Search Results (7,235)

Tumor mutational burden (TMB) is a key pan-cancer biomarker for immunotherapy selection, but its routine assessment by whole-exome sequencing (WES) or large next-generation sequencing (NGS) panels is costly, time-consuming, and constrained by tissue and DNA quality. In parallel, advances in computational pathology have enabled deep learning models to infer molecular biomarkers directly from hematoxylin and eosin (H&E) whole-slide images (WSIs), raising the prospect of a purely digital assay for TMB. In this comprehensive review, we surveyed PubMed and Scopus (2015–2025) to identify original studies that applied deep learning directly to H&E WSIs of human solid tumors for TMB estimation. Across the 17 eligible studies, deep learning models have been applied to predict TMB from H&E WSIs in a variety of tumors, achieving moderate to good discrimination for TMB-high versus TMB-low status. Multimodal architectures tended to outperform conventional CNN-based pipelines. However, heterogeneity in TMB cut-offs, small and imbalanced cohorts, limited external validation, and the black-box nature of these models limit clinical translation. Full article

The use of antiretroviral therapy (ART) as the only effective way to control human immunodeficiency virus (HIV) infection results in HIV drug resistance. Next-generation sequencing (NGS) has become a common method for identifying drug-resistant variants and reducing analysis costs. The aim of this study was to develop an NGS-based protocol for identifying resistance mutations and cell tropism of HIV-1 in adult patients with and without treatment experience in Russia in 2024–2025. Plasma samples from adult HIV-infected patients from Russia were analyzed. Consensus nucleotide sequences of pol and env genes were obtained using NGS. HIV-1 drug resistance analysis was conducted using the Stanford University HIVdb database. CXCR4 cell tropism was predicted using an empirical rule classifier. A protocol for NGS of HIV-1 pol and env genes was developed. The most common HIV-1 surveillance mutations were in the reverse transcriptase. High levels of resistance were observed to non-nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTIs) in treatment-experienced patients and to NNRTIs in treatment-naïve patients. Low levels of resistance were observed to protease and integrase strand transfer inhibitors (INSTIs). CXCR4 cell tropism was extremely rare. NGS allows for the simultaneous processing of large data sets during epidemiological studies. The introduction of NGS-based protocols allows for performing ART efficiency and tropism monitoring at scale. Full article

The Cladia aggregata group of lichen-forming fungi comprises multiple species that are difficult to differentiate based on phenotypic characters. It has a wide distribution across several continents, but is most diverse in Australasia. We aimed to delimit the species complex further, investigate the relatedness of the lineages, and examine their distributional ranges and phenotypic traits. We used Restriction Site Associated DNA Sequencing (RAD-seq) to compare thousands of loci across 91 individuals from the Americas, Asia, and Australasia. All Asian samples formed a distinct, monophyletic clade in all phylogenetic trees, while the American samples divided into two clades, one comprising South American samples and another comprising Caribbean samples, with the latter representing C. aggregata sensu stricto, as the type specimen was collected in Jamaica. Further population-genomic analyses support the conclusion that the Asian samples are genetically distinct and are here described as a new species. The new species, Cladia asiatica, accommodates the Asian samples previously included in C. aggregata. Our analysis highlights the potential of next-generation sequencing to reveal hidden diversity and resolve the phylogeny of this species complex and lichen-forming fungi in general. Full article

Vancomycin-resistant Enterococcus faecium (VREfm) is an emerging pathogen responsible for healthcare-associated infections. For this reason, 44 VREfm isolates collected during 2021–2023 were characterized using phenotypic and genomic approaches. VREfm isolates were identified by MALDI-TOF and antimicrobial susceptibility tests were performed with Vitek 2, Sensititre, or E-test. Sequence type (ST), antibiotic resistance genes, virulence factors and genetic relatedness were determined using Next Generation Sequencing. Forty-three isolates had a VanA phenotype and vanHAX genotype and one had a VanB phenotype and vanHBX genotype. Isolates showed high antibiotic resistance to various antibiotics, but generally remained susceptible to quinupristin/dalfopristin, tigecycline and eravacycline. Two isolates were resistant to linezolid, showing the chromosomal mutation G2576T in domain V of the 23S rRNA gene in one isolate, and the transferable linezolid resistance genes cfr(D) and optrA in the other. Thirty-eight isolates belonged to ST80, one to ST17 (ST80 and ST17 are included in CC17) and one to ST697. Genomic analysis of the ST80 isolates showed that nearly all of them belonged to a single cluster. To prevent further spread of VREfm in the nosocomial environment, in addition to the application of up-to-date infection control strategies and antibiotic stewardship programs, the implementation of genomic surveillance is recommended. Full article

