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Search Results (2,854)

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Keywords = next generation sequencing NGS

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24 pages, 567 KB  
Review
Bioinformatics Tools, Databases, and Data Formats: A Functional Overview for Introductory Sequence-Based and NGS Workflows
by Inês Domingues and João A. M. Santos
Appl. Sci. 2026, 16(13), 6666; https://doi.org/10.3390/app16136666 - 3 Jul 2026
Viewed by 72
Abstract
Bioinformatics has become a central component of biological and biomedical research, supporting the organization, analysis, interpretation, and integration of large-scale biological data. The rapid expansion of high-throughput technologies, particularly next-generation sequencing, has led to the development of numerous tools, databases, and data formats [...] Read more.
Bioinformatics has become a central component of biological and biomedical research, supporting the organization, analysis, interpretation, and integration of large-scale biological data. The rapid expansion of high-throughput technologies, particularly next-generation sequencing, has led to the development of numerous tools, databases, and data formats that address different stages of sequence-based and NGS-oriented bioinformatics workflows. This article presents a structured overview of representative bioinformatics resources and proposes a functional taxonomy for introductory sequence-based and NGS-oriented workflows. The taxonomy organizes resources into major functional categories, including genomic databases and browsers, sequence and data analysis tools, sequence alignment and search tools, gene prediction tools, protein-level interpretation resources, data retrieval and mining platforms, and biological data formats. Representative resources such as the UCSC Genome Browser, Ensembl, NCBI databases, FastQC, Trimmomatic, Cutadapt, trimAl, BLAST, ClustalW, MAFFT, MUSCLE, BWA, Bowtie, GENSCAN, ExPASy, PhosphoSitePlus, PIR, and BioMart as well as widely used data formats are described and compared. By summarizing their purposes, inputs, outputs, strengths, limitations, availability, and common applications, this review provides a systematic reference for students, early-career researchers, and non-specialist users seeking to navigate representative bioinformatics tools, databases, platforms, and data formats within introductory sequence-based and NGS-oriented analytical workflows. Full article
(This article belongs to the Special Issue Bioinformatics, Computational Biology and Multi-Omics Studies)
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13 pages, 11926 KB  
Article
Functional Analysis of IL-6 Genetic Variants and Their Potential Role in Lipid Homeostasis and Inflammatory Regulation in Colombian Athletes
by Diana Carolina Zambrano Ríos, Miguel Ángel Gómez, Juan Manuel Gómez, Felipe Alberto Polo, Betty Oviedo Sarria, Julián Andrés Rivera and Andrés Jenuer Matta
Curr. Issues Mol. Biol. 2026, 48(7), 686; https://doi.org/10.3390/cimb48070686 - 3 Jul 2026
Viewed by 77
Abstract
Obesity and metabolic dysregulation are closely associated with chronic low-grade inflammation, in which interleukin-6 (IL-6) plays a key regulatory role. Genetic variation in the IL-6 gene may influence inflammatory responses and metabolic homeostasis. To identify single-nucleotide variants (SNVs) in the IL-6 gene in [...] Read more.
Obesity and metabolic dysregulation are closely associated with chronic low-grade inflammation, in which interleukin-6 (IL-6) plays a key regulatory role. Genetic variation in the IL-6 gene may influence inflammatory responses and metabolic homeostasis. To identify single-nucleotide variants (SNVs) in the IL-6 gene in a cohort of Colombian high-performance athletes and to evaluate their potential functional and structural consequences using bioinformatic prediction and protein-modeling approaches. A descriptive observational study was conducted in a cohort of 23 high-performance Colombian athletes from Valle del Cauca representing cycling, karate, and weightlifting disciplines. Genomic Deoxyribonucleic Acid (DNA) extracted from peripheral blood samples was analyzed using Next-Generation Sequencing (NGS). Identified variants were evaluated using several in silico prediction tools, including Basic Local Alignment Search Tool (BLAST version 2.16.0), Expert Protein Analysis System (ExPASy version 4.0), Open Reading Frame Finder (ORFfinder version 0.4.3), and population databases such as Genome Aggregation Database (gnomAD version 4.0). Structural modeling was used to explore the potential impact of amino-acid substitutions on IL-6 protein stability. Eight single-nucleotide variants were identified in the IL-6 gene. Among them, the rs1524107 variant generated a missense substitution predicted to modify the amino-acid sequence of the IL-6 protein. Structural modeling suggested a potential alteration in protein stability associated with this variant. The rs1524107 variant may influence IL-6 protein structure according to computational predictions. These findings provide preliminary hypothesis-generating evidence regarding the potential role of IL-6 genetic variation in inflammatory regulation; however, functional validation and larger cohort studies are required to determine their biological significance. Full article
(This article belongs to the Special Issue Mechanisms and Pathophysiology of Obesity)
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27 pages, 526 KB  
Review
β-Thalassemia in Vietnam: Epidemiology, Molecular Characteristics, Diagnosis, Treatment, and Prevention Strategies
by Hong-Quan Duong, Thi-Khanh Tran, Thi-Hue Nguyen and Minh-Cong Hoang
Thalass. Rep. 2026, 16(3), 13; https://doi.org/10.3390/thalassrep16030013 - 2 Jul 2026
Viewed by 101
Abstract
β-thalassemia is one of the most prevalent inherited hemoglobin disorders worldwide and represents a major public health challenge in Southeast Asia, particularly in Vietnam. The disorder is caused by pathogenic variants in the β-globin (HBB) gene, resulting in reduced or absent [...] Read more.
