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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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 Welcome and Opening Remarks 8:30 a.m. James LeDuc, committee chair—The Uniersity of Texas Medical School The workshop in context of the study and the statement of task Session 1: The Current Structure for Oversight 9:00 a.m. 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 Leinson Julia Kiehlbauch, United States Department of • Agriculture, Animal and Plant Health Inspection Serice 

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8 APPENDIX D Rob Weyant, Centers for Disease Control and • Preention—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 Inestigation— • Surveillance of Select Agent list and emerging concerns. Amy Patterson, National Institutes of Health, Office of • Biotechnology Actiities—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 • .0—Representing companies working to harmonize screening techniques. What would they like to know to help the decision making process? Stephen M. Maurer, Uniersity 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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 APPENDIX D 12:15 p.m. Lunch Session 3: Virulence 1:00 p.m. 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 Uniersity—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, Uniersity of Washington—Systems • biology and the difficulty predicting the importance of a sequence. Ralph Baric, Uniersity 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 Break 3:10 p.m. Session 4: Predicting Pathogenicity from Sequence 3:25 p.m. 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, Uniersity of California at Dais— • Phylogenomic inference of protein function and the importance of genomic context.

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0 APPENDIX D Elliot J Lefkowitz, Uniersity of Alabama at • Birmingham—Bioinformatics support for pathogen research; Viral gene discovery and pathogenic potential. John Moult, Uniersity of Maryland Biotechnology • Institute, Center for Adanced Research in Biotechnology—Protein structure and function prediction. Ian Lipkin, Columbia Uniersity, 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