E-probe Diagnostic Nucleic acid Analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics
| Autor: | Ulrich Melcher, Ruchi Verma, Anthony H. Stobbe, Carla D. Garzon, Andres S. Espindola, Francisco M. Ochoa-Corona, William L. Schneider, Jon Daniels, Jacqueline Fletcher |
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| Rok vydání: | 2013 |
| Předmět: |
Microbiology (medical)
Oomycete Genetics Microbiological Techniques Nucleic acid quantitation biology Computational Biology High-Throughput Nucleotide Sequencing RNA virus Computational biology Sequence Analysis DNA biology.organism_classification Microbiology DNA sequencing Nucleic Acid Probes Data sequences Databases Genetic Decoy Molecular Biology Genome size Sequence (medicine) Plant Diseases |
| Zdroj: | Journal of microbiological methods. 94(3) |
| ISSN: | 1872-8359 |
| Popis: | Plant biosecurity requires rapid identification of pathogenic organisms. While there are many pathogen-specific diagnostic assays, the ability to test for large numbers of pathogens simultaneously is lacking. Next generation sequencing (NGS) allows one to detect all organisms within a given sample, but has computational limitations during assembly and similarity searching of sequence data which extend the time needed to make a diagnostic decision. To minimize the amount of bioinformatic processing time needed, unique pathogen-specific sequences (termed e-probes) were designed to be used in searches of unassembled, non-quality checked, sequence data. E-probes have been designed and tested for several selected phytopathogens, including an RNA virus, a DNA virus, bacteria, fungi, and an oomycete, illustrating the ability to detect several diverse plant pathogens. E-probes of 80 or more nucleotides in length provided satisfactory levels of precision (75%). The number of e-probes designed for each pathogen varied with the genome size of the pathogen. To give confidence to diagnostic calls, a statistical method of determining the presence of a given pathogen was developed, in which target e-probe signals (detection signal) are compared to signals generated by a decoy set of e-probes (background signal). The E-probe Diagnostic Nucleic acid Analysis (EDNA) process provides the framework for a new sequence-based detection system that eliminates the need for assembly of NGS data. |
| Databáze: | OpenAIRE |
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