β-thalassemia is one of the most prevalent inherited hemoglobin disorders worldwide and represents a major public health challenge in Southeast Asia, particularly in Vietnam. The disorder is caused by pathogenic variants in the β-globin (HBB) gene, resulting in reduced or absent β-globin synthesis, ineffective erythropoiesis, chronic hemolytic anemia, and progressive multi-organ complications. Vietnam exhibits a high burden of thalassemia and related hemoglobinopathies, with approximately 13.8% of the population carrying a hemoglobinopathy-associated variant and substantial heterogeneity in distribution across ethnic groups and geographic regions. This review provides a comprehensive overview of the epidemiology, molecular characteristics, diagnostic strategies, treatment approaches, and prevention programs for β-thalassemia in Vietnam. Current evidence indicates that a limited number of recurrent HBB variants account for the majority of β-thalassemia alleles in the Vietnamese population, including codon 17 (A>T) (HBB: c.52A>T), codons 41/42 deletion (-TTCT) (HBB: c.126_129delTTCT), codons 71/72 (+A) (HBB: c.216_217insA), codons 95 (+A) (HBB: c.287_288insA), IVS-I-1 (G>T) (HBB: c.92+1G>T), IVS-I-5 (G>C) (HBB: c.92+5G>C), IVS-II-654 (G>T) (HBB: c.316+197C>T), -28 (A>G) (HBB: c.-78A>G), and -88 (C>T) (HBB: c.-138C>T). Diagnostic strategies generally follow a stepwise approach integrating hematological screening and hemoglobin analysis with confirmatory molecular testing. Advances in molecular diagnostics, particularly targeted polymerase chain reaction (PCR)-based assays and next-generation sequencing (NGS), have significantly improved detection of both carriers and affected individuals. Despite these advances, β-thalassemia continues to impose a considerable clinical, economic, and societal burden because many patients require lifelong blood transfusions, iron chelation therapy, and multidisciplinary management of disease-related complications. Major challenges include limited access to screening, prenatal diagnosis, and genetic counseling services, particularly in rural and ethnic minority populations, as well as the financial and technical barriers associated with advanced molecular diagnostics and emerging therapies. Strengthening nationwide screening programs, expanding access to prenatal and preconception genetic services, improving public awareness, and enhancing healthcare infrastructure are essential for reducing disease incidence and improving patient outcomes. In parallel, the integration of advanced molecular diagnostics and emerging gene-based therapies will be critical for advancing long-term disease control. This review highlights current knowledge gaps and proposes strategic priorities to support evidence-based policy development and comprehensive β-thalassemia prevention and management in Vietnam. Full article
(This article belongs to the Collection Feature Papers in Thalassemia Reports)
16 pages, 397 KB  
Article
The Role of Next-Generation Sequencing in the Management of Asymptomatic, Young Slovenian Athletes for Distinction Between Athlete’s Heart and Cardiomyopathy
by Špela Stangler Herodež, Eva Čokolič, Nik Slavic, Tomaž Podlesnikar, Matjaž Vogrin, Nadja Kokalj Vokač and Danijela Krgović
Biomedicines 2026, 14(7), 1505; https://doi.org/10.3390/biomedicines14071505 - 2 Jul 2026
Viewed by 154
Abstract
Background: Intensive, prolonged endurance and strength training in apparently healthy young athletes causes many physiologic and structural adjustments in the heart, known as athlete’s heart. The correct distinction between physiological adaptations and pathological changes is crucial for the athlete, therefore screening programs [...] Read more.
Background: Intensive, prolonged endurance and strength training in apparently healthy young athletes causes many physiologic and structural adjustments in the heart, known as athlete’s heart. The correct distinction between physiological adaptations and pathological changes is crucial for the athlete, therefore screening programs are recommended by medical and sports associations. Nevertheless, a small but not negligible proportion of young competitive athletes die by sudden death. In 25% the cause of sudden cardiac death is genetic. Determining the genetic component is of key importance for distinction between athlete’s heart and cardiomyopathy. Methods: A gene panel next-generation sequencing (NGS) was performed in 41 apparently healthy young athletes without previously known heart disease. Results: Across 174 genes with known associations to different cardiac conditions, we identified nine variants: two pathogenic (P) variants and seven variants of unknown significance (VUSs). For all of them a more detailed follow-up with a cardiologist was advised. Conclusions: The results in our study suggest that targeted sequencing of genes associated with cardiovascular disease is the key that enables correct differentiation between athlete’s heart and cardiomyopathy, leading to fast and accurate clinical intervention where necessary. In this way, initial pathological changes are not confused with physiological ones, which could be fatal for the athlete if they continue with competitive sport. Full article
14 pages, 750 KB  
Brief Report
Molecular Feasibility of Gene Sequencing on Lymph Node Fine-Needle Cytology Samples of Non-Hodgkin Lymphoma
by Angela D’Ardia, Elisabetta Maffei, Sara Gaeta, Teresa Infante, Valentina Giudice, Francesco Sabbatino, Anna Di Filippo, Marco Picardi, Pio Zeppa and Alessandro Caputo
Int. J. Mol. Sci. 2026, 27(13), 5962; https://doi.org/10.3390/ijms27135962 - 2 Jul 2026
Viewed by 105
Abstract
Non-Hodgkin lymphomas (NHL) are lymphoproliferative neoplasms with a heterogenous genetic landscape that require multiple assays to be characterized. Cytological samples are frequently utilized in the diagnosis of NHL. An RNA-based assay was utilized to detect translocations and identify mutations in fine-needle aspiration cytology [...] Read more.
