Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis
Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation betwe...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2013-01-01
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| Series: | Journal of Nucleic Acids |
| Online Access: | http://dx.doi.org/10.1155/2013/801505 |
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| _version_ | 1849405383816249344 |
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| author | John P. Jakupciak Jeffrey M. Wells Richard J. Karalus David R. Pawlowski Jeffrey S. Lin Andrew B. Feldman |
| author_facet | John P. Jakupciak Jeffrey M. Wells Richard J. Karalus David R. Pawlowski Jeffrey S. Lin Andrew B. Feldman |
| author_sort | John P. Jakupciak |
| collection | DOAJ |
| description | Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations. |
| format | Article |
| id | doaj-art-4e29a1913444479f9e02ba84bb0c429e |
| institution | Kabale University |
| issn | 2090-0201 2090-021X |
| language | English |
| publishDate | 2013-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Nucleic Acids |
| spelling | doaj-art-4e29a1913444479f9e02ba84bb0c429e2025-08-20T03:36:41ZengWileyJournal of Nucleic Acids2090-02012090-021X2013-01-01201310.1155/2013/801505801505Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic AnalysisJohn P. Jakupciak0Jeffrey M. Wells1Richard J. Karalus2David R. Pawlowski3Jeffrey S. Lin4Andrew B. Feldman5Cipher Systems, 2661 Riva Road, Annapolis, MD 21401, USACipher Systems, 2661 Riva Road, Annapolis, MD 21401, USACUBRC, Buffalo, NY 14225, USACUBRC, Buffalo, NY 14225, USAThe Johns Hopkins University, Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USAThe Johns Hopkins University, Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USALarge-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.http://dx.doi.org/10.1155/2013/801505 |
| spellingShingle | John P. Jakupciak Jeffrey M. Wells Richard J. Karalus David R. Pawlowski Jeffrey S. Lin Andrew B. Feldman Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis Journal of Nucleic Acids |
| title | Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis |
| title_full | Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis |
| title_fullStr | Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis |
| title_full_unstemmed | Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis |
| title_short | Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis |
| title_sort | population sequencing as a biomarker of burkholderia mallei and burkholderia pseudomallei evolution through microbial forensic analysis |
| url | http://dx.doi.org/10.1155/2013/801505 |
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