Universidad Peruana Cayetano Heredia

Design and use of mouse control DNA for DNA biomarker extraction and PCR detection from urine: Application for transrenal Mycobacterium tuberculosis DNA detection

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dc.contributor.author Bordelon, Hali
dc.contributor.author Ricks, Keersten M.
dc.contributor.author Pask, Megan E.
dc.contributor.author Russ, Patricia K.
dc.contributor.author Solinas, Francesca
dc.contributor.author Baglia, Mark L.
dc.contributor.author Short, Philip A.
dc.contributor.author Nel, Andrew
dc.contributor.author Blackburn, Jonathan
dc.contributor.author Dheda, Keertan
dc.contributor.author Zamudio Fuertes, Carlos Eduardo
dc.contributor.author Cáceres Nakiche, Tatiana
dc.contributor.author Wright, David W.
dc.contributor.author Haselton, Frederick R.
dc.contributor.author Pettit, April C.
dc.date.accessioned 2019-01-25T15:02:22Z
dc.date.available 2019-01-25T15:02:22Z
dc.date.issued 2017
dc.identifier.uri https://hdl.handle.net/20.500.12866/4631
dc.description.abstract Urine samples are increasingly used for diagnosing infections including Escherichia coli, Ebola virus, and Zika virus. However, extraction and concentration of nucleic acid biomarkers from urine is necessary for many molecular detection strategies such as polymerase chain reaction (PCR). Since urine samples typically have large volumes with dilute biomarker concentrations making them prone to false negatives, another impediment for urine-based diagnostics is the establishment of appropriate controls particularly to rule out false negatives. In this study, a mouse glyceraldehyde 3-phosphate dehydrogenase (GAPDH) DNA target was added to retrospectively collected urine samples from tuberculosis (TB)-infected and TB-uninfected patients to indicate extraction of intact DNA and removal of PCR inhibitors from urine samples. We tested this design on surrogate urine samples, retrospective 1milliliter (mL) urine samples from patients in Lima, Peru and retrospective 5mL urine samples from patients in Cape Town, South Africa. Extraction/PCR control DNA was detectable in 97% of clinical samples with no statistically significant differences among groups. Despite the inclusion of this control, there was no difference in the amount of TB IS6110 Tr-DNA detected between TB-infected and TB-uninfected groups except for samples from known HIV-infected patients. We found an increase in TB IS6110 Tr-DNA between TB/HIV co-infected patients compared to TB-uninfected/HIV-infected patients (N=18, p=0.037). The inclusion of an extraction/PCR control DNA to indicate successful DNA extraction and removal of PCR inhibitors should be easily adaptable as a sample preparation control for other acellular sample types. en_US
dc.language.iso eng
dc.publisher Elsevier
dc.relation.ispartofseries Journal of Microbiological Methods
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject Humans en_US
dc.subject Retrospective Studies en_US
dc.subject Animals en_US
dc.subject Sensitivity and Specificity en_US
dc.subject Coinfection en_US
dc.subject South Africa en_US
dc.subject Genetic Markers en_US
dc.subject Base Sequence en_US
dc.subject DNA/isolation & purification en_US
dc.subject Gene Targeting/methods en_US
dc.subject Glyceraldehyde-3-Phosphate Dehydrogenases/genetics en_US
dc.subject HIV Infections/complications en_US
dc.subject Mice/genetics en_US
dc.subject Molecular Diagnostic Techniques/methods en_US
dc.subject Mycobacterium tuberculosis/genetics/isolation & purification en_US
dc.subject Peptide Fragments/genetics en_US
dc.subject Polymerase Chain Reaction/methods en_US
dc.subject Tuberculosis/complications/diagnosis/microbiology/urine en_US
dc.subject Urine/microbiology en_US
dc.title Design and use of mouse control DNA for DNA biomarker extraction and PCR detection from urine: Application for transrenal Mycobacterium tuberculosis DNA detection en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1016/j.mimet.2017.02.010
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#1.06.01
dc.relation.issn 1872-8359


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