Clinical Laboratory Improvement Research Articles

Implementation and Performance of a Point-of-Care COVID-19 Test Program in 4,000 California Schools

To evaluate the feasibility and accuracy of an unprecedented COVID-19 antigen testing program in schools, which required a healthcare provider order, laboratory director, a Clinical Laboratory Improvement Amendments certificate of waiver, as well as training of school personnel. Descriptive report of a point-of-care, school-based antigen testing program in California from August 1st, 2021 through May 30, 2022, in which participants grades K-12 self-swabbed and school personnel performed testing. Participants included 944 009 students, personnel, and community members from 4022 California kindergarten through high schools. Outcomes measured include sensitivity and specificity (with polymerase chain reaction [PCR] as comparator) of the Abbott BinaxNOW antigen test, number of tests performed, and active infections identified. Of 102 022 paired PCR/antigen tests, the overall sensitivity and specificity for the antigen test was 81.2% (95% CI: 80.5%-81.8%) and 99.6% (95% CI: 99.5%-99.6%), respectively, using cycle threshold values<30. During January through March 2022, the highest prevalence period, the positive predictive value of antigen testing was 94.7% and the negative predictive value was 94.2%. Overall, 4022 school sites were enrolled and 3 987 840 million antigen tests were performed on 944 009 individuals. A total of 162 927 positive antigen tests were reported in 135 163 individuals (14.3% of persons tested). Rapidly implementing a school-based testing program in thousands of schools is feasible. Self-swabbing and testing by school personnel can yield accurate results. On-site COVID-19 testing is no longer necessary in schools, but this model provides a framework for future infectious disease threats.

Scalable solutions for global health: the SalivaDirect model

The COVID-19 pandemic caught the world unprepared. Large-scale testing efforts were urgently needed, and diagnostic strategies had to rapidly evolve in response to unprecedented worldwide demand. However, the rollout of diagnostic testing and screening for SARS-CoV-2 was often impeded by logistical challenges, including regulatory delays, workforce shortages, laboratory bottlenecks, and supply chain disruptions. Recognizing these hurdles early on, we developed a testing approach that supported frequent, repeat testing, particularly as communities reopened. We hypothesized and experimentally demonstrated that saliva was a suitable specimen for the detection of SARS-CoV-2. This finding was advanced into the development of open-source, extraction-free reverse transcription polymerase chain reaction protocols using readily available, “off-the-shelf” reagents and equipment for the direct detection of SARS-CoV-2 in saliva (“SalivaDirect’’). Working with the US Food and Drug Administration (FDA), we established a novel regulatory framework wherein the FDA granted Emergency Use Authorization to Yale University to offer the SalivaDirect test protocol to high-complexity diagnostic laboratories (as designated by the Clinical Laboratory Improvement Amendments) with quality oversight provided by Yale. This grew into a network of more than 200 labs across the United States that, as of May 2024, resulted in over 6.5 million SARS-CoV-2 tests. By making the protocol flexible and open-source, laboratories were able to rapidly and economically scale testing using a simple, self-collected saliva specimen. Additionally, fostering a national network of laboratories enabled real-time exchanges, problem solving, and the development of community best practices. Preparing for the next pandemic, or simply the next seasonal epidemic, the SalivaDirect model of deploying a readily available, expandable solution and accompanying network provides a proven method for the successful implementation of pathogen testing in the United States and globally.

Rapid detection of SARS-CoV-2 variants by molecular-clamping technology-based RT-qPCR.

We have developed a multiplex reverse-transcription quantitative real-time PCR (RT-qPCR) testing platform for the rapid detection of SARS-CoV-2 variants using the xenonucleic acid (XNA)-based molecular-clamping technology. The XNA-based RT-qPCR assay can achieve high sensitivity with a limit of detection of about 100 copies/mL for variant detection which is much better than the next-generation sequencing (NGS) assay. Its turnaround time is about 4 hours with lower cost and a lot of Clinical Laboratory Improvement Amendments (CLIA) labs own the instrument and meet skillset requirements. This assay provides a rapid, reliable, and cost-effective testing platform for rapid detection and monitoring of known and emerging SARS-CoV-2 variants. This testing platform can be adopted by laboratories that perform routine SARS-CoV-2 PCR testing, providing a rapid and cost-effective method in lieu of NGS-based assays, for detecting, differentiating, and monitoring SARS-CoV-2 variants. This assay is easily scalable to any new variant(s) should it emerge.

