EGFR/CEP7 high polysomy is separate and distinct from EGFR amplification in glioblastoma as determined by fluorescence in situ hybridization.

EGFR amplification in gliomas is commonly defined by an EGFR/CEP7 ratio of ≥2. In testing performed at a major reference laboratory, a small subset of patients had ≥5 copies of both EGFR and CEP7 yet were not amplified by the EGFR/CEP7 ratio and were designated high polysomy cases. To determine whether these tumors are more closely related to traditionally defined EGFR-amplified or nonamplified gliomas, a retrospective search identified 22 out of 1143 (1.9%) gliomas with an average of ≥5 copies/cell of EGFR and CEP7 with an EGFR/CEP7 ratio of <2 displaying high polysomy. Of these cases, 4 had insufficient clinicopathologic data to include in additional analysis, 15 were glioblastomas, 2 were IDH-mutant astrocytomas, and 1 was a high-grade glial neoplasm, NOS. Next-generation sequencing available on 3 cases demonstrated one with a TERT promoter mutation, TP53 mutations in all cases, and no EGFR mutations or amplifications, which most closely matched the nonamplified cases. The median overall survival times were 42.86, 66.07, and 41.14 weeks for amplified, highly polysomic, and nonamplified, respectively, and were not significantly different (p = 0.3410). High chromosome 7 polysomic gliomas are rare but our data suggest that they may be biologically similar to nonamplified gliomas.

Comparison of three methods for the detection of antibodies against muscle-specific kinase.

OBJECTIVES: To compare 3 different methods for the detection of antibodies against muscle-specific kinase (MuSK). METHODS: MuSK antibody testing was performed in 237 serum samples by enzyme-linked immunosorbent assay (ELISA) and fixed cell-based assay (f-CBA-IFA). One hundred and forty-eight (148) of the sera had previously been tested by RIA during clinical testing: 47 MuSK antibody positive and 101 MuSK antibody negative. Of the MuSK RIA negative antibodies, 46 tested positive for other neural antibodies. Additionally, 89 sera were subsequently tested by all three methods: 70 healthy controls and 19 sera positive for other neural antibodies. RESULTS: Qualitative inter-assay agreement based on tiered RIA values was 100% for results of 1.00 nmol/L or greater by both methods; 81% and 94% for results between 0.21 and 0.99 nmol/L by ELISA and f-CBA-IFA, respectively; and 0% for results of 0.04-0.20 nmol/L by both methods. Negative results showed 100% agreement between RIA and both ELISA and f-CBA-IFA (n = 55). None of the controls positive for other neural autoantibodies or healthy controls were positive in any assay. CONCLUSION: Overall, excellent agreement was observed between the 3 methods used to detect antibodies against MuSK. Both the f-CBA-IFA and ELISA performed comparably to RIA and exhibited excellent overall accuracy for MuSK IgG detection, with the f-CBA-IFA demonstrating higher agreement between positive samples with the RIA than the ELISA without identifying false positives in the control samples. Advantages of non-radioactive methods for the detection of MuSK antibodies include reduced handling and disposal of hazardous materials, potential for automation and the reagents having a longer shelf-life, reducing costs associated with both workflow and lot validations. Thus, commercially available ELISA and transfected cell-based assays are viable alternatives to the traditional radioactive assay used for serologic determination of MuSK IgG.

High level of agreement in a fixed vs. live cell-based assay for antibodies to myelin oligodendrocyte glycoprotein in a real-world clinical laboratory setting.

Introduction: As recognition of myelin oligodendrocyte glycoprotein (MOG) antibody-associated disease becomes more widespread, the importance of appropriately ordering and interpreting diagnostic testing for this antibody increases. Several assays are commercially available for MOG testing, and based on a few small studies with very few discrepant results, some have suggested that live cell-based assays (CBA) are superior to fixed CBA for clinical MOG antibody testing. We aimed to determine the real-world agreement between a fixed and live CBA for MOG using two of the most commonly available commercial testing platforms. Methods: We compared paired clinical samples tested at two national clinical reference laboratories and determined the real-world agreement between the fixed CBA and live CBA. Results: Of 322 paired samples tested on both platforms, 53 were positive and 246 were negative by both methodologies (agreement 92.9%, Cohen's kappa 0.78, [0.69-0.86]). Spearman correlation coefficient was 0.80 (p < 0.0001). Of the discrepant results, only 1 of 14 results positive by the live CBA had a titer greater than 1:100, and only 1 of 9 results positive by the fixed CBA had a titer of greater than 1:80. Lower titers on the fixed CBA correlate to higher titers on the live CBA. Conclusion: Overall, there is excellent agreement between fixed and live CBA for MOG antibody testing in a real-world clinical laboratory setting. Clinicians should be aware of which method they use to assess any given patient, as titers are comparable, but not identical between the assays.

