Assay Performance Characteristics Research Articles

TP53 mutation screening for patients at risk of myeloid malignancy.

6546 Background: Cellular therapy is a promising approach for many diseases but is associated with a risk of subsequent myelodysplastic syndrome and/or acute myeloid leukemia, also known as therapy-related myeloid neoplasms (tMN). This phenomenon has recently been described with allogeneic hematopoietic cell transplantation (HCT) and gene therapy for sickle cell disease (SCD). Mutation(s) in functional domains of TP53 are often associated with the development of tMN but currently no prospective screening or monitoring technology is available. Methods: A next-generation sequencing (NGS) assay with unique molecular identifiers (UMI) and bioinformatic noise-suppression was designed to discover somatic mutations at a variant allele frequency (VAF) 1% throughout the TP53gene. The background error profile at each base position was calculated using blood genomic DNA from healthy donors. The minimal detectable allele fraction with 95% confidence (MDAF) was calculated for all reported known AML/tMN TP53 hotspots. Orthogonal validation was performed using droplet digital PCR (ddPCR). Results: The median error corrected sequencing depth at 62 known TP53 hotspot regions was 14,512 (95% CI: 14,769 – 15,430) with a theoretical median de novo NGS variant discovery limit of 0.058% (range: 0.037% - 0.13%). Experimental evidence of assay performance characteristics was produced using serial dilutions of 4 missense, 2 splicing, and 1 frameshift TP53 variants with 100% discovery specificity observed (lowest detected VAF range: 0.05 – 0.12%). High correlation was observed in quantification using NGS discovery and ddPCR validation ( r = 0.958, p<0.0001). Pre- and post-HCT clinical samples from 19 patients with SCD, 11 of which had graft failure including 4 who developed tMN, were screened for TP53 mutations. In all tMN cases, the AML-associated TP53 variant was detectable at least 6 months and up to 2.5 years prior to clinical diagnosis of myeloid malignancy. In contrast, no pathogenic TP53 variants were detected in 15 SCD patients who underwent HCT but did not develop tMN. Conclusions: This study provides generalizable evidence that ultra-sensitive discovery of TP53 mutations prior to cellular therapy is possible and could be a potentially valuable clinical tool to screen for tMN risk.

A study of the gaps and opportunities with fusion detection beyond NTRKs on 422 patients from the community.

e15186 Background: Gene fusions have important implications for therapeutic selection and patient quality of care and many fusions are targeted effectively in a tumor type agnostic manner. While most assays detect hundreds of fusions at once, typically the results are masked and analyzed according to medical requisition. Unfortunately, patients in the community setting most often are only tested for NTRK fusions, which have a prevalence of ~ 1%, and often following a positive IHC screen result. Here we compared side by side the clinical actionability gap in the community when using panTRK IHC testing and NGS fusion panels for NTRKs or for additional fusions, with both NGS panels selected presenting identical assay performance characteristics and medicare coverage. Methods: Clinical samples (n = 8307) from 33 tumor types were tested for RNA fusions using a hybridization capture RNA-seq based fusionome assay for solid tumors in our clinical laboratory, targeting RNA breakpoints at 1104 genes. Deidentified results were analyzed for either the 19 actionable fusion genes (ALK, BRAF, FGFR1-4, MET, NOTCH1/2, NRG1, NTRK1-3, PDGFB, PDGFRA/B, RAF1, RET and ROS1) reportable under Solid Tumor NGS fusion Panel, or only for NTRK fusions. Pan-TRK IHC results on fusion positive patients were analyzed. All the Deidentified patient data presented, was analyzed according to an IRB-approved protocol. Results: Targeted therapy -associated fusions were present in 422 (5.1%) patients, where 53% of patients were female with a median age of 68 years old, and 47% were male with a median age of 70 years old. However, when filtering only for NTRK fusions, just 104 (1.25%) patients had an actionable fusion (38 NTRK1, 10 NTRK2, 56 NTRK3). The additional 318 (3.8%) patients had other therapy candidate fusions: ALK (0.6%), BRAF 0.3%, FGFRs 0.9%, MET 0.4%, NOTCH2 0.2%, NRG1 0.2%, PDGFRA 0.1%, RAF1 0.2%, RET 0.5%, ROS1 0.2%, excluding NTRK positive cases. There were only 2 (0.02%) cases that were positive for both an NTRK fusion and an additional Targeted Panel fusion gene. Interestingly, we found that IHC testing was able to identify 75% of NTRK1 and 55% NTRK2 positive samples but only 20% of NTRK3 fusion positive patients. Moreover only 54% of the panTRK IHC positive patients expressed and NTRK fusion while 46% expressed one of the other 16 druggable fusions, with FGFRs on 20%, and ALK and ROS1 with 4% each. Conclusions: The data demonstrates that up to 4 -fold more patients can have a fusion matched therapy when testing for these 19 druggable fusions at once as compared to testing only for NTRK fusions or following IHC testing. Moreover, IHC testing as a screening method as very poor sensitivity for NTRK fusions, specially for NTRK3. Changes on the molecular testing paradigm in the community setting is needed to provide more patients with a therapeutic opportunity, when assay performance and financial considerations are equal to increase cancer care access.