Xpert Breast Cancer STRAT4 Assay using fine-needle aspiration biopsy samples in a resource-constrained setting: a prospective diagnostic accuracy study

Use of fine-needle aspiration biopsy (FNAB) specimens on Xpert Breast Cancer STRAT4 Assay (STRAT4; Cepheid, Sunnyvale, CA, USA), a CE-marked in-vitro diagnostic medical device, could potentially increase access to breast cancer biomarker testing in resource-constrained settings. We aimed to assess the performance of a research use-only version of STRAT4 using FNAB specimens in Tanzania. In this prospective diagnostic accuracy study, patients aged 18 years or older with palpable breast masses presenting to the FNAB Clinic at Muhimbili National Hospital (Dar es Salaam, Tanzania) were recruited consecutively. Patients who were pregnant, lactating, or had a previous diagnosis of breast cancer were excluded. STRAT4 testing was performed on off-label FNAB samples using four protocols: the 1 × protocol (using the standard lysate method) on FNAB smears (1 × FNAB), quick lysis and Maui protocols (both on FNAB smears), and the 1 × protocol on formalin-fixed paraffin-embedded (FFPE) cell block material (1 × cell block). For 1 × FNAB and 1 × cell block, tissue was processed using FFPE lysis reagent, incubated at 80°C with proteinase K, and followed by addition of 95% or higher ethanol. Quick lysis was processed using FFPE lysis reagent and 95% or higher ethanol, whereas Maui was processed using a proprietary research-use only lysis reagent. The primary outcomes were overall concordance, sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) of STRAT4 as compared with immunohistochemistry or immunohistochemistry plus fluorescence in-situ hybridisation performed on cell blocks using clinically validated protocols in a Clinical Laboratory Improvement Amendments-accredited laboratory at the University of California, San Francisco (San Francisco, CA, USA). Between Nov 29, 2017, and Dec 17, 2020, 208 patients were enrolled. Of 208 cases, 51 (25%) were excluded from analysis because of insufficient tissue in the cell block or absent cell blocks, leaving 157 participants (all female) for analysis. For oestrogen receptor, 1 × FNAB had the best performance, with an overall concordance of 95% (95% CI 90-100), sensitivity of 94% (85-100), specificity of 97% (90-100), and AUC of 0·96 (0·81-1·00). For progesterone receptor, 1 × cell block had the best overall performance (overall concordance 89% [95% CI 84-95], sensitivity 91% [82-99], and specificity 89% [81-97], with an AUC of 0·93 [0·89-0·99]) and 1 × FNAB performed the best among the smear protocols, with a concordance of 84% (95% CI 74-93), sensitivity of 63% (43-82), specificity of 97% (92-100), and AUC of 0·91 (0·72-0·97). For HER2, Maui had the highest agreement, with an overall concordance of 93% (95% CI 89-98), sensitivity of 96% (88-100), specificity of 92% (87-98), and AUC of 0·95 (0·98-1·00). For Ki67, Maui had the best performance of smear protocols, with a concordance of 73% (95% CI 64-82), sensitivity of 70% (58-81), specificity of 81% (66-96), and AUC of 0·80 (0·54-0·82). Processing FNAB samples with STRAT4 is feasible in Tanzania, and performance for the oestrogen receptor is robust. Further optimisation of STRAT4 for FNAB has the potential to improve timely access to breast cancer diagnostics in resource-constrained settings. US National Institutes of Health; UCSF Global Cancer Program, Helen Diller Family Comprehensive Cancer Center; UCSF Department of Pathology; and Cepheid.

B-113 Beckman Coulter DxI 9000 immunoassay analyzer assay performance meets new CLIA 2024 performance goals with highest proportion of Six Sigma performance amongst all major manufacturers