Trends in Blood Lead Levels Quantified by ICP-MS: A Reference Laboratory Retrospective Study.

BACKGROUND: Exposure to lead may cause severe adverse effects such as anemia, neurologic damage, developmental disorders, and reproductive disorders. Consequently, in 2021, the Centers for Disease Control and Prevention (CDC) reduced its blood lead reference value from 5 µg/dL to 3.5 µg/dL in pediatric patients, 1 to 5 years old. The objective of this study was to perform a retrospective analysis of patient blood lead concentrations reported by ARUP Laboratories to evaluate the frequency of blood lead concentrations greater than 3.5 µg/dL. METHODS: The analysis of blood lead concentration was performed in venous whole blood specimens using inductively coupled plasma mass spectrometry (ICP-MS). In addition, retrospective data analysis was performed to evaluate zinc protoporphyrin (ZPP) concentrations in adult patients with corresponding lead results, using the lead industrial exposure panel. The analysis for ZPP was performed using quantitative hematofluorometry. RESULTS: Retrospective data analysis identified a decline in blood lead concentrations from 2012 to 2021 for pediatric and adult patients. The calculated nonparametric 95% range for ZPP blood was 15 to 43 µg/dL and the ZPP heme ratio 26 to 74 µmol ZPP/mol heme. CONCLUSIONS: Lowering the blood lead reference value (BLRV) to 3.5 µg/dL presents an opportunity for healthcare providers and public health agencies to extend medical or environmental interventions for lead exposure in pediatric patients.

Improvement of lipid and lipoprotein profiles in children and adolescents with cystic fibrosis on CFTR modulator therapy.

BACKGROUND: Association of a high-fat diet with increased risks of cardiovascular disease (CVD) and type 2 diabetes, has prompted evaluation of lipids in people with CF (pwCF). However, most evidence on dyslipidemia was published before CF transmembrane conductance regulator (CFTR) modulators became a standard of care. The main goal of this study was to investigate the effect of CFTR modulator therapies on lipid and lipoprotein profiles in children and adolescents with CF. METHODS: Blood samples were collected from 153 pwCF (10.1 ± 4.7 years of age) and 60 age-matched controls. Most pwCF were pancreatic insufficient on pancreatic enzyme replacement therapy. By the end of the study, 65% of CF participants were on CFTR modulator therapy for >1 month. The results of traditional and advanced lipid testing in pwCF were correlated with clinical and dietary information. RESULTS: Total cholesterol and low-density lipoprotein (LDL) cholesterol were significantly lower in pwCF compared to non-CF participants. Those not receiving CFTR modulators also had significantly lower high-density lipoprotein (HDL) cholesterol and HDL particle number than controls. Individuals with CF on modulator therapy had significantly higher concentrations of anti-atherogenic HDL cholesterol and HDL particles along with lower levels of atherogenic large very-low density lipoprotein (VLDL) particles, total and small LDL particles, and triglycerides compared to those without CFTR modulator therapy. CONCLUSION: CFTR modulator therapy has a beneficial effect on dyslipidemia in CF. It remains to be seen if these positive changes translate into decreased CVD risk later in life given the increasing life expectancy in CF.

Quantitative analysis of ethanolamine plasmalogen species in red blood cells using liquid chromatography tandem mass spectrometry for diagnosing peroxisome biogenesis disorders.

