Development of Internal Controls for Probe-Based Nucleic Acid Diagnostic Assays

1999 ◽  
Vol 270 (2) ◽  
pp. 249-256 ◽  
Author(s):  
Bernard C. Courtney ◽  
Malcolm M. Smith ◽  
Erik A. Henchal
Keyword(s):  
Nucleic Acid ◽  
Internal Controls ◽  
Diagnostic Assays

scholarly journals Efficient design of maximally active and specific nucleic acid diagnostics for thousands of viruses

2020 ◽  
Author(s):  
Hayden C. Metsky ◽  
Nicole L. Welch ◽  
Nicholas J. Haradhvala ◽  
Laurie Rumker ◽  
Yibin B. Zhang ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Genomic Diversity ◽  
Efficient Design ◽  
Full Spectrum ◽  
Diagnostic Assays ◽  
Genome Data ◽  
Species Specific ◽  
Nucleic Acid Assays ◽  
Lower Limits ◽  
Detection Technologies

AbstractHarnessing genomic data and predictive models will provide activity-informed diagnostic assays for thousands of viruses and offer rapid design for novel ones. Here we develop and extensively validate new algorithms that design nucleic acid assays having maximal predicted detection activity over a virus’s full genomic diversity with stringent specificity. Focusing on CRISPR-Cas13a detection, we test a library of ~ 19,000 guide-target pairs and construct a convolutional neural network that predicts Cas13a detection activity better than other techniques. We link our methods by building ADAPT, an end-to-end system that automatically leverages the latest viral genome data. We designed optimal species-specific assays for the 1,933 vertebrate-infecting viral species within 2 hours for most species and 24 hours for all but 3. ADAPT’s designs are sensitive and specific down to the lineage-level for the range of taxa we tested, including ones that pose challenges involving genomic diversity and specificity. They also exhibit significantly higher fluorescence and lower limits of detection, across a virus’s full spectrum of genomic diversity, than designs from standard techniques. ADAPT is available in an accessible software package and can be applied to other detection technologies to enhance critically-needed viral diagnostic and surveillance efforts.

scholarly journals Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay

2020 ◽  
Author(s):  
Melis N. Anahtar ◽  
Bennett Shaw ◽  
Damien Slater ◽  
Elizabeth H Byrne ◽  
Yolanda Botti-Lodovico ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Health Care Providers ◽  
Diagnostic Testing ◽  
Care Providers ◽  
Effective Response ◽  
Diagnostic Assays ◽  
Health Authorities ◽  
Public Health Authorities ◽  
Set Up ◽  
Crisis Conditions

Developing and deploying new diagnostic tests is difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important for an effective response. In the early stages of a pandemic, laboratories play a key role in helping health care providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, polymerase chain reaction (PCR) remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility, and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to fast and accurate diagnostic testing in crisis conditions.

scholarly journals Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay

2021 ◽  
pp. jclinpath-2020-207128
Author(s):  
Melis N Anahtar ◽  
Bennett M Shaw ◽  
Damien Slater ◽  
Elizabeth H Byrne ◽  
Yolanda Botti-Lodovico ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Testing ◽  
Healthcare Providers ◽  
Diagnostic Assays ◽  
Health Authorities ◽  
Public Health Authorities ◽  
Set Up ◽  
Crisis Conditions ◽  
Do So

Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.

scholarly journals Nucleic acid-based differential diagnostic assays for feline coronavirus

2014 ◽  
Vol 208 ◽  
pp. 21-25 ◽  
Author(s):  
Jae-Ik Han ◽  
Shien-Young Kang ◽  
Kyoung-Jin Yoon ◽  
Ki-Jeong Na
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Assays ◽  
Feline Coronavirus

scholarly journals A Robust, Low-Cost Instrument for Real-time Colorimetric Isothermal Nucleic Acid Amplification

2021 ◽  
Author(s):  
Frank Myers ◽  
Brian Moffatt ◽  
Ragheb El Khaja ◽  
Titash Chatterjee ◽  
Gurmeet Marwaha ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Point Of Care ◽  
Low Cost ◽  
Lamp Assay ◽  
Nucleic Acid Amplification ◽  
Diagnostic Assays ◽  
Isothermal Nucleic Acid Amplification ◽  
Point Of Care Diagnostics ◽  
Time Readout

The COVID-19 pandemic has highlighted the need for broader access to molecular diagnostics. Colorimetric isothermal nucleic acid amplification assays enable simplified instrumentation over more conventional PCR diagnostic assays and, as such, represent a promising approach for addressing this need. In particular, colorimetric LAMP (loop-mediated isothermal amplification) has received a great deal of interest recently. However, there do not currently exist robust instruments for performing these kinds of assays in high throughput with real-time readout of amplification signals. To address this need, we developed LARI, the LAMP Assay Reader Instrument. We have deployed over 50 LARIs for routine use in R&D and production environments, with over 12,000 assays run to date. In this paper, we present the design and construction of LARI along with thermal, optical, and assay performance characteristics. LARI can be produced for under $1500 and has broad applications in R&D, point-of-care diagnostics, and global health.

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