Report for Development of a Census Array and Evaluation of the Array to Detect Biothreat Agents and Environmental Samples for DHS

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The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. This report focuses on the design, testing and results of samples on the Census Array. We designed a Census/Detection Array to detect all sequenced viruses (including phage), bacteria (eubacteria), and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection ... continued below

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PDF-file: 12 pages; size: 0.4 Mbytes

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Jaing, C & Jackson, P April 14, 2011.

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Description

The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. This report focuses on the design, testing and results of samples on the Census Array. We designed a Census/Detection Array to detect all sequenced viruses (including phage), bacteria (eubacteria), and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms, and to be unique relative to the human genome. A combination of 'detection' probes with high levels of conservation within a family plus 'census' probes targeting strain/isolate specific regions enabled detection and taxonomic classification from the level of family down to the strain. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. We tested the array with purified bacterial and viral DNA/RNA samples, artificial mixes of known bacterial/viral samples, spiked DNA against complex background including BW aerosol samples and soil samples, and environmental samples to evaluate the array's sensitivity and forensic capability. The data were analyzed using our novel maximum likelihood software. For most of the organisms tested, we have achieved at least species level discrimination.

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PDF-file: 12 pages; size: 0.4 Mbytes

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  • Report No.: LLNL-TR-480650
  • Grant Number: W-7405-ENG-48
  • DOI: 10.2172/1022899 | External Link
  • Office of Scientific & Technical Information Report Number: 1022899
  • Archival Resource Key: ark:/67531/metadc831900

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

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  • April 14, 2011

Added to The UNT Digital Library

  • May 19, 2016, 3:16 p.m.

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  • Dec. 8, 2016, 9:12 p.m.

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Jaing, C & Jackson, P. Report for Development of a Census Array and Evaluation of the Array to Detect Biothreat Agents and Environmental Samples for DHS, report, April 14, 2011; Livermore, California. (digital.library.unt.edu/ark:/67531/metadc831900/: accessed October 22, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.