Within-laboratory reproducibility of Ames test results: Are repeat tests necessary?

The Ames test is required by regulatory agencies worldwide for assessing the mutagenic and carcinogenic potential of chemical compounds. This test uses several strains of bacteria to evaluate mutation induction: positive results in the assay are predictive of rodent carcinogenicity. As an initial step to understanding how well the assay may detect mutagens present as constituents of complex mixtures such as botanical extracts, a cross-sector working group examined the within-laboratory reproducibility of the Ames test using the extensive, publicly available National Toxicology Program (NTP) Ames test database comprising more than 3000 distinct test articles, most of which are individual chemicals. This study focused primarily on NTP tests conducted using the standard Organization for Economic Co-operation and Development Test Guideline 471 preincubation test protocol with 10% rat liver S9 for metabolic activation, although 30% rat S9 and 10 and 30% hamster liver S9 were also evaluated. The reproducibility of initial negative responses in all strains with and without 10% S9, was quite high, ranging from 95% to 99% with few exceptions. The within-laboratory reproducibility of initial positive responses for strains TA98 and TA100 with and without 10% rat liver S9 was ≥90%. Similar results were seen with hamster S9. As expected, the reproducibility of initial equivocal responses was lower, <50%. These results will provide context for determining the optimal design of recommended test protocols for use in screening both individual chemicals and complex mixtures, including botanicals.

Nationwide implementation of a multifaceted tailored strategy to improve uptake of standardized structured reporting in pathology: an effect and process evaluation.

BACKGROUND: Implementation strategies are aimed at improving guideline adherence. Both effect and process evaluations are conducted to provide insights into the success or failure of these strategies. In our study, we evaluate the nationwide implementation of standardized structured reporting (SSR) in pathology. METHODS: An interrupted time series analysis was conducted to evaluate the effect of a previously developed implementation strategy, which consisted of various digitally available elements, on SSR in pathology laboratories. A segmented regression analysis was performed to analyze the change in mean SSR percentages directly after the strategy introduction for pathology reporting and specific subcategories. In addition, we analyzed the change in trend in the weekly percentages after strategy introduction, also for subgroups of tumor groups, retrieval methods, and type of laboratory. The change in SSR use after the strategy introduction was determined for all pathology laboratories. We further conducted a process evaluation in which the exposure to the strategy elements was determined. Experiences of the users with all strategy elements and the remaining barriers and potential strategy elements were evaluated through an eSurvey. We also tested whether exposure to a specific element and a combination of elements resulted in a higher uptake of SSR after strategy introduction. RESULTS: There was a significant increase in an average use of SSR after the strategy introduction for reporting of gastrointestinal (p=.018) and urological (p=.003) oncological diagnoses. A significant increase was present for all oncological resections as a group (p=.007). Thirty-three out of 42 pathology laboratories increased SSR use after the strategy introduction. The "Feedback button", an option within the templates for SSR to provide feedback to the provider and one of the elements of the implementation strategy, was most frequently used by the SSR users, and effectiveness results showed that it increased average SSR use after the strategy introduction. Barriers were still present for SSR implementation. CONCLUSIONS: Nationwide SSR implementation improved for specific tumor groups and retrieval methods. The next step will be to further improve the use of SSR and, simultaneously, to further develop potential benefits of high SSR use, focusing on re-using discrete pathology data. In this way, we can facilitate proper treatment decisions in oncology.

Directrices de laboratorio para la detección y el diagnóstico de la infección por el virus de la viruela del mono / Laboratory Guidelines for the Detection and Diagnosis of Monkeypox Virus Infection

Este documento está basado en la guía provisional de la Organización Mundial de la Salud sobre las pruebas de laboratorio para el virus de la viruela del mono, 23 de mayo de 2022, y tiene por objeto proporcionar orientación a los Laboratorios Nacionales de Referencia sobre la detección del virus de la viruela del mono

This document is based on World Health Organization interim guidance on Laboratory testing for monkeypox virus, 23 May 2022, and is intended to provide guidance to National Reference Laboratories on monkeypox virus laboratory detection

External quality assessment of COVID-19 real time reverse transcription PCR laboratories in India.

