Individual Laboratories Research Articles

A sensitivity analysis of methodological variables associated with microbiome measurements.

The experimental methods employed during metagenomic sequencing analyses of microbiome samples significantly impact the resulting data and typically vary substantially between laboratories. In this study, a full factorial experimental design was used to compare the effects of a select set of methodological choices (sample, operator, lot, extraction kit, variable region, and reference database) on the analysis of biologically diverse stool samples. For each parameter investigated, a main effect was calculated that allowed direct comparison both between methodological choices (bias effects) and between samples (real biological differences). Overall, methodological bias was found to be similar in magnitude to real biological differences while also exhibiting significant variations between individual taxa, even between closely related genera. The quantified method biases were then used to computationally improve the comparability of data sets collected under substantially different protocols. This investigation demonstrates a framework for quantitatively assessing methodological choices that could be routinely performed by individual laboratories to better understand their metagenomic sequencing workflows and to improve the scope of the datasets they produce.IMPORTANCEMethod-specific bias is a well-recognized challenge in metagenomic sequencing characterization of microbiome samples, but rigorous bias quantification is challenging. This report details a full factorial exploration of 48 experimental protocols by systematically varying microbiome sample, iterations of material production, laboratory personnel, DNA extraction kit, marker gene selection, and reference databases. Quantification of the biases associated with each parameter revealed similar magnitudes of variation arising from real biological differences and from varied analysis procedures. Furthermore, these measurement biases varied substantially with taxa, even between closely related genera. However, computational correction of method bias using a reference material was demonstrated that significantly harmonized metagenomic sequencing results collected using different analysis protocols.

A multicenter performance evaluation of cefiderocol MIC results: ComASP in comparison to CLSI broth microdilution.

There are very limited commercial methods available to clinical laboratories for cefiderocol minimum inhibitory concentration (MIC) testing. The Compact Antimicrobial Susceptibility Panel (ComASP) Cefiderocol method includes iron-depleted cation-adjusted Mueller-Hinton broth, which eliminates variability in cefiderocol MIC results based on iron levels. The lyophilized multi-well format of ComASP also provides for room temperature storage. In comparison to what an individual lab may do for method verification, this multi-site, multi-isolate study provides a robust evaluation and greater assurance to clinical microbiologists of the method's accurate and reproducible performance.

A Global Collaborative Comparison of SARS-CoV-2 Antigenicity Across 15 Laboratories.

Setting up a global SARS-CoV-2 surveillance system requires an understanding of how virus isolation and propagation practices, use of animal or human sera, and different neutralisation assay platforms influence assessment of SARS-CoV-2 antigenicity. In this study, with the contribution of 15 independent laboratories across all WHO regions, we carried out a controlled analysis of neutralisation assay platforms using the first WHO International Standard for antibodies to SARS-CoV-2 variants of concern (source: NIBSC). Live virus isolates (source: WHO BioHub or individual labs) or spike plasmids (individual labs) for pseudovirus production were used to perform neutralisation assays using the same serum panels. When comparing fold drops, excellent data consistency was observed across the labs using common reagents, including between pseudovirus and live virus neutralisation assays (RMSD of data from mean fold drop was 0.59). Utilising a Bayesian model, geometric mean titres and assay titre magnitudes (offsets) can describe the data efficiently. Titre magnitudes were seen to vary largely even for labs within the same assay group. We have observed that overall, live Microneutralisation assays tend to have the lowest titres, whereas Pseudovirus Neutralisation have the highest (with a mean difference of 3.2 log2 units between the two). These findings are relevant for laboratory networks, such as the WHO Coronavirus Laboratory Network (CoViNet), that seek to support a global surveillance system for evolution and antigenic characterisation of variants to support monitoring of population immunity and vaccine composition policy.

