TY - JOUR
T1 - Organism identification using a genome sequence-independent universal microarray probe set
AU - Belosludtsev, Yuri Y.
AU - Bowerman, Dawn
AU - Weil, Ryan
AU - Marthandan, Nishanth
AU - Balog, Robert
AU - Luebke, Kevin
AU - Lawson, Jonathan
AU - Johnston, Stephen A.
AU - Lyons, C. Rick
AU - O'Brien, Kevin
AU - Garner, Harold R.
AU - Powdrill, Thomas F.
PY - 2004/10
Y1 - 2004/10
N2 - There has been increasing interest and efforts devoted to developing biosensor technologies for identifying pathogens, particularly in the biothreat area. In this study, a universal set of short 12- and 13-mer oligonucleotide probes was derived independently of a priori genomic sequence information and used to generate unique species-dependent genomic hybridization signatures. The probe set sequences were algorithmically generated to be maximally distant in sequence space and not dependent on the sequence of any particular genome. The probe set is universally applicable because it is unbiased and independent of hybridization predictions based upon simplified assumptions regarding probe-target duplex formation from linear sequence analysis. Tests were conducted on microarrays containing 14,283 unique probes synthesized using an in situ light-directed synthesis methodology. The genomic DNA hybridization intensity patterns reproducibly differentiated various organisms (Bacillus subtilis, Yersinia pestis, Streptococcus pneumonia, Bacillus anthracis, and Homo sapiens), including the correct identification of a blinded "unknown" sample. Applications of this method include not only pathological and forensic genome identification in medicine and basic science, but also potentially a novel method for the discovery of unknown targets and associations inherent in dynamic nucleic acid populations such as represented by differential gene expression.
AB - There has been increasing interest and efforts devoted to developing biosensor technologies for identifying pathogens, particularly in the biothreat area. In this study, a universal set of short 12- and 13-mer oligonucleotide probes was derived independently of a priori genomic sequence information and used to generate unique species-dependent genomic hybridization signatures. The probe set sequences were algorithmically generated to be maximally distant in sequence space and not dependent on the sequence of any particular genome. The probe set is universally applicable because it is unbiased and independent of hybridization predictions based upon simplified assumptions regarding probe-target duplex formation from linear sequence analysis. Tests were conducted on microarrays containing 14,283 unique probes synthesized using an in situ light-directed synthesis methodology. The genomic DNA hybridization intensity patterns reproducibly differentiated various organisms (Bacillus subtilis, Yersinia pestis, Streptococcus pneumonia, Bacillus anthracis, and Homo sapiens), including the correct identification of a blinded "unknown" sample. Applications of this method include not only pathological and forensic genome identification in medicine and basic science, but also potentially a novel method for the discovery of unknown targets and associations inherent in dynamic nucleic acid populations such as represented by differential gene expression.
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U2 - 10.2144/04374rr02
DO - 10.2144/04374rr02
M3 - Article
C2 - 15517977
AN - SCOPUS:6344256775
SN - 0736-6205
VL - 37
SP - 654
EP - 660
JO - BioTechniques
JF - BioTechniques
IS - 4
ER -