STRIP: Systematic Testing using Robotics and Innovation during Pandemics v1

2021 ◽  
Author(s):  
Peter H L Krijger ◽  
Tim A Hoek ◽  
Sanne Boersma ◽  
Lieke I P M Donders ◽  
Maaike M C Broeders ◽  
...  
Keyword(s):  
Diagnostic Testing ◽  
Test Procedure ◽  
Testing Procedure ◽  
Practical Implementation ◽  
Diagnostic Laboratory ◽  
Systematic Testing ◽  
Personnel Costs ◽  
Liquid Handling ◽  
Full Capacity ◽  
Sensitivity Specificity

STRIP is a start-to-end streamlined and automated procedure for COVID-19 testing, centering on a single Tecan Fluent liquid-handling robot that can process over 14,000 samples per day. The sensitivity, specificity, and practical implementation of STRIP have been validated in a clinical study on 1128 individuals, meeting the standards set by the Dutch National Institute for Public Health and the Environment (Dutch CDC). Automation throughout the testing procedure dramatically reduces the workload of diagnostic laboratory personnel and potentially allows the placement of multiple STRIP liquid-handling robots per testing facility, further increasing testing capacity. The entire test procedure also requires only 3 pipet tips per sample, as well as reduced testing reagents due to process miniaturization, which is important given scarcity of testing consumables during the COVID-19 pandemic. Furthermore, STRIP is compatible with reagents from any supplier, and thus less sensitive to supply chain bottlenecks. Finally, the system is open and modular, facilitating adaptation of future developments in diagnostics. Overall, the system enabled substantial savings in personnel and reagents requirements compared with conventional diagnostic testing; when STRIP runs at full capacity, it is possible to rapidly recoup the initial outlay in the liquid-handling system from savings in personnel costs, reagents and materials.

scholarly journals The Laboratory Diagnosis of HIV Infections

2005 ◽  
Vol 16 (1) ◽  
pp. 26-30 ◽  
Author(s):  
Margaret Fearon
Keyword(s):  
Point Of Care ◽  
Diagnostic Testing ◽  
Clinical Information ◽  
Hiv Infections ◽  
Laboratory Diagnosis ◽  
The United States ◽  
Specific Information ◽  
Antibody Testing ◽  
Diagnostic Laboratory ◽  
Laboratory Results

HIV diagnostic testing has come a long way since its inception in the early 1980s. Current enzyme immunoassays are sensitive enough to detect antibody as early as one to two weeks after infection. A variety of other assays are essential to confirm positive antibody screens (Western blot, polymerase chain reaction [PCR]), provide an adjunct to antibody testing (p24 antigen, PCR), or provide additional information for the clinician treating HIV-positive patients (qualitative and quantitative PCR, and genotyping). Most diagnostic laboratories have complex testing algorithms to ensure accuracy of results and optimal use of laboratory resources. The choice of assays is guided by the initial screening results and the clinical information provided by the physician; both are integral to the laboratory's ability to provide an accurate laboratory diagnosis. Laboratories should also provide specific information on specimen collection, storage and transport so that specimen integrity is not compromised, thereby preserving the accuracy of laboratory results. Point of Care tests have become increasingly popular in the United States and some places in Canada over the past several years. These tests provide rapid, on-site HIV results in a format that is relatively easy for clinic staff to perform. However, the performance of these tests requires adherence to good laboratory quality control practices, as well as the backup of a licensed diagnostic laboratory to provide confirmation and resolution of positive or indeterminate results. Laboratory quality assurance programs and the participation in HIV proficiency testing programs are essential to ensure that diagnostic laboratories provide accurate, timely and clinically relevant laboratory results.

scholarly journals The diagnosis of delirium in 80 emergency unit patients

1998 ◽  
Vol 56 (2) ◽  
pp. 176-183
Author(s):  
AFONSO CARLOS NEVES ◽  
RICARDO DE CASTRO CINTRA SESSO ◽  
HENRIQUE BALLALAI FERRAZ ◽  
SÍLVIO FRANCISCO ◽  
JOÃO BAPTISTA DOS REIS-FILHO
Keyword(s):  
Correct Diagnosis ◽  
Diagnostic Testing ◽  
Final Diagnosis ◽  
Initial Diagnosis ◽  
University Hospital ◽  
Emergency Unit ◽  
Predictive Values ◽  
Kappa Test ◽  
History Of ◽  
Sensitivity Specificity

