World at work: research and testing laboratories.
Ontology highlight
ABSTRACT:
SUBMITTER: Emery RJ
PROVIDER: S-EPMC1740981 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundTesting for epidermal growth factor receptor (EGFR) mutations is an essential recommendation in guidelines for metastatic non-squamous non-small-cell lung cancer, and is considered mandatory in European countries. However, in practice, challenges are often faced when carrying out routine biomarker testing, including access to testing, inadequate tissue samples and long turnaround times (TATs).Materials and methodsTo evaluate the real-world EGFR testing practices of European pathology laboratories, an online survey was set up and validated by the Pulmonary Pathology Working Group of the European Society of Pathology and distributed to 64 expert testing laboratories. The retrospective survey focussed on laboratory organisation and daily EGFR testing practice of pathologists and molecular biologists between 2018 and 2021.ResultsTATs varied greatly both between and within countries. These discrepancies may be partly due to reflex testing practices, as 20.8% of laboratories carried out EGFR testing only at the request of the clinician. Many laboratories across Europe still favour single-test sequencing as a primary method of EGFR mutation identification; 32.7% indicated that they only used targeted techniques and 45.1% used single-gene testing followed by next-generation sequencing (NGS), depending on the case. Reported testing rates were consistent over time with no significant decrease in the number of EGFR tests carried out in 2020, despite the increased pressure faced by testing facilities during the COVID-19 pandemic. ISO 15189 accreditation was reported by 42.0% of molecular biology laboratories for single-test sequencing, and by 42.3% for NGS. 92.5% of laboratories indicated they regularly participate in an external quality assessment scheme.ConclusionsThese results highlight the strong heterogeneity of EGFR testing that still occurs within thoracic pathology and molecular biology laboratories across Europe. Even among expert testing facilities there is variability in testing capabilities, TAT, reflex testing practice and laboratory accreditation, stressing the need to harmonise reimbursement technologies and decision-making algorithms in Europe.
| S-EPMC10594022 | biostudies-literature
Project description:Background & objectivesAn outbreak of respiratory illness of unknown aetiology was reported from Hubei province of Wuhan, People's Republic of China, in December 2019. The outbreak was attributed to a novel coronavirus (CoV), named as severe acute respiratory syndrome (SARS)-CoV-2 and the disease as COVID-19. Within one month, cases were reported from 25 countries. In view of the novel viral strain with reported high morbidity, establishing early countrywide diagnosis to detect imported cases became critical. Here we describe the role of a countrywide network of VRDLs in early diagnosis of COVID-19.MethodsThe Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, established screening as well as confirmatory assays for SARS-CoV-2. A total of 13 VRDLs were provided with the E gene screening real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay. VRDLs were selected on the basis of their presence near an international airport/seaport and their past performance. The case definition for testing included all individuals with travel history to Wuhan and symptomatic individuals with travel history to other parts of China. This was later expanded to include symptomatic individuals returning from Singapore, Japan, Hong Kong, Thailand and South Korea.ResultsWithin a week of standardization of the test at NIV, all VRDLs could initiate testing for SARS-CoV-2. Till February 29, 2020, a total of 2,913 samples were tested. This included both 654 individuals quarantined in the two camps and others fitting within the case definition. The quarantined individuals were tested twice - at days 0 and 14. All tested negative on both occasions. Only three individuals belonging to different districts in Kerala were found to be positive.Interpretation & conclusionsSudden emergence of SARS-CoV-2 and its potential to cause a pandemic posed an unsurmountable challenge to the public health system of India. However, concerted efforts of various arms of the Government of India resulted in a well-coordinated action at each level. India has successfully demonstrated its ability to establish quick diagnosis of SARS-CoV-2 at NIV, Pune, and the testing VRDLs.