Sudden emergence and rapid spread of COVID-19 created an inevitable need for expansion of the COVID-19 laboratory testing network across the world. The strategy to test-track-treat was advocated for quick detection and containment of the disease. Being the second most populous country in the world, India was challenged to make COVID-19 testing available and accessible in all parts of the country. The molecular laboratory testing network was augmented expeditiously, and number of laboratories was increased from one in January 2020 to 2951 till mid-September, 2021. This rapid expansion warranted the need to have inbuilt systems of quality control/ quality assurance. In addition to the ongoing inter-laboratory quality control (ILQC), India implemented an External Quality Assurance Program (EQAP) with assistance from World Health Organization (WHO) and Royal College of Pathologists, Australasia. Out of the 953 open system rRTPCR laboratories in both public and private sector who participated in the first round of EQAP, 891(93.4%) laboratories obtained a passing score of > = 80%. The satisfactory performance of Indian COVID-19 testing laboratories has boosted the confidence of the public and policy makers in the quality of testing. ILQC and EQAP need to continue to ensure adherence of the testing laboratories to the desired quality standards.

Laboratory monitoring to reduce adverse drug-related events: a mixed methods study.

BACKGROUND: Therapy with angiotensinconverting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) requires laboratory monitoring to avoid hyperkalemia and acute kidney failure. OBJECTIVE: To assess the frequency of recommended annual serum potassium and creatinine monitoring and determine potential factors associated with care gaps among adults dispensed an ACEI or ARB. METHODS: This mixed-methods study integrated findings from a retrospective cohort study and individual patient interviews. Adults aged 21 years and over within Kaiser Permanente Southern California with at least 180 treatment days of an ACEI and/or ARB in 2015 were included. Patients invited for qualitative interviews included those who did and did not complete the recommended laboratory tests. We assessed the proportion of patients completing both recommended laboratory tests, factors associated with not receiving laboratory monitoring, and patients' insights into barriers and facilitators of recommended monitoring. RESULTS: Of 437,544 patients who received an ACEI or ARB, 9.0% did not receive both a serum potassium and creatinine laboratory test during treatment (defined as a care gap). Lower risk of a care gap was observed for patients with increasing age (rate ratio [RR] per 10-year increase = 0.78, 95% CI = 0.77-0.79); diabetes mellitus (RR = 0.62, 95% CI = 0.60-0.64); hypertension (RR = 0.71, 95% CI = 0.71-0.74); Charlson Comorbidity Index score of at least 2 (RR = 0.62, 95% CI = 0.60-0.64); those who changed medication classes (RR = 0.53, 95% CI = 0.51-0.56); and patients with a cardiologist (RR = 0.81, 95% CI = 0.73-0.90) or nephrologist (RR = 0.60, 95% CI = 0.52-0.69) as their prescribing provider. Twenty-five patients completed the qualitative interviews. Patients often lacked knowledge about the need for laboratory monitoring, cited logistical barriers to accessing the laboratory, and deemed the reminders they received through an outpatient safety program as a facilitator to completing tests. CONCLUSIONS: Given the large patient population on ACEI and ARB medications, monitoring and support strategies such as electronic clinical surveillance could be important in addressing care gaps and potentially reducing adverse drug effects. DISCLOSURES: This project was supported by grant number R01HS024437 from the Agency for Healthcare Research and Quality. The funder had no role in the design of the study; collection, analyses, or interpretation of the data, or decision to submit this manuscript for publication. Harrison, Reynolds, Hahn, Munoz-Plaza, Yi, Fischer, Luong, Sim, Brettler, Handler, and Mittman are employees of the Southern California Permanente Medical Group. Danworth was employed by the Southern California Permanente Medical Group at the time of this study. Singh was partially supported by the Houston VA HSR&D Center for Innovations in Quality, Effectiveness and Safety (CIN13-413). Reynolds reports grants from Novartis, Amgen Inc., and Vital Strategies, Resolve to Save Lives, unrelated to this work. Yi reports grants from Novartis unrelated to this work. Kanter has nothing to disclose.

Tumor BRCA testing in ovarian cancer and EQA scheme: our experience of a critical evaluation.

