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15 pages, 653 KB  
Article
Abundance of Yersinia pestis Nucleic Acids in Soil from Rattus tanezumi Plague Foci in Yunnan Using ddPCR
by Yongmei La, Fan Li, Cunjuan Duan, Jinjiao Kong, Haipeng Zhang, Hongli Tan, Baoxiang Li, Youhong Zhong, Shilong Yang, Peng Wang and Liyuan Shi
Pathogens 2026, 15(6), 616; https://doi.org/10.3390/pathogens15060616 - 9 Jun 2026
Viewed by 149
Abstract
To determine whether Yersinia pestis (Y. pestis) signals were present in the soil, 78 soil samples were collected from 10 counties identified as Rattus tanezumi plague foci and another six counties in non-foci areas in Yunnan, China, from August 2024 to [...] Read more.
To determine whether Yersinia pestis (Y. pestis) signals were present in the soil, 78 soil samples were collected from 10 counties identified as Rattus tanezumi plague foci and another six counties in non-foci areas in Yunnan, China, from August 2024 to May 2025. Nucleic acids were extracted using the DNeasy PowerSoil Pro Kit (Qiagen) and detected with a Bio-Rad QX200 droplet digital PCR (ddPCR) system targeting two Y. pestis genes (caf1 and ypo0392). Our sampling design also considered two additional dimensions: nine soil types and three habitat types. The raw data obtained from ddPCR were copy numbers. A gene was considered positive when its copy number exceeded the limit of detection (LoD). A sample was considered positive if the copy number of ypo0392 exceeded its LoD (regardless of caf1), or if both genes exceeded their respective LoDs. No correlation was detected between the positivity rate of Y. pestis and the division of sampling sites into plague focus and non-focus regions (p = 0.758). Similarly, the Mann–Whitney U test revealed non-significant differences in pathogen copy number across the two site categories, with p = 0.603 for the caf1 gene and p = 0.372 for the ypo0392 gene. No statistical difference in positivity rate was found for either soil types or habitat types. However, for both the grouping variables, a statistical difference in copy number was observed. Our results indicated that quantifying nucleic acid abundance by copy number provided richer information than a simple positive/negative determination. The detection of Y. pestis signals was associated with soil type, rather than with whether an area was classified as a focus or non-focus region. Accordingly, future research on the preservation mechanism of Y. pestis should not be restricted to the concept of natural foci but should adopt a broader perspective. Full article
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44 pages, 1508 KB  
Review
Circulating Tumor DNA as Emerging Predictive and Prognostic Biomarker in Prostate Cancer
by Bicky Thapa, Jacopo Venturini, Atish D. Choudhury and Edoardo Francini
Cancers 2026, 18(11), 1702; https://doi.org/10.3390/cancers18111702 - 23 May 2026
Viewed by 313
Abstract
A circulating tumor DNA (ctDNA) assay is an emerging non-invasive diagnostic approach providing real-time insights into the heterogeneous tumor molecular landscape of advanced prostate cancer, overcoming the limitations of traditional tissue biopsies and PSA. Detection methods include droplet digital PCR, next-generation sequencing, and [...] Read more.