Extending the Calgary Audit and Feedback Framework into the virtual environment: a process evaluation and empiric evidence

BackgroundThe Calgary Audit and Feedback Framework (CAFF) is a pragmatic, evidence-based approach for the design and implementation of in-person social learning interventions using Audit and Group Feedback (AGF). This report describes extension of CAFF into the virtual environment as part of a multifaceted intervention bundle to reduce redundant daily laboratory testing in hospitals. We evaluate the process of extending CAFF in the virtual environment and share resulting evidence of participant engagement with planning for practice change.MethodsWe describe an innovative virtually facilitated AGF intervention based on the CAFF. The AGF intervention was part of an intervention bundle which included individual physician laboratory test utilization reports and educational tools to reduce redundant daily laboratory testing in hospitals. We used data from recorded and transcribed virtual AGF sessions, post AGF session surveys and detailed field notes maintained by project team members. We used simple descriptive statistics for quantitative data and analyzed qualitative data according to the elements of CAFF.ResultsEighty-three physicians participated over twelve virtual AGF sessions conducted across four tertiary care hospitals during the study period. We demonstrate that all prerequisite activities for CAFF (relationship building, question choice and data representation) were present in every virtual AGF session. Virtual facilitation was effective in supporting the transition of participants through different steps of CAFF in each session to lead to change talk and planning. All participants contributed to discussion during the AGF sessions. The post AGF session surveys were filled by 66% of participants (55/83), with over 90% of respondents reporting that the session helped them improve practice. 46% of participants (38/83) completed personal commitment to change forms at the end of the sessions.ConclusionsVirtual AGF sessions, developed and implemented with fidelity to the CAFF approach, successfully engaged physicians in a group learning environment that led to change planning. Further studies are needed to determine the generalizability of our findings and to add to the literature on evidence-based virtual facilitation techniques.

Epidemiological cut-off values for Vibrio parahaemolyticus calculated from minimal inhibitory concentration data generated at 35 and 28°C.

This work was performed to generate the data needed to set epidemiological cut-off values for minimal inhibitory concentrations (MICs) of 10 antimicrobial agents against Vibrio parahaemolyticus determined using standardised broth microdilution protocols. Eight laboratories performed broth microdilution tests with incubation at 35°C for 16 to 20 h, and 7 also performed tests on the same isolates with incubation at 28°C for 24 to 28 h. Data were analysed by the ECOFFinder and normalised resistance interpretation algorithms. The cut-off values calculated for ceftazidime, florfenicol and trimethoprim/sulfamethoxazole, 1, 1 and 0.25/4.75 µg ml-1, respectively, were the same when calculated from data obtained at both temperatures. The cut-off values calculated from data obtained at 35°C and from data obtained at 28°C were 0.25 and 0.5 µg ml-1 for enrofloxacin, 2 and 4 µg ml-1 for gentamicin, 0.5 and 1 µg ml-1 for oxolinic acid and 2 and 1 µg ml-1 for oxytetracycline, respectively. The influence of incubation temperature on MIC values was investigated by comparing MICs obtained at 35 and 28°C for a specific antimicrobial agent with a particular isolate by an individual laboratory. Results showed that 56% of 1473 of these paired MIC values were identical, while 38% differed from one another by not more than 1 dilution step. The data generated in this work will be submitted to the Clinical and Laboratory Standards Institute for consideration in their setting of internationally agreed epidemiological cut-off values for V. parahaemolyticus that are essential for interpreting antimicrobial susceptibility testing data of this species.

Harmonization of anti-nuclear antibody testing (ANA) by indirect immunofluorescence assay: Results from ten years of UK NEQAS external quality assessment.