Non-Hodgkin lymphomas (NHL) are lymphoproliferative neoplasms with a heterogenous genetic landscape that require multiple assays to be characterized. Cytological samples are frequently utilized in the diagnosis of NHL. An RNA-based assay was utilized to detect translocations and identify mutations in fine-needle aspiration cytology (FNAC) samples of NHL. Fragmentation index and RNA concentration were evaluated in 54 FNAC and eight corresponding histological samples of NHL to establish first the material adequacy before sequencing. To sequence FusionPlex Lymphoma (ArcherDX, Boulder, USA), an anchored multiplex polymerase chain reaction-based RNA targeting 125 genes was used. The sequencing data processing was entirely carried out on the ArcherDX online platform. Mutations were detected in 21 of 62 samples (34%), and in 41 of 62 samples (66%), no genomic alterations were found. The FusionPlex assay detected five BCL6 translocations (three IGH-BCL6 and two EIF4A2-BCL6), six IGH-BCL2 translocations, two IGH-CCND1 translocations, two TP53 point mutations, two MYD88 mutation and four uncommon translocations (two EIF4E3-FOXP1, one TBL1XR1-TP63, one LOC105370537-FUT8). In eight out of eight cases, there was NGS (Next Generation Sequencing) results concordance between corresponding cytological and histological samples (100% concordance). FNAC samples of NHL are suitable for molecular assessment by NGS and FusionPlex Lymphoma assay is an effective method for this purpose. NGS allows the detection of mutations and the identification of translocations on cytological samples also with scanty diagnostic material. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
29 pages, 1485 KB  
Review
Advancements and Clinical Applications Prospects of Epigenetic Biomarkers in Liquid Biopsy for Oral Squamous Cell Carcinoma
by Yuan Li, Yao Liu, Yuyi Cong, Juan Liu, Wen Pan, Xiaobing Guan and Jiaqi Wang
Curr. Issues Mol. Biol. 2026, 48(7), 680; https://doi.org/10.3390/cimb48070680 - 1 Jul 2026
Viewed by 104
Abstract
Oral squamous-cell carcinoma (OSCC) is a prevalent malignancy of the head and neck region. A delay in the diagnosis of OSCC often results in a high metastatic tendency, which is the main reason for the high patient mortality. Dynamic monitoring and management of [...] Read more.
Oral squamous-cell carcinoma (OSCC) is a prevalent malignancy of the head and neck region. A delay in the diagnosis of OSCC often results in a high metastatic tendency, which is the main reason for the high patient mortality. Dynamic monitoring and management of the onset and progression of OSCC are critical for improving patient survival rates. Liquid biopsy technology—characterized by its non-invasive nature, procedural convenience, and capacity for longitudinal monitoring—is a promising adjunct to histopathological examination for the early diagnosis of OSCC. Epigenetic alterations, characterized by reversibility and long-term stability in physiological fluids, are critical enablers of liquid biopsy and its clinical utility. Advances in detection technologies, including quantitative polymerase chain reaction (qPCR), digital droplet PCR (ddPCR), next-generation sequencing (NGS), and electrochemical biosensors, have significantly facilitated the research and clinical translation of epigenetic biomarkers in oral liquid biopsies. However, translating epigenetic biomarkers from research discovery to clinical practice for OSCC remains hindered by several critical challenges: the scarcity of large-scale, rigorously designed cohort studies, limited multicenter validation, inconsistent preprocessing protocols, and a lack of harmonized analytical platforms. Finally, we propose a conceptual framework to outline potential clinical application models for these biomarkers. Full article
(This article belongs to the Special Issue Oral Cancer: Prophylaxis, Etiopathogenesis and Treatment, 2nd Edition)
21 pages, 896 KB  
Article
Clinical Utility of NGS-Based Diagnosis in Primary Ciliary Dyskinesia: Experience from a Brazilian Pediatric Cohort at a Reference Center for Rare Diseases
by Patrícia F. Barreto M. Costa, Danielle de Freitas F. M. Fins, Isabelle de Oliveira Moraes, Tania Wrobel Folescu, Renata Wrobel Folescu Cohen, Natana Chaves Rabelo, Leticia Azevedo Barreto, Julia Vieira da Cunha Moreira, Bianca Barbosa Abdala, Mariana Naccarato Teixeira Lopes Andrade, Juan Llerena, Dafne Horovitz, Maria Eduarda Gomes and Sayonara Gonzalez
Genes 2026, 17(7), 767; https://doi.org/10.3390/genes17070767 - 30 Jun 2026
Viewed by 158
Abstract
Background: Primary ciliary dyskinesia (PCD) is a rare and genetically heterogeneous disorder that remains underdiagnosed in low- and middle-income countries, largely due to limited access to specialized diagnostic tests. Genetic analysis has become an essential component of PCD diagnosis, particularly where functional [...] Read more.