Abstract Background The Clinical Laboratory Improvement Act (CLIA) proficiency testing (PT) criteria will be updated in July 2024 with some goals tightening by up to 40%. It is assumed, but not known, that all assays and instruments will be able to achieve these goals. Using these new CLIA 2024 goals, estimates of current instrument group performance from an international proficiency testing (PT) survey have shown significant differences in quality, calling into question which assays can achieve the new CLIA goals. Currently, the highest performing diagnostic instrument achieves only 35.2% 6-Sigma, while the majority of instruments have less than 15% 6-Sigma performance indicating a higher probability of future PT failures. Methods Eighteen assays that will be governed by new CLIA 2024 goals were assessed for Sigma metric performance on the DxI 9000 immunoassay analyzer: Alpha Fetoprotein (AFP), Beta hCG, Carcinoembryonic antigen (CEA), Cortisol, Creatine Kinase MB (CK-MB), Estradiol, Ferritin, Folate, Follicle-Stimulating Hormone (FSH), Prolactin, Para-thyroid hormone (PTH), Total Prostate specific antigen (Total PSA), Testosterone, Thyroid Stimulating Hormone (TSH), Total Triiodothyronine (TT3),high sensitivity Troponin I, Total Thyroxine (TT4) and Vitamin B12. Precision and bias were determined following CLSI EP5 and EP9 guidelines, measured across 3 reagent lots. CLIA 2024 PT criteria provides the allowable total error for the standard Sigma-metric calculation: Sigma-metric = (TEa - |bias|) / SD Performance of the other major analyzers was assessed using the methodology introduced in 2006 by Westgard JO and Westgard SA. The Sigma-metric predicts future problems with PT and potential optimization of QC procedure opportunities, including fewer Westgard Rules, control levels, even reduced QC frequency and materials leading to less cost and time saved. Results Half (50%) of the assays on DxI 9000 achieves 6-Sigma, outperforming all other major manufacturers in the market who range from only 5% to 35% 6-Sigma. Further, over 78% of the DxI 9000 performance was 4Sigma and higher. Less than 8% of performance fell below 3-Sigma, which was observed at the extreme ends of the reportable range. Conclusions The DxI 9000 assay performance is well designed to meet CLIA 2024’s new PT criteria and has the highest prevalence of 6-sigma assay performance observed on market when compared to the top 5 major instrument manufacturers. Assays with Sigma metrics at 4-Sigma and higher are unlikely to face analytical PT difficulties and can be optimized for reduced Westgard Rules, control levels, and potentially even QC frequency.

A-196 Using Aggregated Proficiency Testing Results to Identify Systematic Error

Abstract Background Proficiency testing (PT) should identify systematic errors, which are likely to recur. The Clinical Laboratory Improvement Amendments of 1988 (CLIA) acceptance limits (ALs) include 3SD and concentration limits. We investigated the ability of PT to detect systematic error, especially as affected by the AL type. Methods Ungradable, duplicate, and irregular scores were removed from 2008 to 2018 CLIA laboratory PT results. For analytes that had at least 200 events and at least 200 participating laboratories, we calculated the overall sample miss rate, the unsatisfactory event rate, i.e., less than 80, and event rates for Score 100 to 0. We used paired t-tests and the Wilcoxon Signed-Rank test to compare miss rates and unsatisfactory event rates between short- and long-term participants. We used the binomial distribution to model the expected event scores under the assumption that all errors may be independent (random); see Figure. For each analyte and each of the possible PT scores, we compared observed event scores with their expected values as a ratio. Results 40,596 laboratories produced 15,140,128 event scores for 75 analytes. The distribution of event scores was over-weighted with higher-order event errors (Score 0 - Score 60) compared to the predicted distribution. Miss rates and unsatisfactory rates were significantly higher for short-term laboratories. Plotting the log ratio of observed versus expected rates for event scores showed that the degree of systematic effect increased progressively for each analyte. The magnitude of the effect was less for 3SD ALs. Conclusions In an event, PT errors are often dependent. Concentration and 3SD ALs were similarly sensitive to detect systematic error; both were more sensitive than ALs for qualitative or dilution assays. Expressing systematic error using PT data could help to identify remediable analytical issues.

A-003 Beckman Coulter DxI 9000 Immunoassay Analyzer’s High Sensitivity Troponin I achieves &amp;gt;90% six sigma performance when assessed against clia 2024 performance goals

Abstract Background In July 2024, the Clinical Laboratory Improvement Act (CLIA) proficiency testing (PT) criteria will directly regulate Troponin I performance for the very first time. The new CLIA goal is 0.9 ng/mL or 30%, whichever is greater. CAP previously set a goal of 30% or 3 times the group standard deviation (SD), whichever is greater, a more permissive setting. Estimates of current instrument group performance from an international proficiency testing (PT) survey have shown none of the 5 major diagnostic instruments can achieve the biological minimum goal at a 6-Sigma level, while 4 of the 5 instruments perform at 3 Sigma or below. Performance of these platforms was assessed using the methodology introduced in 2006 by Westgard JO and Westgard SA. The DxI 9000 high sensitivity Troponin I assay was assessed to determine if it could achieve the new CLIA 2024 goals. Methods The DxI 9000 high sensitivity Troponin I assay was assessed with three reagent lots, on both serum and Lithium Heparin (LiHep) samples, following Clinical Laboratory Standards Institute (CLSI) protocols EP05 and EP09 to estimate imprecision and bias. The new CLIA 2024 PT criteria supplied the allowable total error for the standard Sigma-metric calculation: Sigma-metric = (TEa - |bias|) / SD The Sigma-metric predicts not only future problems with PT, but also potential optimization of QC procedures, including fewer Westgard Rules, control levels, even reduced QC frequency which can lead to less cost, time, and materials. Results The majority (91.7%) of data points across the analytical measuring range for DxI 9000’s high sensitivity Troponin I assay from both serum and LiHep samples achieved 6-Sigma performance. For serum, only 8.3% of samples achieved 5-sigma performance. For LiHep, only 4.2% of the performance was 4 Sigma. None of the performance was 3 Sigma or lower. Conclusions The superior precision observed on DxI 9000 high sensitivity Troponin I delivers overwhelming 6-sigma performance when assessed by CLIA’s 2024 goal. This assay is highly unlikely to face PT difficulties and can be optimized for reduced Westgard Rules, reduced control levels leading to a reduction in time, materials, and cost.