External quality assurance (EQA) programs play a pivotal role in monitoring laboratory practices, allowing each laboratory to evaluate the consistency of results across different methods as well the ability of individual laboratories to compare and improve over time their own performance. The objective of our study was to analyze the UK NEQAS EQA reports for the "Antibodies to Nuclear and Related Antigens" program from 2013 to 2023, to assess the overall level of harmonization of the responses for anti-nuclear antibody (ANA) testing by indirect immunofluorescence (IIF), in terms of both pattern and titer consensus. As a second aim, we analyzed the impact of the introduction in UK NEQAS EQA reports of the International Consensus on ANA Patterns (ICAP) nomenclature and of digital image recognition on the harmonization of the ANA HEp-2 IIF test. The percentage of consensus for positive/negative results was significantly higher (90.9 ± 1.4) in 2023 than in 2013 (64.0 ± 7.8, p < 0.001). Common to all years in the investigated period, consensus on pattern recognition was significantly lower for the homogenous pattern (70.5 ± 16.0) compared to the centromere (84.9 ± 14.9), the speckled (90.3 ± 12.3), and the negative (84.5 ± 18.6, p < 0.001) samples, while it was significantly higher for titers 1:80-1:320 than for titers > 1:320 (p < 0.001). The difference between manual reading and digital reading was not significant (93.8 % vs. 92.4 %; p = 0.078), but it was significant between the pre- and post-use of the ICAP nomenclature (82.6 % vs. 93.8 %; p < 0.001). This study shows that the variability in ANA recognition and reporting is pattern (homogeneous > speckled > centromere) and titer (high titer > low titer) dependent. While we did not find any difference between the use of manual reading compared to digital reading, the adoption of the ICAP nomenclature greatly improved the harmonization of ANA reporting.

Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology

10X Visium, a popular Spatial transcriptomics (ST) method, faces limited adoption due to its high cost and restricted sample usage per slide. To address these issues, we propose Microarray Integrated Spatial Transcriptomics (MIST), combining conventional tissue microarray (TMA) with Visium, using laser-cutting and 3D printing to enhance slide throughput. Our design facilitates independent replication and customization in individual labs to suit specific experimental needs. We provide a step-by-step guide from designing TMAs to the library preparation step. We demonstrate MIST’s cost-effectiveness and technical benefits over Visium and GeoMx Nanostring. We also introduce ‘AnnotateMap’, a novel computational tool for efficient analysis of multiple ROIs processed through MIST.

An Open Access Resource for Marmoset Neuroscientific Apparatus.

The use of the common marmoset (Callithrix jacchus) for neuroscientific inquiry has grown precipitously over the past two decades. Despite windfalls of grant support from funding initiatives in North America, Europe, and Asia to model human brain diseases in the marmoset, marmoset-specific apparatus are of sparse availability from commercial vendors and thus are often developed and reside within individual laboratories. Through our collective research efforts, we have designed and vetted myriad designs for awake or anesthetized magnetic resonance imaging (MRI), positron emission tomography (PET), computed tomography (CT), as well as focused ultrasound (FUS), electrophysiology, optical imaging, surgery, and behavior in marmosets across the age-span. This resource makes these designs openly available, reducing the burden of de novo development across the marmoset field. The computer-aided-design (CAD) files are publicly available through the Marmoset Brain Connectome (MBC) resource (https://www.marmosetbrainconnectome.org/apparatus/) and include dozens of downloadable CAD assemblies, software and online calculators for marmoset neuroscience. In addition, we make available a variety of vetted touchscreen and task-based fMRI code and stimuli. Here, we highlight the online interface and the development and validation of a few yet unpublished resources: Software to automatically extract the head morphology of a marmoset from a CT and produce a 3D printable helmet for awake neuroimaging, and the design and validation of 8-channel and 14-channel receive arrays for imaging deep structures during anatomical and functional MRI.

A collaborative study to establish the second national standard for antithrombin concentrate in Korea

This study aimed to establish a second national standard for antithrombin (AT) concentrate that can be used for potency assays of AT products. A collaborative study was conducted involving four laboratories, including national control laboratories and manufacturers in Korea, and the suitability of a candidate material to serve as the second national standard for AT concentrate was evaluated. The candidate material was manufactured using a process approved for Good Manufacturing Practices. The potency of the candidate was determined using the heparin cofactor chromogenic method. The candidate was calibrated against the third International Standard for AT concentrate (code 06/166). Participants provided data from 58 independent assays. Combined potency estimates were calculated by determining the geometric means of the results obtained from all assays performed at individual laboratories. The overall potency assessments were subsequently established as the geometric means of all results collected from all laboratories. According to the collaborative study results, the intra- and inter-laboratory variability showed acceptable geometric coefficient of variation of 1.2 %–3.4 % and 2.4 % respectively, and it deemed to serve as the Korean national standard for AT concentrate with the assigned potency as follows: 32.1 IU/vial (95 % confidence interval; 31.7–32.5 IU/vial).

