ArticleAnnals of clinical microbiology and antimicrobials2008
Predicting the sensitivity and specificity of published real-time PCR assays.
Article in Annals of clinical microbiology and antimicrobials, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 56 citations in OpenAlex.
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- Simplifying the estimation of diagnostic testing accuracy over time for high specificity tests in the absence of a gold standard.Biometrics · 2023Article
- Enhanced Arbovirus Surveillance with High-Throughput Metatranscriptomic Processing of Field-Collected Mosquitoes.Viruses · 2022Article
- Review
- Meta-Analysis of qPCR for Bovine Respiratory Disease Based on MIQE Guidelines.Frontiers in molecular biosciences · 2022Article
- Comparison of traditional methods and high-throughput genetic sequencing in the detection of pathogens in pulmonary infectious diseases.Annals of translational medicine · 2021Article
- PANDAA intentionally violates conventional qPCR design to enable durable, mismatch-agnostic detection of highly polymorphic pathogens.Communications biology · 2021Article
- Liquid biopsy in oncology: a consensus statement of the Spanish Society of Pathology and the Spanish Society of Medical Oncology.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2020Article
- GoPrime: Development of an In Silico Framework to Predict the Performance of Real-Time PCR Primers and Probes Using Foot-and-Mouth Disease Virus as a Model.Pathogens (Basel, Switzerland) · 2020Article
- In silico re-assessment of a diagnostic RT-qPCR assay for universal detection of Influenza A viruses.Scientific reports · 2019Article
- Simultaneous Detection of Different Zika Virus Lineages via Molecular Computation in a Point-of-Care Assay.Viruses · 2018Article
- Techniques of using circulating tumor DNA as a liquid biopsy component in cancer management.Computational and structural biotechnology journal · 2018Review
- Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics.PLoS neglected tropical diseases · 2017Article
- Evaluation of TaqMan qPCR System Integrating Two Identically Labelled Hydrolysis Probes in Single Assay.Scientific reports · 2017Article
- Targeted amplification for enhanced detection of biothreat agents by next-generation sequencing.BMC research notes · 2015Article
- The presence of cariogenic and periodontal pathogens in the oral cavity of one-year-old infants delivered pre-term with very low birthweights: a case control study.BMC oral health · 2014Article
- Analytical characteristics of a qPCR-based molecular diagnostic assay - conceptual considerations for laboratory personnel.Journal of biomedical research · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn recent years real-time PCR has become a leading technique for nucleic acid detection and quantification. These assays have the potential to greatly enhance efficiency in the clinical laboratory. Choice of primer and probe sequences is critical for accurate diagnosis in the clinic, yet current primer/probe signature design strategies are limited, and signature evaluation methods are lacking.
methodsWe assessed the quality of a signature by predicting the number of true positive, false positive and false negative hits against all available public sequence data. We found real-time PCR signatures described in recent literature and used a BLAST search based approach to collect all hits to the primer-probe combinations that should be amplified by real-time PCR chemistry. We then compared our hits with the sequences in the NCBI taxonomy tree that the signature was designed to detect.
resultsWe found that many published signatures have high specificity (almost no false positives) but low sensitivity (high false negative rate). Where high sensitivity is needed, we offer a revised methodology for signature design which may designate that multiple signatures are required to detect all sequenced strains. We use this methodology to produce new signatures that are predicted to have higher sensitivity and specificity.
conclusionWe show that current methods for real-time PCR assay design have unacceptably low sensitivities for most clinical applications. Additionally, as new sequence data becomes available, old assays must be reassessed and redesigned. A standard protocol for both generating and assessing the quality of these assays is therefore of great value. Real-time PCR has the capacity to greatly improve clinical diagnostics. The improved assay design and evaluation methods presented herein will expedite adoption of this technique in the clinical lab.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.