Abstract 1312: A study of the clinical utility of NTRKs only vs. comprehensive gene fusion panel testing from a single assay platform

Abstract Background: Gene fusions have important implications for therapeutic selection and patient quality of care, and though they have a low prevalence individually, many fusions are targeted effectively, agnostic of any tumor type. Unfortunately, patients in the community oncology setting are most often only tested for NTRK fusions, which have a prevalence of around 1%. Here, we compared side by side the actual clinical actionability differences using real-world testing data between broad vs. NTRK fusion only panels offered by our clinical laboratory, both with identical assay performance characteristics, reimbursement, and cost levels. Methods: Clinical samples(n=8307) from 33 tumor types were tested for known and novel RNA fusions using our hybridization capture RNA-seq based Solid Tumor Fusion Panels in our clinical laboratory, which targets RNA breakpoints at 1104 genes. Deidentified results were analyzed before or after filtering for fusions based on either a Targeted Solid Tumor NGS fusion Panel (16 drug targetable genes) or only NTRKs fusions. Deidentified patient data presented was analyzed according to an IRB-approved protocol. Results: The prevalence of fusions in the cohort was 30.5% involving any of the 1104 targeted genes by the assay (27% in frame, 20% out of frame, and 41% others). Druggable fusions were present in 5.1% (422) of patients, where 53% were female with a median age of 68 years old, and 47% were male with a median age of 70. However, when filtering only for NTRK fusions, only 104 patients had an NTRK fusion (38 NTRK1, 10 NTRK2, 56 NTRK3), while an additional 318 patients had detected fusions from the Targeted Panel. These druggable fusions had the following prevalences; ALK 0.6 %, BRAF 0.3%, FGFR1 0.2%, FGFR2 0.3%, FGFR3 0.4%, FGFR4 0.0% n=4, MET 0.4%, NOTCH1 0.0% n=1, NOTCH2 0.2%, NRG1 0.2%, PDGFB 0.0% n=3, PDGFRA 0.1%, PDGFRB 0% n=0, RAF1 0.2%, RET 0.5%, ROS1 0.2%, excluding NTRK positive cases. The incidence of NTRK 1/2/3 fusions was 1.25%, while 3.8% of patients have other fusions included on the Targeted Panel in the absence of an NTRK fusion. Two (2, 0.02%) patients had both an NTRK fusion and an additional fusion covered on one of the other 16 genes in the Targeted NGS fusion panel. Conclusion: Actionable fusions showed a combined prevalence in the clinical setting of 5.1%. This study demonstrates that when fusion testing is performed, four times more patients can benefit from a therapeutic option than when testing for these 16 genes compared to the widespread panel of the current clinicians’ favorite choice of only NTRK fusions. More data and education are needed to change the testing paradigm of treating physicians to test broader sets of fusions when assay performance and financial considerations are equal to increase cancer care access. Citation Format: Chaugiang Duong, Steven Lau-Rivera, Rory Jackson, Pathum Kanagasunderam, Roya Hariri, Nathan Montgomery, Derek Lyle, Fernando Lopez Diaz. A study of the clinical utility of NTRKs only vs. comprehensive gene fusion panel testing from a single assay platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1312.

Accurate redox state indication by in situ derivatization with N-ethylmaleimide - Profiling of transsulfuration and glutathione pathway metabolites by UPLC-MS/MS

BackgroundReduced and oxidized glutathione play an important role for the intracellular detoxification of reactive oxygen species. The iron-dependent formation of such reactive oxygen species in conjunction with the inhibition of the redox-balancing enzyme glutathione peroxidase 4 underlie an imbalance in the cellular redox state, thereby resulting in a non-apoptotic form of cell death, defined as ferroptosis, which is relevant in several pathologies. MethodsHere we present a rapid ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) based method providing the accurate quantification of 12 glutathione pathway metabolites after in situ derivatization with N-Ethylmaleimide (NEM). The method was validated regards linearity, recovery and accuracy as well as precision. The assay includes glutathione and its oxidized form glutathione disulfide. Furthermore, the related precursors cysteine, cystine, glutamic acid, γ-glutamylcysteine and cysteinylglycine, biomarkers of protein crosslinking such as cystathionine and lanthionine, as well as metabolites of the transsulfuration pathway, methionine, homocysteine and serine are simultaneously determined. ResultsTwelve glutathione pathway metabolites were simultaneously analyzed in four different human cell line extracts within a total LC run time of 5.5 min. Interday coefficients of variation (1.7 % to 12.0 %), the mean observed accuracy (100.0 % ± 5.2 %), linear quantification ranges over three orders of magnitude for all analytes and sufficient metabolite stability after NEM-derivatization demonstrate method reliability. Immediate derivatization with NEM at cell harvesting prevents autooxidation of glutathione, ensures accurate results for the GSH/GSSG redox ratio and thereby allows interpretation of cellular redox state. ConclusionThe described UPLC-MS/MS method provides a sensitive and selective tool for a fast and simultaneous analysis of glutathione pathway metabolites, its direct precursors and related compounds. Assay performance characteristics demonstrate the suitability of the method for applications in different cell cultures. Therefore, by providing glutathione related functional metabolic readouts, the method enables investigations in mechanisms of ferroptosis and alterations in oxidative stress levels in several pathophysiologies.

