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Purpose: Data sharing through ClinVar offers a unique opportunity to identify interpretation differences between laboratories. As part of a ClinGen initiative, four clinical laboratories (Ambry, GeneDx, Partners Healthcare Laboratory for Molecular Medicine, and University of Chicago Genetic Services Laboratory) collaborated to identify the basis of interpretation differences and to investigate if data sharing and reassessment resolve interpretation differences by analyzing a subset of variants. Methods: ClinVar variants with submissions from at least two of the four participating laboratories were compared. For a subset of identified differences, laboratories documented the basis for discordance, shared internal data, independently reassessed with the American College of Medical Genetics and Genomics–Association for Molecular Pathology (ACMG-AMP) guidelines, and then compared interpretations. Results: At least two of the participating laboratories interpreted 6,169 variants in ClinVar, of which 88.3% were initially concordant. Laboratories reassessed 242/724 initially discordant variants, of which 87.2% (211) were resolved by reassessment with current criteria and/or internal data sharing; 12.8% (31) of reassessed variants remained discordant owing to differences in the application of the ACMG-AMP guidelines. Conclusion: Participating laboratories increased their overall concordance from 88.3 to 91.7%, indicating that sharing variant interpretations in ClinVar—thereby allowing identification of differences and motivation to resolve those differences—is critical to moving toward more consistent variant interpretations. Genet Med advance online publication 09 March 2017

Laboratory-acquired infections due to a variety of bacteria, viruses, parasites, and fungi have been described over the last century, and laboratory workers are at risk of exposure to these infectious agents. However, reporting laboratory-associated infections has been largely voluntary, and there is no way to determine the real number of people involved or to know the precise risks for workers. In this study, an international survey based on volunteering was conducted in biosafety level 3 and 4 laboratories to determine the number of laboratory-acquired infections and the possible underlying causes of these contaminations. The analysis of the survey reveals that laboratory-acquired infections have been infrequent and even rare in recent years, and human errors represent a very high percentage of the cases. Today, most risks from biological hazards can be reduced through the use of appropriate procedures and techniques, containment devices and facilities, and the training of personnel.

Computerized assessments are already used to derive accurate and reliable measures of cognitive function. Web-based cognitive assessment could improve the accessibility and flexibility of research and clinical assessment, widen participation, and promote research recruitment while simultaneously reducing costs. However, differences in context may influence task performance. This study aims to determine the comparability of an unsupervised, web-based administration of the Cambridge Neuropsychological Test Automated Battery (CANTAB) against a typical in-person lab-based assessment, using a within-subjects counterbalanced design. The study aims to test (1) reliability, quantifying the relationship between measurements across settings using correlational approaches; (2) equivalence, the extent to which test results in different settings produce similar overall results; and (3) agreement, by quantifying acceptable limits to bias and differences between measurement environments. A total of 51 healthy adults (32 women and 19 men; mean age 36.8, SD 15.6 years) completed 2 testing sessions, which were completed on average 1 week apart (SD 4.5 days). Assessments included equivalent tests of emotion recognition (emotion recognition task [ERT]), visual recognition (pattern recognition memory [PRM]), episodic memory (paired associate learning [PAL]), working memory and spatial planning (spatial working memory [SWM] and one touch stockings of Cambridge), and sustained attention (rapid visual information processing [RVP]). Participants were randomly allocated to one of the two groups, either assessed in-person in the laboratory first (n=33) or with unsupervised web-based assessments on their personal computing systems first (n=18). Performance indices (errors, correct trials, and response sensitivity) and median reaction times were extracted. Intraclass and bivariate correlations examined intersetting reliability, linear mixed models and Bayesian paired sample t tests tested for equivalence, and Bland-Altman plots examined agreement. Intraclass correlation (ICC) coefficients ranged from ρ=0.23-0.67, with high correlations in 3 performance indices (from PAL, SWM, and RVP tasks; ρ≥0.60). High ICC values were also seen for reaction time measures from 2 tasks (PRM and ERT tasks; ρ≥0.60). However, reaction times were slower during web-based assessments, which undermined both equivalence and agreement for reaction time measures. Performance indices did not differ between assessment settings and generally showed satisfactory agreement. Our findings support the comparability of CANTAB performance indices (errors, correct trials, and response sensitivity) in unsupervised, web-based assessments with in-person and laboratory tests. Reaction times are not as easily translatable from in-person to web-based testing, likely due to variations in computer hardware. The results underline the importance of examining more than one index to ascertain comparability, as high correlations can present in the context of systematic differences, which are a product of differences between measurement environments. Further work is now needed to examine web-based assessments in clinical populations and in larger samples to improve sensitivity for detecting subtler differences between test settings.