Evaluating the Effectiveness of External Molecular Proficiency Testing in the Global Polio Laboratory Network, 2021-2022.

In the Global Poliovirus Laboratory Network (GPLN), participation and successful completion in annual proficiency test (PT) panels has been a part of the WHO accreditation process for decades. The PT panel is a molecular external quality assessment (mEQA) that evaluates laboratory preparedness, technical proficiency, the accuracy of data interpretation, and result reporting. Using the Intratypic Differentiation (ITD) real-time RT-PCR kits from CDC, laboratories run screening assays and report results in accordance with the ITD algorithm to identify and type polioviruses. The mEQA panels consisted of 10 blinded, non-infectious lyophilized RNA transcripts, including programmatically relevant viruses and targets contained in the real-time PCR assays. Sample identities included wildtype, vaccine-derived (VDPV), Sabin-like polioviruses, enterovirus, and negatives, as well as categories of invalid and indeterminate. The performance of individual laboratories was assessed based on the laboratory's ability to correctly detect and characterize the serotype/genotype identities of each sample. The scoring scheme assessed the laboratory readiness following GPLN guidelines. Laboratories receiving mEQA scores of 90 or higher passed the assessment, scores of less than 90 failed and required remedial actions and re-evaluation. In 2021 and 2022, 123 and 129 GPLN laboratories were invited to request the annual PT panel, and 118 and 127 laboratories submitted results, respectively. The overall results were good, with 86% and 91.5% of laboratories passing the PT panel on their first attempt in 2021 and 2022, respectively. Most labs scored the highest score of 100, and less than one quarter scored between 90 and 95. Less than 10% of submitting laboratories failed the PT, resulting in in-depth troubleshooting to identify root causes and remediations. Most of these laboratories were issued a second PT panel for repeat testing, and almost all laboratories passed the repeat PT panel. The results of the 2021 and 2022 annual mEQA PTs showed that, despite the COVID-19 pandemic, the performance remained high in the GPLN, with most labs achieving the highest score. For these labs, the real-time PCR assay updates that were implemented during 2021-2022 were carried out with full adherence to procedures and algorithms. Even initially failing labs achieved passing scores after remediation.

Predicting Leptospirosis Using Baseline Laboratory Tests and Geospatial Mapping of Acute Febrile Illness Cases Through Machine Learning-Based Algorithm.

Introduction Leptospirosis is a zoonotic infection caused by Leptospira bacteria, which is reemerging in various regions and often poses a diagnostic challenge due to its nonspecific symptoms. While most infections are mild, severe cases occur in 5-10% of patients and are associated with high mortality, especially in areas with poor sanitation and urbanization. This study aims to investigate the association of specific parameters with leptospirosis diagnosis using a machine learning model and geographic mapping tools to identify spatial patterns and high-risk areas for the disease. Methods An observational retrospective study conducted at a tertiary care center analyzed patients clinically suspected of leptospirosis over the course of one year. The study utilized laboratory investigations, geographic mapping, and machine learning models to explore the association between various laboratory parameters and the predictive diagnosis of leptospirosis. Results The study, conducted over one year at All India Institute of Medical Sciences, Kalyani, India, included 325 patients, of whom 43 (13.2%) tested positive for leptospirosis by IgM ELISA. Geographic mapping revealed case clusters around nearby districts of West Bengal, with a few cases from Tripura and Bangladesh. The study found no significant association between individual laboratory parameters and leptospirosis diagnosis. However, machine learning models, particularly k-nearest neighbors (KNN), demonstrated moderate predictive accuracy (accuracy: 74%, area under the curve: 0.6). Conclusion Geographic mapping identified clusters of leptospirosis cases; however, no significant association was found between individual laboratory parameters and the disease diagnosis. Machine learning models, particularly KNN, demonstrated moderate predictive accuracy. The study also highlighted the overlapping clinical features of leptospirosis, dengue, and scrub typhus in West Bengal, although it noted the absence of detailed clinical data as a limitation.