| S-EPMC7258754 | biostudies-literature
Project description:Digital technologies, especially if used in novel ways, provide a number of potential advantages to clinical research in trials related to human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS) and may greatly facilitate operations as well as data collection and analysis. These technologies may even allow answering questions that are not answerable with older technologies. However, they come with a variety of potential concerns for both the participants and the trial sponsors. The exact challenges and means for alleviation depend on the technology and on the population in which it is deployed, and the rapidly changing landscape of digital technologies presents a challenge for creating future-proof guidelines for technology application.The aim of this study was to identify and summarize some common themes that are frequently encountered by researchers in this context and highlight those that should be carefully considered before making a decision to include these technologies in their research.In April 2016, the Global HIV Vaccine Enterprise surveyed the field for research groups with recent experience in novel applications of digital technologies in HIV clinical research and convened these groups for a 1-day meeting. Real-world uses of various technologies were presented and discussed by 46 attendees, most of whom were researchers involved in the design and conduct of clinical trials of biomedical HIV prevention and treatment approaches. After the meeting, a small group of organizers reviewed the presentations and feedback obtained during the meeting and categorized various lessons-learned to identify common themes. A group of 9 experts developed a draft summary of the findings that was circulated via email to all 46 attendees for review. Taking into account the feedback received, the group finalized the considerations that are presented here.Meeting presenters and attendees discussed the many successful applications of digital technologies to improve research outcomes, such as those for recruitment and enrollment, participant identification, informed consent, data collection, data quality, and protocol or treatment adherence. These discussions also revealed unintended consequence of technology usage, including risks to study participants and risks to study integrity.Key lessons learned from these discussions included the need to thoroughly evaluate systems to be used, the idea that early success may not be sustained throughout the study, that some failures will occur, and considerations for study-provided devices. Additionally, taking these key lessons into account, the group generated recommendations on how to move forward with the use of technology in HIV vaccine and biomedical prevention trials.
| S-EPMC5556256 | biostudies-other
Project description:Once a fixture of research in the social and behavioral sciences, volunteer subjects are now only rarely used in human subjects research. Yet volunteers are a potentially valuable resource, especially for research conducted online. We argue that online volunteer laboratories are able to produce high-quality data comparable to that from other online pools. The scalability of volunteer labs means that they can produce large volumes of high-quality data for multiple researchers, while imposing little or no financial burden. Using a range of original tests, we show that volunteer and paid respondents have different motivations for participating in research, but have similar descriptive compositions. Furthermore, volunteer samples are able to replicate classic and contemporary social science findings, and produce high levels of overall response quality comparable to paid subjects. Our results suggest that online volunteer labs represent a potentially significant untapped source of human subjects data.
| S-EPMC6713332 | biostudies-literature
Project description:Pharmacogenetic (PGx) testing involves the analysis of genes known to affect response to medications. The field has been projected as a leading application of personalized or precision medicine, but the use of PGx tests has been stymied, in part, by the lack of clinical evidence of utility and reported low provider awareness. Another factor is the availability of testing. The range and types of PGx tests available have not been assessed to date. In the period September 2017-January 2018 we analyzed the numbers and types of PGx tests offered by clinical testing laboratories in the US. Of the 111 such labs that we identified, we confirmed that 76 offered PGx testing services. Of these, 31 offered only tests for single genes; 30 offered only tests for multiple genes; and 15 offered both types of tests. Collectively, 45 laboratories offered 114 multigene panel tests covering 295 genes. The majority of these tests did not have any clinical guidelines. PGx tests vary in type and makeup, which presents challenges in appropriate test evaluation and selection for providers, insurers, health systems, and patients alike.
| S-EPMC6642061 | biostudies-literature
Project description:KRAS mutation testing helps oncologists decide whether patients diagnosed with metastatic colorectal cancer (CRC) should be treated with epidermal growth factor receptor (EGFR) inhibitors. These drugs block the EGFR signaling pathway in tumor cells, and thus can slow tumor progression. Mutated KRAS is found in 30?45% of all CRC tumors, with mutations occurring at codons 12 and 13 being the most common. Patients with a mutated KRAS found in tumor tissue show limited clinical response to EGFR inhibitor therapy. Several factors can influence the results of KRAS mutation testing in tumor specimens. Variation can result from tumor heterogeneity, sample handling, DNA preparation, and differences in assay design and methodology. The purpose of this study was to evaluate comparability of KRAS test results among five labs currently used to determine KRAS mutation status of colorectal cancer specimens in a large multi-center study.Three commercial labs (Genzyme, Clarient, Quest Diagnostics), one clinical lab (Henry Ford Health System), and one research lab (Oregon Health Sciences University) were contracted to analyze KRAS mutational status; all are Clinical Laboratory Improvement Amendments (CLIA) certified. Twenty formalin-fixed paraffin-embedded (FFPE) human CRC samples that had been previously tested for KRAS mutations were selected based on mutation status (7 wild type samples, 7 with codon 12 mutations, and 6 with codon 13 mutations) from two clinical settings (Kaiser Permanente Colorado and Northwest). To ensure sufficient sample quantity, only surgical specimens from colon resections were used. Before being sent to each lab, the FFPE samples were reviewed by a pathologist to determine that the sample was of sufficient quality and quantity for testing. We asked each lab to use their standard clinical testing procedures. Clarient uses a polymerase chain reaction (PCR) method for mutation detection, Genzyme uses single nucleotide primer extension assay with fragment analysis by capillary electrophoresis, and the other three labs all use sequencing. Preliminary data (n=11 samples tested to date) suggests good agreement across laboratories despite differences in mutation detection methodologies.