The bacterial microbiome in aquaria plays an essential role in system stability by metabolizing toxic compounds like ammonia. This study monitored microbiome changes in seven zoo aquatic systems during their first year to assess responses to external influences. Over one year (October 2021–October 2022), water and swab samples were collected from one seawater tank and six filtration systems at regular intervals. Bacterial cultivation included total bacterial counts. Metagenomic analysis was performed on samples corresponding to environmental events using Oxford Nanopore sequencing. Taxonomical analysis at the phylum and genus levels used EPI2ME software. Diversity analyses and statistical tests were performed using R. Total bacterial counts increased steadily after inoculation and stabilized by the end of the collection period. Diversity analysis revealed significant differences within and between freshwater and saltwater tanks. Each aquarium exhibited a distinct bacterial community with frequent compositional changes. Despite environmental conditions and maintenance interventions and resulting disturbances that affected the microbiome, the overall nitrifying capacity remained unaffected. Nitrifying taxa emerged as potential indicators for environmental effects. Combined with investigations of ecological function, next-generation sequencing could facilitate the development of aquarium management protocols, ultimately improving fish welfare. Full article

The gut plays a central role in fish nutrition, immunity, and overall health, making it key in aquaculture research. The microbiota, crucial to gut function, is increasingly studied as an indicator of health and nutritional status. This study characterized the gut microbiota of juvenile meagre (Argyrosomus regius) (initial weight 4.6 ± 0.4 g) fed for seven weeks on diets in which fishmeal (FM) and fish oil (FO) were replaced by increased proportions of plant-based ingredients, with the aim of identifying microbial profiles associated with nutritional challenge. Fish were fed a FM/FO control diet (CTRL; 55.1% FM, 11.3% FO), a low FM/FO diet (CD; 15% FM, 7% FO), or a very low FM/FO diet (ED; 5% FM, 5% FO). Next-generation sequencing analysis of gut mucosa and digesta revealed no significant differences in alpha or beta diversity among different dietary groups. Firmicutes dominated all samples, particularly Bacilli, Mycoplasmatales, Mycoplasmataceae, and Mycoplasma. Significant differences were only observed in low-abundance taxa (<1%), with higher abundance of Thermoactinomycetales (p = 7.71 × 10⁻⁴), Thermoactinomycetaceae (p = 7.71 × 10⁻⁴), Kroppenstedtia (p = 1.70 × 10⁻³), and Pseudogracilibacillus (p = 0.039) in challenged groups. This study highlights the potential of low-abundance microbial groups as targets to establish gut health biomarkers in fish. Full article

Tuberculosis (TB) remains one of the leading causes of death from a single infectious agent worldwide, a burden further exacerbated by HIV co-infection and the increasing prevalence of drug-resistant strains. Although a wide range of laboratory diagnostic methods are currently available, their applicability, implementation, and clinical impact vary substantially across healthcare settings with different levels of complexity and resources. This review provides a comprehensive overview of the main laboratory diagnostic methods for active and latent TB, emphasizing their clinical applicability, implementation challenges, and role within integrated diagnostic strategies. Conventional approaches, such as smear microscopy and culture, are discussed alongside modern diagnostic technologies, including automated nucleic acid amplification tests (NAATs), loop-mediated isothermal amplification (LAMP), line probe assays (LPAs), next-generation sequencing (NGS), and lateral flow assays, highlighting their strengths and limitations in distinct epidemiological and operational contexts. Unlike existing WHO guidelines and prior reviews that predominantly focus on test performance and recommendation status, this review adopts an implementation-oriented perspective, critically examining diagnostic methods in light of real-world constraints, regional disparities, and evidence gaps. Particular attention is given to limitations related to laboratory infrastructure, biosafety, workforce capacity, and sustainability, as well as to under-addressed areas such as latent TB, metagenomic approaches, and the investigation of co-pathogens. By integrating WHO guidance with contextual and operational considerations, this review aims to support rational test selection and the development of flexible, integrated diagnostic workflows tailored to local health system capacity, patient populations, and clinical scenarios, thereby strengthening the effectiveness and equity of TB diagnostic strategies. Full article