Multiplexing projects: supervising undergraduate research projects with larger cohorts

Almost all undergraduate students in the UK complete a final year research project or dissertation. In the molecular biosciences field, these projects are often based in individual research laboratory. However, with increasing student numbers, falling staff/student ratios and decreased funding for consumables, these projects are becoming unstainable. At the University of Nottingham, we have developed a new model for cohort-based projects. These projects allow students to be taught key skills as a group, and then to apply their knowledge to individual projects. By streamlining communications, we are able to involve multiple members of staff and cover for staff absences. Feedback from these new-style projects has been extremely positive, and student engagement is high. Here, we share our experience of running multiplexed projects and discuss the adaptations we have made to enhance the student and staff experience.

Strategic genetic insights and integrated approaches for successful management of blackleg in canola/rapeseed farming

AbstractThis review describes a triumphant narrative in the battle against the devastating plant pathogen complex, Leptosphaeria maculans and L. biglobosa, and the success of the world's second‐largest oilseed crop, canola/oilseed rape. Emphasizing global collaborations, the article explores successfully mitigating this destructive disease in canola/rapeseed production across Australia, Canada and Europe. It highlights how strategies may vary between continents to adapt to specific contexts. While initial resistance (R) genes proved effective, the evolution of the pathogen under crop‐induced disease pressure led to the breakdown of these genes. Now, growers in these regions have been equipped with new tools, allowing them to make informed decisions that help to keep the disease at generally low levels. A pivotal factor in this success has been a deepened understanding of the intricate science underlying the host–pathogen interaction. Concerted efforts of individual laboratories and collaborative initiatives have played an essential role in this success, including novel methods for disease control based on extensive research that has translated into developing highly resistant varieties, enhanced pathogen monitoring, improved cultivar recommendation and integrated management strategies. The review showcases many milestone advancements, including the cloning of numerous avirulence genes within the pathogen, characterization of specific R genes, the development of various molecular tools for monitoring both pathogen and host, the introduction of groundbreaking disease management strategies such as R gene labelling, rotation and stacking, and establishment of a universal pathogen isolate collection that facilitates the exchange of information among multiple laboratories and adds a new dimension to this triumph.

The EuroFlow PIDOT external quality assurance scheme: enhancing laboratory performance evaluation in immunophenotyping of rare lymphoid immunodeficiencies.

The development of External Quality Assessment Schemes (EQAS) for clinical flow cytometry (FCM) is challenging in the context of rare (immunological) diseases. Here, we introduce a novel EQAS monitoring the primary immunodeficiency Orientation Tube (PIDOT), developed by EuroFlow, in both a 'wet' and 'dry' format. This EQAS provides feedback on the quality of individual laboratories (i.e.,accuracy, reproducibility and result interpretation), while eliminating the need for sample distribution. In the wet format, marker staining intensities (MedFIs) within landmark cell populations in PIDOT analysis performed on locally collected healthy control (HC) samples, were compared to EQAS targets. In the dry format, participants analyzed centrally distributed PIDOT flow cytometry data (n=10). We report the results of six EQAS rounds across 20 laboratories in 11 countries. The wet format (212 HC samples) demonstrated consistent technical performance among laboratories (median %rCV on MedFIs=34.5 %; average failure rate 17.3 %) and showed improvement upon repeated participation. The dry format demonstrated effective proficiency of participants in cell count enumeration (range %rCVs 3.1-7.1 % for the major lymphoid subsets), and in identifying lymphoid abnormalities (79.3 % alignment with reference). The PIDOT-EQAS allows laboratories, adhering to the standardized EuroFlow approach, to monitor interlaboratory variations without the need for sample distribution, and provides them educational support to recognize rare clinically relevant immunophenotypic patterns of primary immunodeficiencies (PID). This EQAS contributes to quality improvement of PID diagnostics and can serve as an example for future flow cytometry EQAS in the context of rare diseases.