Ibrutinib Added to Standard Conditioning and As Consolidation Therapy Following Autologous Hematopoietic Stem Cell Transplantation (AutoHCT) for Relapsed/Refractory Activated-B-Cell Subtype Diffuse Large B-Cell Lymphoma (ABC-DLBCL): Primary Analysis of the US Intergroup Double-Blind Randomized Phase III Study Alliance A051301/BMT-CTN 1201

Introduction: AutoHCT is an effective therapy for patients (pts) with DLBCL who are refractory or relapse following first-line chemotherapy, but long term outcomes remain suboptimal. The BTK inhibitor ibrutinib has shown promising activity in pts with ABC-DLBCL (Wilson et al, Nat Med 2015). In 2016 we launched a randomized phase III clinical trial to evaluate the addition of ibrutinib to AutoHCT as part of conditioning and as consolidation therapy for pts with relapsed/refractory ABC-DLBCL. Patients and Methods: Following assessment of open-label treatment in a safety cohort of 6 pts, we randomly assigned pts with chemotherapy-sensitive persistent or relapsed ABC-DLBCL to receive ibrutinib 560 mg [Arm A] or placebo [Arm B] concurrently with conditioning on days -6 to -1 of AutoHCT (Cycle 1). Following count recovery and resolution of acute toxicities, pts continued ibrutinib 560 mg in Arm A or placebo in Arm B for 12 additional 28-day cycles. Crossover to Arm A using single agent ibrutinib was allowed for pts progressing on Arm B. Central pathology review was performed for disease confirmation and subtype assignment. Initially, ABC subtype assignment was performed using the Nanostring Lymphoma Subtyping Test (LST) but the study was amended to use the IHC-based Hans classifier for non-GCB on 8/15/19. Other key eligibility criteria included receipt of no more than 3 prior regimens, no active CNS involvement, no need for long-term anticoagulation, and no prior progression on Ibrutinib. Pts were stratified by time to relapse (<=12 mos vs >12 mos), type of conditioning (BEAM or CBV) and prior ibrutinib use. The original design required 296 patients with 82% power to detect a difference in 2-year progression-free survival (PFS) rates of 67% vs. 50% with a two-sided alpha of 0.05. A revised statistical design allowed an interim futility analysis to be conducted after 40 pts were enrolled and followed for 2 years. Even though the study met criteria to continue accrual to a target of 160 pts, we decided to close it early due to declining accrual on 12/20/2022. We hereby present the primary analysis of the evaluable patients enrolled (data as of 07/17/2023). Results: Between 2/6/17 and 8/24/18, we screened 255 pts but enrolled only 34 (13%) largely due to long assay turnaround times and performance characteristics with the LST. Following the switch to the IHC-based Hans classifier (after 8/15/19), 60 out of 110 pts screened were enrolled (54%) in line with our a priori expectation. In total, 45 pts were randomized to Arm A vs. 43 to Arm B, with 39 and 38, respectively, being evaluable for the primary endpoint at this time. Median age was 61 years (range 20-75 years), median number of prior lines of therapy was 2, 46% of the pts were female, 21% were refractory or had early relapse, 94% were planned to receive BEAM conditioning. Overall, 87% of pts in Arm A and 88% in Arm B underwent conditioning while 70% and 67% respectively, started maintenance therapy. The median number of cycles received was 6 in Arm A vs. 5 in Arm B. The primary endpoint of 2-year PFS was 57.6% (95% CI: 42.1%, 78.8%) in Arm A vs. 40.8% (95% CI: 26.5, 62.8%) in Arm B (HR=0.54; 95% CI: 0.26, 1.10; log-rank p = 0.087). Median PFS was 26.5 months (95% CI: 10.2, not reached [NR]) in Arm A vs. 8.1 months (95% CI: 5.4, NR) in Arm B. Only one pt crossed over to Arm A after progression on Arm B. The most common grade 3-4 AEs in each of the arms were: neutropenia (A: 14%, B: 14%), febrile neutropenia (A: 11%, B: 9%), and thrombocytopenia (A: 11%, B: 7%). Rates of any grade atrial fibrillation were similar between arms (12.8% in Arm A vs. 10.5% in Arm B); one patient had grade 3 and one patient had grade 4 atrial fibrillation, both in Arm B. Six pts had reported grade 5 events (Arm A: 2 sepsis, 1 COVID-19, 1 respiratory failure and 1 disease progression and Arm B: 1 disease progression) but only one grade 5 event (sepsis, Arm A) was deemed probably related to treatment. Conclusions: Despite an early high rate of screen failures and declining accruals due to competition with CAR-T cell therapy, the primary analysis suggests that ibrutinib with and following AutoHCT in relapsed/refractory ABC-DLBCL is well-tolerated and may improve PFS in this high-risk patient population. This trial was supported by: U10CA180821, U10CA180882, U24CA196171; U10CA180820, UG1CA233234 (ECOG-ACRIN); U10CA180868 (NRG); U10CA180888 (SWOG) ClinicalTrials.gov Identifier: NCT02443077 https://acknowledgments.alliancefound.org

Development of a proficiency testing program for HPV serology assays used to evaluate antibody responses in vaccine trials

