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A high-throughput pipeline for designing microarray-based pathogen diagnostic assays

BACKGROUND: We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for identifying target organisms in environmental or clinical samples. The design...

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Autores principales: Vijaya Satya, Ravi, Zavaljevski, Nela, Kumar, Kamal, Reifman, Jaques
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375140/
https://www.ncbi.nlm.nih.gov/pubmed/18402679
http://dx.doi.org/10.1186/1471-2105-9-185
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author Vijaya Satya, Ravi
Zavaljevski, Nela
Kumar, Kamal
Reifman, Jaques
author_facet Vijaya Satya, Ravi
Zavaljevski, Nela
Kumar, Kamal
Reifman, Jaques
author_sort Vijaya Satya, Ravi
collection PubMed
description BACKGROUND: We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for identifying target organisms in environmental or clinical samples. The design process is implemented in a high-performance computing software pipeline that incorporates major algorithmic improvements over a previous version to both reduce computation time and improve specificity assessment. RESULTS: The algorithmic improvements result in significant reduction in runtimes, with the updated pipeline being nearly up to five-times faster than the previous version. The improvements in specificity assessment, based on multiple specificity criteria, result in robust and consistent evaluation of cross-hybridization with nontarget sequences. In addition, the multiple criteria provide finer control on the number of resulting fingerprints, which helps in obtaining a larger number of fingerprints with high specificity. Simulation tests for Francisella tularensis and Yersinia pestis, using a well-established hybridization model to estimate cross-hybridization with nontarget sequences, show that the improved specificity criteria yield a larger number of fingerprints as compared to using a single specificity criterion. CONCLUSION: The faster runtimes, achieved as the result of algorithmic improvements, are critical for extending the pipeline to process multiple target genomes. The larger numbers of identified fingerprints, obtained by considering broader specificity criteria, are essential for designing probes for hard-to-distinguish target sequences.
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spelling pubmed-23751402008-05-09 A high-throughput pipeline for designing microarray-based pathogen diagnostic assays Vijaya Satya, Ravi Zavaljevski, Nela Kumar, Kamal Reifman, Jaques BMC Bioinformatics Methodology Article BACKGROUND: We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for identifying target organisms in environmental or clinical samples. The design process is implemented in a high-performance computing software pipeline that incorporates major algorithmic improvements over a previous version to both reduce computation time and improve specificity assessment. RESULTS: The algorithmic improvements result in significant reduction in runtimes, with the updated pipeline being nearly up to five-times faster than the previous version. The improvements in specificity assessment, based on multiple specificity criteria, result in robust and consistent evaluation of cross-hybridization with nontarget sequences. In addition, the multiple criteria provide finer control on the number of resulting fingerprints, which helps in obtaining a larger number of fingerprints with high specificity. Simulation tests for Francisella tularensis and Yersinia pestis, using a well-established hybridization model to estimate cross-hybridization with nontarget sequences, show that the improved specificity criteria yield a larger number of fingerprints as compared to using a single specificity criterion. CONCLUSION: The faster runtimes, achieved as the result of algorithmic improvements, are critical for extending the pipeline to process multiple target genomes. The larger numbers of identified fingerprints, obtained by considering broader specificity criteria, are essential for designing probes for hard-to-distinguish target sequences. BioMed Central 2008-04-10 /pmc/articles/PMC2375140/ /pubmed/18402679 http://dx.doi.org/10.1186/1471-2105-9-185 Text en Copyright © 2008 Satya et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Vijaya Satya, Ravi
Zavaljevski, Nela
Kumar, Kamal
Reifman, Jaques
A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
title A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
title_full A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
title_fullStr A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
title_full_unstemmed A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
title_short A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
title_sort high-throughput pipeline for designing microarray-based pathogen diagnostic assays
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375140/
https://www.ncbi.nlm.nih.gov/pubmed/18402679
http://dx.doi.org/10.1186/1471-2105-9-185
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