We evaluated the initial and final diagnosis of 80 patients with delirium arriving at the emergence unit of a university hospital in a large Brazilian city over a period of 30 months up to December 1991. The diagnosis was based on the DSM-IIIR criteria. Patients with a known history of head trauma or epileptic seizure and patients younger than 13 years were excluded. Only patients with a disease of up to 7 days were included.The patients were subdivided into four etiologic groups: vascular; associated with the use of alcohol; infectious-parasitic; miscellaneous.The results showed a rate of correct diagnosis ranging from 65 to 80% with the use of kappa test (standard good to excelent). Sensitivity, specificity, positive predictive and negative predictive values had results showing different conditions for initial diagnosis in each group. This study can help the initial diagnosis of delirium and the choice for diagnostic testing.

scholarly journals Large-scale, in-house production of viral transport media to support SARS-CoV-2 PCR testing in a multi-hospital healthcare network during the COVID-19 pandemic

2020 ◽  
Author(s):  
Kenneth P Smith ◽  
Annie Cheng ◽  
Amber Chopelas ◽  
Sarah DuBois-Coyne ◽  
Ikram Mezghani ◽  
...  
Keyword(s):  
Large Scale ◽  
Medical Center ◽  
Diagnostic Testing ◽  
Diagnostic Laboratory ◽  
Healthcare Network ◽  
Research Division ◽  
Viral Transport ◽  
Accelerated Stability ◽  
House Production ◽  
Transport Tube

The COVID-19 pandemic has severely disrupted worldwide supplies of viral transport media (VTM) due to widespread demand for SARS-CoV-2 RT-PCR testing. In response to this ongoing shortage, we began production of VTM in-house in support of diagnostic testing in our hospital network. As our diagnostic laboratory was not equipped for reagent production, we took advantage of space and personnel that became available due to closure of the research division of our medical center. We utilized a formulation of VTM described by the CDC that was simple to produce, did not require filtration for sterilization, and used reagents that were available from commercial suppliers. Performance of VTM was evaluated by several quality assurance measures. Based on Ct values of spiking experiments, we found that our VTM supported highly consistent amplification of the SARS-CoV-2 target (coefficient of variation = 2.95%) using the Abbott RealTime SARS-CoV-2 EUA assay on the Abbott m2000 platform. VTM was also found to be compatible with multiple swab types and, based on accelerated stability studies, able to maintain functionality for at least four months at room temperature. We further discuss how we met logistical challenges associated with large-scale VTM production in a crisis setting including use of staged, assembly line for VTM transport tube production.

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.

scholarly journals Has the Pandemic Triggered a ‘Paperdemic’? Towards an Assessment of Diagnostic Indicators for COVID-19

2021 ◽  
Author(s):  
AISDL
Keyword(s):  
Predictive Value ◽  
Diagnostic Testing ◽  
Supporting Evidence ◽  
The Novel ◽  
Scientific Publications ◽  
Widespread Belief ◽  
Novel Method ◽  
Consistency Problem ◽  
Novel Coronavirus ◽  
Sensitivity Specificity

This paper is a preliminary step towards the assessment of an alarming widespread belief that victims of the novel coronavirus SARS-CoV-2 include the quality and accuracy of scientific publications about it. Our initial results suggest that this belief cannot be readily ignored, denied, dismissed or refuted, since some genuine supporting evidence can be forwarded for it. This evidence includes an obvious increase in retractions of papers published about the COVID-19 pandemic plus an extra-ordinary phenomenon of inconsistency that we report herein. In fact, we provide a novel method for validating any purported set of the four most prominent indicators of diagnostic testing (Sensitivity, Specificity, Positive Predictive Value, and Negative Predictive Value), by observing that these indicators constitute three rather than four independent quantities. This observation has virtually been unheard of in the open medical literature, and hence researchers have not taken it into consideration. We define two functions, which serve as consistency criteria, since each of them checks consistency for any set of four numerical values (naturally belonging to the interval [0.0,1.0]) claimed to be the four basic diagnostic indicators. Most of the data we came across in various international journals met our criteria for consistency, but in a few cases, there were obvious unexplained blunders. We explored the same consistency problem for some diagnostic data published in 2020 concerning the ongoing COVID-19 pandemic and observed that the afore-mentioned unexplained blunders tended to be on the rise. A systematic extensive statistical assessment of this resumed tendency is warranted.

