Modified genome comparison method: A new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example

Neshani, A. and Kakhki, R. K. and Sankian, M. and Zare, H. and Chichaklu, A. H. and Sayyadi, M. and Ghazvini, K. (2018) Modified genome comparison method: A new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example. BMC Infectious Diseases, 18 (1).

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Abstract

Background: The first step of designing any genome-based molecular diagnostic test is to find a specific target sequence. The modified genome comparison method is one of the easiest and most comprehensive ways to achieve this goal. In this study, we aimed to explain this method with the example of Mycobacterium tuberculosis complex and investigate its efficacy in a diagnostic test. Methods: A specific target was identified using modified genome comparison method and an in-house PCR test was designed. To determine the analytical sensitivity and specificity, 10 standard specimens were used. Also, 230 specimens were used to determine the clinical sensitivity and specificity. Results: The identity and query cover of our new diagnostic target (5KST) were ≥ 90 with M. tuberculosis complex. The 5KST-PCR sensitivity was 100 for smear-positive, culture-positive and 85.7 for smear-negative, culture-positive specimens. All of 100 smear-negative, culture-negative specimens were negative in 5KST-PCR (100 clinical specificity). Analytical sensitivity of 5KST-PCR was approximately 1 copy of genomic DNA per microliter. Conclusions: Modified genome comparison method is a confident way to find specific targets for use in diagnostic tests. Accordingly, the 5KST-PCR designed in this study has high sensitivity and specificity and can be replaced for conventional TB PCR tests. © 2018 The Author(s).

Item Type: Article
Additional Information: Cited By :4 Export Date: 16 February 2020 CODEN: BIDMB Correspondence Address: Ghazvini, K.; Antimicrobial Resistance Research Center, Mashhad University of Medical SciencesIran; email: Ghazvinik@mums.ac.ir
Uncontrolled Keywords: 5KST Genome comparison method Mycobacterium tuberculosis complex PCR Specific target bacterial DNA bacterial genome chemistry genetic database genetics genomics human isolation and purification metabolism microbiology Mycobacterium tuberculosis polymerase chain reaction procedures tuberculosis Databases, Genetic DNA, Bacterial Genome, Bacterial Humans
Subjects: WF Respiratory System
QZ pathology-neoplasms-Genetics
Divisions: Mashhad University of Medical Sciences
Depositing User: lib2 lib2 lib2
Date Deposited: 07 May 2020 07:34
Last Modified: 07 May 2020 07:34
URI: http://eprints.mums.ac.ir/id/eprint/17454

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