Terahertz wireless communication offers ultra-high bandwidth, enabling an extremely high data rate for next-generation networks. However, it faces challenges including severe propagation loss and atmospheric absorption, which limits the transmission rate and transmission distance. To address the problem, polarization division multiplexing (PDM) and antenna diversity techniques are utilized in this work to increase system capacity without changing the bandwidth of transmitted signals. Meanwhile, duobinary shaping is used to solve the problem of bandwidth limitation of components in the system, and the final duobinary signals are recovered by maximum likelihood sequence detection (MLSD). A Gaussian mixture model (GMM)-enhanced duobinary unsupervised adaptive convolutional neural network (DB-UACNN) is proposed, to further deal with channel noise. Based on the technologies above, a 2 × 2 multiple-input multiple-output (MIMO) photonic-aided terahertz wireless transmission system at 300 GHz is demonstrated. Experimental results have proved that the signal-to-noise ratio (SNR) gain of duobinary shaping is up to 1.87 dB and 1.70 dB in X-polarization and Y-polarization. The proposed GMM-enhanced DB-UACNN also shows extra SNR gain of up to 2.59 dB and 2.63 dB in X-polarization and Y-polarization, compared to the conventional duobinary filter. The high transmission rate of 100 Gbit/s over the distance of 200 m is finally realized under a 7% hard-decision forward error correction (HD-FEC) threshold. Full article

Background: KMT2A rearrangements are a frequent genetic abnormality associated with Acute myeloid leukemia (AML), historically linked to varied prognoses and outcomes. The prognosis for patients with this rearrangement remains controversial, necessitating further research to stratify risk and guide treatment. Methods: In this retrospective study, a total of 3468 adolescent and adult AML patients were screened, and 181 patients harboring KMT2A rearrangements were analyzed. We used FISH, RT-PCR, and next-generation sequencing, including transcriptome and targeted panels, for diagnosis and mutation profiling. All patients received intensive chemotherapy. We evaluated overall survival and event-free survival using Kaplan–Meier and Cox regression models, with HSCT analyzed as a time-dependent variable. Results: The incidence of KMT2A-rearranged AML in our newly diagnosed cohort was 5.9%. Among the 181 patients included in the final analysis, 89 (49.2%) were male and 92 (50.8%) were female, with a median age of 33 years (range: 13–65). The distribution of fusion partners included KMT2A::MLLT3 (n = 39), KMT2A::AFDN (n = 27), KMT2A::MLLT10 (n = 25), KMT2A::ELL (n = 24), and others (n = 12). Seventy-four patients underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT) in first complete remission (CR1). The median follow-up for survivors was 17.53 months (range 1.47–112.57), and the 3-year overall survival (OS) and event-free survival (EFS) for the entire cohort were 42.0% and 32.1%, respectively. Patients with KMT2A::ELL exhibited superior OS compared to other subtypes (3-year OS [ELL vs. non-ELL]: 59.8% vs. 39.3%, p = 0.023). Concomitant mutations did not significantly impact the prognosis of KMT2A-rearranged AML patients. In multivariate analysis, age and HSCT in CR1 were independently associated with OS and EFS (OS: HR = 1.022, p = 0.026 [age]; HR = 0.238, p < 0.001 [HSCT]; EFS: HR = 1.027, p = 0.002 [age]; HR = 0.155, p < 0.001 [HSCT]). Patients aged over 20 years were more likely to benefit from HSCT than those aged 20 years or younger (p < 0.001 [age > 20], p = 0.780 [age ≤ 20]). Conclusions: Our study revealed the heterogeneous outcomes of KMT2A-rearranged AML patients and clarified the impact of HSCT across different age groups. Full article