In this community effort, we compare measurements between 34 laboratories from 19 countries, utilizing mixtures of labelled authentic synthetic standards, to quantify by mass spectrometry four clinically used ceramide species in the NIST (National Institute of Standards and Technology) human blood plasma Standard Reference Material (SRM) 1950, as well as a set of candidate plasma reference materials (RM 8231). Participants either utilized a provided validated method and/or their method of choice. Mean concentration values, and intra- and inter-laboratory coefficients of variation (CV) were calculated using single-point and multi-point calibrations, respectively. These results are the most precise (intra-laboratory CVs ≤ 4.2%) and concordant (inter-laboratory CVs < 14%) community-derived absolute concentration values reported to date for four clinically used ceramides in the commonly analyzed SRM 1950. We demonstrate that calibration using authentic labelled standards dramatically reduces data variability. Furthermore, we show how the use of shared RM can correct systematic quantitative biases and help in harmonizing lipidomics. Collectively, the results from the present study provide a significant knowledge base for translation of lipidomic technologies to future clinical applications that might require the determination of reference intervals (RIs) in various human populations or might need to estimate reference change values (RCV), when analytical variability is a key factor for recall during multiple testing of individuals. Here, the authors compared measurements between 34 laboratories from 19 countries, to quantify by mass spectrometry four ceramides of clinical relevance in human blood plasma Standard Reference Materials. The main goals were to evaluate concordance obtained in a large inter-laboratory trial and to report absolute concentrations of four circulating lipids in a publicly available standard.

Purpose: While the diagnostic success of genomic sequencing expands, the complexity of this testing should not be overlooked. Numerous laboratory processes are required to support the identification, interpretation, and reporting of clinically significant variants. This study aimed to examine the workflow and reporting procedures among US laboratories to highlight shared practices and identify areas in need of standardization. Methods: Surveys and follow-up interviews were conducted with laboratories offering exome and/or genome sequencing to support a research program or for routine clinical services. The 73-item survey elicited multiple choice and free-text responses that were later clarified with phone interviews. Results: Twenty-one laboratories participated. Practices highly concordant across all groups included consent documentation, multiperson case review, and enabling patient opt-out of incidental or secondary findings analysis. Noted divergence included use of phenotypic data to inform case analysis and interpretation and reporting of case-specific quality metrics and methods. Few laboratory policies detailed procedures for data reanalysis, data sharing, or patient access to data. Conclusion: This study provides an overview of practices and policies of experienced exome and genome sequencing laboratories. The results enable broader consideration of which practices are becoming standard approaches, where divergence remains, and areas of development in best practice guidelines that may be helpful. Genet Med advance online publication 03 Novemeber 2016

Context.—Substantial variability between different antibody titration methods prompted development and introduction of uniform methods in 2008. Objective.—To determine whether uniform methods consistently decrease interlaboratory variation in proficiency testing. Design.—Proficiency testing data for antibody titration between 2009 and 2013 were obtained from the College of American Pathologists. Each laboratory was supplied plasma and red cells to determine anti-A and anti-D antibody titers by their standard method: gel or tube by uniform or other methods at different testing phases (immediate spin and/or room temperature [anti-A], and/or anti-human globulin [AHG: anti-A and anti-D]) with different additives. Interlaboratory variations were compared by analyzing the distribution of titer results by method and phase. Results.—A median of 574 and 1100 responses were reported for anti-A and anti-D antibody titers, respectively, during a 5-year period. The 3 most frequent (median) methods performed for anti-A antibody were uniform tube room temperature (147.5; range, 119–159), uniform tube AHG (143.5; range, 134–150), and other tube AHG (97; range, 82–116); for anti-D antibody, the methods were other tube (451; range, 431–465), uniform tube (404; range, 382–462), and uniform gel (137; range, 121–153). Of the larger reported methods, uniform gel AHG phase for anti-A and anti-D antibodies had the most participants with the same result (mode). For anti-A antibody, 0 of 8 (uniform versus other tube room temperature) and 1 of 8 (uniform versus other tube AHG), and for anti-D antibody, 0 of 8 (uniform versus other tube) and 0 of 8 (uniform versus other gel) proficiency tests showed significant titer variability reduction. Conclusion.—Uniform methods harmonize laboratory techniques but rarely reduce interlaboratory titer variance in comparison with other methods.