Plasmalogens are glycerophospholipids characterized by a vinyl-ether bond with a fatty alcohol at the sn-1 position, a polyunsaturated fatty acid at the sn-2 position, and a polar head at the sn-3 position, commonly phosphoethanolamine. Plasmalogens play crucial roles in several cellular processes. Reduced levels have been associated with Alzheimer's and Parkinson's disease progression. Markedly reduced plasmalogens are a classic feature of peroxisome biogenesis disorders (PBD) because plasmalogen synthesis requires functional peroxisomes. Particularly, severe plasmalogen deficiency is the biochemical hallmark of rhizomelic chondrodysplasia punctata (RCDP). Traditionally, plasmalogens are evaluated in red blood cells (RBCs) by gas-chromatography/mass-spectrometry (GC-MS), which cannot distinguish individual species. We developed a liquid-chromatography/tandem mass-spectrometry (LC-MS/MS) method to quantify eighteen phosphoethanolamine plasmalogens in RBCs to diagnose PBD patients, especially RCDP. Validation results showed a specific, robust, and precise method with broad analytical range. Age-specific reference intervals were established; control medians were used to assess plasmalogen deficiency in patients' RBCs. Clinical utility was also confirmed in Pex7 deficient mouse models recapitulating severe and milder RCDP clinical phenotypes. To our knowledge, this is the first attempt to replace the GC-MS method in the clinical laboratory. In addition to diagnosing PBDs, structure-specific plasmalogen quantitation could help understand disease pathogenesis and monitor therapy.

LC-MS/MS Method for Measurement of Thiopurine Nucleotides (TN) in Erythrocytes and Association of TN Concentrations With TPMT Enzyme Activity.

Monitoring concentrations of thiopurine metabolites is used clinically to prevent adverse effects in patients on thiopurine drug therapy. We developed a LC-MS/MS method for the quantification of 6-thioguanine (6-TG) and 6-methylmercaptopurine (6-MMP) in red blood cells (RBCs). This method utilizes an automated cell washer for RBC separation from whole blood samples and washing of the separated RBCs. The lower limit of quantification of the method was 0.2 µmol/L for 6-TG (∼50 pmol/8 × 108 RBC) and 4 µmol/L for 6-MMP (∼1,000 pmol/8 × 108 RBC). The total imprecision of the assay was <3.0%. The upper limit of linearity for 6-TG and 6-MMP was 7.5 µmol/L and 150 µmol/L, respectively. The stability of the thiopurine metabolites under pre- and post-analytically relevant conditions was also evaluated. A good agreement was observed between this method and validated LC-MS/MS methods from three laboratories, except for ∼40% low bias for 6-MMP observed in one of the methods. The assessment of the association between 6-TG and 6-MMP concentrations with thiopurine S-methyltransferase (TPMT) phenotype and genotype demonstrated a statistically significant difference in the thiopurine metabolite concentrations between the TPMT groups with normal and intermediate activity of 6-MMP (p < 0.0001), while the difference in 6-TG concentrations was statistically not significant (p = 0.096). Among the samples with normal TPMT activity, higher concentrations of 6-MMP (p = 0.015) were observed in pediatric samples than in the samples of adults. No statistically significant differences were observed in the distributions of 6-TG and 6-MMP concentrations among the evaluated genotypes.

Assessment of a Line Immunoassay for the Detection of Mi-2 Antibodies: Results From a Single Academic Center Investigation.

OBJECTIVES: To evaluate the performance characteristics of a line immunoassay (LIA) for the detection of Mi-2 antibodies associated with dermatomyositis (DM). METHODS: In total, 432 consecutive patient specimens were tested for Mi-2 antibodies concurrently by LIA (Mi-2α or Mi-2ß) or immunoprecipitation (IP) test and antinuclear antibody by indirect immunofluorescence assay using HEp-2 substrate. Following antibody evaluation, results for patients positive in any of the assays for Mi-2 antibody had a retrospective chart review for diagnostic categorization. The performance of all tests was evaluated based on the extracted clinical data. RESULTS: Forty patients were positive in at least one of the Mi-2 assays. The frequency of Mi-2ß antibody by LIA was highest (75.0%), followed by Mi-2 by IP (35.0%) and Mi-2α by LIA (20.0%), respectively. Mi-2 by IP had the best total percent agreement for DM (95.0%) compared with 70.0% and 25.0% for the LIA Mi-2α and Mi-2ß, respectively. Positivity of the Mi-2ß antibody was significantly associated with non-DM diagnosis. CONCLUSIONS: Agreement for DM with assays for detecting Mi-2 is variable. Additional studies are required to validate Mi-2 immunoassays for routine patient evaluation.

Establishing age-stratified red blood cell fatty acid reference ranges using model-based clustering and iterative application of the harris-boyd method.