Objectives: Respiratory syncytial virus (RSV) is a leading cause of hospitalization for acute lower respiratory tract infections (ALRIs) in children, with bacterial coinfection complicating diagnosis and often driving antibiotic overuse. This study aimed to develop and validate a clinical prediction model using common laboratory biomarkers to enable early, accurate identification of clinically significant bacterial coinfection in children with RSV infection. Methods: A single-center, retrospective cohort study was conducted at Fujian Children’s Hospital, enrolling 518 hospitalized children with RSV infection, which was confirmed via targeted next-generation sequencing (tNGS). Patients were randomly divided into a training set (n = 363) and a test set (n = 155) at a 7:3 ratio. The primary outcome, bacterial coinfection, was defined by a composite reference standard integrating etiological evidence from tNGS with clinical, inflammatory, and imaging data, and adjudicated by a blinded expert panel. LASSO regression identified independent predictors, followed by multivariable logistic regression modeling. Model performance was assessed via discrimination (AUC), calibration (Hosmer–Lemeshow test), and clinical utility (Decision Curve Analysis) in both sets. Results: Neutrophil-to-lymphocyte ratio (NLR), C-reactive protein (CRP), and serum amyloid A (SAA) were selected as predictors. The model achieved an AUC of 0.832 (95% CI: 0.788–0.875) in the training set and 0.811 (95% CI: 0.737–0.885) in the test set, with well-calibrated predictions (p > 0.05). Decision curve analysis demonstrated net clinical benefit across 10–80% threshold probabilities. A nomogram was developed for practical application. Conclusions: This study established a model integrating NLR, CRP, and SAA. It offers a reliable tool for the early detection of bacterial coinfection in RSV-infected children, enabling targeted antibiotic stewardship and improving clinical outcomes. Full article

Circulating tumor cells (CTCs) are shed from the primary tumor into the bloodstream and represent dynamic molecular biomarkers for monitoring the progression of cancer. While profiling tumor tissues with over expression of cell surface markers, such as PD-L1 or HER2, is standard in guiding therapy, tissue samples are often inaccessible and inadequate, especially post-surgery or in cases of recurrence. Emerging clinical evidence indicates that CTC counts and biomarker surface expression can predict prognosis and therapeutic resistance more accurately than imaging or tissue-based approaches. Recent advancements in the CTC detection methods, based on physical properties or surface markers (e.g., EpCAM), coupled with next-generation sequencing (NGS) have enabled the isolation of these rare cells and their molecular characterization. Consequently, CTCs provide a real-time alternative, enabling repeated, longitudinal assessment of tumor phenotype and therapeutic response. This review emphasizes the translational potential of surface protein biomarkers on CTCs for profiling, namely PD-L1, HER2, and EGFR, as a clinically actionable approach to stratify patients, guide immunotherapy decisions, and monitor minimal residual disease (MRD), especially when longitudinal tissue biopsies are not feasible. Full article

Introduction: Epilepsy syndromes show marked clinical and genetic heterogeneity, with numerous functionally diverse genes involved in their etiology. Next-generation sequencing (NGS) has facilitated the identification of many monogenic epilepsy syndromes and enables earlier, more accurate diagnosis in pediatric patients. Materials and Methods: This study analyzes the molecular profiles of 87 pediatric patients with various forms of epilepsy in whom pathogenic or likely pathogenic variants were identified. Next-generation sequencing (NGS) using multi-gene epilepsy panels or whole-exome sequencing (WES) was performed. Results: A total of 88 pathogenic or likely pathogenic variants were detected in 48 epilepsy-related genes; 30 variants occurred de novo. SCN1A and KCNQ2 were the most frequent contributors (12.6% and 9.2%, respectively). The highest percentage of positive diagnoses (48%) was observed in patients with developmental and epileptic encephalopathy (DEE), with variants identified in genes including ALG13, ATP1A2, CACNA1A, CDKL5, CHD2, GABRG2, ITPA, KCNQ2, PCDH19, SCN1A, SCN2A, SCN3A, SCN8A, SMC1A, SPTAN1, STXBP1, and UBA5. Pathogenic variants in ANKRD11 were found in four patients with KBG syndrome, while other genes appeared sporadically. Conclusions: Targeted massively parallel sequencing is an effective diagnostic tool for pediatric epilepsy. The presence of numerous single-case findings highlights the high genetic heterogeneity of epilepsy. This approach enabled more precise diagnoses that would not have been achieved through clinical evaluation alone, underscoring the importance of genetic testing for prognosis and treatment planning in pediatric patients with unexplained epilepsy. Full article

