Validation of targeted next-generation sequencing panels in a cohort of Polish patients with epilepsy: assessing variable performance across clinical endophenotypes and uncovering novel genetic variants

Introduction

Targeted Next-Generation Sequencing Panels (TNGSP) have become a standard in global clinical practice. Instead of questioning the necessity of next-generation sequencing in epilepsy patients, contemporary large-scale research focuses on factors such as the size of TNGSP, the comparative advantages of exome or genome-wide sequencing over TNGSP, and the impact of clinical, electrophysiological, and demographic variables on genetic test performance. This study aims to elucidate the demographic and clinical factors influencing the performance of TNGSP in 138 Polish patients with epilepsy, recognizing the pivotal role of genetic testing in guiding patient management and therapy.

Methods

A retrospective analysis was conducted on patients from a genetic clinic in Poznań, Poland, who underwent commercial gene panel studies at Invitae Corporation (USA) between 2020 and 2022. Patient groups were defined based on the age of onset of the first epileptic seizures, seizure type, gender, fever dependence of seizures, presence of intellectual disability or developmental delay, abnormalities in MRI, and the presence of dysmorphic features or congenital malformations. Seizure classification followed the 2017 ILAE criteria.

Results

Among the 138 patients, 30 (21.7%) exhibited a pathogenic or likely pathogenic variant, with a distribution of 20.7% in males and 22.5% in females. Diagnostic performance correlated with the patient's age at the onset of the first seizure and the type of seizure. Predominant variants were identified in the SCN1A, PRRT2, CDKL5, DEPDC5, TSC2, and SLC2A1 genes. Additionally, 12 genes (CACNA1A, SCN2A, GRIN2A, KCNQ2, CHD2, DYNC1H1, NEXMIF, SCN1B, DDX3X, EEF1A2, NPRL3, UBE3A) exhibited single instances of damage. Notably, novel variants were discovered in DEPDC5, SCN1A, TSC2, CDKL5, NPRL3, DYNC1H1, CHD2, and DDX3X.

Discussion

Identified variants were present in genes previously recognized in both European and non-European populations. A thorough examination of Variants of Uncertain Significance (VUSs), specifically focusing on gene copy number changes, may unveil more extensive chromosomal aberrations. The relatively frequent occurrence of pathological variants in X chromosome-linked genes in girls warrants further investigation, challenging the prevailing notion of male predominance in X-linked epilepsy.

MicroRNA panels as diagnostic biomarkers for colorectal cancer: A systematic review and meta-analysis

Background

Circulating microRNAs (miRNA) have emerged as promising diagnostic biomarkers for several diseases, including cancer. However, the diagnostic accuracy of miRNA panels in colorectal cancer (CRC) remains inconsistent and there is still lack of meta-analyses to determine whether miRNA panels can serve as robust biomarkers for CRC diagnosis.

Methods

This study performed a systematic review and meta-analysis to evaluate the clinical utility of miRNA panels as potential biomarkers for the diagnosis of CRC. The investigation systematically searched PubMed, Medline, Web of Science, Cochrane Library, and Google Scholar (21-year span, between 2000 and 2021) to retrieve articles reporting the diagnostic role of miRNA panels in detecting CRC. Diagnostic meta-analysis of miRNA panels used diverse evaluation indicators, including sensitivity, specificity, Positive Likelihood Ratio (PLR), Negative Likelihood Ratio (NLR), Diagnostic Odds Ratio (DOR), and the area under the curve (AUC) values.

