Open AccessThe Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers
Author(s) -
Jason W. Sahl,
Adam J. Vazquez,
Carina M. Hall,
Joseph D. Busch,
Apichai Tuanyok,
Mark Mayo,
James M. Schupp,
Madeline Lummis,
Talima Pearson,
Kenzie Shippy,
Rebecca E. Colman,
Christopher J. Allender,
Vanessa Theobald,
Derek S. Sarovich,
Erin P. Price,
Alex Hutcheson,
Jonas Korlach,
John J. LiPuma,
Jason T. Ladner,
Sean Lovett,
Galina Koroleva,
Gustavo Palacios,
Direk Limmathurotsakul,
Vanaporn Wuthiekanun,
Gumphol Wongsuwan,
Bart J. Currie,
Paul Keim,
David M. Wagner
Publication year - 2016
Publication title -
mbio
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.562
H-Index - 121
eISSN - 2161-2129
pISSN - 2150-7511
DOI - 10.1128/mbio.00846-16
Subject(s) - genome , computational biology , identification (biology) , false positive paradox , biology , burkholderia pseudomallei , genomics , bacterial genome size , comparative genomics , genetics , gene , computer science , bacteria , botany , machine learning
Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives.
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