Background: Primary ciliary dyskinesia (PCD) is a rare and genetically heterogeneous disorder that remains underdiagnosed in low- and middle-income countries, largely due to limited access to specialized diagnostic tests. Genetic analysis has become an essential component of PCD diagnosis, particularly where functional and ultrastructural evaluations are unavailable. Methods: We conducted an investigational study including children and adolescents with clinical suspicion of PCD followed at a Brazilian tertiary center. Clinical characterization included detailed phenotyping and calculation of the PICADAR score. Molecular investigation was performed using exome sequencing as a frontline diagnostic approach. Results: Among 27 individuals evaluated, 10 (37%) received a confirmed molecular diagnosis of PCD. An additional 6 (22%) individuals had inconclusive molecular findings, mainly due to variants of uncertain significance (VUS), and were classified as likely PCD based on combined clinical and molecular evidence. Higher PICADAR scores were more frequently observed among individuals with confirmed or likely molecular diagnosis, with 9 of 10 confirmed cases presenting a score above 5. Beyond PCD-associated findings, exome sequencing also enabled the identification of clinically relevant additional diagnoses, including cystic fibrosis, FGFR3-related hypochondroplasia, and ACMG-reportable secondary finding involving BRCA2. Some unresolved cases may also reflect inherent technical limitations of exome sequencing, including restricted sensitivity for copy-number variants, suboptimal coverage of highly homologous or GC-rich regions, and limited detection of deep intronic and other variants. Additional factors include challenges in variant interpretation and incomplete knowledge of disease-associated genes. Conclusions: Frontline exome sequencing is a valuable diagnostic tool for PCD, particularly when integrated with robust clinical phenotyping. Clinical scoring systems such as PICADAR may help prioritize individuals for genetic testing and optimize diagnostic yield in resource-limited settings. Full article
(This article belongs to the Special Issue Genetic Diagnosis and Treatment of Rare Diseases)
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13 pages, 740 KB  
Article
Comparison of Amplicon-Based Next-Generation Sequencing Testing and Immunohistochemical Staining in Detecting Anaplastic Lymphoma Kinase Fusion Genes in Non-Small-Cell Lung Cancer: A Large Single-Centre Cohort Study
by Yuichiro Suzukawa, Yuto Tagawa, Seigo Katakura, Shuhei Teranishi, Tetsuro Kondo, Haruhiro Saito and Shuji Murakami
Cancers 2026, 18(13), 2125; https://doi.org/10.3390/cancers18132125 - 30 Jun 2026
Viewed by 169
Abstract
Background/Objectives: Anaplastic lymphoma kinase (ALK) fusion is a driver gene translocation detected in 3–5% of patients with non-small-cell lung cancer (NSCLC). Next-generation sequencing (NGS)-based tests are the standard of care for detecting actionable gene alterations; however, false negatives remain a [...] Read more.
Background/Objectives: Anaplastic lymphoma kinase (ALK) fusion is a driver gene translocation detected in 3–5% of patients with non-small-cell lung cancer (NSCLC). Next-generation sequencing (NGS)-based tests are the standard of care for detecting actionable gene alterations; however, false negatives remain a concern. Immunohistochemical staining is another reliable, rapid, and low-cost method for detecting ALK fusions. Previous studies have reported high concordance with NGS, although further studies are needed to draw definitive conclusions. Methods: A retrospective analysis was conducted on consecutive patients with NSCLC who were tested using the Oncomine Dx Target Test (ODxTT), an amplicon-based DNA and RNA NGS test for NSCLC, and ALK-immunohistochemistry (IHC) at our institution between 8 August 2019 and 11 April 2025. Results: Of 919 eligible patients included in this study, ALK fusion was detected in 30 (3.26%) patients, whereas ALK-IHC was positive in 35 (3.80%) patients. The concordance and κ coefficient of the two tests were 99.4% and 0.920, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value of ALK-IHC for ODxTT were 100%, 99.4%, 85.7%, and 100%, respectively. Five discordant patients were NGS negative and IHC positive. Among the five discordant cases, one had a false-negative NGS result, whereas the remaining four had false-positive ALK-IHC results, including three patients with neuroendocrine carcinomas. Conclusions: ALK-IHC shows diagnostic accuracy comparable to ODxTT, although prudent interpretation is needed for patients without adenocarcinoma. Our findings suggest the complementary role of ALK-IHC alongside NGS-based testing, particularly in patients with a high pre-test probability of harbouring ALK fusions. Full article
(This article belongs to the Section Cancer Biomarkers)
14 pages, 272 KB  
Article
PURA-Related Neurodevelopmental Disorder: Insight from Eight New Cases
by Agnieszka Madej-Pilarczyk, Marzena Gawlik, Beata Chałupczyńska, Jagoda Błaszkiewicz, Dorota Wicher, Agata Cieślikowska, Anila Babameto-Laku, Krystyna Chrzanowska and Elżbieta Ciara
Genes 2026, 17(7), 765; https://doi.org/10.3390/genes17070765 - 30 Jun 2026
Viewed by 159
Abstract
Background: PURA-related neurodevelopmental disorder (PURA-NDD; OMIM #616158) is a rare autosomal dominant condition caused by pathogenic variants in the PURA gene encoding Purα, a multifunctional protein involved in DNA replication, transcriptional regulation, and RNA transport. Since its initial description [...] Read more.
