National Academies Press: OpenBook

Sequence-Based Classification of Select Agents: A Brighter Line (2010)

Chapter: Appendix D: 2009 Workshop Agenda

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Suggested Citation:"Appendix D: 2009 Workshop Agenda." National Research Council. 2010. Sequence-Based Classification of Select Agents: A Brighter Line. Washington, DC: The National Academies Press. doi: 10.17226/12970.
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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

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

Suggested Citation:"Appendix D: 2009 Workshop Agenda." National Research Council. 2010. Sequence-Based Classification of Select Agents: A Brighter Line. Washington, DC: The National Academies Press. doi: 10.17226/12970.
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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 **

Suggested Citation:"Appendix D: 2009 Workshop Agenda." National Research Council. 2010. Sequence-Based Classification of Select Agents: A Brighter Line. Washington, DC: The National Academies Press. doi: 10.17226/12970.
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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.

Suggested Citation:"Appendix D: 2009 Workshop Agenda." National Research Council. 2010. Sequence-Based Classification of Select Agents: A Brighter Line. Washington, DC: The National Academies Press. doi: 10.17226/12970.
×

 

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

Suggested Citation:"Appendix D: 2009 Workshop Agenda." National Research Council. 2010. Sequence-Based Classification of Select Agents: A Brighter Line. Washington, DC: The National Academies Press. doi: 10.17226/12970.
×
Page 147
Suggested Citation:"Appendix D: 2009 Workshop Agenda." National Research Council. 2010. Sequence-Based Classification of Select Agents: A Brighter Line. Washington, DC: The National Academies Press. doi: 10.17226/12970.
×
Page 148
Suggested Citation:"Appendix D: 2009 Workshop Agenda." National Research Council. 2010. Sequence-Based Classification of Select Agents: A Brighter Line. Washington, DC: The National Academies Press. doi: 10.17226/12970.
×
Page 149
Suggested Citation:"Appendix D: 2009 Workshop Agenda." National Research Council. 2010. Sequence-Based Classification of Select Agents: A Brighter Line. Washington, DC: The National Academies Press. doi: 10.17226/12970.
×
Page 150
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Select Agents are defined in regulations through a list of names of particularly dangerous known bacteria, viruses, toxins, and fungi. However, natural variation and intentional genetic modification blur the boundaries of any discrete Select Agent list based on names. Access to technologies that can generate or 'synthesize' any DNA sequence is expanding, making it easier and less expensive for researchers, industry scientists, and amateur users to create organisms without needing to obtain samples of existing stocks or cultures. This has led to growing concerns that these DNA synthesis technologies might be used to synthesize Select Agents, modify such agents by introducing small changes to the genetic sequence, or create entirely new pathogens. Amid these concerns, the National Institutes of Health requested that the Research Council investigate the science and technology needed to replace the current Select Agent list with an oversight system that predicts if a DNA sequence could be used to produce an organism that should be regulated as a Select Agent.

A DNA sequence-based system to better define when a pathogen or toxin is subject to Select Agent regulations could be developed. This could be coupled with a 'yellow flag' system that would recognize requests to synthesize suspicious sequences and serve as a reference to anyone with relevant questions, allowing for appropriate follow-up.

Sequence-Based Classification of Select Agents finds that replacing the current list of Select Agents with a system that could predict if fragments of DNA sequences could be used to produce novel pathogens with Select Agent characteristics is not feasible. However, it emphasized that for the foreseeable future, any threat from synthetic biology and synthetic genomics is far more likely to come from assembling known Select Agents, or modifications of them, rather than construction of previously unknown agents. Therefore, the book recommends modernizing the regulations to define Select Agents in terms of their gene sequences, not by their names, and called this 'sequence-based classification.'

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