B-109 Six Sigma Analysis for Enhancing Biochemistry Internal Quality Control in a Private Laboratory in India

Abstract Background This abstract outlines a comprehensive study on the application of Six Sigma methodologies to optimize internal quality control processes in a private biochemistry laboratory in India. Data collection was performed using Bio-Rad Assayed Chemistry Control on the Roche cobas 6000 instrument, facilitated by Bio-Rad Unity software. The study adheres to Clinical Laboratory Improvement Amendments (CLIA) 2024 guidelines, specifically focusing on Total Error (TEa). Methods The analytical performances of Cobas c501 insturment as analyse by running biochemical tests (urea, creatinine, uric acid, total bilirubin, AST, Amylase, Lipase, CK, LD, ALT, ALP, LDH, HDL-C, Ca2+, cholesterol, TG, HDL LDL, total protein, albumin, Na+, K+, and Cl−) and glucose on Cobas 400 were evaluated. Biases and CV were obtained from internal quality control programs using biorad unity software. The performance of each instrument was assessed using the σ scale; the benchmark performance was &amp;lt;3 σ (improvement needed); “world-class” quality was six sigma. Results Analytes such as “Alk PO4,” “ALT,” “Amylase,” “Bilirubin,” “CK,” “GGT,” “LD,” “Phosphorus,” “HDL,” “LDL Cholesterol,” “Triglycerides,” and “Uric acid” exhibited impressive sigma scores exceeding 6. Meanwhile, analytes including “Calcium,” “Total Cholesterol,” “Potassium,” “Total Protein,” “Urea,” and “Glucose” achieved sigma scores between 4 and 6, demonstrating noteworthy performance within acceptable bounds. Conclusions This study contributes valuable insights to laboratory management, specifically in the context of biochemistry testing in private Indian laboratories. The adoption of Six Sigma principles, coupled with adherence to CLIA 2024 guidelines and the utilization of advanced instrumentation and software, ensures compliance with regulatory requirements and fosters a culture of continuous improvement. This positions the laboratory to deliver high-quality and reliable results in the dynamic landscape of healthcare diagnostics.

A-118 Sigma Metric Performance of Chemistry Assays on 4 Instrument Systems

Abstract Background Chemistry panels play a crucial role in determining a person’s general health and well-being. These tests evaluate electrolyte balance and the status of several major organs. The Comprehensive Metabolic Panel (CMP) and Lipid Panel constitute approximately 87% of the blood tests prescribed in medical laboratories. Laboratories monitor assay performance by performing proficiency testing using quality controls (QC). College of American Pathologists (CAP) data is useful for laboratories to compare their proficiency testing performance to other laboratories and instrument systems. Sigma metrics serve as a valuable tool for laboratories to assess the quality and accuracy of their tests. Sigma scores vary from 0 to 6, with the 6 score designated as world-class performance, 5 as excellent, 4 as good, 3 as marginal, and 2 as poor. The analytical performance of 16 clinical assays from Abbott, Beckman, Roche, and Siemens instrument systems were compared using Sigma metrics. Methods Sigma metrics of 16 chemistry analytes were compared across 4 instruments system using CAP data from three reports (C-A 2023, C-C 2023 and C-B 2022). The 4 systems evaluated were Abbott Alinity ci, Beckman AU, Roche COBAS c500/c303 and Siemens Atellica CH. Method imprecision was estimated for each assay using the cumulative coefficient of variation or standard deviation for each assay at a single QC concentration and calculating the average sigma. Since sigma levels can be concentration-dependent, an equivalent CAP sample concentration was chosen for each instrument system evaluation. Method bias was estimated by evaluating each method QC mean to the peer group mean. Sigma values were calculated for each method as Sigma = (TEa - |Bias|) / Precision using the allowable total error from 2014 Clinical Laboratory Improvement Amendments (CLIA) proposed acceptance limits. Average Sigma values were generated for each analyte and graded as an optimal Sigma score. Results The sigma scores varied across assays and instrument systems. Abbott demonstrated the best overall performance. Specifically, the Abbott Alinity system had the highest number (7/16, 44%) of assays at 5 sigma or higher, with Siemens showing the lowest number of assays at 5 Sigma or higher (1/16, 6%). Of the 16 assays evaluated, Abbott has the fewest assays at or below the 3 sigma threshold (5/16) when compared to Roche (7/16), Beckman (7/16), and Siemens (9/16). Sigma scores were comparable between the Abbott ARCHITCT and Alinity clinical chemistry systems. Conclusions Sigma metrics are useful in assessing the performance of clinical assays. Assays with high Sigma have better performance due to lower imprecision and higher accuracy. None of the instrument systems demonstrated optimal six sigma performance for all analytes. However, Abbott demonstrated the best overall performance.