Background: PURA-related neurodevelopmental disorder (PURA-NDD; OMIM #616158) is a rare autosomal dominant condition caused by pathogenic variants in the PURA gene encoding Purα, a multifunctional protein involved in DNA replication, transcriptional regulation, and RNA transport. Since its initial description in 2014, PURA-NDD has been increasingly recognized as a distinct clinical entity with early onset and a broad phenotypic spectrum. The clinical presentation is characterized primarily by neonatal hypotonia, global developmental delay, intellectual disability, feeding difficulties, and epilepsy, along with additional features such as respiratory insufficiency, movement disorders, hypersomnolence, and variable dysmorphic traits. Despite a relatively recognizable core phenotype, marked inter-individual variability often limits the ability to establish a definitive clinical diagnosis based on phenotype alone. This underscores the essential role of molecular genetic testing in the differential diagnosis of rare neurodevelopmental disorders. Patients and methods: We report a cohort of eight individuals (four males and four females) aged 17 months to 15.5 years with PURA-related neurodevelopmental disorder (PURA-NDD), evaluated using a genotype-first diagnostic strategy supported by comprehensive genomic testing, including next-generation sequencing (NGS) panels and whole-genome sequencing (WGS). Patients were referred for the evaluation of nonspecific neurodevelopmental features, including neonatal hypotonia, respiratory distress, and epilepsy, in the absence of a definitive clinical diagnosis. Results: Molecular analysis identified eight heterozygous variants in PURA, of which four (50%) were novel: c.311T>G p.(Met104Arg), c.406_407del p.(Gln136Glyfs64), c.515A>C p.(Gln172Pro), and c.885delinsGC p.(His296Profs21). The remaining variants included previously reported missense and frameshift changes associated with PURA-NDD, as well as one variant previously reported in ClinVar. Conclusions: Our findings not only confirm the core clinical features of PURA-related neurodevelopmental disorder but also contribute to a more comprehensive delineation of its phenotypic spectrum. The detailed characterization of our cohort broadens the range of recognized clinical manifestations and further highlights the marked phenotypic heterogeneity of PURA-NDD. In addition, the identification of both novel and previously reported pathogenic variants expands the mutational spectrum of PURA and underscores the importance of integrating clinical, molecular, and bioinformatic data for accurate variant interpretation. Although genotype–phenotype correlations remain incompletely understood, emerging evidence suggests potential associations between variant type or location and clinical severity, warranting further investigation in larger cohorts. The recognition of characteristic neonatal features may facilitate earlier diagnosis and implementation of supportive multidisciplinary management. Overall, this study illustrates how genomic technologies not only improve diagnostic yield in rare disorders but also refine disease definition, enhance the understanding of underlying pathogenic mechanisms, and support the development of more precise genotype–phenotype correlations. Further studies involving larger cohorts and long-term follow-up are needed to better define the full clinical and molecular spectrum of PURA-NDD. Full article
(This article belongs to the Special Issue Advances in Molecular Genetics of Rare Disorders)
15 pages, 849 KB  
Article
High-Touch, High-Risk: An Exploratory Microbiome Analysis of Hospital Wheelchairs
by Luca Dalle Carbonare, Anna Vareschi, Kevin Dervishi, Michela Deiana, Elena Locatelli, Arianna Minoia, Francesca Cristiana Piritore, Alessandra Ruggiero, Ilda Czobor Barbu, Donato Zipeto, Chiara Piubelli and Maria Teresa Valenti
Pathogens 2026, 15(7), 693; https://doi.org/10.3390/pathogens15070693 - 30 Jun 2026
Viewed by 175
Abstract
In this exploratory pilot study, quantitative analyses were performed on seven leather wheelchairs and the protective barrier was evaluated on three leather wheelchairs, while shotgun metagenomic sequencing (Illumina and Oxford Nanopore) was conducted on pooled samples obtained from seven leather and three fabric [...] Read more.
