SAIC Biological Defense/ BioTechnology in Huntsville

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Presentation for FLC Mid-Atlantic Region 21
September 2006
R. Paul Schaudies, Ph.D. Doreen A. Robinson,
Ph.D. 703-298-3720
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Molecular RadarTM Biological Forensic
Identification Technology

• Highly multiplexed nucleic acid hybridization
  based approach
• Target only unique and informative genetic
  regions
• Microarray format allows for identification of
  tens of thousands of individual sequences in
  parallel
• Complete genetic characterization within 4-24
  hours
• Customizable levels of resolution

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Capabilities Offered

• Functional equivalent of a 10,000-fold
  multiplexed PCR reaction
• Simultaneously identify multiple organisms
• Strain level resolution
• Identify virulence factors
• Identify antibiotic resistance genes
• Identify signs of genetic engineering
• Characterize unknown organisms
• No sample dilution for multiple analyses
• Technology is adaptable to multiple platforms and
  applications

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System Concept
Assay Development
Routine Sample Analysis

• Computer identification of informative DNA/RNA
  sequences
• Identification of candidate oligonucleotides
• On-chip synthesis of oligos

• Whole-genome amplification with label
  incorporation
• Hybridization on chip
• Spot profile identifies sequences present in
  original sample

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Bacillus anthracis Ames vs Sterne on SAIC VER 1
Array
ID Spot Color
pXO1 Blue
pXO2 Yellow
Genomic Red
Controls Purple
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SAIC VER1 Array Hybridizations
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Three-Dimensional Data Presentation

• Three hybridizations using identical arrays
• Each data point represents the performance of a
  specific oligonucleotide in three separate
  hybridizations
• Unique sequences fall on the axes
• Conserved sequences fall on the planes or at the
  top center if present in all three organisms

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Virulence Factors for Bacillus
of Spots 2 Virulence
B. anthracis Ames
of Spots 16 Virulence 313 pX01 47 Genomic
of Spots 10 Virulence 2 mRNA 2 Genomic
B. cereus G9421
B. thuringiensis 97-27
of Spots 17 Genomic
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Virulence Factors for Yersinia
Y. pestis CO92
of Spots 16 Virulence 10 Genomic
of Spots 6 Virulence 14 pCD1 92 Genomic
Y. enterocolitica 9610
Y. pseudotuberculosis 11960
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Summary

• Molecular RadarTM provides high fidelity forensic
  identification and characterization of
  microorganisms
• We have achieved resolution down to the level of
  strain for pathogens and near-neighbor organisms
• We can design and validate arrays for any DNA or
  RNA containing organism at desired level of
  resolution

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Contact Information

• R. Paul Schaudies, Ph.D.
• 703-298-3720
• schaudiesr_at_saic.com
• Doreen A. Robinson, Ph.D.
• 703-298-3720
• robinsond2_at_saic.com