Evaluating the Radiation Sensitivity Index and 12-chemokine gene expression signature for clinical use in a CLIA laboratory.

The radiation sensitivity index (RSI) and 12-chemokine gene expression signature (12CK GES) are two gene expression signatures (GES) that were previously developed to predict tumor radiation sensitivity or identify the presence of tertiary lymphoid structures in tumors, respectively. To advance the use of these GES into clinical trial evaluation, their assays must be assessed within the context of the Clinical Laboratory Improvement Amendments (CLIA) process. Using HG-U133Plus 2.0 arrays, we first established CLIA laboratory proficiency. Then the accuracy (limit of detection and macrodissection impact), precision (variability by time and operator), sample type (surgery vs. biopsy), and concordance with reference laboratory were evaluated. RSI and 12CK GES were reproducible (RSI: 0.01 mean difference, 12CK GES 0.17 mean difference) and precise with respect to time and operator. Taken together, the reproducibility analysis of the scores indicated a median RSI difference of 0.06 (6.47% of range) across samples and a median 12CK GES difference of 0.92 (12.29% of range). Experiments indicated that the lower limit of input RNA is 5 ng. Reproducibility with a second CLIA laboratory demonstrated reliability with the median RSI score difference of 0.065 (6% of full range) and 12CK GES difference of 0.93 (12 % of observed range). Overall, under CLIA, RSI and 12CK GES were demonstrated by the Moffitt Cancer Center Advanced Diagnostic Laboratory to be reproducible GES for clinical usage.

A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples.

Vaginitis is a widespread issue for women worldwide, yet current diagnostic tools are lacking. Bacterial vaginosis (BV) is the most prevalent type of vaginitis, found in 10-50% of reproductive-aged women. Current diagnostic methods for BV rely on clinical criteria, microscopy, or the detection of a few microbes by qPCR. However, many vaginal infections lack a single etiological agent and are characterized by changes in the vaginal microbiome community structure (e.g., BV is defined as a loss of protective lactobacilli resulting in an overgrowth of anaerobic bacteria). Shotgun metagenomic sequencing provides a comprehensive view of all the organisms present in the vaginal microbiome (VMB), allowing for a better understanding of all potential etiologies. Here, we describe a robust VMB metagenomics sequencing test with a sensitivity of 93.1%, a specificity of 90%, a negative predictive value of 93.4%, and a positive predictive value of 89.6% certified by Clinical Laboratory Improvement Amendments (CLIA), the College of American Pathologist (CAP), and the Clinical Laboratory Evaluation Program (CLEP). We sequenced over 7000 human vaginal samples with this pipeline and described general findings and comparisons to US census data.

Analytical Validation of Esopredict, an Epigenetic Prognostic Assay for Patients with Barrett's Esophagus.

EsopredictTM is a prognostic assay that risk-stratifies Barrett's esophagus patients to predict future progression to high-grade dysplasia (HGD) or esophageal adenocarcinoma (EAC). Established based on foundational studies at Johns Hopkins University, a risk algorithm was developed and clinically validated in two independent studies (n = 320). EsopredictTM is currently offered as a clinical test under the Clinical Laboratory Improvement Amendments (CLIA) guidelines. Here we present the analytical validation by repeated testing of FFPE tissues (n = 26 patients), cell lines, and contrived DNA controls to determine assay performance regarding analytical sensitivity (as defined by the limit of detection (LOD)), analytical specificity (as defined by the limit of blank (LOB)), accuracy as determined from the average positive and negative agreement, repeatability, and reproducibility. The LOD for the assay at 1.5% DNA methylation was significantly higher than the LOB, as determined by an unmethylated DNA control (0% methylated DNA). Inter- and intra-assay average positive agreement (APA) were 88% and 94%, respectively, while average negative agreement (ANA) values were 90% and 94%, respectively. Average inter- and intra-assay precision were <9% and <5% coefficient of variation (CV), respectively. These results confirm that EsopredictTM is a highly reproducible, sensitive, and specific risk categorization assay for the prediction of progression to HGD or EAC within 5 years.