Next generation sequencing (NGS) is a widespread molecular biology method integrated into clinical practice to detect genetic variants, for diagnostic and prognostic purposes. The scheduled external quality assessments (EQA) is integral part of clinical molecular laboratory quality assurance. The EQA provides an efficient system to compare analytic test performances among different laboratories, which is essential to evaluate consistency of molecular test. EQA failures demands targeted corrective action plans. In this context, the complexity of the NGS techniques requires careful and continuous quality control procedures. We report a tumor BRCA1/2 (tBRCA) testing benchmark discrepancy provided by the European Molecular Genetics Quality Network in our laboratory during a round of EQA for somatic mutation testing of BRCA genes in relation to ovarian cancer. The critical analysis emerging from the tBRCA EQA is presented. We underline that harmonization processes are still required for the EQA in the molecular biology field, especially if applied to the evaluation of methods characterized by high complexity.

Evaluation of commercial SARS-CoV-2 serological assays in Canadian public health laboratories.

The COVID-19 pandemic has led to the influx of immunoassays for the detection of antibodies towards severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into the global market. The Canadian Public Health Laboratory Network Serology Task Force undertook a nationwide evaluation of twelve laboratory and 6 point-of-care based commercial serological assays for the detection of SARS-CoV-2 antibodies. We determined that there was considerable variability in the performance of individual tests and that an orthogonal testing algorithm should be prioritized to maximize the accuracy and comparability of results across the country. The manual enzyme immunoassays and point-of-care tests evaluated had lower specificity and increased coefficients of variation compared to automated enzyme immunoassays platforms putting into question their utility for large-scale sero-surveillance. Overall, the data presented here provide a comprehensive approach for applying accurate serological assays for longitudinal sero-surveillance and vaccine trials while informing Canadian public health policy.

Efficiency of pooled surveillance testing in academic labs to detect and inhibit COVID-19 outbreaks.

Robust surveillance testing is a key strategic plan to prevent COVID-19 outbreaks and slow the spread of the SARS-CoV-2 pandemic; however, limited resources, facilities and time often impair the implementation of a widespread surveillance effort. To mitigate these resource limitations, we employed a strategy of pooling samples, reducing reagent cost and processing time. Through utilizing academic faculty and labs, successful pooled surveillance testing was conducted throughout Fall 2020 semester to detect positive SARS-CoV-2 infections in a population of 4400 students. During the semester, over 25,000 individual COVID status evaluations were made by pooling eight individual samples into one quantitative reverse transcription polymerase chain reaction. This pooled surveillance strategy was highly effective at detecting infection and significantly reduced financial burden and cost by $3.6 million.

Mutation Spectrum of EGFR From 21,324 Chinese Patients With Non-Small Cell Lung Cancer (NSCLC) Successfully Tested by Multiple Methods in a CAP-Accredited Laboratory.

Genotyping epidermal growth factor receptor (EGFR) gene in patients with advanced non-small cell lung cancers (NSCLC) is essential for identifying those patients who may benefit from targeted therapies. Systemically evaluating EGFR mutation detection rates of different methods currently used in clinical setting will provide valuable information to clinicians and laboratory scientists who take care of NSCLC patients. This study retrospectively reviewed the EGFR data obtained in our laboratory in last 10 years. A total of 21,324 NSCLC cases successfully underwent EGFR genotyping for clinical therapeutic purpose, including 5,244 cases tested by Sanger sequencing, 13,329 cases tested by real-time PCR, and 2,751 tested by next-generation sequencing (NGS). The average EGFR mutation rate was 45.1%, with 40.3% identified by Sanger sequencing, 46.5% by real-time PCR and 47.5% by NGS. Of these cases with EGFR mutations identified, 93.3% of them harbored a single EGFR mutation (92.1% with 19del or L858R, and 7.9% with uncommon mutations) and 6.7% harbored complex EGFR mutations. Of the 72 distinct EGFR variants identified in this study, 15 of them (single or complex EGFR mutations) were newly identified in NSCLC. For these cases with EGFR mutations tested by NGS, 65.3% of them also carried tumor-related variants in some non-EGFR genes and about one third of them were considered candidates of targeted drugs. NGS method showed advantages over Sanger sequencing and real-time PCR not only by providing the highest mutation detection rate of EGFR but also by identifying actionable non-EGFR mutations with targeted drugs in clinical setting.

Limitations of currently available in vitro oestrogenicity bioassays for effect-based testing of whole foods as the basis for decision making.