National recommendations of the Croatian Chamber of Medical Biochemists and Working group for Laboratory hematology of the Croatian Society of Medical Biochemistry and Laboratory Medicine: Management of samples with suspected EDTA-induced pseudothrombocytopenia.

Pseudothrombocytopenia (PTCP) is defined by the occurence of spouriously low platelet count as a consequence of in vitro platelet aggregation. It is a rare and benign artifact, not associated with any specific disorder or therapy, that becomes clinically relevant when it is not timely and reliably recognized. Thus, it may result in inappropriate clinical decisions (i.e. unnecessary further testing, misdiagnoses and potential patients' mismanagement) unavoidably compromising patient safety. The most common form of PTCP is caused by ethylenediaminetetraacetic acid (EDTA). Several approaches for the management of samples with EDTA-induced PTCP have been described in the literature. However, expert recommendations are scarce. The scope of these recommendations is to assist in achieving national harmonisation in laboratory management (i.e. detecting and reporting platelet counts) of samples with EDTA-induced PTCP. These minimal recommendations were prepared by the members of the joint working group of the Croatian Chamber of Medical Biochemists and Working group for Laboratory Hematology of the Croatian Society of Medical Biochemistry and Laboratory Medicine, and might be customized according to specific conditions (i.e. personnel and equipment) of each individual laboratory. These recommendations are primarily intended to all laboratory professionals involved in the management of samples with EDTA-induced PTCP, but also to other healthcare professionals involved in collecting samples and interpreting complete blood count results.

B-355 Assessment of Calcitonin Cutoff Values for Post-Thyroidectomy Surveillance in Patients with Medullary Thyroid Carcinoma: Findings from a Single-Center Investigation

Abstract Background Patients with sporadic or hereditary Medullary Thyroid Carcinoma (MTC) often undergo total thyroidectomy and lymph node dissection, with postoperative surveillance relying on serum calcitonin levels and ultrasound examinations. According to American Thyroid Association (ATA) guidelines, detectable levels of serum calcitonin and Carcinoembryonic Antigen (CEA) post-thyroidectomy suggest potential disease persistence or recurrence, necessitating frequent monitoring for early detection. This study sought to reassess the role of postoperative calcitonin levels in identifying possible tumor recurrence. Methods A retrospective analysis was conducted using Siemens Atellica to test calcitonin levels in 562 samples collected between 09/27/2022 and 08/11/2023, at least 3 months post-total thyroidectomy. Imaging studies performed within 6 months of the calcitonin assessment were also reviewed. Sample pools with calcitonin concentrations near 3.00 and 5.00 pg/mL were utilized to determine the limit of quantification (LoQ). CEA results were included for comparison. Additionally, 16 serum samples were analyzed using the Roche Cobas system at a reference laboratory. Results Precision analysis around 3.00 and 5.00 pg/mL revealed coefficients of variation (CVs) of 16.49% and 8.87%, respectively. Comparison of calcitonin levels between Siemens Atellica and Roche Cobas systems demonstrated consistent levels &amp;lt; 5.00 pg/mL in 15 out of 16 samples, indicating alignment and reliability between the platforms. A calcitonin cutoff of 1.89 pg/mL yielded 43% sensitivity and 67% specificity, while a cutoff of 5.00 pg/mL resulted in 0% sensitivity and 100% specificity. Conclusions Our findings suggest that a 5 pg/mL calcitonin cutoff on the Siemens Atellica platform may be suitable for identifying tumor persistence or recurrence in post-thyroidectomy patients within our institution. However, individual laboratories should establish their LoQ criteria when interpreting calcitonin levels for postoperative monitoring of tumor recurrence.

