and thinking that supports the creation of such a cancer cell map across a range of tissue types, as well as how such a resource can be used to match patient genomes with prognostic and predictive outcomes. 
BIO:
Trey Ideker is a systems biologist working to elucidate and model the genetic networks inside cells. He has introduced a variety of influential approaches for mapping and analyzing networks, including Cytoscape, an open software platform cited more than 10,000 times. He holds positions as Professor of Genetics in the Department of Medicine at the University of California at San Diego and leads the Program in Genomes and Networks at UCSD Moores Cancer Center. Dr. Ideker serves on the Editorial Boards of Cell, Cell Reports, and Molecular Systems Biology; is a fellow of the American Association for the Advancement of Science; was named one of the Top 10 Innovators of 2006 by Technology Review magazine; and is the 2009 recipient of the Overton Prize from the International Society for Computational Biology.
SUMMARY:
Topic: The Cancer Cell Map Initiative
Speaker: Trey Ideker, Ph.D.
Date: Wednesday, March 2, 2016
Time: 11 AM – 12 PM ET
You are invited to listen to Dr. Ideker's presentation in Room 2W910-912 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: A screencast of the presentation will be available for viewing after the event on the NCI CBIIT Speaker Series YouTube Playlist 
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About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
Our ability to deeply investigate the cancer genome is outpacing our ability to relate these changes to the phenotypes that they produce. Transformational change is possible but we will need to address several fundamental challenges including: (1) accurate phenotyping across entire populations of cancer patients, (2) sharing of clinical, imaging, and sequencing data associated with cancer biospecimens, and (3) processing of complex, high-dimensional data in combination with clinical data. In this CBIIT talk, I will share our experiences in two different open-source, NCI-funded projects to develop technology that can help address these fundamental challenges: The TIES Cancer Research Network is a federated network of Cancer Centers that enables collaborative access to deidentified and NLP-processed data, images, and biospecimens across all institutions. A network “trust” agreement among all TCRN institutions, and policies for managing the network make it possible for investigators to easily access this large dataset. TCRN is based on a scalable model that could support a national clinical data and resource sharing network for Precision Medicine. The Cancer Deep Phenotyping project (DeepPhe) is a new collaboration with the Boston Children’s Hospital cTAKES team, that focuses on development of advanced methods for phenotype extraction and representation. Expected outcomes of this project will include software pipelines for processing clinical documents to extract summarizations of key cancer phenotype variables over time including stage, tumor extent, recurrence and outcome.
SYNOPSIS:
Rebecca Crowley Jacobson, M.D., M.S., is a Professor of Biomedical Informatics at the University of Pittsburgh School of Medicine, with secondary faculty appointments in the University of Pittsburgh Cancer Institute, Intelligent Systems Program, and Department of Pathology. She is the Chief Information Officer for the Institute for Personalized Medicine and also Director of the National Library of Medicine funded Graduate Training Program in Biomedical Informatics. Her research interests include federated data sharing, the development and evaluation of natural language processing systems to enable translational research, and the development and use of ontologies and knowledge-based systems. She was elected as a Fellow of the American College of Medical Informatics in 2010, and is the author of over 75 manuscripts. Her work has been funded by the National Cancer Institute, National Library of Medicine, Fogarty International Center, National Center for Research Resources, and the Agency for Health Care Research and Quality.
SUMMARY:
Topic: How We Can Use Federated Data Sharing, Natural Language Processing, and Deep Phenotyping to Advance Precision Medicine
Speaker: Rebecca Crowley Jacobson, M.D., M.S.
Date: Wednesday, February 17, 2016
Time: 11 AM – 12 PM ET
You are invited to listen to Dr. Rebecca Crowley Jacobson's presentation in Room 2W910-912 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: A screencast of the presentation will be available for viewing after the event on the NCI CBIIT Speaker Series YouTube Playlist
.
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