In this study, a proficiency panel was created for evaluation of assay performance and inter- and intra-laboratory assay comparisons, especially the ability to accurately measure negative, low, intermediate, and high levels of HPV type-specific antibodies. Comprised of 80 deidentified samples, this panel is designed for individual labs to evaluate assay performance characteristics on a biennial basis, to promote standardization of methodology and harmonization of data from human papillomavirus (HPV) serology tests in vaccine trials. The proficiency panel was qualified using 2 types of assays (singleplex Enzyme-Linked Immunosorbent Assays [ELISAs] or Multiplex antibody-binding assays and Pseudovirion-based neutralization assays [PBNAs]) in 10 laboratories from 7 countries, monitoring HPV antibody responses for up to 9 HPV types and using 3 different analysis methods. Sensitivity, specificity, and correlations (concordance, accuracy, and precision) were evaluated for each HPV type. In laboratories that tested all 80 samples, results from most (74/80) samples were reported with 100% accuracy across all 9 HPV types. The average sensitivity and specificity for singleplex and multiplex antibody binding assays ranged from 86.7% to 98.3% (sensitivity) and 84.2% to 94.3% (specificity), while the average sensitivity and specificity for the Pseudovirion (PsV)-based neutralization assays (PBNA) ranged from 87.6% to 99.4% (sensitivity) and 52.4% to 94.4% (specificity). This proficiency panel will help with assessing performance characteristics of HPV serology assays used in clinical trial studies and assure the data generated from these assays is harmonized.

FRI480 Uncovering The Mystery Of Macro TSH

Abstract Disclosure: F. Anwar: None. Z.I. Saeed: None. Introduction: An isolated elevation in TSH level, while uncommon, may result in incorrect diagnosis and improper treatment. We present a case of suspected hypothyroidism that was later found to be caused by macroTSH in the blood. Clinical Case: A 21-year-old asymptomatic female was diagnosed with hypothyroidism and started on levothyroxine at age 16 when routine lab work revealed TSH of 34.2 MCU (0.550-4.780 MCU) and free T4 of 1.1 ng/dl (0.89-1.76 ng/dl). She denied any personal or family history of thyroid disorders in the past. Patient later reported symptoms including palpitations and weight loss leading to discontinuation of levothyroxine. Repeat lab work showed TSH of 0.112 MCU and free T4 of 1.71 ng/dl. After discontinuing levothyroxine, TSH levels were found in range of 89.26 MCU to 106 MCU (0.550-4.780 MCU). Free T4 levels remained normal, even when tested using dialysis method. Total T3 level also remained normal at 87 ng/dl (80-200 ng/dl). TPO antibodies were slightly elevated at 9.3 IU/mL (0.0-9.0 IU/ml), TSI and TSH receptor antibodies were negative. Patient's high TSH level, lack of symptoms, and normal free T4 levels prompted the use of different assays to test TSH. We contacted Mayo Clinic Lab for further testing. One assay (Roche Elecsys) showed TSH level of 90.8 mIU/L, but this result was not significantly changed when sample was incubated with a commercial heterophile antibody blocking reagent. Another assay (Beckman Coulter Access TSH) produced a significantly different but still elevated result of 43.1 mIU/L. For research purposes, the sample was further tested for macroTSH using polyethylene glycol (PEG) precipitation, which resulted in TSH level of 5.8 mIU/L which was reduced from 90.8 mIU/L (94% reduction). These results were higher than the mean +/- 2 standard deviations of the control group (range 0% to 65% reduction in TSH with PEG in controls). This suggested presence of macroTSH, although the assay's performance characteristics and reference ranges had not been established at the time of testing for this patient. Patient's TSH levels remain high and she was advised not to begin the medication unless circulating thyroid hormone levels are abnormal. Conclusion: Macro TSH is a combination of monomeric TSH and anti-TSH antibodies, similar to macro-prolactin. It is considered inactive and has an estimated prevalence of 0.6-1.6%. In a review of over 150 patients, more than 50% of documented thyroid interferences, including macro TSH, led to incorrect diagnosis and improper treatment. This case demonstrates the significance of identifying macro TSH to avoid misdiagnosis and inappropriate management of euthyroid patients with isolated TSH elevation. Presentation: Friday, June 16, 2023

B-302 Increased False-Positives vs Increased Interference Flags: Using the AU 5800 to Compare Two Ethyl Glucuronide Assays

