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Sequence-Based Classiﬁcation of Select Agents: A Brighter Line Appendix D 2009 Workshop Agenda Scientific Milestones for the Development of a Gene-Sequence-Based Classification System for Oversight of Select Agents Thursday, Sept. 3rd, 2009 The National Academy of Sciences Building: Lecture Room 2100 C St., N.W. • Washington, D.C. 20037 AGENDA 8:30 a.m. Welcome and Opening Remarks James LeDuc, committee chair—The University of Texas Medical School The workshop in context of the study and the statement of task 9:00 a.m. Session 1: The Current Structure for Oversight What are the current forms of oversight? Are there gaps in the oversight, and if so, are these gaps emerging as a result of new technology, new user communities, or new perceptions? How might a sequence based system be helpful in addressing these gaps/concerns? *Moderator: Rachel Levinson • Julia Kiehlbauch, United States Department of Agriculture, Animal and Plant Health Inspection Service
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Sequence-Based Classiﬁcation of Select Agents: A Brighter Line • Rob Weyant, Centers for Disease Control and Prevention—Synthetic DNA and the Select Agent Regulations. • Claudia Mickelson, Massachusetts Institute of Technology—IBC, RAC guidelines and concerns about sequences. • Edward You, Federal Bureau of Investigation—Surveillance of Select Agent list and emerging concerns. • Amy Patterson, National Institutes of Health, Office of Biotechnology Activities—Comprehensive view and the need for this study. Panel discussion: ~30 min 10:30 a.m. Break 10:45 a.m. Session 2: Current Mechanisms and Criteria for Screening and Surveillance What is currently being done? How are sequences chosen to monitor? What is a “sequence of concern”? *Moderator—John Mulligan • Pete Pesenti, Department of Homeland Security—What are the factors and process used for risk assessment? What are the criteria or characteristics of agents (or sequences) considered a threat? • John Mulligan, Blue Heron Biotechnology—What are the current screening practices, standards, and procedures in the industry? What are challenges and concerns? • Marcus Graf, GeneArt and Claes Gustafsson, DNA 2.0—Representing companies working to harmonize screening techniques. What would they like to know to help the decision making process? • Stephen M. Maurer, University of California at Berkeley—Interface of biosecurity, synthetic biology, and industry. Panel discussion: ~30 min ** Ed You, FBI will join panel **
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Sequence-Based Classiﬁcation of Select Agents: A Brighter Line 12:15 p.m. Lunch 1:00 p.m. Session 3: Virulence What is virulence? Why is it so hard to predict? What attributes make a pathogen a threat to biosecurity? —to public health? Is there a difference? *Moderator—Stan Falkow • Stan Falkow, Stanford University—Overview of virulence, meaning of genomics in prediction. • Jeff Taubenberger, National Institutes of Health, National Institute of Allergy and Infectious Diseases—Influenza virulence and the role of genotype-phenotype relationships. • Michael Katze, University of Washington—Systems biology and the difficulty predicting the importance of a sequence. • Ralph Baric, University of North Carolina at Chapel Hill—SARS, systems genetics and pathogenesis. • Ramon Felciano, Ingenuity Systems—Systems biology and pathway modeling of pathogenesis and host response. Panel discussion: ~30 min 3:10 p.m. Break 3:25 p.m. Session 4: Predicting Pathogenicity from Sequence Speakers will address gaps, challenges, and timeframe for milestones. *Moderator—Sean Eddy • Sean Eddy, Howard Hughes Medical Institute, Janelia Farm Research Campus—Overview of sequence analysis; how reliably can protein function be predicted from protein sequence? • Jonathon Eisen, University of California at Davis—Phylogenomic inference of protein function and the importance of genomic context.
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Sequence-Based Classiﬁcation of Select Agents: A Brighter Line • Elliot J Lefkowitz, University of Alabama at Birmingham—Bioinformatics support for pathogen research; Viral gene discovery and pathogenic potential. • John Moult, University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology—Protein structure and function prediction. • Ian Lipkin, Columbia University, Mailman School of Public Health—Identification of emerging or novel microorganisms—pathogen surveillance. Panel discussion: ~30 min 5:45 p.m. Closing Remarks 6:00 p.m. Adjourn