Results

Among the 313 articles identified, 20 studies met the inclusion criteria. The pooled estimates of miRNA panels for the diagnosis of CRC were 0.85 (95% CI: 0.84-0.86), 0.79 (95% CI: 0.78-0.80), 4.06 (95% CI: 3.89-4.23), 0.20 (95% CI: 0.19-0.20), 22.50 (95% CI: 20.81-24.32) for sensitivity, specificity, PLR, NLR, and DOR, respectively. Moreover, the summary receiver operating characteristics (SROC) curve revealed an AUC value of 0.915 (95% CI: 0.914-0.916), suggesting an outstanding diagnostic accuracy for overall miRNA panels. Subgroup and meta-regression analyses demonstrated that miRNA panels have the highest diagnostic accuracy within serum samples, rather than in other sample-types - with a sensitivity, specificity, PLR, NLR, DOR, and AUC of 0.87, 0.86, 7.33, 0.13, 55.29, and 0.943, respectively. Sensitivity analysis revealed that DOR values did not differ markedly, which indicates that the meta-analysis had strong reliability. Furthermore, this study demonstrated no proof of publication bias for DOR values analyzed using Egger's regression test (P > 0.05) and funnel plot. Interestingly, miR-15b, miR-21 and miR-31 presented the best diagnostic accuracy values for CRC with sensitivity, specificity, PLR, NLR, DOR, and AUC values of 0.95, 0.94, 17.19, 0.05, 324.81, and 0.948, respectively.

Conclusion

This study's findings indicated that miRNA panels, particularly serum-derived miRNA panels, can serve as powerful and promising biomarkers for early CRC screening.

Systematic review registration

[www.crd.york.ac.uk/prospero], identifier [CRD42021268172].

Immunocytochemistry for diagnostic cytopathology-A practical guide

Cytological specimens, which are obtained by minimally invasive methods, are an excellent source of diagnostic material. Sometimes they are the only material available for diagnosis as well as for prognostic/predictive markers. When cytomorphology is not straightforward, ancillary tests may be required for a definitive diagnosis to guide clinical management. Immunocytochemistry (ICC) is the most common and practical ancillary tool used to reach a diagnosis when cytomorphology is equivocal, to differentiate entities with overlapping morphological features, and to determine the cell lineage and the site of origin of a metastatic neoplasm. Numerous immunomarkers are available, and some are expressed in multiple neoplasms. To rule out entities within a differential diagnosis, the use of more than one marker, sometimes panels, is necessary. ICC panels for diagnostic purposes should be customised based on the clinical context and cytomorphology, and the markers should be used judiciously to preserve material for additional tests for targeted therapies in the appropriate setting. This review offers a practical guide for the use of ICC for diagnostic cytopathology, covering the most commonly encountered non-hematolymphoid diagnostic scenarios in various body sites.

Biological Markers in Anxiety Disorders

Anxiety disorders are one of the most commonly reported disorders in psychiatry, causing a high medical and socio-economic burden. Recently, there has been a soaring interest in the biological basis of anxiety disorders, which is reflected in an increasing number of articles related to the topic. Due to the ambiguity of the diagnosis and a large number of underdiagnosed patients, researchers are looking for laboratory tests that could facilitate the diagnosis of anxiety disorders in clinical practice and would allow for the earliest possible implementation of appropriate treatment. Such potential biomarkers may also be useable in monitoring the efficacy of pharmacological therapy for anxiety disorders. Therefore this article reviews the literature of potential biomarkers such as components of saliva, peripheral blood, cerebrospinal fluid (CSF), and neuroimaging studies. There are promising publications in the literature that can be useful. The most valuable and promising markers of saliva are cortisol, lysozyme, and α-amylase (sAA). In the blood, in turn, we can distinguish serotonin, brain-derived serum neurotrophic factor (BDNF), cortisol, and microRNA. Structural changes in the amygdala and hippocampus are promising neuroimaging markers, while in CSF, potential markers include oxytocin and 5-Hydroxyindoleacetic acid (5-HIAA). Unfortunately, research in the field of biomarkers is hampered by insufficient knowledge about the etiopathogenesis of anxiety disorders, the significant heterogeneity of anxiety disorders, frequent comorbidities, and low specificity of biomarkers. The development of appropriate biomarker panels and their assessment using new approaches may have the prospective to overcome the above-mentioned obstacles.

