Dataset Information

Fluorescence Polarization Based Nucleic Acid Testing for Rapid and Cost-Effective Diagnosis of Infectious Disease.

ABSTRACT: A new nucleic acid detection method was developed for a rapid and cost-effective diagnosis of infectious disease. This approach relies on the three unique elements: 1)?detection probes that regulate DNA polymerase activity in response to the complementary target DNA; 2)?universal reporters conjugated with a single fluorophore; and 3)?fluorescence polarization (FP) detection. As a proof-of-concept, the assay was used to detect and sub-type Salmonella bacteria with sensitivities down to a single bacterium in less than three hours.

SUBMITTER: Park KS

PROVIDER: S-EPMC4816641 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Fluorescence Polarization Based Nucleic Acid Testing for Rapid and Cost-Effective Diagnosis of Infectious Disease.

Park Ki Soo KS Charles Richelle C RC Ryan Edward T ET Weissleder Ralph R Lee Hakho H

Chemistry (Weinheim an der Bergstrasse, Germany) 20150930 46

A new nucleic acid detection method was developed for a rapid and cost-effective diagnosis of infectious disease. This approach relies on the three unique elements: 1) detection probes that regulate DNA polymerase activity in response to the complementary target DNA; 2) universal reporters conjugated with a single fluorophore; and 3) fluorescence polarization (FP) detection. As a proof-of-concept, the assay was used to detect and sub-type Salmonella bacteria with sensitivities down to a single b ...[more]

PMID: 26420633

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Project description:Global pandemics such as COVID-19 have resulted in significant global social and economic disruption. Although polymerase chain reaction (PCR) is recommended as the standard test for identifying the SARS-CoV-2, conventional assays are time-consuming. In parallel, although artificial intelligence (AI) has been employed to contain the disease, the implementation of AI in PCR analytics, which may enhance the cognition of diagnostics, is quite rare. The information that the amplification curve reveals can reflect the dynamics of reactions. Here, we present a novel AI-aided on-chip approach by integrating deep learning with microfluidic paper-based analytical devices (µPADs) to detect synthetic RNA templates of the SARS-CoV-2 ORF1ab gene. The µPADs feature a multilayer structure by which the devices are compatible with conventional PCR instruments. During analysis, real-time PCR data were synchronously fed to three unsupervised learning models with deep neural networks, including RNN, LSTM, and GRU. Of these, the GRU is found to be most effective and accurate. Based on the experimentally obtained datasets, qualitative forecasting can be made as early as 13 cycles, which significantly enhances the efficiency of the PCR tests by 67.5% (∼40 min). Also, an accurate prediction of the end-point value of PCR curves can be obtained by GRU around 20 cycles. To further improve PCR testing efficiency, we also propose AI-aided dynamic evaluation criteria for determining critical cycle numbers, which enables real-time quantitative analysis of PCR tests. The presented approach is the first to integrate AI for on-chip PCR data analysis. It is capable of forecasting the final output and the trend of qPCR in addition to the conventional end-point Cq calculation. It is also capable of fully exploring the dynamics and intrinsic features of each reaction. This work leverages methodologies from diverse disciplines to provide perspectives and insights beyond the scope of a single scientific field. It is universally applicable and can be extended to multiple areas of fundamental research. Graphical abstract Image, graphical abstract

Project description:BackgroundYaws is a non-venereal treponemal infection caused by Treponema pallidum subspecies pertenue. The disease is targeted by WHO for eradication by 2020. Rapid diagnostic tests (RDTs) are envisaged for confirmation of clinical cases during treatment campaigns and for certification of the interruption of transmission. Yaws testing requires both treponemal (trep) and non-treponemal (non-trep) assays for diagnosis of current infection. We evaluate a sequential testing strategy (using a treponemal RDT before a trep/non-trep RDT) in terms of cost and cost-effectiveness, relative to a single-assay combined testing strategy (using the trep/non-trep RDT alone), for two use cases: individual diagnosis and community surveillance.MethodsWe use cohort decision analysis to examine the diagnostic and cost outcomes. We estimate cost and cost-effectiveness of the alternative testing strategies at different levels of prevalence of past/current infection and current infection under each use case. We take the perspective of the global yaws eradication programme. We calculate the total number of correct diagnoses for each strategy over a range of plausible prevalences. We employ probabilistic sensitivity analysis (PSA) to account for uncertainty and report 95% intervals.ResultsAt current prices of the treponemal and trep/non-trep RDTs, the sequential strategy is cost-saving for individual diagnosis at prevalence of past/current infection less than 85% (81-90); it is cost-saving for surveillance at less than 100%. The threshold price of the trep/non-trep RDT (below which the sequential strategy would no longer be cost-saving) is US$ 1.08 (1.02-1.14) for individual diagnosis at high prevalence of past/current infection (51%) and US$ 0.54 (0.52-0.56) for community surveillance at low prevalence (15%).DiscussionWe find that the sequential strategy is cost-saving for both diagnosis and surveillance in most relevant settings. In the absence of evidence assessing relative performance (sensitivity and specificity), cost-effectiveness is uncertain. However, the conditions under which the combined test only strategy might be more cost-effective than the sequential strategy are limited. A cheaper trep/non-trep RDT is needed, costing no more than US$ 0.50-1.00, depending on the use case. Our results will help enhance the cost-effectiveness of yaws programmes in the 13 countries known to be currently endemic. It will also inform efforts in the much larger group of 71 countries with a history of yaws, many of which will have to undertake surveillance to confirm the interruption of transmission.

Dataset Information

Fluorescence Polarization Based Nucleic Acid Testing for Rapid and Cost-Effective Diagnosis of Infectious Disease.

Publications

Fluorescence Polarization Based Nucleic Acid Testing for Rapid and Cost-Effective Diagnosis of Infectious Disease.

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