The idea that previously unknown hazards can be readily revealed in complex mixtures such as foods is a seductive one, giving rise to the hope that data from effect-based assays of food products collected in market surveys is of suitable quality to be the basis for data-driven decision-making. To study this, we undertook a comparative study of the oestrogenicity of blinded cereal samples, both in a number of external testing laboratories and in our own facility. The results clearly showed little variance in the activities of 9 samples when using a single method, but great differences between the activities from each method. Further exploration of these findings suggest that the oestrogenic activity is likely an inherent part of the natural food matrix which the varying sample preparation methods are able to release and extract to differing degrees. These issues indicate the current poor suitability of these types of datasets to be used as the basis for consumer advice or food decision-making. Data quality must be improved before such testing is used in practice.

Performance of HIV detection in Zhejiang province in China: The Pareto principle at work.

BACKGROUND: Timely detection of HIV infection is critical for curbing the AIDS epidemic, and building an extensive and effective HIV laboratory network is of great importance. Therefore, improving quality management of the laboratory network and optimizing detection strategies are desirable research issues. METHODS: We assessed the applicability of the Pareto principle to HIV detection performance. We conducted a retrospective review of basic information and numbers of screening tests among an HIV laboratory network (1,452 laboratories) in Zhejiang province in 2014 and statistically analyzed HIV testing data for different population categories. RESULTS: Approximately, 80% of the cumulative HIV screening tests and positive screening tests originated from 17.3% (251/1,452) and 11.7% (170/1,452) of the laboratories in the whole province, respectively, and similar patterns were observed at the prefectural level. We found that the top five population screening categories (25%, 5/20) had the highest contribution (approximately 80%) to not only the number of screening tests (77.2%) but also the numbers of positive (76.4%) and confirmed positive tests (81.5%). CONCLUSIONS: The Pareto principle provides a method for identifying noteworthy laboratories to deliver prior quality supervision and developing highly efficient screening strategies that best suit local needs.

A guided-inquiry investigation of genetic variants using Oxford nanopore sequencing for an undergraduate molecular biology laboratory course.

Next Generation Sequencing (NGS) has become an important tool in the biological sciences and has a growing number of applications across medical fields. Currently, few undergraduate programs provide training in the design and implementation of NGS applications. Here, we describe an inquiry-based laboratory exercise for a college-level molecular biology laboratory course that uses real-time MinION deep sequencing and bioinformatics to investigate characteristic genetic variants found in cancer cell-lines. The overall goal for students was to identify non-small cell lung cancer (NSCLC) cell-lines based on their unique genomic profiles. The units described in this laboratory highlight core principles in multiplex PCR primer design, real-time deep sequencing, and bioinformatics analysis for genetic variants. We found that the MinION device is an appropriate, feasible tool that provides a comprehensive, hands-on NGS experience for undergraduates. Student evaluations demonstrated increased confidence in using molecular techniques and enhanced understanding of NGS concepts. Overall, this exercise provides a pedagogical tool for incorporating NGS approaches in the teaching laboratory as way of enhancing students' comprehension of genomic sequence analysis. Further, this NGS lab module can easily be added to a variety of lab-based courses to help undergraduate students learn current DNA sequencing methods with limited effort and cost.

Influence of laboratory procedures on postthawing cell viability and hematopoietic engraftment after autologous peripheral blood stem cell transplantation.

BACKGROUND: The kinetics of hematopoietic recovery after autologous stem cell transplantation (ASCT) may be affected by laboratory procedures. The aim of this study was to evaluate the influence of characteristics of the cryopreserved units of peripheral blood stem cells (PBSC) on postthawing cell viability and engraftment outcomes after ASCT. STUDY DESIGN AND METHODS: This was a retrospective cohort study including individuals referred for ASCT. Cryopreservation was conducted at a single processing facility between 2014 and 2019, and patients received clinical care at six transplant centers. Covariates and outcome data were retrieved from participants' records. RESULTS: The study population comprised 619 patients (345 [55.7%] male). Median age was 53 years. Multiple myeloma was the most common diagnosis (62.7%). Higher preapheresis CD34+ cell count, lower nucleated cell (NC) concentration per cryobag, and composition of the cryoprotectant solution (5% dimethyl sulfoxide [DMSO] and 6% hydroxyethyl starch) were statistically significantly associated with higher postthawing cell viability. The linear regression model for time to neutrophil and platelet engraftment included the infused CD34+ cell dose and the composition of the cryoprotectant solution. Patients who had PBSC cryopreserved using 10% DMSO solution presented six times higher odds (odds ratio [OR] = 6.9; 95% confidence interval [CI]: 2.2-21.1; p = .001) of delayed neutrophil engraftment (>14 days) and two times higher odds (OR = 2.3, 95%CI: 1.4-3.7; p = .001) of prolonged hospitalization (>18 days). DISCUSSION: The study showed that mobilization efficacy, NC concentration, and the composition of the cryoprotectant solution significantly affected postthawing cell viability. In addition, the composition of the cryoprotectant solution significantly impacted engraftment outcomes and time of hospitalization after ASCT.

