scholarly journals SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay

2021 ◽  
Vol 6 ◽  
pp. 9
Author(s):  
Michael D. Buck ◽  
Enzo Z. Poirier ◽  
Ana Cardoso ◽  
Bruno Frederico ◽  
Johnathan Canton ◽  
...  
Keyword(s):  
Diagnostic Testing ◽  
Lamp Assay ◽  
Cost Effective ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
Testing Strategies ◽  
Clinical Diagnostic ◽  
Alternative Testing ◽  
Biomedical Research Institute ◽  
Alternative Testing Strategies

The ongoing pandemic of SARS-CoV-2 calls for rapid and cost-effective methods to accurately identify infected individuals. The vast majority of patient samples is assessed for viral RNA presence by RT-qPCR. Our biomedical research institute, in collaboration between partner hospitals and an accredited clinical diagnostic laboratory, established a diagnostic testing pipeline that has reported on more than 252,000 RT-qPCR results since its commencement at the beginning of April 2020. However, due to ongoing demand and competition for critical resources, alternative testing strategies were sought. In this work, we present a clinically-validated procedure for high-throughput SARS-CoV-2 detection by RT-LAMP in 25 minutes that is robust, reliable, repeatable, sensitive, specific, and inexpensive.

scholarly journals SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay

2021 ◽  
Vol 6 ◽  
pp. 9
Author(s):  
Michael D. Buck ◽  
Enzo Z. Poirier ◽  
Ana Cardoso ◽  
Bruno Frederico ◽  
Johnathan Canton ◽  
...  
Keyword(s):  
Diagnostic Testing ◽  
Lamp Assay ◽  
Cost Effective ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
Testing Strategies ◽  
Clinical Diagnostic ◽  
Alternative Testing ◽  
Biomedical Research Institute ◽  
Alternative Testing Strategies

The ongoing pandemic of SARS-CoV-2 calls for rapid and cost-effective methods to accurately identify infected individuals. The vast majority of patient samples is assessed for viral RNA presence by RT-qPCR. Our biomedical research institute, in collaboration between partner hospitals and an accredited clinical diagnostic laboratory, established a diagnostic testing pipeline that has reported on more than 252,000 RT-qPCR results since its commencement at the beginning of April 2020. However, due to ongoing demand and competition for critical resources, alternative testing strategies were sought. In this work, we present a clinically-validated procedure for high-throughput SARS-CoV-2 detection by RT-LAMP that is robust, reliable, repeatable, specific, and inexpensive.

scholarly journals Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay

2020 ◽  
Keyword(s):  
Diagnostic Testing ◽  
Lamp Assay ◽  
Standard Operating Procedure ◽  
Cost Effective ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
Testing Strategies ◽  
Clinical Diagnostic ◽  
Standard Operating ◽  
Biomedical Research Institute

AbstractThe ongoing pandemic of SARS-CoV-2 calls for rapid and cost-effective methods to accurately identify infected individuals. The vast majority of patient samples is assessed for viral RNA presence by RT-qPCR. Our biomedical research institute, in collaboration between partner hospitals and an accredited clinical diagnostic laboratory, established a diagnostic testing pipeline that has reported on more than 40,000 RT-qPCR results since its commencement at the beginning of April 2020. However, due to ongoing demand and competition for critical resources, alternative testing strategies were sought. In this work, we present a clinically-validated standard operating procedure (SOP) for high-throughput SARS-CoV-2 detection by RT-LAMP in 25 minutes that is robust, reliable, repeatable, sensitive, specific, and inexpensive.

Effects of Population Structure and Admixture on Exact Tests for Association Between Loci

Genetics ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 381-387
Author(s):  
B Law ◽  
J S Buckleton ◽  
C M Triggs ◽  
B S Weir
Keyword(s):  
Population Subdivision ◽  
Data Sets ◽  
Multilocus Genotype ◽  
Test Statistic ◽  
Exact Test ◽  
Testing Strategies ◽  
Different Populations ◽  
Alternative Testing ◽  
Sparse Data Sets ◽  
Alternative Testing Strategies

Abstract The probability of multilocus genotype counts conditional on allelic counts and on allelic independence provides a test statistic for independence within and between loci. As the number of loci increases and each sampled genotype becomes unique, the conditional probability becomes a function of total heterozygosity. In that case, it does not address between-locus dependence directly but only indirectly through detection of the Wahlund effect. Moreover, the test will reject the hypothesis of allelic independence only for small values of heterozygosity. Low heterozygosity is expected for population subdivision but not for population admixture. The test may therefore be inappropriate for admixed populations. If individuals with parents in two different populations are always considered to belong to one of the populations, then heterozygosity is increased in that population and the exact test should not be used for sparse data sets from that population. If such a case is suspected, then alternative testing strategies are suggested.