BD Vacutainer™ Urine Culture & Sensitivity Preservative PLUS Plastic Tubes Minimize the Harmful Impact of Stressors Dependent on Temperature and Time Storage in Uropathogenic Bacteria.

Background: Urinary tract infection is a worldwide health problem. According to the Clinical Laboratory Improvement Amendments and the European Urinalysis Guideline, urine samples should be tested within 2 h of collection. Thus, using chemical preservatives that guarantee the pre-analytical conditions is a practical tool. However, the effects of temperature and storage time as uropathogenic bacteria stressors are unclear. Methods: Gram-negative and -positive ATTC strains, E. coli, P. mirabilis, E. faecalis, and S. aureus, were used in this study. Strains in liquid media were stored at 4, 25, and 37 °C for 0, 2, 12, 24, and 48 h in tubes with and without preservatives. Then, reactive oxygen species (ROS) levels, viable but non-culturable bacteria (VBNC), and bacteria growth were analyzed. Results: A high ROS level was associated with the presence of VBNC and dead bacteria with low CFU counts, but a low ROS level increased the CFU number, depending on temperature and storage time in tubes without preservatives (boric acid, sodium borate, and formate). The BD Vacutainer™ Urine Culture & Sensitivity Preservative PLUS Plastic Tubes (C&S-PP) prevent this ROS increase, maintaining the CFU number for longer. Conclusions: C&S-PP tubes minimize the stressor effects (temperature and time storage) on uropathogenic bacteria when stored, improving the pre-analytical conditions of cultures realized by the clinical laboratory.

Strengthening the Application of the DAIDS GCLP Guidelines: The Implementation of an Integrated Laboratory Oversight Framework.

The Division of AIDS (DAIDS) Good Clinical Laboratory Practice (GCLP) Guidelines establish a framework to guide the oversight of laboratories supporting DAIDS-sponsored clinical research or trials. Compliance with these guidelines promotes data reliability, validity, and safety of the clinical research or trial participants and laboratory staff and ensures adherence to regulatory requirements. Acknowledgment and adoption of the DAIDS GCLP Guidelines are critical in building laboratory capacity and preparedness for conducting clinical trials. In collaboration with DAIDS, laboratory experts support the implementation of the DAIDS Integrated Laboratory Oversight Framework (Framework) activities. This article describes the implementation of the GCLP Guidelines, the Framework activities, and the coordinated efforts to strengthen laboratory performance. The Framework activities include four components: Quality Assurance Oversight, GCLP Audits, GCLP Training, and Laboratory Quality Improvement. Comparison of GCLP Guidelines with other regulations or standards, including U.S. Clinical Laboratory Improvement Amendments regulation 42 CFR 493, College of American Pathologists, World Health Organization GCLP, and International Organization for Standardization, ISO 15189:2012 standards, highlighted the differences and similarities to guide integration and harmonization efforts. Processes related to the Framework activities are outlined in detail, including key data derived from the managed activities of over 175 laboratories worldwide. Via the evolution of the DAIDS GCLP Guidelines and laboratory oversight workflows, the laboratories participating in DAIDS-sponsored clinical research and trials have successfully participated in internal and external regulatory audits. The collaborative and integrated oversight approach promotes knowledge-sharing and accountability to support the implementation of the DAIDS GCLP Guidelines and compliance monitoring. Lessons learned have helped with the implementation of the DAIDS integrated laboratory oversight approach and quality oversight programs at multiple laboratories worldwide.

Beyond the basics: Sigma scores in laboratory medicine with variable total allowable errors (TEa)