Manual de laboratorio para el diagnóstico por PCR en tiempo real en laboratorios descentralizados y vigilancia genómica de SARS-CoV-2 / Laboratory manual for real-time PCR diagnosis in decentralized laboratories and genomic surveillance of SARS-CoV-2

En los antecedentes, brinda detalles técnicos de enfermedades previas al COVID-19 y sigue esta consigna internacional: "Sin embargo, a la luz de la posible introducción de un caso sospechoso relacionado con el 2019-nCoV en la Región de las Américas, la Organización Panamericana de la Salud / Organización Mundial de la Salud (OPS / OMS) recomienda a los Estados Miembros garantizar su identificación oportuna, el envío de las muestras a laboratorios Nacionales o de referencia y la implementación del protocolo de detección molecular para 2019-nCoV, según la capacidad del laboratorio." Aborda las tres mutaciones del virus conocidas hasta la fecha del documento y las tres variantes conocidas: Reino Unido e Irlanda del Norte, República de Sudáfrica y Brasil, siendo la de mayor transmisibilidad, según el documento, la del Reino Unido. El primero de los objetivos del documento es: "Brindar los lineamientos generales para la toma de muestra, conservación, transporte y diagnóstico del SARS-Cov-2 en los laboratorios descentralizados bajo la técnica de Reacción en Cadena de la Polimerasa (PCR) en tiempo Real, en atención a pacientes que cumplen con la definición de caso y se tipifica como "sospechoso inusitado"." Incluye como anexo 2 el documento: "Lineamientos para el abordaje de casos positivos para SARS-COV-2 de viajeros que ingresan al país por el aeropuerto internacional "La Aurora" (AILA)"

Improving Malignancy Detection Rates in Body Fluids Submitted to the Hematology Laboratory for Nucleated Cell Count and Differential: A Quality Improvement Study.

CONTEXT.­: Body fluid specimens are regularly submitted to the hematology laboratory for cell count and differential. Unless there is high clinical suspicion for malignancy, most cases lack concurrent cytology review and may not benefit from more focused examination for malignancy. OBJECTIVE.­: To compare rates of malignancy detection before and after fluid-focused training for hematology technologists as part of a quality improvement initiative. DESIGN.­: During an 8-week pretraining period, body fluids submitted to the cytology laboratory were correlated with concurrent hematology specimens. After slide review and training sessions for the hematology technologists, the same data were collected for a 4-week period. Discrepant cases were reviewed by hematology laboratory supervisors and pathologists. RESULTS.­: We collected 465 pretraining and 249 posttraining body fluids with concurrent cytology and hematology evaluation. In the pretraining cohort, 48 cases (10.3%) were diagnosed as malignant by cytology; of those, 33 were detected by hematology. In the posttraining cohort, 30 cases (12.0%) were diagnosed as malignant by cytology of which 27 were detected by hematology. Of the 18 discrepant cases (all carcinomas), hematology slide review showed definite features of malignancy in 15 and no tumor cells in 3. The malignancy detection rate by the hematology laboratory significantly improved after training (68.8% versus 90.0%, P = .01). CONCLUSIONS.­: We demonstrate the comparatively lower malignancy detection rate for body fluid specimens processed in our hematology laboratory, particularly for carcinomas. Hematology technologist education/training improved the malignancy detection rate, an important quality improvement given the large proportion of body fluids undergoing hematology evaluation without concurrent cytology reviews.