In this exploratory pilot study, quantitative analyses were performed on seven leather wheelchairs and the protective barrier was evaluated on three leather wheelchairs, while shotgun metagenomic sequencing (Illumina and Oxford Nanopore) was conducted on pooled samples obtained from seven leather and three fabric wheelchairs to characterize microbial DNA recovered from wheelchair surfaces under routine clinical conditions. Microbial DNA and biomass were detected on all sampled surfaces, with median DNA concentrations of approximately 0.015 ng/µL, median cell counts of approximately 4.8 × 10⁵ cells/mL, and median OD600 values of approximately 0.038, although variability among wheelchairs was observed. NGS analysis revealed heterogeneous microbial communities composed mainly of taxa associated with human skin microbiota and environmental sources. Opportunistic taxa including Escherichia coli, Staphylococcus haemolyticus, Achromobacter xylosoxidans, and Clostridioides difficile DNA were detected. Differences in microbial composition were observed between the pooled fabric and leather samples, with fabric samples characterized by the dominance of specific taxa and leather samples exhibiting a more heterogeneous microbial profile. In addition, median DNA concentration, cell counts, and OD600 values were reduced by approximately 98–100% on the protective barrier compared with uncovered wheelchair surfaces, with statistically significant differences between conditions. Overall, these findings suggest that hospital wheelchairs may harbor measurable levels of microbial biomass and microbial DNA despite routine sanitation procedures. Lower contamination levels were observed on the protective barrier under the conditions tested. Due to the exploratory nature of the study, the small sample size, and the use of pooled samples for metagenomic analyses, these observations should be interpreted with caution and require confirmation in larger studies. Full article
(This article belongs to the Section Bacterial Pathogens)
11 pages, 791 KB  
Case Report
Clinical and Molecular Heterogeneity of MYH3-Related Arthrogryposis with a Novel MYH3 Variant
by Annalidia Donato, Davide Vecchio, Caterina Marinaro, Rossella Brando, Alessia Bauleo, Elena Falcone and Daniela Concolino
Genes 2026, 17(7), 762; https://doi.org/10.3390/genes17070762 - 30 Jun 2026
Viewed by 113
Abstract
Background: Arthrogryposis consists of a heterogeneous group of congenital disorders characterized by multiple joint contractures. Distal arthrogryposes (DAs) are often caused by pathogenic variants in fast-twitch muscle protein genes, including MYH3, nosologically linked to DA2A and DA2B. Methods: We evaluated two siblings [...] Read more.
Background: Arthrogryposis consists of a heterogeneous group of congenital disorders characterized by multiple joint contractures. Distal arthrogryposes (DAs) are often caused by pathogenic variants in fast-twitch muscle protein genes, including MYH3, nosologically linked to DA2A and DA2B. Methods: We evaluated two siblings with features suggestive of arthrogryposis through detailed clinical examination, radiographic imaging, audiological assessment, and targeted next-generation sequencing (NGS) for skeletal dysplasias and an arthrogryposis panel, including MYH3. Variants were confirmed by Sanger sequencing, and segregation analysis was performed in available relatives. Results: Both patients harbored three heterozygous MYH3 variants: two maternally inherited in cis (c.749G>A and c.787G>T) and one paternally inherited in trans (c.4130_4138del), currently classified as variants of uncertain significance (VUS) and likely pathogenic, respectively. The female patient presented with a short neck, hand contractures, cubitus valgus, a widened internipple distance, and severe thoracolumbar scoliosis. The male sibling showed craniofacial dysmorphisms, more extensive musculoskeletal anomalies, and moderate-to-severe sensorineural hearing loss. The segregation analysis suggests an MYH3 autosomal recessive inheritance pattern. Conclusions: This report broadens the phenotypic spectrum of MYH3-related disorders, suggesting potential involvement in atypical DA phenotypes resembling DA4 (scoliosis) and DA6 (hearing loss), for which causative genes remain unknown. Comprehensive molecular testing and segregation analysis are essential to clarify genotype–phenotype correlations in congenital contracture syndromes. Full article
(This article belongs to the Special Issue Genes and Pediatrics)
31 pages, 1508 KB  
Review
HER2 Alterations in Squamous Cell Lung Cancer: Biology, Therapeutic Landscape, and Emerging Precision Approaches
by Dina Elantably, Isabella Meerzaman, Alicia Y. Hou, Ahmed Abdelhakeem and Yanyan Lou
Cancers 2026, 18(13), 2121; https://doi.org/10.3390/cancers18132121 - 30 Jun 2026
Viewed by 259
Abstract
Squamous cell lung cancer (SqCLC) accounts for 20–30% of non-small cell lung cancer (NSCLC) and remains associated with a poorer prognosis compared with adenocarcinoma. Despite advances in treatment, 5-year overall survival for advanced (stage IV) disease remains below 10–15%. Unlike non-squamous NSCLC, SqCLC [...] Read more.