Abstract Background Ethyl glucuronide (EtG) is a metabolite of ethanol that can be detected in urine for up to three to five days following consumption of alcohol. Urine specimens are routinely screened for EtG to assess ethanol exposure for compliance and/or abuse with presumptive positive samples being confirmed using quantitative Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). LC-MS/MS is costly and labor intensive. Therefore, providing a sensitive and specific screening option for EtG in urine is beneficial, with it being more cost-effective, efficient, and widely available. Evaluation of the performance characteristics of different EtG assays can aid in identifying an assay that most closely agrees with LC-MS/MS. Methods To evaluate agreement, 100 residual urine specimens (approximately 50 positive/50 negatives identified using ARK Ethyl Glucuronide Assay) were thawed, mixed, and analyzed. Specimen were analyzed using ARK and Immunalysis Ethyl Glucuronide Urine HEIA on the Beckman Coulter AU 5800. Discrepant results were investigated using LC-MS/MS. Additionally, 15 false-positive samples (identified positive by ARK but confirmed negative by LC-MS/MS) were evaluated on both ARK and Immunalysis assays. Lastly, 7 samples were analyzed on ARK and Immunalysis because of the inability to quantitate by LC-MS/MS due to interfering substance. Results were evaluated using EP Evaluator and Microsoft Excel. Results Of the 100 samples analyzed, 8 samples were identified as discrepant between the two immunoassays. These 8 discrepant samples tested positive on ARK and negative on Immunalysis, resulting in an 83.3% positive agreement and a 100.0% negative agreement between ARK and Immunalysis. For these 8 discrepant samples, LC-MS/MS confirmed 7 samples negative and 1 sample positive suggesting that using ARK would result in 14.6% of presumptive positives confirming negative. Of the initial 100 samples, 7 samples resulted with interference flags by Immunalysis, indicating the presence of an unknown interfering substance within the sample. Of these samples with interference flags, 3 were among the 8 discrepant samples. Evaluation of identified false-positive samples (n = 15) by ARK resulted in 90.9% negative agreement for Immunalysis compared to 0.0% negative agreement by ARK. Of these 15 false-positive samples tested, 3 had interference flags identified using Immunalysis. Between agreement samples (n = 100) and false-positive samples (n = 15), a total of 10 interference flags were identified by Immunalysis, 6 of which were observed to have discrepant results between ARK and Immunalysis. ARK identified no interference flags. Interference was confirmed for 7 samples using LC-MS/MS, with Immunalysis detecting interference in 57% of those samples, and ARK reported no interference flags. In total, LC-MS/MS results were obtained for 37 samples, of which, only 2 false-positive and 1 false-negative samples were observed using Immunalysis. Conclusion While the assays offered by ARK and Immunalysis are similar in that they screen for EtG, we observed the accuracy between the two assays to be quite different, when compared to LC-MS/MS. Using ARK reagents would result in greater number of presumptive positives. Of note, the instrument flags accompanying Immunalysis results appear to be indicative of an interfering substance that ARK is not detecting and then subsequently reports as (falsely) positive.

B-031 Digital Elisatotal 25-Hydroxyvitamin D

Abstract Evaluation of digital ELISA using a high-resolution computational optical system for measurement of total 25-hydroxyvitamin D Background Biomarkers such as vitamin D occur at very low concentrations in blood, and sensitive detection methods are required in order to measure them. It is difficult to accurately measure low-concentration biomarkers using conventional enzyme-linked immunosorbent assays (ELISA) with fluorescence staining. By developing a digital ELISA (DELISA, Small Machines, Seoul, Korea) platform, a low concentration substance was realized by analyzing the digitalized signal through a high-resolution computational optical system in a microfluidic chip. We evaluated DELISA for measurement of total 25-hydroxyvitamin D (25OHD) in a fluidic chip. Methods The sample with monoclonal antibody bead conjugates mixture was incubated for 20 min at 37°C, then 30 uL sample mixture was applied to inlet of the chip. After additional incubation for 2 min at room temperature and 2 min after sample application, 120 uL of washing buffer was applied onto the washing hole and the chip was incubated for 10 min. 25OHD molecules in the sample bond to magnetic beads coupled with anti-25OHD at the end of the membrane. Chips were inserted into DELISA, and 25OHD results were derived by analysis of the computational method of microscopic imaging, proportional to the concentration of 25OHD. Assay performance characteristics of the limit of detection (LoD), precision and analytical measurement interval (AMI) using Vitamin D Depleted, Low and High Serum (Molecular Depot, San Diego, CA) were determined according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. 87 Samples for method comparison studies were obtained from routine clinical samples submitted for 2 OHD determination or from apparently healthy normal volunteers. The study was approved by the Institutional Review Board of Dongguk University Ilsan Hospital (202207024). Results LoD was 10.3 ng/mL and within-laboratory precision was 11, 12, and 10% coefficient of variation at 14.1, 56.6, and 113.2 ng/mL, respectively. The best fit polynomial was a cubic equation from 14.1 to 113.2 ng/mL and the difference between the third-order equation and the first-order equation at Level 3 and 4 concentrations was outside the non-linearity limit. Comparison with chemiluminescent assay (Elecsys Vitamin D total II, Roche Diagnostics, Mannheim, Germany) yielded a 0.904 of correlation coefficient and 0.921 slope in the range from 7.0 to 57.9 ng/mL. Conclusions The DELISA 25OHD assay has a suitable LoD and precision, however, it is necessary to improve the AMI at high concentration values and correlation with the automated analyzer.

HDV RNA assays: Performance characteristics, clinical utility, and challenges.