Background In countries with a high prevalence of TB, such as Ethiopia, direct sputum smear microscopy remains the most cost-effective tool for diagnosing patients with infectious tuberculosis and monitoring their progress on treatment . However, poor-quality sputum microscopy services may lead to the failure to detect persons with active tuberculosis and may cause unnecessary anti-TB treatment for non-TB cases. Proficiency level is the percentage agreement between participants'readings and the reference panel results. The aim of this study was to assess proficiency and associated factors of laboratory professionals in sputum smear microscopy for acid-fast bacilli at selected peripheral public and private diagnostic laboratories in East Gojjam Zone, Northwest Ethiopia, in 2023. Method An institutional-based cross-sectional study design was conducted from March 2023 to June 2023 at selected peripheral public diagnostic laboratories in East Gojjam Zone. 65 laboratory professionals were selected randomly from 41 peripheral public diagnostic laboratories in the study area. A validated questionnaire and 10 panel slides were used as data collection tools. The panel consisted of 5 pre-stained and 5 unstained slides. Data were entered and analyzed using the Statistical Package for Social Sciences software (SPSS version 20). P values less than 0.05 were considered statistically significant when looking for associations between dependent and independent variables. Result The overall proficiency level of laboratory professionals in tuberculosis smear microscopy was 81.92% with 95% CI [78.46–85.38]. Previous TB smear microscopy training, work experience, and institution of education had a significant association with the overall performance of laboratory professionals in TB smear microscopy. Conclusion The overall TB smear microscopy performance level of laboratory professionals at peripheral diagnostic laboratories in Ethiopia, was satisfactory, indicating a good level of competence. However, notable technical errors related to smear reading and reporting were observed. Thus, higher education institutions, especially private institutions, and the Zonal Health Department, should implement educational and training interventions to address the identified gaps and ultimately contribute to the national TB control program.

Customers can also benefit from the regularity of the data that is produced by Emerald's standardized hardware and software environment. Because each piece of data is linked permanently to the unambiguous script with which it was produced, \"it puts this very rigid, searchable ontology on top of everything\", explains Frezza. STANDARD OPERATING PROCEDURE Ginkgo Bioworks, a biotechnology company in Boston, Massachusetts, has built a syntheticbiology foundry - a facility where, with the help of lab-automation firm Strateos of Menlo Park, California, they automate the design and testing of engineered organisms. Paul Jaschke, a biological engineer at Macquarie University in Sydney, recalls working with Transcriptic, a lab-automation company in Menlo Park, while he was a postdoctoral researcher at Stanford University in California in 2015. Realizing this change might involve replacing manual verification with consistency checks embedded in software, developing business models that separate design and analysis work from experimental execution, or simply communicating a more precise description of what virtualization can offer.

[...]many laboratories use a locally developed system of Microsoft Word or similar documents for their policies and perform document control using a combination of spreadsheets and manual updating and version control. Very often this is managed by the laboratory itself, without any significant technical or administrative support from the institution. Because these products have only limited access and version controls, the medical director may not always know if a document has been altered. [...]the commit message becomes the primary means of navigating between versions.

Aims Histochemical staining of tissue is a fundamental technique in tissue diagnosis and research, but it suffers from significant variability. Efforts to address this include laboratory quality controls and quality assurance schemes, but these rely on subjective interpretation of stain quality, are laborious and have low reproducibility. We aimed (1) to develop a method for histochemical stain quantification using whole slide imaging and image analysis and (2) to demonstrate its usefulness in measuring staining variation. Methods A method to quantify the individual stain components of histochemical stains on virtual slides was developed. It was evaluated for repeatability and reproducibility, then applied to control sections of an appendix to quantify H&E staining (H/E intensities and H:E ratio) between automated staining machines and to measure differences between six regional diagnostic laboratories. Results The method was validated with <0.5% variation in H:E ratio measurement when using the same scanner for a batch of slides (ie, it was repeatable) but was not highly reproducible between scanners or over time, where variation of 7% was found. Application of the method showed H:E ratios between three staining machines varied from 0.69 to 0.93, H:E ratio variation over time was observed. Interlaboratory comparison demonstrated differences in H:E ratio between regional laboratories from 0.57 to 0.89. Conclusions A simple method using whole slide imaging can be used to quantify and compare histochemical staining. This method could be deployed in routine quality assurance and quality control. Work is needed on whole slide imaging devices to improve reproducibility.