Improved HPLC Determination of Plasma and Urine Oxalate in the Clinical Diagnostic Laboratory

1992 ◽  
Vol 15 (3) ◽  
pp. 501-511 ◽  
Author(s):  
A. Brega ◽  
A. Quadri ◽  
P. Villa ◽  
P. Prandini ◽  
Ji-Qing Wei ◽  
...  
Keyword(s):  
Hplc Determination ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
Clinical Diagnostic ◽  
Urine Oxalate

scholarly journals GenomeDiver: A platform for phenotype-guided medical genomic diagnosis

2020 ◽  
Author(s):  
Nathaniel Pearson ◽  
Christian Stolte ◽  
Kevin Shi ◽  
Faygel Beren ◽  
Noura S. Abul-Husn ◽  
...  
Keyword(s):  
Diagnostic Testing ◽  
Diagnostic Process ◽  
Genomic Sequencing ◽  
Sequencing Data ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
Phenotypic Data ◽  
Human Phenotype ◽  
Phenotype Data

ABSTRACTPurposeMaking a diagnosis from clinical genomic sequencing requires well-structured phenotypic data to guide genotype interpretation. A patient’s phenotypic features can be documented using the Human Phenotype Ontology (HPO), generating terms used to prioritize genes potentially causing the patient’s disease. We have developed GenomeDiver to provide a user interface for clinicians that allows more effective collaboration with the clinical diagnostic laboratory, with the goal of improving the success of the diagnostic process.MethodsGenomeDiver is designed to prompt reverse phenotyping of patients undergoing genetic testing, enriching the amount and quality of structured phenotype data for the diagnostic laboratory, and helping clinicians to explore and flag diseases potentially causing their patient’s presentation.ResultsWe show how GenomeDiver communicates the clinician’s informed insights to the diagnostic lab in the form of HPO terms for interpretation of genomic sequencing data. We describe our user-driven design process, the engineering of the software for efficiency, security and portability, and an example of the performance of GenomeDiver using simulated genomic testing data.ConclusionsGenomeDiver is a first step in a new approach to genomic diagnostics that enhances laboratory-clinician interactions, with the goal of directly engaging clinicians to improve the outcome of genomic diagnostic testing.

Leveraging the new predictive toxicology paradigm: alternative testing strategies in regulatory decision-making

2016 ◽  
Vol 3 (6) ◽  
pp. 1380-1395 ◽  
Author(s):  
Timothy Malloy ◽  
Elizabeth Beryt
Keyword(s):  
Safety Data ◽  
Health And Safety ◽  
Risk Prevention ◽  
Toxicity Data ◽  
Predictive Toxicology ◽  
Regulatory Decision ◽  
Testing Strategies ◽  
Comprehensive Health ◽  
Alternative Testing ◽  
Alternative Testing Strategies

Although toxicity data is critical to effective risk prevention and management, comprehensive health and safety data is not available for the vast majority of chemicals in use today.

Detecting Antimicrobial Resistance

2019 ◽  
Author(s):  
Lynette Phee ◽  
David Wareham
Keyword(s):  
Phenotypic Expression ◽  
Ease Of Use ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
Clinical Diagnostic ◽  
Control And Prevention ◽  
Antimicrobial Susceptibility Tests ◽  
Susceptibility Tests ◽  
Phenotypic Methods ◽  
Cost Of Materials

● To optimize antimicrobial therapy for the management of individual patient’s infection. ● For surveillance purposes, which in turn inform local/national/international clinical guidelines. ● For the management of infection control and prevention. Broadly speaking, resistance is detected by observing its phenotypic expression (activity of the candidate drug(s) against the target bacterium) or detecting the underlying genotypic determinant (resistance genes). Commonly used methods in clinical diagnostic laboratories generally fall under the ‘phenotypic’ category. These share similar traits— ease of use, reproducibility, scalability, quick turnaround of results and relative low cost of materials/reagents required. Moreover, decades of experience and fine-tuning have seen them established as methods of choice in most microbiology laboratories. Most phenotypic test methods are reliant on the use of clinical breakpoints set by national and international bodies (e.g. EUCAST and CLSI) to determine susceptibility/resistance. These guidelines are regularly subject to updates with input from leading experts and latest research findings. It is important for clinical diagnostic laboratories to adhere to best practice guidance set out by these bodies and keep up-to-date with the latest guidelines. Growth characteristics (on artificial media) of the bacterium of interest are extremely important in conventional phenotypic methods. As this presents a big obstacle for slow growers and ‘unculturable’ pathogens (e.g. Mycobacterium tuberculosis, Mycoplasma spp.) it has led to the introduction of genotypic methods of resistance detection in the clinical diagnostic laboratory. meteoric rise in the world of microbiology. Compared with conventional phenotypic methods, molecular genotypic-based tests are better suited for automation and reduce dependence on skilled workers for result interpretation. They therefore deliver the rapid turnaround demanded by modern medicine. Antimicrobial susceptibility tests (ASTs) is a term used to describe a range of phenotypic methods that employ direct observation of the action of antimicrobials against a target microorganism. This is the most commonly used method in clinical diagnostic laboratories for detecting resistance in bacteria. A. Disc diffusion Growth medium: Standardized agar plates (usually unsupplemented, but addition(s) may be necessary for bacteria with specific growth requirements). Antibacterial component: Fixed dose in standard size circular paper discs or tablets.

scholarly journals The role of alternative testing strategies in environmental risk assessment of engineered nanomaterials

2017 ◽  
Vol 4 (2) ◽  
pp. 292-301 ◽  
Author(s):  
Rune Hjorth ◽  
Patricia A. Holden ◽  
Steffen Foss Hansen ◽  
Benjamin P. Colman ◽  
Khara Grieger ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Environmental Risk ◽  
Environmental Risk Assessment ◽  
Engineered Nanomaterials ◽  
Animal Testing ◽  
Test Systems ◽  
Testing Strategies ◽  
Alternative Testing ◽  
Alternative Testing Strategies

Within toxicology there is a pressure to find new test systems to replace, reduce and refine animal testing. In nanoecotoxicology this raises a number of questions.

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