Evaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome.

2.50
Hdl Handle:
http://hdl.handle.net/10033/70596
Title:
Evaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome.
Authors:
Dötsch, Andreas; Pommerenke, Claudia ( 0000-0002-9448-416X ) ; Bredenbruch, Florian; Geffers, Robert; Häussler, Susanne
Abstract:
BACKGROUND: Whole genome sequencing techniques have added a new dimension to studies on bacterial adaptation, evolution and diversity in chronic infections. By using this powerful approach it was demonstrated that Pseudomonas aeruginosa undergoes intense genetic adaptation processes, crucial in the development of persistent disease. The challenge ahead is to identify universal infection relevant adaptive bacterial traits as potential targets for the development of alternative treatment strategies. RESULTS: We developed a microarray-based method applicable for discovery of single nucleotide polymorphisms (SNPs) in P. aeruginosa as an easy and economical alternative to whole genome sequencing. About 50% of all SNPs theoretically covered by the array could be detected in a comparative hybridization of PAO1 and PA14 genomes at high specificity (> 0.996). Variations larger than SNPs were detected at much higher sensitivities, reaching nearly 100% for genetic differences affecting multiple consecutive probe oligonucleotides. The detailed comparison of the in silico alignment with experimental hybridization data lead to the identification of various factors influencing sensitivity and specificity in SNP detection and to the identification of strain specific features such as a large deletion within the PA4684 and PA4685 genes in the Washington Genome Center PAO1. CONCLUSION: The application of the genome array as a tool to identify adaptive mutations, to depict genome organizations, and to identify global regulons by the "ChIP-on-chip" technique will expand our knowledge on P. aeruginosa adaptation, evolution and regulatory mechanisms of persistence on a global scale and thus advance the development of effective therapies to overcome persistent disease.
Affiliation:
Helmholtz Centre for Infection Research, Braunschweig, Germany. andreas.doetsch@helmholtz-hzi.de
Citation:
Evaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome. 2009, 10:29 BMC Genomics
Journal:
BMC genomics
Issue Date:
2009
URI:
http://hdl.handle.net/10033/70596
DOI:
10.1186/1471-2164-10-29
PubMed ID:
19152677
Type:
Article
Language:
en
ISSN:
1471-2164
Appears in Collections:
publications of the research group chronic pseudomonas infections (CPI)

Full metadata record

DC FieldValue Language
dc.contributor.authorDötsch, Andreasen
dc.contributor.authorPommerenke, Claudiaen
dc.contributor.authorBredenbruch, Florianen
dc.contributor.authorGeffers, Roberten
dc.contributor.authorHäussler, Susanneen
dc.date.accessioned2009-06-16T13:09:44Zen
dc.date.available2009-06-16T13:09:44Zen
dc.date.issued2009en
dc.identifier.citationEvaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome. 2009, 10:29 BMC Genomicsen
dc.identifier.issn1471-2164en
dc.identifier.pmid19152677en
dc.identifier.doi10.1186/1471-2164-10-29en
dc.identifier.urihttp://hdl.handle.net/10033/70596en
dc.description.abstractBACKGROUND: Whole genome sequencing techniques have added a new dimension to studies on bacterial adaptation, evolution and diversity in chronic infections. By using this powerful approach it was demonstrated that Pseudomonas aeruginosa undergoes intense genetic adaptation processes, crucial in the development of persistent disease. The challenge ahead is to identify universal infection relevant adaptive bacterial traits as potential targets for the development of alternative treatment strategies. RESULTS: We developed a microarray-based method applicable for discovery of single nucleotide polymorphisms (SNPs) in P. aeruginosa as an easy and economical alternative to whole genome sequencing. About 50% of all SNPs theoretically covered by the array could be detected in a comparative hybridization of PAO1 and PA14 genomes at high specificity (> 0.996). Variations larger than SNPs were detected at much higher sensitivities, reaching nearly 100% for genetic differences affecting multiple consecutive probe oligonucleotides. The detailed comparison of the in silico alignment with experimental hybridization data lead to the identification of various factors influencing sensitivity and specificity in SNP detection and to the identification of strain specific features such as a large deletion within the PA4684 and PA4685 genes in the Washington Genome Center PAO1. CONCLUSION: The application of the genome array as a tool to identify adaptive mutations, to depict genome organizations, and to identify global regulons by the "ChIP-on-chip" technique will expand our knowledge on P. aeruginosa adaptation, evolution and regulatory mechanisms of persistence on a global scale and thus advance the development of effective therapies to overcome persistent disease.en
dc.language.isoenen
dc.subject.meshAdaptation, Biologicalen
dc.subject.meshComparative Genomic Hybridizationen
dc.subject.meshDNA, Bacterialen
dc.subject.meshGenome, Bacterialen
dc.subject.meshOligonucleotide Array Sequence Analysisen
dc.subject.meshPolymorphism, Single Nucleotideen
dc.subject.meshPseudomonas aeruginosaen
dc.subject.meshSensitivity and Specificityen
dc.subject.meshSequence Alignmenten
dc.subject.meshSequence Analysis, DNAen
dc.titleEvaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome.en
dc.typeArticleen
dc.contributor.departmentHelmholtz Centre for Infection Research, Braunschweig, Germany. andreas.doetsch@helmholtz-hzi.deen
dc.identifier.journalBMC genomicsen

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