SENSITIVITY, SPECIFICITY, AND PREDICTIVE VALUE OF PHYSICAL EXAMINATION, CULTURE, AND OTHER LABORATORY STUDIES IN THE DIAGNOSIS DURING EARLY INFANCY OF VERTICALLY ACQUIRED HUMAN IMMUNODEFICIENCY VIRUS INFECTION

PEDIATRICS ◽  
1994 ◽  
Vol 94 (2) ◽  
pp. 274-275
Author(s):  
Susan E. Pacheco ◽  
William T. Shearer
Keyword(s):  
Clinical Trials ◽  
Physical Examination ◽  
Hiv Infection ◽  
Laboratory Studies ◽  
Diagnostic Laboratory ◽  
Predictive Values ◽  
P24 Antigen ◽  
Aids Clinical Trials ◽  
Sensitivity Specificity ◽  
Hiv 1

Purpose of the Study. To determine the HIV vertical transmission rate in an unselected group of infants born to HIV-infected mothers, and to examine the sensitivity, specificity, and positive and negative predictive values of physical examination and diagnostic laboratory studies (HIV culture, serum quantitative immunoglobulins and HIV-1 p24 antigen) in the diagnosis of HIV infection. Study Population. A group of 142 infants referred solely because they were born to HIV-infected mothers were selected for this study. Methods. Epidemiological and clinical data were obtained retrospectively from the Baylor Pediatric AIDS Clinical Trials Group HIV Infection Registry and medical records. The information recorded included results of physical examination and diagnostic laboratory tests (HIV culture, serum quantitative immunoglobulins, and HIV-1 p24 antigen). HIV cultures were performed according to a consensus protocol developed for the National Institute of Allergy and Infectious Diseases AIDS Clinical Trials Group. Results. Of 142 infants whose HIV infection status was known at the time of the study, 17 (20%) had confirmed infection, and 68 (80%) had seroreverted with no evidence of infection. All HIV-infected infants were at least 3 months old when abnormal physical exam findings became apparent (lymphadenopathy and hepatosplenomegaly), but similar findings were noted in an equal number of HIV-uninfected infants. All infected infants available were HIV culture positive by 6 months of age (16/16). There was no positive cultures reported in the infants who seroreverted (32/32). Elevated immunoglobulins (IgG, IgA, IgM) were present by 6 months of age in a high percentage of infected infants. Nearly one-half of the uninfected infants had elevated immunoglobulin levels during the first 6 months of life, but in 50% of the cases it was IgG alone.

scholarly journals Diagnostic value of mean platelet volume in neonatal sepsis

2019 ◽  
Vol 59 (6) ◽  
pp. 289-93
Author(s):  
Kristopher May Pamudji ◽  
I Made Kardana
Keyword(s):  
Neonatal Sepsis ◽  
Predictive Value ◽  
Mean Platelet Volume ◽  
Severe Disease ◽  
Diagnostic Testing ◽  
Clinical Signs ◽  
Diagnostic Value ◽  
Platelet Volume ◽  
Good Potential ◽  
Sensitivity Specificity

Background Neonatal sepsis is a severe disease with potentially serious impacts if not treated early. However, the symptoms and clinical signs are not specific. Several studies have been conducted to find early infection markers for detection of neonatal sepsis, but without satisfactory results. Mean platelet volume (MPV) is a new marker of infection that has good potential for diagnosing neonatal sepsis. Objective To assess the diagnostic value of MPV in early detection of neonatal sepsis. Methods This retrospective study with diagnostic testing was done with data collected from medical records of neonates with neonatal sepsis who were admitted to the Neonatology Department in Sanglah Hospital, Denpasar from December 2018 to March 2019. Mean platelet volume cut-off point was determined using a receiver-operating characteristic (ROC) curve. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of MPV in neonatal sepsis were determined using a 2x2 table. Results Of 82 subjects, 55 subjects were male (67%). Positive blood culture results were found in 25 subjects (30%). Mean platelet volume with a cut-off point of 7.44 fL had 80% sensitivity, 84.2% specificity, 69% PPV, and 90.6% NPV. Conclusion Mean platelet volume with a cut-off point of 7.44 fL can be used to diagnose neonatal sepsis with a sensitivity of 80% and specificity of 84.2%.

