Page Banner

United States Department of Agriculture

Agricultural Research Service

Title: Evaluating the performance of Q-PCR primers for the detection of Xanthomonas fragariae with ROC analysis

Authors
item Turechek, William
item Hartung, John

Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: April 1, 2007
Publication Date: July 28, 2007
Citation: Turechek, W., Hartung, J.S. 2007. Evaluating the performance of Q-PCR primers for the detection of Xanthomonas fragariae with ROC analysis. Phytopathology 97:5116.

Technical Abstract: Angular leaf spot is an important disease of strawberry. The EPPO lists X. fragariae as an A2 quarantine pathogen and in certain European markets, nurseries must certify plants pathogen free if they wish to export to Europe. Quantitative PCR is the desired tool for certification because of its sensitivity, specificity and ease of use. Q-PCR, however, is neither perfectly sensitive, particularly when pathogen prevalence is low, or perfectly specific, resulting in false positive test results. ROC analysis provides a statistical means for quantifying these attributes for PCR or any diagnostic test, as well as providing the means for comparing multiple tests for the same pathogen. ROC analysis was used to analyze the performance of three Q-PCR primer sets (q241, q245, and q295) for their ability to detect the target DNA in dilutions of purified DNA, whole cell suspensions, and plant extract/bacteria mixtures at tolerance thresholds of 0, 10, and 100 cells. All primer pairs performed equivalently across all thresholds and preparations with the exception of q295 which performed poorer than 241 and 245 in whole cell preparations at the detection threshold of 0 cells. Sensitivity was greatest with preparations of purified DNA and the plant/bacteria mixture, followed by whole cells. The specificity decreased as the tolerance increased. The results can be used as a guide for selecting suitable thresholds for the detection of X. fragariae.

Last Modified: 8/21/2014
Footer Content Back to Top of Page