Coinfection with HBV and HDV results in hepatitis D, the most severe form of chronic viral hepatitis, frequently leading to liver decompensation and HCC. Pegylated interferon alpha, the only treatment option for chronic hepatitis D for many years, has limited efficacy. New treatments are in advanced clinical development, with one recent approval. Diagnosis and antiviral treatment response monitoring are based on detection and quantification of HDV RNA. However, the development of reliable HDV RNA assays is challenged by viral heterogeneity (at least 8 different genotypes and several subgenotypes), intrahost viral diversity, rapid viral evolution, and distinct secondary structure features of HDV RNA. Different RNA extraction methodologies, primer/probe design for nucleic acid tests, lack of automation, and overall dearth of standardization across testing laboratories contribute to substantial variability in performance characteristics of research-based and commercial HDV RNA assays. A World Health Organization (WHO) standard for HDV RNA, available for about 10 years, has been used by many laboratories to determine the limit of detection of their assays and facilitates comparisons of RNA levels across study centers. Here we review challenges for robust pan genotype HDV RNA quantification, discuss particular clinical needs and the importance of reliable HDV RNA quantification in the context of drug development and patient monitoring. We summarize distinct technical features and performance characteristics of available HDV RNA assays. Finally, we provide considerations for the use of HDV RNA assays in the context of drug development and patient monitoring.

State-of-the-Art Review: Neurosyphilis.

We review key concepts in the diagnosis, treatment, and follow-up of individuals with neurosyphilis. We describe the epidemiology of syphilis in the United States, highlight populations that are markedly affected by this infection, and attempt to estimate the burden of neurosyphilis. We describe the cardinal clinical features of early and late (tertiary) neurosyphilis and characterize the clinical significance of asymptomatic neurosyphilis in the antibiotic era. We review the indications for cerebrospinal fluid (CSF) examination and the performance characteristics of different CSF assays including treponemal and lipoidal antibodies, white cell count, and protein concentration. Future biomarkers and the role of imaging are briefly considered. We review preferred and alternative treatments for neurosyphilis and evidence for their use, including evidence for the use of enhanced intramuscular benzathine penicillin G to supplement intravenous penicillin.

Analytical and diagnostic performance characteristics of reverse-transcriptase loop-mediated isothermal amplification assays for dengue virus serotypes 1-4: A scoping review to inform potential use in portable molecular diagnostic devices.

Dengue is a mosquito-borne disease caused by dengue virus (DENV) serotypes 1-4 which affects 100-400 million adults and children each year. Reverse-transcriptase (RT) quantitative polymerase chain reaction (qPCR) assays are the current gold-standard in diagnosis and serotyping of infections, but their use in low-middle income countries (LMICs) has been limited by laboratory infrastructure requirements. Loop-mediated isothermal amplification (LAMP) assays do not require thermocycling equipment and therefore could potentially be deployed outside laboratories and/or miniaturised. This scoping literature review aimed to describe the analytical and diagnostic performance characteristics of previously developed serotype-specific dengue RT-LAMP assays and evaluate potential for use in portable molecular diagnostic devices. A literature search in Medline was conducted. Studies were included if they were listed before 4th May 2022 (no prior time limit set) and described the development of any serotype-specific DENV RT-LAMP assay ('original assays') or described the further evaluation, adaption or implementation of these assays. Technical features, analytical and diagnostic performance characteristics were collected for each assay. Eight original assays were identified. These were heterogenous in design and reporting. Assays' lower limit of detection (LLOD) and linear range of quantification were comparable to RT-qPCR (with lowest reported values 2.2x101 and 1.98x102 copies/ml, respectively, for studies which quantified target RNA copies) and analytical specificity was high. When evaluated, diagnostic performance was also high, though reference diagnostic criteria varied widely, prohibiting comparison between assays. Fourteen studies using previously described assays were identified, including those where reagents were lyophilised or 'printed' into microfluidic channels and where several novel detection methods were used. Serotype-specific DENV RT-LAMP assays are high-performing and have potential to be used in portable molecular diagnostic devices if they can be integrated with sample extraction and detection methods. Standardised reporting of assay validation and diagnostic accuracy studies would be beneficial.

Standardising the biochemical confirmation of adult male hypogonadism: A joint position statement by the Society for Endocrinology and Association of Clinical Biochemistry and Laboratory Medicine.

Inter-assay variation between different immunoassays and different mass spectrometry methods hampers the biochemical confirmation of male hypogonadism. Furthermore, some laboratories utilise assay manufacturer reference ranges that do not necessarily mirror assay performance characteristics, with the lower limit of normality ranging from 4.9 nmol/L to 11 nmol/L. The quality of the normative data underlying commercial immunoassay reference ranges is uncertain. A working group reviewed published evidence and agreed upon standardised reporting guidance to augment total testosterone reports. Evidence-based guidance on appropriate blood sampling, clinical action limits, and other major factors likely to affect the interpretation of results are provided. This article aims to improve the quality of the interpretation of testosterone results by non-specialist clinicians. It also discusses approaches for assay harmonisation which have been successful in some but not all healthcare systems.

Standardising the biochemical confirmation of adult male hypogonadism; a joint position statement by the Society for Endocrinology and Association of Clinical Biochemistry and Laboratory Medicine.

Background: Inter-assay variation between different immunoassays and different mass spectrometry methods hampers the biochemical confirmation of male hypogonadism. Furthermore, some laboratories utilis eassay manufacturer reference ranges that do not necessarily mirror assay performance characteristics, with the lower limit of normality ranging from 4.9 nmol/L to 11 nmol/L. The quality of the normative data underlying commercial immunoassay reference ranges is uncertain.Design: A working group reviewed published evidence and agreed upon standardised reporting guidance to augment total testosterone reports. Results: Evidence-based guidance on appropriate blood sampling, clinical action limits, and other major factors likely to affect the interpretation of results are provided. Conclusions: This article aims to improve the quality of the interpretation of testosterone results by non-specialist clinicians. It also discusses approaches for assay harmonisation which have been successful in some but not all healthcare systems.

