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Suggested Citation:"Appendix C: Glossary." Institute of Medicine and National Research Council. 2015. BioWatch PCR Assays: Building Confidence, Ensuring Reliability: Abbreviated Version. Washington, DC: The National Academies Press. doi: 10.17226/21658.
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Appendix C

Glossary

Agent: See Biological agent.

Air sampling: Collecting quantities and types of atmospheric contaminants from a representative sample of air.

Amplicon (PCR): A piece of nucleic acid representing a specific product of the amplification reaction.

Assay: A quantitative or qualitative evaluation of the presence or amount of a given target in a particular sample.

Biological agent: A microorganism (or a toxin derived from it) that causes disease in humans, plants, or animals and is used in bioterrorism or biological warfare.

Biosurveillance: The process of active data-gathering with appropriate analysis and interpretation of biosphere data that might relate to disease activity and threats to human or animal health—whether infectious, toxic, metabolic, or otherwise, and regardless of intentional or natural origin—in order to achieve early warning of health threats, early detection of health events, and overall situational awareness of disease activity.

BioWatch Actionable Result: A determination that occurs when analysis of a filter from a BioWatch sampler indicates the confirmed presence of a target organism’s nucleic acid signature.

BioWatch jurisdiction: A major metropolitan area—which may include one or more city, county, state, or regional decision-making bodies—where BioWatch air samplers are operational.

Suggested Citation:"Appendix C: Glossary." Institute of Medicine and National Research Council. 2015. BioWatch PCR Assays: Building Confidence, Ensuring Reliability: Abbreviated Version. Washington, DC: The National Academies Press. doi: 10.17226/21658.
×

BioWatch program: An activity funded by the Department of Homeland Security that uses sets of air samplers in more than 30 jurisdictions to collect airborne particles onto filters that are subsequently transported to laboratories for analysis for the presence of genetic material from certain biological agents.

BioWatch system: The collection of operational components (which are themselves systems) that produce information from air sampling and feed it into a public health decision-making process to determine the appropriate response to a BioWatch Actionable Result (BAR).

Detection: The determination or recognition of the presence of an object or state of interest.

Detector: A data collection and processing technology that both collects and evaluates data.

Environmental background panel: In the context of a biological agent detection assay, a set of organisms that may be present in the environment, against which the detection assay is tested to determine whether the assay potentially cross-reacts with nucleic acid from these organisms.

Environmental sampling: In the context of the BioWatch system, physical sampling of the environment around a collector associated with a positive PCR assay result to provide decision makers with additional situational assessment and to inform appropriate response actions.

Environmental surveillance: Monitoring of the environment to evaluate potential exposure to harmful agents and damage to living organisms.

Exclusivity strain panel: In the context of a biological agent detection assay, a set of organisms such as closely related bacterial or viral strains and species, against which the detection assay is tested to determine whether the assay potentially cross-reacts with nucleic acid from these organisms.

False negative: A negative result for a given target when the target is present.

False positive: A positive result for a given target when the target is not present.

Inclusivity strain panel: In the context of a biological agent detection assay, the set of organisms, such as bacterial or viral strains and species, against which the detection assay is tested to determine whether the assay is successfully able to detect nucleic acid from these organisms.

Laboratory Response Network: A national network of local, state, and federal public health, health care, food, agriculture, veterinary, and environmental testing laboratories that provide the laboratory infra-

Suggested Citation:"Appendix C: Glossary." Institute of Medicine and National Research Council. 2015. BioWatch PCR Assays: Building Confidence, Ensuring Reliability: Abbreviated Version. Washington, DC: The National Academies Press. doi: 10.17226/21658.
×

structure and capacity to respond to biological and chemical terrorism and other public health emergencies.

Limit of detection: The minimum concentration of a substance that an assay can detect above background with a certain degree of statistical confidence probability (frequently with 95 percent confidence).

Monitoring: Periodic or continuous surveillance or testing to determine the presence or level of a substance of interest in various media or in humans, plants, and animals.

Multiplex (PCR assay): A type of PCR assay designed to simultaneously amplify and detect multiple target regions of nucleic acid in a single sample. It is distinguished from procedures that perform one molecular assay at a time (see Singleplex assay).

Nucleic acid signature: Nucleotide sequence that is considered distinctive for an organism, or a subset of organisms, and can be used in testing for the presence of nucleic acid from this organism.

Polymerase chain reaction (PCR): A technique in molecular biology that is used to reproduce enzymatically (amplify) selected sections of DNA. It permits the analysis of any short sequence of DNA (or RNA) without the need for cloning.

Plasmid: A small piece of DNA found within a bacterial cell that is separate from the chromosomal DNA of the organism.