A-156 Comparison of blast and variant lymphocyte flagging between the Alinity hq from Abbott and XN-1000 from Sysmex

Abstract Background Blast cells are immature white blood cells (WBC). The presence of blasts in the peripheral blood may be associated with certain diseases such as myelodysplastic syndrome and acute myelogenous leukemia. Variant lymphocytes (i.e., reactive lymphocytes, atypical lymphocytes) are WBCs produced by the immune system in reaction to infections caused by pathogens such as Epstein-Barr virus, cytomegalovirus, etc. It is clinically useful that the automated hematology analyzer is capable of flagging these cells. In this study, the blast (shown as ‘BLAST’ on the Alinity hq and ‘Blast/Abn Lympho?’ or ‘Blast?’ on XN-1000) and variant lymphocyte (shown as ‘VAR LYM’ on the Alinity hq, and ‘Atypical Lympho?’ on XN-1000) flagging was compared between the Alinity hq from Abbott and XN-1000 from Sysmex. Alinity hq has different sensitivity settings available for BLAST and VAR LYM flagging. In this study, the default setting for Alinity hq was used. For XN-1000, the Q-Flag default setting is 100. In this study, the setting was 120 for ‘Blast/Abn Lympho’ and 100 for “Atypical lympho?’. Methods Blood specimens were tested on the Alinity hq and XN-1000 analyzers. Two smears per specimen were made manually or by the Alinity hs slide maker stainer and read by two independent readers. The specimens showing any of the following flagging were included in the analysis: ‘BLAST’ on Alinity hq, ‘VAR LYM’ on Alinity hq, ‘Blast/Abn Lympho?’ or ‘Blast?’ on XN-1000, ‘Atypical lympho?’ on XN-1000. The flagging reports of these samples from both analyzers were compared to the smear review to determine if each analyzer's blast and variant lymphocyte flagging were true positive, false positive, true negative, or false negative. Results A total of 520 specimens were tested, yielding 41 specimens for blast flagging analysis and 80 specimens for variant lymphocyte flagging analysis. Due to the scarce availability of true positive samples from the manual review, true positive and false negative rate were not compared. For blast flagging using smear results of &amp;gt;=1% or &amp;gt;=5% as the positive criterion, Alinity hq yielded a 9.8% (=4/41) false positive rate and 87.8% (=36/41) true negative rate. XN-1000 yielded a 75.6% (=31/41) false positive rate and 22.0% (=9/41) true negative rate. For variant lymphocyte flagging using smear results of &amp;gt;=5% as the positive criterion, Alinity hq yielded a 6.3% (=5/80) false positive rate and 92.5% (=74/80) true negative rate. XN-1000 yielded a 91.3% (=73/80) false positive rate and 7.5% (=6/80) true negative rate. Conclusions This study demonstrated that Alinity hq achieved a much lower false positive rate and much higher true negative rate for both blast and variant lymphocyte flagging when compared to the XN-1000. Manual blast and variant lymphocyte morphology classification is laboratory- and technician-dependent. Both analyzers allow different sensitivity/specificity levels to flag blasts and variant lymphocytes. Each individual laboratory should evaluate and choose the setting that is most suitable for their specific patient populations to obtain the desired flagging rate.