BACKGROUND: The current assessment of nutritional status and diagnosis of essential fatty acids deficiency (EFAD) utilizes the analysis of long-chain fatty acids (LCFAs) in serum or plasma; however, these concentrations do not represent habitual LCFA intake. LCFAs in red blood cells (RBCs) are less prone to intra-individual variability and exclude the need for fasting, which is unrealistic in pediatric populations. Our study objective was to characterize the RBC LCFA profiles in pediatric and adult reference populations and establish age-specific reference intervals (RIs). METHODS: Twenty-one LCFAs in RBCs were measured in 523 pediatric and adult controls by gas chromatography-mass spectrometry. Model-based clustering was used to identify possible age subgroups. After removing outliers by the Tukey method, initial age subgroups were then compared using the Harris-Boyd method in an iterative manner. RIs (95%), with confidence intervals (90%), in the final age groups were established using parametric or non-parametric statistics. RESULTS: Our data showed heterogeneous changes in the concentrations of most LCFAs and the EFAD biomarkers (mead acid, Triene/Tetraene ratio) during infancy. Model-based clustering identified six initial age subgroups per fatty acid, on average. Our application of the iterative Harris-Boyd method decreased the average number of age groups to three per fatty acid, with 13 total unique age cut-offs. Finally, using these age groups, we established age-specific RIs for 21 fatty acids, six group totals, and the Triene/Tetraene ratio. CONCLUSION: Our study revealed significant age-dependent changes in RBC fatty acid profiles warranting separate pediatric and adults RIs. Model-based clustering and the iterative application of the Harris-Boyd method were successfully used to establish RBC fatty acid RIs for an objective assessment of long-term nutritional status in pediatric and adult populations.

Retrospective comparison of results for simultaneous orders for LDL particle count, apolipoprotein B, and LDL-C.

BACKGROUND: Analysis of lipoprotein size and composition by nuclear magnetic resonance (NMR) has been advocated as a method for identifying individuals at high CVD risk. We compared risk stratification between NMR-based LDL particle number (LDL-PNUM), LDL-cholesterol (LDL-C), and apolipoprotein B (apoB). METHODS: Retrospective data from patients with simultaneous orders for LDL-PNUM, LDL-C, and apoB were analyzed and included data from an NMR assay (Numares). Quantitative and qualitative analyses were performed. Additional lipid parameters were investigated for patients with discordant risk classifications in LDL-related measurements. The percent change of LDL-PNUM was compared to the percent change of LDL-C or apoB for patients with serial measurements. RESULTS: We observed good quantitative and qualitative correlation when comparing LDL-PNUM to either LDL-C or apoB (Spearman's ρ ≥ 0.83, percent agreements ≥ 85%). Among the patients with discordant risk stratification, most had increased LDL-PNUM and normal LDL-C and apoB. For patients with serial measurements, a strong correlation between the LDL-PNUM percent change and the LDL-C or apoB percent change was observed (Spearman's ρ > 0.93). CONCLUSION: For many patients, risk stratification of LDL-PNUM is similar to apoB or LDL-C using cut-offs proposed by guidelines.

Augmented Human Intelligence and Automated Diagnosis in Flow Cytometry for Hematologic Malignancies.

OBJECTIVES: Clinical flow cytometry is laborious, time-consuming, and expensive given the need for data review by highly trained personnel such as technologists and pathologists as well as the significant number of normal cases. Given these issues, automation in analysis and diagnosis holds the key to major efficiency gains. The objective was to design an automated pipeline for the diagnosis of B-cell malignancies in flow cytometry and evaluate its performance against our standard clinical diagnostic flow cytometry process. METHODS: Using 3,417 cases of peripheral blood data over 6 months from our 10-color B-cell screening tube, we used a newly described method for feature extraction and dimensionality reduction called UMAP on the raw flow cytometry data followed by random forest classification to classify cases without gating on specific population. RESULTS: Our automated classifier was able to achieve greater than 95% accuracy in diagnosing all B-cell malignancies, and even better performance for specific malignancies for which the panel was designed, such as chronic lymphocytic leukemia. By adjusting classifier cutoffs, 100% sensitivity could be achieved with an albeit low 14% specificity. Hypothetically, this would allow 11% of the cases to be autoverified without human intervention. CONCLUSIONS: These results suggest that a clinical implementation of this pipeline can greatly assist in quality control, improve turnaround time, and decrease staff workloads.