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Sequence-Based Classification of Select Agents A Brighter Line (2010) / Chapter Skim
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Pages 1-8

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From page 1...
... , which considered the effects of synthetic biology and DNA synthesis technology on biosecurity and the current Select Agent Regulations. The principal concerns that it addressed were that • DNA synthesis technology is rapidly diminishing barriers to acquisi tion of pathogens, because an increasing variety of organisms may be instantiated by whole genome synthesis, rather than by transfer of samples of existing organism stocks or cultures; • Natural variation and intentional genetic modification blur the bound aries around any discrete list based on taxonomic names • Synthetic biology may enable the accidental or deliberate creation of entirely novel pathogens unrelated to current ones.
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From page 2...
... Some properties historically considered in assigning an organism to the Select Agent list are not biological properties, and therefore, can never be determined from the organism's genome sequence. • High-level biological phenotypes -- such as pathogenicity, transmissi bility, and environmental stability -- cannot plausibly be predicted with the degree of certainty required for regulatory purposes, either now or in the foreseeable future.
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From page 3...
... For the purposes of regulation, a discrete taxonomic list of Select Agents, augmented by sequence-based classification to better cir cumscribe taxonomic distinctions blurred by natural and synthetic variation and modification, is a reasonable strategy to maintain for the foreseeable future. Sequence-based classification is strictly operational -- a set of tools for drawing decision boundaries around known sequences that do or do not belong to a desired classification.
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From page 4...
... Sequence-based classification strategies would more sharply de fine the Select Agent Regulations to deal with issues raised by DNA synthesis and natural variation, and would thus establish a "brighter line": an unambiguous procedure for deciding when a genome sequence is assigned one of the taxonomic names on the Select Agent list. The problem of classifying a sequence as a complete Select Agent genome (subject to the Select Agent Regulations)
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From page 5...
... A comprehensive sequence database would thoroughly cover naturally occurring genetic variation based on geographic distribution, ecological or laboratory adaptations, and those as sociated with clinical severity or attenuation. The database would include not only Select Agent sequences, but also a representative set of near-neighbors for each Select Agent.
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From page 6...
... • Long-term areas of research include: Protein structure and function; Gene expression and regulation; Pathogenic mechanisms Animal models of disease Data and information management for systems biology Synthetic biology M etagenomics and phylogenomic, including the human microbiome The near-term milestones and long-term research aim either to expand the general frontiers of biological knowledge or to apply existing knowledge to the Select Agent Regulations. Our committee was deeply uncomfortable with research programs that would seek to expand knowledge solely for the purpose of improving the Select Agent Regulations.
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From page 7...
... Our principal finding is that sequence-based prediction of Select Agent properties is not feasible, now or in the foreseeable future; any dedicated research effort solely for this purpose is likely to have only negative consequences. When the committee's report was in the final stages of completion, the White House issued on July 2, 2010, a new Executive Order, "Optimizing the Security of Biological Select Agents and Toxins in the United States." Although the committee did not have time to consider fully the implications of this Executive Order, it notes that several issues are particularly relevant to this report; these are briefly discussed in Box 1.2.
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Key Terms

  • select agents
  • agent regulations
  • agent list
  • genome sequence
  • yellow flag

  • sequence database
  • taxonomic names
  • dna synthesis
  • discrete taxonomic
  • genome sequences

  • biological knowledge
  • complete select
  • agent sequences
  • agent properties
  • taxonomic name

  • natural variation
  • synthesis technology
  • specific agents
  • biological select
  • actual select

  • defining select
  • themselves select
  • identify select
  • current select
  • predict select

  • agent genome
  • agent taxonomic
  • agent sta
  • agent pathogenicity
  • agent subject


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