Platelet factor 4 triggers thrombo-inflammation by bridging innate and adaptive immunity.

Platelet factor 4 (PF4, synonym: CXCL4) is an evolutionary old chemokine with proposed roles in hemostasis and antimicrobial defense. In addition, PF4 has attracted considerable attention as a crucial mediator of one of the most prothrombotic adverse drug effects affecting blood cells, heparin-induced thrombocytopenia (HIT). Interest in PF4 substantially increased in 2021 when it was identified as the target antigen in the life-threatening adverse effect, vaccine-induced immune thrombotic thrombocytopenia (VITT). We address the concept that a major biological function of PF4-a strongly cationic chemokine-is to bind to negatively-charged prokaryotic microorganisms, resulting in structural changes in PF4 that trigger a danger signal recognized by the adaptive immune system. Application of biophysical tools has provided substantial insights into the molecular mechanisms by which PF4 becomes immunogenic, providing insights into a new mechanism of autoimmunity. Binding of autoantibodies with high affinity induces conformational change(s) in the endogenous protein, which are then recognized as foreign antigen, as exemplified by the prothrombotic disorders, autoimmune HIT and VITT. The final part of our review summarizes current assays for HIT and VITT, explaining how structural aspects of anti-PF4 pathobiology relate to assay design and performance characteristics. Currently, functional (platelet activation) assays using washed platelets detect HIT antibodies when heparin is added, and VITT antibodies when PF4 is added. Solid-phase PF4-dependent immunoassays using microtiter plates are sensitive for both HIT and VITT antibodies, while rapid immunoassays, in which the PF4/heparin antigen is coated on beads, are sensitive and specific for HIT, but not for VITT antibodies.

Evaluation of a Semiautomated System for the Quantitation of Human Adenovirus DNA from Clinical Samples.

Human adenoviruses (HAdVs) cause severe disease in immunocompromised patients. Quantitation of HAdV DNA in peripheral blood is used to assess the risk of disseminated disease and to monitor response to therapy. The lower limit of detection, precision, and linearity of the semiautomated AltoStar adenovirus quantitative PCR (qPCR) was evaluated using reference HAdV-E4 in EDTA plasma and respiratory virus matrix. Qualitative and quantitative agreement was determined using 122 clinical EDTA plasma specimens previously tested using a laboratory-developed HAdV qPCR. The 95% lower limit of detection (LLOD) was 33 IU/mL (95% confidence interval [CI], 10 to 56) for EDTA plasma and 188 IU/mL (95% CI, 145 to 304) for respiratory swab matrix. In both matrices, the AltoStar HAdV qPCR was linear from 7.0 to 2.0 log10 IU/mL. For the clinical specimens, overall agreement was 96.7% (95% CI, 91.8 to 99.1), positive percent agreement was 95.5% (95% CI, 87.6 to 98.5), and negative percent agreement was 98.2% (95% CI, 88.5 to 99.7). Passing-Bablok analysis of specimens quantifiable by both methods revealed a regression line of Y = 1.11 · X + 0.00; there was positive proportional bias (95% CI of the slope, 1.05 to 1.22) but no systematic bias (95% CI of the Y-intercept, -0.43 to 0.23) compared to the reference. The AltoStar platform provides accurate quantitation of HAdV DNA and provides a semiautomated option for the clinical monitoring of HAdV following transplantation. IMPORTANCE Accurate quantification of human adenovirus DNA in the peripheral blood plays a critical role in the management of adenovirus infections in transplant recipients. Many laboratories utilize in-house laboratory-based PCR assays for the quantification of human adenovirus, as there are few commercial options available. Here, we describe the analytical and clinical performance of the semiautomated AltoStar adenovirus quantitative PCR (Altona Diagnostics). This platform provides sensitive, precise, and accurate quantification of adenovirus DNA that is well suited for virological testing following transplantation. Prior to implementing a new quantitative test in the clinical laboratory, a rigorous evaluation is required to determine assay performance characteristics and to correlate results to current in-house methods of quantitation.

Assessment of the clinical and analytical performance of the Aptima SARS-CoV-2 assay using the VALCOR protocol

BackgroundThe COVID-19 pandemic highlighted the importance of diagnostic testing against curbing the spread of SARS-CoV-2. The urgent need and scale for diagnostic tools resulted in manufacturers of SARS-CoV-2 assays receiving emergency authorization that lacked robust analytical or clinical evaluation. As it is highly likely that testing for SARS-CoV-2 will continue to play a central role in public health, the performance characteristics of assays should be evaluated to ensure reliable diagnostic outcomes are achieved.MethodsVALCOR or “VALidation of SARS-CORona Virus-2 assays” is a study protocol designed to set up a framework for test validation of SARS-CoV-2 virus assays. Using clinical samples collated from VALCOR, the performance of Aptima SARS-CoV-2 assay was assessed against a standard comparator assay. Diagnostic test parameters such as sensitivity, specificity and overall per cent agreement were calculated for the clinical performance of Aptima SARS-CoV-2 assay.ResultsA total of 180 clinical samples were tested with an addition of 40 diluted clinical specimens to determine the limit of detection. When compared to the standard comparator assay Aptima had a sensitivity of 100.0% [95% CI 95.9–100.0] and specificity of 96.7% [95% CI 90.8–99.3]. The overall percent agreement was 98.3% with an excellent Cohen’s coefficient of κ = 0.967 [95% CI 0.929–1.000]. For the limit of detection, Aptima was able to detect all of the diluted clinical samples.ConclusionIn conclusion. validation of Aptima SARS-CoV-2 assay using clinical samples collated through the VALCOR protocol showed excellent test performance. Additionally, Aptima demonstrated high analytical sensitivity by detecting all diluted clinical samples corresponding to a low limit of detection.