| S-EPMC3251394 | biostudies-other
Project description:Managing environmental risk is essential to ensure organisations minimise their impact on the environment, comply with environmental legislation and maintain their reputation in an increasingly environmentally aware society. Organisations frequently use management systems to plan and execute routine environmental assessments, however environmental impacts may still arise from routine activities or accidents that could be avoided by effective environmental management. Currently there is no method for an organisation to assess the level of awareness their employees have of activities that may lead to an environmental impact, or the level of uptake of environmental management processes. Therefore, the Environmental Management Performance Assessment (EMPA) process was developed to enable organisations to self-assess existing environmental management processes by survey of their employees. The EMPA process was aligned to key phases of the Deming Cycle and involves development and distribution of a survey to organisation employees. The responses are then used to recognise areas for improvement by progression through a bespoke flow chart integrated with the initial survey. This enables demonstration of how particular hazards arise from insufficient awareness at different stages in the Deming Cycle and how these hazards can have wider, reputational, economic, and legislative consequences. The process was trialled by surveying academic researchers on the environmental management processes in their laboratories as a sample set.
| S-EPMC9280376 | biostudies-literature
Project description:Widespread testing is required to limit the current public health crisis caused by the COVID-19 pandemic. Multiple tests protocols have been authorized by the food and drugs administration (FDA) under an emergency use authorization (EUA). The majority of these protocols are based on the gold-standard RT-qPCR test pioneered by the U.S. Centers for Disease Control and Prevention (CDC). However, there is still a widespread lack of testing in the US and many of the clinical diagnostics protocols require extensive human labor and materials that could face supply shortages and present biosafety concerns. Given the need to develop alternative reagents and approaches to provide nucleic-acid testing in the face of heightened demand and potential shortages, we have developed a simplified SARS-CoV-2 testing protocol adapted for its use in research laboratories with minimal molecular biology equipment and expertise. The protocol utilizes TRIzol to purify the viral RNA from different types of clinical specimens, requires minimal BSL-1 precautions and, given its high sensitivity, can be easily adapted to pooling samples strategies.
| S-EPMC7748277 | biostudies-literature
Project description:Regular proficiency testing of forensic examiners is required at accredited laboratories and widely accepted as an important component of a functioning quality assurance program. Yet, unlike in other testing industries, the majority of forensic laboratories testing programs rely entirely on declared proficiency tests. Some laboratories, primarily federal forensic facilities, have adopted blind proficiency tests, which are also used in the medical and drug testing industries. Blind tests offer advantages. They must resemble actual cases, can test the entire laboratory pipeline, avoid changes in behavior from an examiner knowing they are being tested, and are one of the only methods that can detect misconduct. However, the forensic context present both logistical and cultural obstacles to the implementation of blind proficiency tests. In November 2018, we convened a meeting of directors and quality assurance managers of local and state laboratories to discuss obstacles to the adoption of blind testing and assess successful and potential strategies to overcome them. Here, we compare the situation in forensic science to other testing disciplines, identifying obstacles to the implementation of blind proficiency testing in forensic contexts, and proposing ways to address those issues and increase the ecological validity of proficiency tests at forensic laboratories.
| S-EPMC7552087 | biostudies-literature
Project description:BackgroundLaboratory testing is helpful when evaluating patients with suspected Lyme disease (LD). A 2-tiered antibody testing approach is recommended, but single-tier and nonvalidated tests are also used. We conducted a survey of large commercial laboratories in the United States to assess laboratory practices. We used these data to estimate the cost of testing and number of infections among patients from whom specimens were submitted.MethodsLarge commercial laboratories were asked to report the type and volume of testing conducted nationwide in 2008, as well as the percentage of positive tests for 4 LD-endemic states. The total direct cost of testing was calculated for each test type. These data and test-specific performance parameters available in published literature were used to estimate the number of infections among source patients.ResultsSeven participating laboratories performed approximately 3.4 million LD tests on approximately 2.4 million specimens nationwide at an estimated cost of $492 million. Two-tiered testing accounted for at least 62% of assays performed; alternative testing accounted for <3% of assays. The estimated frequency of infection among patients from whom specimens were submitted ranged from 10% to 18.5%. Applied to the total numbers of specimens, this yielded an estimated 240 000 to 444 000 infected source patients in 2008.DiscussionLD testing is common and costly, with most testing in accordance with diagnostic recommendations. These results highlight the importance of considering clinical and exposure history when interpreting laboratory results for diagnostic and surveillance purposes.
| S-EPMC4646413 | biostudies-literature