Comparison of etonogestrel bioanalytical assay results in plasma and serum within and across laboratories

ObjectivesTo compare performance characteristics of etonogestrel bioanalytical assays across laboratories. Study designWe conducted a blinded, six laboratory study: five academic laboratories and one contracted commercial laboratory (reference). Etonogestrel was quantitated at each laboratory in both prepared serum and/or plasma samples of six known etonogestrel concentrations, and in 60 clinical samples from participants using etonogestrel-containing contraceptive methods. Per regulatory guidance, laboratory accuracy (percent bias) and precision (coefficient of variation; CV) were defined as ±15% of the nominal prepared concentration. We compared inter- and intra-laboratory agreement using a Kendall’s Tau-B and Passing-Bablok regression. ResultsFor prepared samples, six laboratories analyzed serum and three laboratories analyzed plasma. All etonogestrel results were within ±15% for accuracy across all concentrations at four labs, including the reference laboratory. All labs demonstrated high precision, with only one occurrence of CV >15%. We found a positive association between prepared plasma and serum etonogestrel results (Kendall’s Tau-B 0.80–0.88). For clinical samples, five laboratories analyzed serum and three laboratories analyzed plasma. Compared to the reference laboratory, inter-laboratory serum etonogestrel concentrations were positively correlated (Kendall’s Tau-B 0.76–0.95). Proportional bias was observed, meaning individual lab etonogestrel results were consistently higher (slope estimates 0.78–0.95) or lower (slope estimates 1.05–1.10) than the reference laboratory. In clinical samples, intra-laboratory results were well associated between plasma and serum (Kendall’s Tau-B 0.92–0.96). ConclusionsThere was good intra-laboratory agreement, irrespective of sample matrix; however, there was inter-laboratory variability in etonogestrel results. Differences between laboratory results should be considered when comparing etonogestrel pharmacokinetics across studies. ImplicationsEtonogestrel concentrations were highly precise within each laboratory and were comparable between serum and plasma. Results varied between laboratories (5–28% higher to 5–9% lower compared to the Organon commercial laboratory). To minimize variability, we recommend utilizing a single laboratory that conducts routine proficiency testing for etonogestrel analysis within a study.

Diagnosis Based on Population Data versus Personalized Data: The Evolving Paradigm in Laboratory Medicine.

The diagnosis of diseases is a complex process involving the integration of multiple parameters obtained from various sources, including laboratory findings. The interpretation of laboratory data is inherently comparative, necessitating reliable references for accurate assessment. Different types of references, such as reference intervals, decision limits, action limits, and reference change values, are essential tools in the interpretation of laboratory data. Although these references are used to interpret individual laboratory data, they are typically derived from population data, which raises concerns about their reliability and consequently the accuracy of interpretation of individuals' laboratory data. The accuracy of diagnosis is critical to all subsequent steps in medical practice, making the estimate of reliable references a priority. For more precise interpretation, references should ideally be derived from an individual's own data rather than from population averages. This manuscript summarizes the current sources of references used in laboratory data interpretation, examines the references themselves, and discusses the transition from population-based laboratory medicine to personalized laboratory medicine.

O-GlcNAc informatics: advances and trends.

As a post-translational modification, protein glycosylation is critical in health and disease. O-Linked β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), as an intracellular monosaccharide modification on proteins, was discovered 40 years ago. Thanks to technological advances, the physiological and pathological significance of O-GlcNAcylation has been gradually revealed and widely appreciated, especially in recent years.O-GlcNAc informatics has been quickly evolving. Clearly, O-GlcNAc informatics tools have not only facilitatedO-GlcNAc functional studies, but also provided us a unique perspective on proteinO-GlcNAcylation. In this article, we review O-GlcNAc-focused software tools and servers that have been developed forO-GlcNAc research over the past four decades. Specifically, we will (1) survey bioinformatics tools that have facilitated O-GlcNAc proteomics data analysis, (2) introduce databases/servers forO-GlcNAc proteins/sites that have been experimentally identified by individual research labs, (3) describe software tools that have been developed to predictO-GlcNAc sites, and (4) introduce platforms cataloging proteins that interact with the O-GlcNAc cycling enzymes (i.e., O-GlcNAc transferaseand O-GlcNAcase). We hope these resources will provide useful information to both experienced researchers and new incomers to the O-GlcNAc field. We anticipate that this review provides a framework to stimulate the future development of more sophisticated informatic tools for O-GlcNAc research.