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Title: Rapid Accurate Identification of Bacterial and Viral Pathogens

Abstract

The goals of this program were to develop two assays for rapid, accurate identification of pathogenic organisms at the strain level. The first assay "Quantitative Genome Profiling or QGP" is a real time PCR assay with a restriction enzyme-based component. Its underlying concept is that certain enzymes should cleave genomic DNA at many sites and that in some cases these cuts will interrupt the connection on the genomic DNA between flanking PCR primer pairs thereby eliminating selected PCR amplifications. When this occurs the appearance of the real-time PCR threshold (Ct) signal during DNA amplification is totally eliminated or, if cutting is incomplete, greatly delayed compared to an uncut control. This temporal difference in appearance of the Ct signal relative to undigested control DNA provides a rapid, high-throughput approach for DNA-based identification of different but closely related pathogens depending upon the nucleotide sequence of the target region. The second assay we developed uses the nucleotide sequence of pairs of shmi identifier tags (-21 bp) to identify DNA molecules. Subtle differences in linked tag pair combinations can also be used to distinguish between closely related isolates..

Authors:
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
973575
Report Number(s):
BNL-91058-2007
DOE Contract Number:
DE-AC02-98CH10886
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Dunn, John. Rapid Accurate Identification of Bacterial and Viral Pathogens. United States: N. p., 2007. Web. doi:10.2172/973575.
Dunn, John. Rapid Accurate Identification of Bacterial and Viral Pathogens. United States. doi:10.2172/973575.
Dunn, John. Fri . "Rapid Accurate Identification of Bacterial and Viral Pathogens". United States. doi:10.2172/973575. https://www.osti.gov/servlets/purl/973575.
@article{osti_973575,
title = {Rapid Accurate Identification of Bacterial and Viral Pathogens},
author = {Dunn, John},
abstractNote = {The goals of this program were to develop two assays for rapid, accurate identification of pathogenic organisms at the strain level. The first assay "Quantitative Genome Profiling or QGP" is a real time PCR assay with a restriction enzyme-based component. Its underlying concept is that certain enzymes should cleave genomic DNA at many sites and that in some cases these cuts will interrupt the connection on the genomic DNA between flanking PCR primer pairs thereby eliminating selected PCR amplifications. When this occurs the appearance of the real-time PCR threshold (Ct) signal during DNA amplification is totally eliminated or, if cutting is incomplete, greatly delayed compared to an uncut control. This temporal difference in appearance of the Ct signal relative to undigested control DNA provides a rapid, high-throughput approach for DNA-based identification of different but closely related pathogens depending upon the nucleotide sequence of the target region. The second assay we developed uses the nucleotide sequence of pairs of shmi identifier tags (-21 bp) to identify DNA molecules. Subtle differences in linked tag pair combinations can also be used to distinguish between closely related isolates..},
doi = {10.2172/973575},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Fri Mar 09 00:00:00 EST 2007},
month = {Fri Mar 09 00:00:00 EST 2007}
}

Technical Report:

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