Two-Year Experience of the Implementation of the Milan for Reporting Salivary Gland Cytopathology at a Private Medical Laboratory.

This study aimed to present the 2-year experience of the implementation of the Milan System for Reporting Salivary Gland Cytopathology at Alpha Prolipsis Medical Laboratories, a private medical laboratory located in Athens, Greece. A totaI of 102 Fine Needle Aspirations (FNAs) performed since 2018 were included in the study. Reports were issued according to the Milan System for Reporting Salivary Gland Cytopathology. Aspirates were prepared with both conventional and liquid-based cytological methods and were evaluated by two or three Board-certified cytopathologists. Diagnostic reproducibility and accuracy were evaluated. All cases included in this study had histologic follow-up. The diagnostic accuracy of FNA for differentiating between benign and malignant disease according to MSRSGC classification was 93.3%, the specificity was 97.5% and the sensitivity was 82.2%. The positive and negative predictive values were 93.2 and 87.2%, respectively. Our results show that FNA is a valuable examination technique in the preoperative evaluation of salivary gland lesions. The integration of the 2018 Milan System for Reporting Salivary Gland Cytopathology is effective, with an overall accuracy around 95%.

Establishment of a cell processing laboratory to support hematopoietic stem cell transplantation and chimeric antigen receptor (CAR)-T cell therapy.

Cell processing laboratories are an important part of cancer treatment centers. Cell processing laboratories began by supporting hematopoietic stem cell (HSC) transplantation programs. These laboratories adapted closed bag systems, centrifuges, sterile connecting devices and other equipment used in transfusion services/blood banks to remove red blood cells and plasma from marrow and peripheral blood stem cells products. The success of cellular cancer immunotherapies such as Chimeric Antigen Receptor (CAR) T-cells has increased the importance of cell processing laboratories. Since many of the diseases successfully treated by CAR T-cell therapy are also treated by HSC transplantation and since HSC transplantation teams are well suited to manage patients treated with CAR T-cells, many cell processing laboratories have begun to produce CAR T-cells. The methods that have been used to process HSCs have been modified for T-cell enrichment, culture, stimulation, transduction and expansion for CAR T-cell production. While processing laboratories are well suited to manufacture CAR T-cells and other cellular therapies, producing these therapies is challenging. The manufacture of cellular therapies requires specialized facilities which are costly to build and maintain. The supplies and reagents, especially vectors, can also be expensive. Finally, highly skilled staff are required. The use of automated equipment for cell production may reduce labor requirements and the cost of facilities. The steps used to produce CAR T-cells are reviewed, as well as various strategies for establishing a laboratory to manufacture these cells.

Lineamientos para el abordaje de casos positivos para secuenciación de SARS-CoV-2 para pacientes que asisten a hospitales privados, públicos y al Instituto Guatemalteco de Seguridad Social ­IGSS- / Guidelines for addressing positive cases for SARS-CoV-2 sequencing for patients attending private and public hospitals and the Guatemalan Social Security Institute -IGSS-

En los antecedentes se presentan estadísticas del COVID-19 a la fecha en la que se elaboró el documento (enero 2021) y aborda las tres mutaciones del virus conocidas hasta la fecha del documento. "La caracterización genética de patógenos virales es la base para el desarrollo de protocolos de diagnóstico, vacunas y medicamentos antivirales. Esta estrategia también es una herramienta útil en salud pública para el seguimiento a brotes y control de enfermedades mediante estudios de epidemiología molecular." "…la secuenciación genómica del SARS-CoV-2 y la liberación oportuna de la información no solo permitió la caracterización del agente etiológico involucrado en el brote inicial, sino también el desarrollo oportuno de protocolos de diagnóstico y seguimiento a la evolución de la pandemia de COVID-19. Así, la secuenciación genómica se ha convertido en una herramienta esencial para generar datos virológicos de SARS-CoV-2, para impulsar la respuesta de laboratorio, y entender mejor los patrones de dispersión y evolución de SARS-CoV-2" De manera que el objetivo del documento es: "Generar información genética mediante la vigilancia genómica de casos confirmados de COVID-19 de pacientes que asisten a los servicios de salud públicos y privados del país, así como del Instituto Guatemalteco de Seguridad Social ­IGSS-."