Squamous cell lung cancer (SqCLC) accounts for 20–30% of non-small cell lung cancer (NSCLC) and remains associated with a poorer prognosis compared with adenocarcinoma. Despite advances in treatment, 5-year overall survival for advanced (stage IV) disease remains below 10–15%. Unlike non-squamous NSCLC, SqCLC is characterized by a high tumor mutational burden and complex genomic landscape dominated by alterations in tumor suppressor genes and lineage survival pathways including TP53, CDKN2A, PIK3CA, FGFR1, SOX2, and the NFE2L2/KEAP1 oxidative stress pathway, as well as dysregulation of the NOTCH signaling pathway, but it harbors relatively few actionable oncogenic drivers, resulting in limited treatments for targeted therapy. HER2 alterations can occur by multiple mechanisms, including activating mutations, gene amplifications, and protein overexpression. They comprise a very small percentage of NSCLC, with HER2 mutations reported in approximately 1–3% and HER2 amplifications observed roughly in 2–4%. While HER2 alterations are well characterized in lung adenocarcinoma, the prevalence, genomic context, and clinical significance of HER2 alterations in SqCLC remain incompletely defined. Advances in next-generation sequencing have led to improved ability to detect HER2 alterations and facilitated the development of HER2 targeted therapies. Available treatments for advanced/metastatic SqCLC have been historically limited to platinum-doublet chemotherapy, with immune checkpoint inhibitors such as anti-PD-1/PD-L1 newly emerging in the past decade. Selective HER2 tyrosine kinase inhibitors and HER2 antibody/drug conjugates have shown improved efficacy in HER2-altered NSCLC as shown in DESTINY-LUNG02 and BEAMION LUNG-1 trials; however, most of the enrolled patients had non-squamous histology, with minimal or no SqCLC-specific efficacy data reported. Future progress in HER2-altered SqCLC will require inclusion of SqCLC in HER2 basket trials, incorporation of comprehensive molecular profiling and standardized HER2 testing in squamous histology. This review summarizes the current state of knowledge of HER2 biology in SqCLC and highlights areas for future directions for precision oncology in SqCLC. Full article
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15 pages, 1445 KB  
Article
Promoter Methylation and Somatic Mutations in Cancer-Related Genes Are Associated with Hyperprogressive Disease in Patients with Malignant Melanoma and Renal Cell Carcinoma Receiving Anti-PD-1/PD-L1 Immunotherapy
by Adem Deligonul, Mehmet Sarimahmut, Ahmet Bilgehan Sahin, Elif Erturk, Engin Atli, Hazal Sezginer Guler, Erdem Cubukcu, Hulya Ozturk Nazlioglu, Saduman Balaban Adim, Turkkan Evrensel and Ferda Ari
J. Clin. Med. 2026, 15(13), 5089; https://doi.org/10.3390/jcm15135089 - 30 Jun 2026
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Abstract
Background and Objectives: A subset of cancer patients treated with immune checkpoint inhibitors may experience rapid tumor progression rather than therapeutic benefit, a phenomenon described as hyperprogressive disease (HPD), which is linked to poor prognosis and shortened survival. Reliable biomarkers capable of predicting [...] Read more.
Background and Objectives: A subset of cancer patients treated with immune checkpoint inhibitors may experience rapid tumor progression rather than therapeutic benefit, a phenomenon described as hyperprogressive disease (HPD), which is linked to poor prognosis and shortened survival. Reliable biomarkers capable of predicting HPD remain lacking. To better understand the molecular background of HPD, we analyzed promoter region methylation and somatic mutation profiles in cancer-related genes in patients with malignant melanoma (MM) and renal cell carcinoma (RCC) undergoing anti-PD-1/PD-L1 treatment. Methods: Patients diagnosed with MM or RCC and treated with anti-PD-1/PD-L1 agents between 2011 and 2020 were included, and FFPE tumor samples along with paired normal tissues were analyzed. A diagnosis of HPD was assigned to patients with RECIST 1.1-defined progressive disease who demonstrated a ≥2-fold acceleration in tumor growth kinetics after initiation of immune checkpoint inhibitor therapy. Methylation-specific real-time PCR was performed on 54 samples (15 MM tumors, 22 RCC tumors, 17 RCC-matched adjacent normal samples) to assess promoter methylation of PIK3CA, BAP1, PTEN, and TP53. Next-generation sequencing (NGS) with an 86-gene pan-cancer panel was conducted on 9 HPD samples. Results: Promoter hypermethylation involving PIK3CA, BAP1, PTEN, and TP53 was more pronounced in HPD-associated tumor samples (n = 16) than in tumors without HPD (n = 21). Within the MM cohort, PTEN and TP53 methylation levels demonstrated statistically significant differences between the two groups (p = 0.005 and p = 0.028, respectively), while no comparable associations were observed in RCC patients. NGS analysis detected missense mutations classified as pathogenic or likely pathogenic in 5 of 9 HPD patients (55.6%), involving KIT, PTEN, and VHL. Conclusions: Promoter region hypermethylation in cancer-related genes may contribute to the aggressive tumor behavior observed in HPD. The somatic variants identified in HPD patients are consistent with known oncogenic pathways. These findings support further investigation of epigenetic and genomic biomarkers for HPD risk stratification in larger, prospective cohorts. Full article
(This article belongs to the Section Oncology)
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21 pages, 3023 KB  
Article
Genomic Profiling, Induction Response, and Transplant Outcomes in Pediatric Acute Myeloid Leukemia: A Single-Center Retrospective Cohort Study
by Ana Maria Bicǎ, Andra Daniela Marcu, Cristina Georgiana Jercan, Iuliana Iordan, Letiția Elena Radu, Irina Avramescu, Cerasela Jardan, Dumitru Jardan, Onda Tabita Cǎlugǎru, Anda Mocanu, Andrei Colițǎ and Anca Colițǎ
Int. J. Mol. Sci. 2026, 27(13), 5832; https://doi.org/10.3390/ijms27135832 - 28 Jun 2026
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Abstract
Pediatric acute myeloid leukemia (AML) is biologically heterogeneous, and genomic profiling increasingly informs risk stratification and treatment. We evaluated the relationship between induction response, genomic risk, transplant allocation, and survival in pediatric AML. We retrospectively analyzed 38 pediatric patients with newly diagnosed AML, [...] Read more.