Peripheral Markers of Depression

Major Depressive Disorder (MDD) is a leading cause of disability worldwide, creating a high medical and socioeconomic burden. There is a growing interest in the biological underpinnings of depression, which are reflected by altered levels of biological markers. Among others, enhanced inflammation has been reported in MDD, as reflected by increased concentrations of inflammatory markers-C-reactive protein, interleukin-6, tumor necrosis factor-α and soluble interleukin-2 receptor. Oxidative and nitrosative stress also plays a role in the pathophysiology of MDD. Notably, increased levels of lipid peroxidation markers are characteristic of MDD. Dysregulation of the stress axis, along with increased cortisol levels, have also been reported in MDD. Alterations in growth factors, with a significant decrease in brain-derived neurotrophic factor and an increase in fibroblast growth factor-2 and insulin-like growth factor-1 concentrations have also been found in MDD. Finally, kynurenine metabolites, increased glutamate and decreased total cholesterol also hold promise as reliable biomarkers for MDD. Research in the field of MDD biomarkers is hindered by insufficient understanding of MDD etiopathogenesis, substantial heterogeneity of the disorder, common co-morbidities and low specificity of biomarkers. The construction of biomarker panels and their evaluation with use of new technologies may have the potential to overcome the above mentioned obstacles.

Validation of Aztreonam-Avibactam Susceptibility Testing Using Digitally Dispensed Custom Panels

Aztreonam-avibactam is a combination antimicrobial agent with activity against carbapenemase-producing Enterobacteriaceae (CPE) with metallo-β-lactamases (MβLs). Although aztreonam-avibactam is not yet approved by the U.S. Food and Drug Administration (FDA), clinicians can administer this combination by using two FDA-approved drugs: aztreonam and ceftazidime-avibactam. This combination of drugs is recommended by multiple experts for treatment of serious infections caused by MβL-producing CPE. At present, in vitro antimicrobial susceptibility testing (AST) of aztreonam-avibactam is not commercially available; thus, most clinicians receive no laboratory-based guidance that can support consideration of aztreonam-avibactam for serious CPE infections. Here, we report our internal validation for aztreonam-avibactam AST by reference broth microdilution (BMD) according to Clinical and Laboratory Standards Institute (CLSI) guidelines. The validation was performed using custom frozen reference BMD panels prepared in-house at the Centers for Disease Control and Prevention (CDC). In addition, we took this opportunity to evaluate a new panel-making method using a digital dispenser, the Hewlett Packard (HP) D300e. Our studies demonstrate that the performance characteristics of digitally dispensed panels were equivalent to those of conventionally prepared frozen reference BMD panels for a number of drugs, including aztreonam-avibactam. We found the HP D300e digital dispenser to be easy to use and to provide the capacity to prepare complex drug panels. Our findings will help other clinical and public health laboratories implement susceptibility testing for aztreonam-avibactam.

The Influence of Processing and Particle Size on Binderless Particleboards Made from Arundo donax L. Rhizome

The giant reed (Arundo donax L.) is considered one of the world's 100 worst invasive species. The main method by which this species propagates is by growth of scattered fragments of rhizome, spreading without control with very strong, deep roots. Agricultural waste consists of lignocellulosic materials that can substitute natural wood and offer a suitable alternative with which to manufacture boards for furniture, packaging and building purposes. The objectives of this work were to obtain binderless particleboards using giant reed rhizome as the raw material, to evaluate their mechanical and physical properties according to the applicable European standards and to assess the self-binding mechanism of the particles in the board. Six types of boards (12 classes) were manufactured with giant reed rhizome biomass. They were manufactured with a temperature of 110 °C, a pressure of 2.5 MPa and pressing times of 7 and 15 min, applying one or two pressing cycles. The results achieved for modulus of rupture (14.2 N/mm2), modulus of elasticity (2052.45 N/mm2) and internal bonding strength (1.12 N/mm2) show that the mechanical properties were improved by using a smaller rhizome particle size and two pressing cycles.

Genetics in mainstream medicine: Finally within grasp to influence healthcare globally

A modern genomics ecosystem has emerged. This commentary describes recent trends in clinical genomics that enable its successful integration in mainstream medicine. The rapid expansion of clinical genomics will have a positive impact on the healthcare of individuals worldwide.

