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Sequence-Based Classification of Select Agents: A Brighter Line.

PB2011102498

Publication Date	2010
Page Count	236
Abstract	In 2006, the National Science Advisory Board for Biosecurity (NSABB) released a report, Addressing Biosecurity Concerns Related to the Synthesis of Select Agents (NSABB 2006), 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 acquisition 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 boundaries 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. One of the NSABB recommendations proposed that a group of experts from the scientific community be assembled to determine if an alternative framework based on predicted features and properties encoded by nucleic acids, such as virulence or pathogenicity, can be developed and utilized in lieu of the current finite list of specific agents and taxonomic definitions. (NSABB 2006) Thus, the present study was initiated with the title Scientific Milestones for the Development of a Gene Sequence-Based Classification System for Oversight of Select Agents on the basis of this recommendation. The committee was specifically charged with identifying: the scientific advances that would be necessary to permit serious consideration of developing and implementing an oversight system for Select Agents that is based on predicted features and properties encoded by nucleic acids rather than a relatively static list of specific agents and taxonomic definitions. (Appendix A) It is implicit in the charge that a predictive oversight system is not now feasible. It is also implicit that gene sequence-based classification, is synonymous with predicting features and properties encoded by nucleic acids. However, it soon became clear that the committee was confronted by two quite different tasks, one of which is feasible and one is not. It is possible to classify a new sequence as belonging within a group of known sequences; it is not feasible to predict the function(s) that sequence encodes. Thus, it is essential to distinguish sequence-based classification from sequence-based prediction of biological function.
Keywords	Classification Biosecurity Genetic modification Genome DNA Sequence Oversight frameworks Encoding Taxonomy Definitions Names Recommendations Regulations Information systems National Science Advisory Board for Biosecurity(NSAAB) Select agent regulations
Source Agency	National Academy of Science National Research Council National Institutes of Health
NTIS Subject Category	57B - Biochemistry 74D - Chemical, Biological, & Radiological Warfare 57E - Clinical Medicine 95C - Biomedical Instrumentation & Bioengineering
Corporate Authors	National Research Council, Washington, DC.; National Institutes of Health, Bethesda, MD.
Supplemental Notes	Prepared in cooperation with National Institutes of Health, Bethesda, MD.
Document Type	Technical Report
NTIS Issue Number	201107
Contract Number	NO1-OD-4-2139

Sequence-Based Classification of Select Agents: A Brighter Line.

Sequence-Based Classification of Select Agents: A Brighter Line.
PB2011102498

Publication Date	2010
Page Count	236
Abstract	In 2006, the National Science Advisory Board for Biosecurity (NSABB) released a report, Addressing Biosecurity Concerns Related to the Synthesis of Select Agents (NSABB 2006), 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 acquisition 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 boundaries 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. One of the NSABB recommendations proposed that a group of experts from the scientific community be assembled to determine if an alternative framework based on predicted features and properties encoded by nucleic acids, such as virulence or pathogenicity, can be developed and utilized in lieu of the current finite list of specific agents and taxonomic definitions. (NSABB 2006) Thus, the present study was initiated with the title Scientific Milestones for the Development of a Gene Sequence-Based Classification System for Oversight of Select Agents on the basis of this recommendation. The committee was specifically charged with identifying: the scientific advances that would be necessary to permit serious consideration of developing and implementing an oversight system for Select Agents that is based on predicted features and properties encoded by nucleic acids rather than a relatively static list of specific agents and taxonomic definitions. (Appendix A) It is implicit in the charge that a predictive oversight system is not now feasible. It is also implicit that gene sequence-based classification, is synonymous with predicting features and properties encoded by nucleic acids. However, it soon became clear that the committee was confronted by two quite different tasks, one of which is feasible and one is not. It is possible to classify a new sequence as belonging within a group of known sequences; it is not feasible to predict the function(s) that sequence encodes. Thus, it is essential to distinguish sequence-based classification from sequence-based prediction of biological function.
Keywords	Classification Biosecurity Genetic modification Genome DNA Sequence Oversight frameworks Encoding Taxonomy Definitions Names Recommendations Regulations Information systems National Science Advisory Board for Biosecurity(NSAAB) Select agent regulations
Source Agency	National Academy of Science National Research Council National Institutes of Health
NTIS Subject Category	57B - Biochemistry 74D - Chemical, Biological, & Radiological Warfare 57E - Clinical Medicine 95C - Biomedical Instrumentation & Bioengineering
Corporate Authors	National Research Council, Washington, DC.; National Institutes of Health, Bethesda, MD.
Supplemental Notes	Prepared in cooperation with National Institutes of Health, Bethesda, MD.
Document Type	Technical Report
NTIS Issue Number	201107
Contract Number	NO1-OD-4-2139