Performance characteristics of diagnostic assays for schistosomiasis in Ontario, Canada.

Due to lower intensity of infection and greater intervals from last exposure, parasitologic detection methods for schistosomiasis are poorly sensitive in non-endemic areas, challenging accurate diagnosis. We evaluated parasitologic versus indirect detection methods for schistosomiasis. We included specimens submitted for Schistosoma serology, and stool for ova and parasite microscopy. Three real-time PCR assays targeting Schistosoma mansoni and S. haematobium were performed. Primary outcome measures were sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), where both microscopy and serology were the composite reference standard against serum PCR. Of 8168 serum specimens submitted for Schistosoma serology, 638 (7.8%) were reactive and 6705 (82.1%) were non-reactive. Of 156,771 stool specimens submitted for ova and parasite testing, 46 (0.03%) were positive for eggs of S. mansoni. Four (0.5%) urine specimens were positive for eggs of S. haematobium. Combined serum PCRs targeting S. mansoni had a sensitivity and specificity of 27.8% (95% CI = 18.3-39.1%) and 100% (95% CI = 83.9-100%), respectively, with PPV of 100% (95% CI = 100%) and NPV of 26.9% (95% CI = 24.3-29.7%). The one serum sample positive for S. haematobium was also detectable by our S. haematobium PCR. No cross-reactivity was observed for all three PCR assays. Although serology is highly sensitive, parasitologic tests signify active infection, but are limited by low population-level sensitivity, particularly in non-endemic settings. Although serum PCR offered no performance advantage over stool microscopy, its role in diagnostic parasitology should be pursued due to its high-throughput and operator-independent nature.

Highly sensitive liquid biopsy Duplex sequencing complements tissue biopsy to enhance detection of clinically relevant genetic variants.

Liquid biopsy (LB) is a promising complement to tissue biopsy for detection of clinically relevant genetic variants in cancer and mosaic diseases. A combined workflow to enable parallel tissue and LB analysis is required to maximize diagnostic yield for patients. We developed and validated a cost-efficient combined next-generation sequencing (NGS) workflow for both tissue and LB samples, and applied Duplex sequencing technology for highly accurate detection of low frequency variants in plasma. Clinically relevant cutoffs for variant reporting and quantification were established. We investigated assay performance characteristics for very low amounts of clinically relevant variants. In plasma, the assay achieved 100% sensitivity and 92.3% positive predictive value (PPV) for single nucleotide variants (SNVs) and 91.7% sensitivity and 100% PPV for insertions and deletions (InDel) in clinically relevant hotspots with 0.5-5% variant allele frequencies (VAFs). We further established a cutoff for reporting variants (i.e. Limit of Blank, LOB) at 0.25% VAF and a cutoff for quantification (i.e. Limit of Quantification, LOQ) at 5% VAF in plasma for accurate clinical interpretation of analysis results. With our LB approach, we were able to identify the molecular cause of a clinically confirmed asymmetric overgrowth syndrome in a 10-year old child that would have remained undetected with tissue analysis as well as other molecular diagnostic approaches. Our flexible and cost-efficient workflow allows analysis of both tissue and LB samples and provides clinically relevant cutoffs for variant reporting and precise quantification. Complementing tissue analysis by LB is likely to increase diagnostic yield for patients with molecular diseases.

Characterization by image analysis of the dose vs response curve for a qualitative serum hCG lateral flow immunoassay

BackgroundAs an adjunct to verification of performance characteristics of a qualitative serum hCG lateral flow immunoassay (LFI), we performed image analysis to characterize the dose vs response curve (visibility of the test line), as a means of understanding the transition from negative to positive as a function of increasing [hCG]. MethodsUsing serum samples of known [hCG], device images were obtained using a scanner at the prescribed reading time (5 min). Image analysis (using Python and R) was used to obtain the integral (S) of the test-line color as a function of [hCG]. ResultsData for S as a function of [hCG] were well characterized by a simple hyperbola: S = Smax [hCG]/([hCG] + K), where K = 202 mIU/ml (r = 0.997). Replicates of S at K had CV of 7.3 %. By eye, uncertainty of test results among users occurred only below the assay's stated sensitivity of 10 mIU/ml, in region of S < 3 % of Smax, and signal:noise ratio < 3. ConclusionsBy image analysis, the dose vs response (Test line integral) for this qualitative serum hCG LFI was a simple hyperbola. Characterization of the dose vs response curve was useful in verification of the assay's performance characteristics.