Primer (PCR): A short oligonucleotide that is complementary to part of the target nucleic acid sequence that defines the region that will be selectively amplified by the PCR. During PCR, the primer hybridizes to its complementary sequence and polymerase extends the primer in the amplified region. A pair of primers is used, flanking the target amplification region.

Probe: A short oligonucleotide that is complementary to part of the target region; the probe is labeled in a manner that enables it to detect amplification (e.g., by exploiting fluorescence quenching).

Quality assurance: A comprehensive system and infrastructure that ensures that a program or laboratory meets standards of quality.

Quality control: A process that focuses on the performance of specific testing activities.

Screening: In the context of the BioWatch system, analysis of air sampler filters for a preliminary genetic signature of a particular pathogen.

Sensitivity: The probability that a system will correctly indicate the presence of a particular substance when the substance is present above a certain concentration.

Signature: See Nucleic acid signature.

Suggested Citation:"Appendix C: Glossary." Institute of Medicine and National Research Council. 2015. BioWatch PCR Assays: Building Confidence, Ensuring Reliability: Abbreviated Version. Washington, DC: The National Academies Press. doi: 10.17226/21658.
×

Singleplex (PCR assay): An assay that is designed to amplify and detect a single target region of nucleic acid per sample. Used in comparison to multiplex PCR assay.

Specificity: The ability to correctly identify the absence of a target substance when it is not present.

Threshold cycle (Ct): In the context of a real-time PCR assay, the cycle number at which the amplification curve crosses a specified threshold level, indicating that amplification of the target region is above a background level. The greater the number of cycles required to cross this threshold, the lower the starting concentration of target nucleic acid in the sample.

Validation: The process of ensuring and documenting that a thing, such as a test, device, or process, fulfills the purpose for which it is intended.

Verification: A process that affirms that a given laboratory can obtain the anticipated results and assay performance from a validated assay.

Suggested Citation:"Appendix C: Glossary." Institute of Medicine and National Research Council. 2015. BioWatch PCR Assays: Building Confidence, Ensuring Reliability: Abbreviated Version. Washington, DC: The National Academies Press. doi: 10.17226/21658.
×
Page 167
Suggested Citation:"Appendix C: Glossary." Institute of Medicine and National Research Council. 2015. BioWatch PCR Assays: Building Confidence, Ensuring Reliability: Abbreviated Version. Washington, DC: The National Academies Press. doi: 10.17226/21658.
×
Page 168
Suggested Citation:"Appendix C: Glossary." Institute of Medicine and National Research Council. 2015. BioWatch PCR Assays: Building Confidence, Ensuring Reliability: Abbreviated Version. Washington, DC: The National Academies Press. doi: 10.17226/21658.
×
Page 169
Suggested Citation:"Appendix C: Glossary." Institute of Medicine and National Research Council. 2015. BioWatch PCR Assays: Building Confidence, Ensuring Reliability: Abbreviated Version. Washington, DC: The National Academies Press. doi: 10.17226/21658.
×
Page 170
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BioWatch is an air monitoring system deployed in jurisdictions around the country with the goal of detecting the presence of certain high risk pathogenic microorganisms. It relies on a network of federal and nonfederal collaborative relationships to be successful, and is one part of a larger array of disease surveillance, intelligence-gathering, and biomonitoring activities in support of public safety and health. The assays used in the BioWatch system to detect the presence of pathogens in collected samples rely on the technique of polymerase chain reaction (PCR) to sensitively and specifically amplify target nucleic acid sequences.

BioWatch PCR Assays evaluates and provides guidance on appropriate standards for the validation and verification of PCR tests and assays in order to ensure that adequate performance data are available to public health and other key decision makers with a sufficient confidence level to facilitate the public health response to a BioWatch Actionable Response. This report discusses principles of performance standards, reviews information from several existing guidance documents and standards that might be applicable to BioWatch, and discusses assay testing efforts that have occurred or are ongoing. BioWatch PCR Assays provides recommendations on general principles and approaches for a performance standard and validation framework to meet BioWatch's mission. The report also considers how developments in technology, particularly in multiplex PCR and next-generation sequencing, can contribute to the ability of the BioWatch program to meet current and future challenges.

This report has been determined to contain information exempt from disclosure under 5 U.S.C. 552(b). Section 15 of the Federal Advisory Committee Act provides that the National Academies shall make its final report available to the public unless the National Academies determines that the report would disclose matters described in one or more of the exemption provisions under the Freedom of Information Act (FOIA). In such case, the National Academies "shall make public an abbreviated version of the report that does not disclose those matters." This unrestricted, abbreviated version of the report represents, in so far as possible, the committee's findings, recommendations, and other substantive material without disclosing materials described in 5 U.S.C. 552(b).

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