Pediatric acute myeloid leukemia (AML) is biologically heterogeneous, and genomic profiling increasingly informs risk stratification and treatment. We evaluated the relationship between induction response, genomic risk, transplant allocation, and survival in pediatric AML. We retrospectively analyzed 38 pediatric patients with newly diagnosed AML, treated between 2020 and 2025. Clinical, cytogenetic, molecular, treatment, and outcome data were collected. Genomic alterations were assessed using cytogenetics, fluorescence in situ hybridization (FISH), molecular testing, and next-generation sequencing (NGS). Survival was estimated by Kaplan–Meier analysis, and prognostic factors for event-free survival (EFS) were assessed using univariable Cox regression. This study is exploratory given the limited sample size and should be interpreted accordingly. Complete remission (CR) after the first course of induction was achieved in 25/38 patients (65.8%), partial remission (PR) in 3/38 (7.9%), and refractory disease in 10/38 (26.3%). Twenty-four patients underwent allogeneic hematopoietic stem cell transplantation; 17/24 (70.8%) were alive at last follow-up, with a 2-year overall survival rate of 72.9%. Both induction response and genomic risk stratification showed suggestive associations with outcome; descriptively, induction response showed the strongest prognostic discrimination, with achievement of CR associated with markedly improved survival. High cytogenetic risk and FLT3-ITD were significantly associated with inferior EFS. Post-induction measurable residual disease (MRD) positivity was detected in 16 of 38 patients (42.1%) and was associated with suboptimal induction response; MRD negativity did not uniformly preclude adverse outcomes, particularly in the high-risk genomic subgroup. Genomic profiling refined biological risk and post-remission treatment allocation. Integrated assessment of genomic risk, induction response, and MRD status may improve therapeutic stratification in pediatric AML. Full article
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17 pages, 3109 KB  
Article
Analytical Validation and Clinical Implementation of a 1080-Gene Comprehensive Genomic Profiling Assay with Integrated Cloud-Based Analysis for Solid Tumor Molecular Oncology
by Ashutosh Vashisht, Ashis K. Mondal, Vishakha Vashisht, Pankaj K. Ahluwalia, Saloni Andhari, Jaspreet Farmaha, Jana Woodall and Ravindra Kolhe
Biomedicines 2026, 14(7), 1462; https://doi.org/10.3390/biomedicines14071462 - 27 Jun 2026
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Abstract
Background: Comprehensive genomic profiling (CGP) via next-generation sequencing (NGS) is pivotal for precision oncology, yet many laboratories face challenges with incomplete genomic coverage, complex bioinformatics workflows, and limited integration of key biomarkers. Methods: We evaluated the analytical performance and clinical utility of [...] Read more.
Background: Comprehensive genomic profiling (CGP) via next-generation sequencing (NGS) is pivotal for precision oncology, yet many laboratories face challenges with incomplete genomic coverage, complex bioinformatics workflows, and limited integration of key biomarkers. Methods: We evaluated the analytical performance and clinical utility of a CGP assay using 119 tumor samples representing 18 types of cancer, previously analyzed with an orthogonal NGS panel. Concordance was assessed across 81 genes, covering 176 single-nucleotide variants (SNVs), eight copy number variations (CNVs), four deletions, one duplication, and four gene fusions. Limit of detection (LOD) studies employed AcroMetrix Mutant Hotspot Control and SeraSeq Lung and Brain CNV Mix. Microsatellite instability (MSI) and tumor mutational burden (TMB) were quantified. Inter- and intra-run reproducibility were evaluated to assess precision. Results: The CGP assay demonstrated high analytical performance, with >99% sensitivity, 100% specificity, and complete accuracy for variant detection. LOD studies revealed robust detection of SNVs at ≤5% variant allele frequencies (VAF) and CNVs at three copies. MSI and TMB results were consistent with clinical expectations, showing minimal bias compared to the orthogonal panel. Inter- and intra-run testing confirmed 100% reproducibility, indicating strong assay precision. Post-sequencing variant reporting was streamlined using the iCare platform, enabling direct FASTQ-to-report generation without intermediate bioinformatic steps. Conclusions: These findings support the present assay’s clinical utility in personalized oncology assessment. Full article
(This article belongs to the Special Issue Genome Engineering Technologies for Diseases)
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