Technologies to Enable Autonomous Detection for BioWatch Ensuring Timely and Accurate Information for Public Health Officials: Workshop Summary (2014) / Chapter Skim
Currently Skimming:
Appendix I: White Paper 4: State of the Art for Autonomous Detection Systems Using Genomic Sequencing
Appendix I: White Paper 4: State of the Art for Autonomous Detection Systems Using Genomic Sequencing
Pages 197-214
The Chapter Skim interface presents what we've algorithmically identified as the most significant single chunk of text within every page in the chapter.
Select key terms on the right to highlight them within pages of the chapter.
From page 197... ...
A white paper prepared for the June 25–26, 2013, workshop on Strategies for Cost-Effective and Flexible Biodetection Systems That Ensure Timely and Accurate Information for Public Health Officials, hosted by the Institute of Medicine's Board on Health Sciences Policy and the National Research Council's Board on Life Sciences. The authors are responsible for the content of this article, which does not necessarily represent the views of the Institute of Medicine or the National Research Council.
|
From page 198... ...
Major decreases in the resources required for BioWatch as well as improvements in the overall efficiency and effectiveness can be achieved through technical advances that provide for field in situ detection and identification (an autonomous deployed detector) to eliminate sample transport and laboratory analysis costs; amplification-free nucleic acid detection to decrease reagent costs; reagent-free detection to decrease reagent costs, eliminate the need for environmental engineering controls, and minimize the need for electrical power for the deployed autonomous detector; inexpensive analysis of agent recognition events within the autonomous detector to decrease sensor unit production cost and maintenance; and system modularity to minimize technology refresh costs.
|
From page 199... ...
Some are small, benchtop models, able to produce large amounts of data in a relatively short time and for a relatively low cost. The rapid advancement in NGS technologies will soon enable pathogen detection devices to rely on sequencing to provide a wealth of information about the environment in a cost-effective and timely manner.
|
From page 200... ...
NGS technologies require that DNA molecules are converted to NGS libraries. RNA is always converted to DNA first, as currently there are no direct RNA sequencing technologies (although the potential exists with the Pacific Biosciences (PacBio)
|
From page 201... ...
Comparative analysis to known pathogens, the presence of virulence genes, and recombinant engineering markers and phylogenetic placement would provide indication of novel threat agents. This is highly relevant, especially for rapidly evolving and highly diverse organisms, such as RNA viruses and Burkholderia spp.
|
From page 202... ...
Can run on standard electrical systems. Roche454 Full size One to two Includes All standard library Roche454 GS individuals are sufficient preparation and FLX+ needed for software for sequence run rea Upper assembly sample receipt data gents can be pur 74.3×69.8 through generation and a chased ×36.1 cm sequence data multitude of directly from (W×D×H)
|
From page 203... ...
a Separate personnel required for sequence generation and sequence analysis due to the highly specific training required for each skill. NOTE: When comparing the current NGS technologies consisting of Illumina, IonTorrent, PacBio, and 454, each technology has its own strengths and weaknesses, including the cost of sequencing.
|
From page 204... ...
Even though NGS is unlikely to replace the current rapid and portable pathogen detection platforms in the next couple of years, in many cases it will provide actionable information faster than the rapid systems. This is mainly due to the comprehensive information provided by an organism's entire sequence versus a few selected segments of the genome.
|
From page 205... ...
The simplest process includes detection of known pathogens and determination of some of their features, such as antibiotic resistance. More complex processes will involve identification of novel pathogens in mixed samples (clinical or environmental samples such as BioWatch aerosol samples)
|
From page 206... ...
in a sample is that a small amount of pathogen DNA can be overwhelmed by the background, so clever enrichment strategies may significantly increase the sensitivity. For example, some of the current NGS platforms isolate and amplify individual nucleic acid segments in oil vesicles leading to clonal nucleic acid samples for analysis.
|
From page 207... ...
could be identified and shared with interested sequencing platform developers to establish collaborative research and development initiatives. Flexibility Multiplexing with standard protocols is a strength of the current sequencing platforms and will likely remain so for future devices.
|
From page 208... ...
The second stage would involve the data being remotely ported to a larger comparative analysis server farm capable of doing a much more extensive analysis and confirmatory target identification. This greater level of analysis would support the BioWatch Actionable Result assessment process involving multiple participants.
|
From page 209... ...
. In doing this today, one may use amplicon sequencing of fewer primer pairs in rapid mode versus many primer sets in detailed mode.
|
From page 210... ...
Currently available and validated primer sets can be easily utilized in this approach, but many others can be added. Amplicon sequencing can detect many known pathogens and their phenotypic features (antibiotic resistance markers and virulence factors)
|
From page 211... ...
nucleic acids may be desirable or required. Since all NGS platforms require library preparation, sample-to-result time would still be 6 to 10 hours following sample collection.
|
From page 212... ...
Reagent costs could be decreased and have an analysis time of less than 10 hours following sample collection. Complexity of system fluidics would require routine maintenance.
|
From page 213... ...
In summary, the inherent information content from sequencing and analysis should meet all the needs of BioWatch, addressing false-positive and false-negative issues. However, for at least the Tier 1 and Tier 2 timelines, significant engineering challenges will have to be overcome to adapt the existing reagent-based systems into an autonomous biodetector with desired attributes.
|
Key Terms
This material may be derived from roughly machine-read images, and so is provided only to facilitate research.
More
information on Chapter Skim is available.