scholarly journals The Laboratory Diagnosis ofHaemophilus ducreyi

2005 ◽  
Vol 16 (1) ◽  
pp. 31-34 ◽  
Author(s):  
Michelle Alfa
Keyword(s):  
Diagnostic Testing ◽  
Laboratory Diagnosis ◽  
Primary Method ◽  
Sample Collection ◽  
Culture Methods ◽  
Transmitted Infection ◽  
Diagnostic Laboratory ◽  
Sexually Transmitted ◽  
Alternative Approaches ◽  
Genetic Amplification

Chancroid is a sexually transmitted infection caused byHaemophilus ducreyi. This fastidious, Gram-negative coccobacilli dies rapidly outside the human host, making diagnostic testing using culture methods difficult. This genital ulcer infection is not common in Canada and, therefore, can often be misdiagnosed. The objective of the present paper is to provide practical approaches for the diagnosis of chancroid in Canadian patients where the prevalence of this infection is low. Issues related to sample collection, sample transport and available diagnostic tests are reviewed, and several alternative approaches are outlined. Although antigen detection, serology and genetic amplification methods have all been reported forH ducreyi, none are commercially available. Culture is still the primary method available to most laboratories. However, the special media necessary for direct bedside inoculation is often not available; therefore, communication with the diagnostic laboratory and rapid specimen transport are essential when chancroid is suspected

A Surface-Directed Microfluidic Scheme for Parallel Nanoliter PCR Array Suitable for Point-of-Care Testing

2009 ◽  
Author(s):  
Naveen Ramalingam ◽  
Long-Qing Chen ◽  
Xin-Hao Yang ◽  
Liqun Deng ◽  
Qing-Hui Wang ◽  
...  
Keyword(s):  
Point Of Care ◽  
Mixture Distribution ◽  
Hydrophobic Surface ◽  
Pcr Primers ◽  
Pcr Array ◽  
Diagnostic Laboratory ◽  
Sample Distribution ◽  
Liquid Handling ◽  
Resource Limited ◽  
Micro Reactors

In resource-limited settings, it is impractical to get access to a diagnostic laboratory having sophisticated instruments, and it is desirable to use disposable point-of-care diagnostic chips that do not require liquid handling or pumping instruments for sample distribution among an array of reactors. In addition to the pump-less sample loading method, the challenge to seal an array of reactors without the use of microvalves or mechanical parts still persists. Implementation of microvalve array adds complexity to the chip fabrication and operation processes, and also reduces the space on the microchip. In this paper, we report the development of a high-throughput quantitative PCR chip platform for parallel analyses of multiple gene targets. The PCR mixture distribution among an array of 80 microreactors and subsequent isolation of the reactors were solely realized by a two-step surface tension-based microfluidic scheme, which eliminates the use of pumps, valves and liquid handling instruments. Confinement of the PCR mixture inside the micro reactors was achieved by implementing hybrid flow-restriction passive valves. The microreactors were isolated from each other by the flow of a curable liquid sealant delivered through microchannels by capillary action. We also investigated the effect of detergents that are present in most commercial PCR buffers. Presence of detergents makes the PCR buffer much more wetting on the passive capillary valve surface and this imposes another challenge to the design of the conventional hydrophobic patch valves which has been successfully used for deionized water. We demonstrated a successful capillary valve array with a common air venting channel having a hydrophobic surface for restricting the flow of PCR buffer containing surfactant. The interconnected microreactor array was fabricated on a glass chip substrate with approximate volume of 250 nl microreactor volume for PCR. A different set of PCR primers were preloaded into different microreactor on the PCR array chip for simultaneous amplification of multiple genes. Fluorescent signals from all the microreactors were simultaneously detected at every PCR thermal cycle using EvaGreen fluorescent dye on an in-house real-time PCR instrument. The capability of the scalable PCR array chip was demonstrated by amplifying a fragment of uidA gene for beta-glucuronidase of E. coli genome. Key technical issues related to chip operation such as PCR inhibition on the acid-washed glass substrate, and PCR compatibility of the sealant in both the uncured and cured states have been addressed.

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