BackgroundTo diagnose diseases, track the effectiveness of treatments and make well-informed clinical decisions, doctors rely on results from laboratories. Accurate and precise results minimize the necessity for additional testing, saving time and money while enhancing patient satisfaction.. Internal quality control and an external quality assurance scheme(EQAS) are metrics used to evaluate a clinical laboratory’s performance. One of the numerous quality indicators that can be used to gauge the amount of errors is sigma metrics. To calculate the sigma scores bias%, CV%, and Total Error Allowable (TEa) are needed. Total Error allowable(TEa) is a crucial benchmark that establishes allowed limits on the degree of deviation from the target value for a certain analyte. Nevertheless, a proper consensus for establishing a TEa goal has not been reached and the impact of this limiting factor in standard laboratory practice and sigma calculation has not been sufficiently established. Choosing the right Total Error allowable(TEa) goal is one of the greatest challenges when employing sigma metrics as depending on the source, several measurands of TEa values may exhibit alteration. Material and methodsOur study aims to determine the sigma scores of 20 routine chemistry parameters using six different TEa sources: Clinical Laboratory Improvement Amendment (CLIA 88′), CLIA(Clinical Laboratory Improvement Amendment) 24, BDV (Biological Variation Desirable), RCPA(Royal College of Pathologists of Australasia), RiliBak(Guideline of the German Medical Association for Quality Assurance of Laboratory Medical Examinations), and EMC/Spain(Measurement and Control Scheme) over a 12-month period using the bias percent from the External Quality Assessment Scheme (EQAS) and coefficient of variation (CV) from the Internal Quality Control (IQC). Detection system was automated, multi-channel, selective analyzer, the Beckman Coulter AU680 which works on the principle of spectrophotometry. To compute the Sigma metrics, formula used was Sigma = (TEa – Bias%) / CV%. By comparing the sigma values from the different TEa sources, TEa variance on the evaluation of the sigma metric was ascertained after which an internal quality control plan and QGI(Quality Goal Index) for underperforming parameters were devised. ResultsThe study discovered that the sigma values of common chemical parameters varied significantly based on the TEa sources used. Maximum parameters in the above three-sigma zone were TBil, HDL, CK, ALP, amylase and uric acid in CLIA’88 while RCPA and Biological variation were determined to be the most severe, with the highest performing parameters falling below three sigma zones. Rilibaek was the most liberal, with only sodium in the lower three sigma zones along with CLIA’88. The findings indicate that there is the substantial influence of various Total Error Allowable (TEa) sources on the sigma metric evaluation. A quality control plan was devised depending on different sigma scores of the analytes using biorad unity 2.0 software(westgard sigma multirules). The origins of errors that resulted in low sigma ratings liked enhanced cleaning of electrodes, electrode replacement, ageing of reagents, instrument maintainence were pinpointed and addressed. ConclusionThe study highlights the necessity of harmonizing and standardizing sigma metrics, stressing the significance of choosing suitable total error allowable goals (TEa). The creation of worldwide standards and recommendations for total error allowable (TEa) can lead to its harmonization. Establishing a consensus on the acceptable levels of error for various laboratory tests would necessitate the cooperation of specialists from many nations and organizations in order to set such guidelines and standards.

Genomic landscape of malignant phyllodes tumors reveals multiple targetable opportunities.

Malignant phyllodes tumors (MPT) are rare fibroepithelial breast cancers with no known effective systemic therapy; metastatic progression portends a dismal prognosis. We sought to describe the genomic landscape of MPTs through genomic profiling and immunotherapeutic biomarker analysis. Cases of sequenced MPT were identified from a Clinical Laboratory Improvement Amendments-certified, College of American Pathologists-accredited laboratory (Foundation Medicine). All cases underwent genomic profiling using adaptor ligation-based, next-generation sequencing assay of 324 genes. Tumor agnostic immunotherapy biomarkers, microsatellite instability, tumor mutational burden (TMB), and programmed death-ligand 1 (PD-L1) expression were evaluated. Fisher's Exact Tests and analysis of variance were used to test for differences between groups and for continuous variables as appropriate. Of 135 MPT cases identified; 94 (69.6%) were localized/locally recurrent and 41 (30.4%) were metastatic. Median age was 54 years (range 14-86). The median TMB was 2.5 mut/Mb and 3 were TMB-high (≥10 mut/Mb). 21.4% were PD-L1+ via Dako 22C3 assay (CPS ≥1). Most commonly altered genes included TERT-promoter (69.7%), CDKN2A (45.9%), TP53 (37.8%), NF1 (35.6%), CDKN2B (33.3%), MED12 (28.9%), MTAP (27.7%), KMT2D (22.2%), PIK3CA (20.0%), PTEN (18.5%), and RB1 (18.5%). Several tumors harboring genomic alterations with US Food and Drug Administration-approved indications in other tumor types were found including NF1, PIK3CA, EGFR Exon 19/20 insertions, and BRAF V600E mutations. In the largest genomic evaluation of MPT to date, multiple clinically actionable mutations were found. Routine sequencing of metastatic MPT may provide additional information to guide treatment decisions and clinical trial enrollment.

High-resolution melting assay for rapid, simultaneous detection of JAK2, MPL and CALR variants

AimsIdentification of recurrent genetic alterations in JAK2, MPL and CALR remains crucial in the diagnosis of Philadelphia-negative myeloproliferative neoplasms (MPNs). Current laboratory testing algorithms may entail batching and/or sequential testing,...