Health Care Expenditure and Income: A Global Perspective

This paper investigates the long-run economic relationship between healthcare expenditure and income in the world using data on 167 countries over the period 1995-2012, collected from the World Bank data set. The analysis is carried using panel data methods that allow one to account for unobserved heterogeneity, temporal persistence, and cross-section dependence in the form of either a common factor model or a spatial process. We estimate a global measure of income elasticity using all countries in the sample, and for sub-groups of countries, depending on their geo-political area and income. Our findings suggest that at the global level, health care is a necessity rather than a luxury. However, results vary greatly depending on the sub-sample analysed. Our findings seem to suggest that size of income elasticity depends on the position of different countries in the global income distribution, with poorer countries showing higher elasticity. Copyright © 2016 John Wiley & Sons, Ltd.

Prescriptive appropriateness using inhalant and food allergen panels: a comparison between General Practitioners' and Allergists' prescription in Genoa (Italy)

Background. Prescriptive appropriateness is an actual claim in healthcare, and it also concerns in vitro tests used in the allergy work-up, such as the serum allergen-specific IgE (sIgE) assay. In the Liguria Region, two panels were defined (for inhaled and food allergens) including 12 allergens. Their composition changed over time. Objectives. The aims of the present retrospective study were: i) to evaluate the percentage of positive tests, and ii) to compare the findings of sIgE assay on the basis of the general practictioners' (GPs) or specialist' prescription, considering both the old panels and the new panels. Methods. This retrospective study considered a population of adult patients, which consisted of 2368 subjects (68% females; mean age 50 years; age range: 10-103 years). Serum sIgE were measured by ImmunoCap system. Results. The percentages of positive tests were very low for food allergens and low for inhaled ones (ranging between 5% to 35%). There was change of prevalent prescriptor with new panels. Conclusions. This study underlines the relevance of prescriptive appropriateness in the allergy work-up. The sIgE assay should be limited to those allergens that have a clinical relevance, based on clinical history.

Sustainable Phenolic Fractions as Basis for Furfuryl Alcohol-Based Co-Polymers and Their Use as Wood Adhesives

Furfuryl alcohol is a very interesting green molecule used in the production of biopolymers. In the present paper, the copolymerization in acid environment with natural, easily-available, phenolic derivatives is investigated. The processes of polymerization of the furfuryl alcohol with: (i) spent-liquor from the pulping industry and (ii) commercial tannin from acacia mimosa were investigated though viscometry and IR-spectroscopy. The curing kinetics of the formulations highlighted the importance of the amount of furfuryl alcohol and catalyst as well as the effect of temperature for both phenolic-furanic polymers. Evidence of covalent copolymerization has been observed through infrared spectrometry (FT-IR) combined with principal component analysis (PCA) and confirmed with additional solubility tests. These bio-based formulations were applied as adhesives for solid wood and particleboards with interesting results: at 180 °C, the spent-liquor furanic formulations allow wood bonding slightly with lower performance than PVA in dry conditions, while mixed formulations allow the gluing of particleboard with only satisfactory internal bonding tests.

Estimating a reasonable patient panel size for primary care physicians with team-based task delegation

PURPOSE Primary care faces the dilemma of excessive patient panel sizes in an environment of a primary care physician shortage. We aimed to estimate primary care panel sizes under different models of task delegation to nonphysician members of the primary care team. METHODS We used published estimates of the time it takes for a primary care physician to provide preventive, chronic, and acute care for a panel of 2,500 patients, and modeled how panel sizes would change if portions of preventive and chronic care services were delegated to nonphysician team members. RESULTS Using 3 assumptions about the degree of task delegation that could be achieved (77%, 60%, and 50% of preventive care, and 47%, 30%, and 25% of chronic care), we estimated that a primary care team could reasonably care for a panel of 1,947, 1,523, or 1,387 patients. CONCLUSIONS If portions of preventive and chronic care services are delegated to nonphysician team members, primary care practices can provide recommended preventive and chronic care with panel sizes that are achievable with the available primary care workforce.