Background/Objectives: Cardiac arrhythmias are among the leading causes of sudden cardiac death (SCD). Pathogenic variants in potassium channel genes play a key role in inherited arrhythmia syndromes, yet their contribution in Central Asian populations remains poorly characterized. Methods: We performed targeted next-generation sequencing (NGS) using a 96-gene custom Haloplex panel in 79 Kazakhstani patients with clinically diagnosed arrhythmias, including atrioventricular block, sick sinus syndrome, and atrial fibrillation. Detected variants in potassium channel genes were classified according to ACMG guidelines and correlated with clinical phenotypes. Results: A total of 52 variants were identified across 11 potassium channel genes. Two likely pathogenic variants (KCNH2 p.Cys66Gly and p.Arg176Trp) and six variants of uncertain significance (VUS) in KCNQ1, KCNE2, KCNE3, and KCNJ8 were detected. Two novel previously unreported variants were found in KCNE5 and KCND3. Patients harboring pathogenic variants commonly presented with early-onset arrhythmias or a positive family history of cardiovascular disease. Carriers of KCNH2 variants exhibited mild QT prolongation and recurrent syncope. Conclusions: This is the first genetic study of potassium channel gene mutations in Kazakhstani patients with cardiac arrhythmias. The detection of pathogenic and novel variants highlights the clinical utility of integrating genetic testing into diagnostic and management pathways for arrhythmia syndromes. Population-specific genomic data are essential for improving risk stratification, guiding medication safety, and enabling cascade family screening in Central Asia. Full article

Background/Objectives: In severe peripheral artery disease (PAD) with limb ischemia, hypercholesterolemia (HC) is associated with impaired neovascularization. Extracellular vesicles (EVs) are present within ischemic muscles, and they contain microRNAs (miRs) involved in several biological functions, including angiogenesis and neovascularization. Methods: We used a mouse model of PAD and compared the response to hindlimb ischemia in hypercholesterolemic ApoE^−/− vs. normocholesterolemic mice. Next-generation sequencing (NGS) was used to perform full miR expression profiling in ischemic skeletal muscles and in EVs of varying sizes—large EVs (lEVs) and small EVs (sEVs)—within these muscles. Results: We identified several miRs with potential pro-angiogenic effects (angiomiRs) that are reduced by HC in lEVs (Let-7b-5p, miR-151-3p, Let-7c-5p) or sEVs (miR-21a-5p, miR-196b-5p, miR-340-5p). As proof of principle, we showed that the overexpression of Let-7b-5p in lEVs, or miR-21a-5p in sEVs, can significantly increase the angiogenic capacity of these EVs in vitro. HC also impaired the enrichment of specific angiomiRs in lEVs (miR-100-5p), sEVs (miR-142a-3p), or in both lEVs and sEVs (miR-146b-5p). In silico approaches, including the prediction of miR targets, pathway unions, and gene unions, identified the resulting predictive effects of HC-modulated miRs in EVs on processes with key roles in the modulation of angiogenesis and neovascularization, such as the regulation of the actin cytoskeleton and focal adhesion and the HIF-1, MAPK, AMPK, and PI3K-Akt signaling pathways. Conclusions: Our results constitute an important first step towards the identification of specific miRs that could be targeted to improve EV angiogenic function in hypercholesterolemic conditions and reduce tissue ischemia in patients with severe PAD. Full article

Background: Thymic epithelial tumors (TETs), including thymic carcinomas and thymomas, are rare malignancies originating in the mediastinum. Therapeutic options remain limited for patients experiencing disease progression following platinum-based chemotherapy. High tumor mutational burden (TMB) is uncommon in thymic malignancies but may predict response to immunotherapy. We report a patient with TMB-high TET who participated in the KOSMOS-II study in South Korea and achieved a durable response to atezolizumab without developing immune-related adverse events (irAEs). Case presentation: A 73-year-old woman who had been treated for thymoma 20 years ago presented with a left neck mass. A biopsy of the neck mass confirmed recurrent thymoma, type B3, and her disease progressed despite platinum-based chemotherapy and subsequent pemetrexed treatment. TMB-high thymoma is very rare, but based on the next-generation sequencing (NGS) results, she was diagnosed with TMB-high (20.3 mutations/Mb) thymoma. As TMB-based immunotherapy is not approved in Korea, she was enrolled in the KOSMOS-II study and initiated on atezolizumab following molecular tumor board review. She achieved stable disease after three cycles and has remained progression-free for 14 months, completing 20 cycles without significant irAEs. Notably, her underlying myasthenia gravis did not worsen during treatment. Conclusions: This case demonstrates a favorable outcome with biomarker-directed ICI treatment in recurrent thymoma with limited treatment options, highlighting the importance of appropriate molecular markers to predict drug response. Although TMB-based immunotherapy is FDA-approved in the U.S., it remains unavailable in Korea, underscoring the need to explore flexible access pathways, including the potential use of immunotherapy beyond current indications, to improve treatment options for patients with life-threatening conditions. Full article