title: E-probe Diagnostic Nucleic acid Analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics.
abstract: 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.
authors.affiliation: Oklahoma State University, Department of Biochemistry and Molecular Biology, USA.
authors.forename: Anthony H
authors.initials: AH
authors.lastname: Stobbe
authors.forename: Jon
authors.initials: J
authors.lastname: Daniels
authors.forename: Andres S
authors.initials: AS
authors.lastname: Espindola
authors.forename: Ruchi
authors.initials: R
authors.lastname: Verma
authors.forename: Ulrich
authors.initials: U
authors.lastname: Melcher
authors.forename: Francisco
authors.initials: F
authors.lastname: Ochoa-Corona
authors.forename: Carla
authors.initials: C
authors.lastname: Garzon
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Fletcher
authors.forename: William
authors.initials: W
authors.lastname: Schneider
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008828:Microbiological Techniques / Q000379:methods*; D015341:Nucleic Acid Probes; D010935:Plant Diseases / Q000382:microbiology; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D015341:Nucleic Acid Probes
keywords: Bioinformatics; Next-generation sequencing; Pathogen detection