Sigma performance evaluations for clinical chemistry and immunoassays in a tertiary care hospital laboratory based on Clinical Laboratory Improvement Amendments (CLIA) 1988 and 2024 Guidelines

Sigma performance evaluations for clinical chemistry and immunoassays in a tertiary care hospital laboratory based on Clinical Laboratory Improvement Amendments (CLIA) 1988 and 2024 Guidelines

Analytical Validation of a DNA Methylation Biomarker Test for the Diagnosis of Barrett's Esophagus and Esophageal Adenocarcinoma from Samples Collected Using EsoCheck®, a Non-Endoscopic Esophageal Cell Collection Device.

Barrett's esophagus (BE) is a known precursor to esophageal adenocarcinoma (EAC). Guidelines recommend BE screening in populations with multiple risk factors, for which non-endoscopic esophageal cell collection with biomarker testing is considered as an acceptable alternative to esophagogastroduodenoscopy (EGD). The aim of this study was to evaluate analytical performance characteristics of EsoGuard® (EG), a DNA methylation biomarker assay, as a laboratory-developed test (LDT) in esophageal samples collected with the swallowable EsoCheck® (EC) device. EG is a next-generation sequencing (NGS) assay that evaluates methylated vimentin (VIM) and cyclin A1 (CCNA1), clinically validated biomarkers for the detection of BE and EAC. The studies were conducted according to standards of College of American Pathology (CAP), Clinical Laboratory Improvement Amendments (CLIA), and New York (NY) state requirements for the analytical validation of molecular assays. Comparison to Sanger sequencing showed that EG was 100% accurate at all 31 CpG sites evaluated by the assay. The analytical sensitivity, specificity, and accuracy of the assay were 89%, 100%, and 96%, respectively. Intra- and inter-assay precision was 100%. The limit of detection (LOD) was 1 in 400 methylated cells, and the reference range was 84%. In summary, EsoGuard demonstrates high analytical accuracy, repeatability, and reproducibility in samples collected using the EsoCheck device.

Precision medicine-based platform to guide the treatment of EML4-ALK driven lung cancers and other NSCLC in real time.

215 Background: Lung cancer (LC) is the top cause of cancer-associated mortality worldwide, with a 10-year overall survival rate of 5%. Although most LCs are smoking related, in the US, 25% of non-small cell LC (NSCLC) are diagnosed in persons with little or no smoking history. Fusions involving anaplastic lymphoma kinase (ALK) are the oncogenic driver in ~3–7% of NSCLC. While inhibitors targeting the kinase domain of ALK (TKIs) have proven extremely effective, inevitably, resistance develops with limited treatment options beyond second line TKIs. Additionally, NSCLCs without identified molecular alterations have even more limited tumor specific treatment options. Methods: We developed a precision medicine-based platform (PMP) to screen patient-derived, minimally cultured, organoid material (PDM) directly from resections with curated panels of drugs. PDM collected during clinically indicated procedures is plated in 3D-culture to generate patient-derived organoids (PDOs) and screened with drugs tailored to each tumor type. PDOs are screened at therapeutically relevant doses, drawing from pharmacokinetic data for each drug. We have optimized an assay to rapidly screen for EML4-ALK fusions and can perform next-generation sequencing in real time (~7 days) to integrate with drug screening results. Our organoid cultures retain the full spectrum of tumor microenvironment present in the original sample. Results: To date, we have analyzed 83 cases, including 8 EML4-ALK NSCLC. We have demonstrated the ability to produce high quality data from low input samples (biopsies). In one EML4-ALK NSCLC we were able to collect PDM from two distinct anatomic spaces (pleural effusion and peritoneal fluid) and screen with the same panel of drugs, with nearly identical results, highlighting the reproducibility and consistency of our assay. Screening of EML4-ALK tumors which have progressed to second or higher line TKIs, demonstrate sensitivity to earlier generation ALK TKIs, a known phenomenon. Characterization of tumors with unknown clinical drivers identifies that ~1/3 tumors which have no actionable or hypothetically prioritized variants, and they exhibit particularly poor response to chemotherapies. Our results recapitulate known resistance/progression in samples previously exposed to therapy, demonstrating a strong negative predictive value. Longitudinal assessment is being tracked to robustly assess positive predictive value (PPV). Conclusions: Our PMP captures robust and reproducible results that are consistent with known clinical pathogenesis. Moving forward, we are collecting longitudinal data from enrolled patients in parallel with clinical trials to demonstrate the PPV of our PMP. We additionally strive to demonstrate reproducibility to obtain Clinical Laboratory Improvement Amendments approval and to deliver results to patients and physicians to help guide clinical care.