A circulating tumor DNA (ctDNA) assay is an emerging non-invasive diagnostic approach providing real-time insights into the heterogeneous tumor molecular landscape of advanced prostate cancer, overcoming the limitations of traditional tissue biopsies and PSA. Detection methods include droplet digital PCR, next-generation sequencing, and new epigenomic and fragmentomic strategies (investigational) designed to improve sensitivity in cases of low ctDNA shedding. While ctDNA’s role in localized prostate cancer is limited, it offers significant prognostic value in metastatic cases, where high ctDNA levels correlate with shorter survival. Additionally, longitudinal ctDNA monitoring can predict treatment response and identify emerging resistance mechanisms, including androgen receptor alterations associated with androgen receptor pathway inhibitor therapy and BRCA reversion mutations linked to PARP inhibitors. Importantly, liquid biopsy enables genomic characterization to inform treatment decision-making, particularly in clinical scenarios where tissue biopsy is challenging, such as bone-only disease. However, the widespread clinical implementation of ctDNA analysis is hindered by several analytical challenges, including low sensitivity in localized disease and low disease burden, and the risk of false positives due to clonal hematopoiesis. Furthermore, greater efforts are required to standardize pre-analytical workflows and post-analytical data interpretation and reporting across institutions. This review aims to summarize the evolving role of cfDNA technologies in localized and advanced prostate cancer, highlighting their prognostic and predictive value and their role in uncovering mechanisms of treatment resistance. Full article
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30 pages, 2276 KB  
Review
Advances and Challenges in the Diagnosis of Vector-Borne Protozoal Infections in Veterinary Medicine
by Ana María Cevallos, Tomas Meraz-Tay and Roberto Hernández
Pathogens 2026, 15(6), 561; https://doi.org/10.3390/pathogens15060561 - 22 May 2026
Viewed by 424
Abstract
Vector-borne protozoal infections—including babesiosis, theileriosis, hepatozoonosis, trypanosomosis, and leishmaniosis—impose a substantial burden on livestock and companion animal health worldwide and carry important zoonotic and public health implications. Accurate diagnosis is essential yet challenging, given the diversity of parasite genera, their markedly different tissue [...] Read more.
Vector-borne protozoal infections—including babesiosis, theileriosis, hepatozoonosis, trypanosomosis, and leishmaniosis—impose a substantial burden on livestock and companion animal health worldwide and carry important zoonotic and public health implications. Accurate diagnosis is essential yet challenging, given the diversity of parasite genera, their markedly different tissue tropisms, and the uneven distribution of diagnostic resources across veterinary settings. This review provides an integrated overview of the principal diagnostic approaches available, structured around the biological logic that guides test selection in practice. Microscopic examination remains the first-line method; its strengths and limitations are discussed for intraerythrocytic parasites (Plasmodium spp., Babesia spp., Theileria spp., Cytauxzoon spp.—the latter two with additional extra-erythrocytic schizont stages in leukocytes and tissue macrophages, respectively), leukocyte-associated forms (Hepatozoon spp.), extracellular trypanosomes, and tissue-stage parasites, including emerging applications of artificial intelligence. Serological methods—enzyme-linked immunosorbent assay (ELISA), indirect fluorescence antibody test (IFAT), and point-of-care lateral flow assays—are evaluated for their role in exposure detection, population screening, and international trade certification, with attention to cross-reactivity and the active-versus-past-infection distinction. Molecular diagnostics, encompassing conventional PCR, qPCR, droplet digital PCR, isothermal amplification, and next-generation sequencing, are reviewed with respect to target selection, sensitivity, and point-of-care applicability. Finally, diagnostic challenges are contextualised within a One Health framework, highlighting the fragmentation of veterinary surveillance and the need for integrated, cross-sector approaches to detect emerging threats. Full article
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12 pages, 1418 KB  
Article
Evaluation of Droplet Digital PCR Assay for the Detection of Microsatellite Instability in Colorectal, Gastric, and Endometrial Cancers
by Yousun Chung, Sujin Oh, Soo Kyung Nam, Hyunji Kim, Cheol Lee, Gyeong Hoon Kang, Hyeon Jeong Oh, Hye Seung Lee and Kyoung Un Park
Diagnostics 2026, 16(10), 1550; https://doi.org/10.3390/diagnostics16101550 - 20 May 2026
Viewed by 686
Abstract
Background: Microsatellite instability (MSI) is an important biomarker for the diagnosis of Lynch syndrome and for guiding immunotherapy in various solid tumors. Droplet digital PCR (ddPCR) has emerged as a highly sensitive method for detecting MSI, particularly in circulating tumor DNA (ctDNA). [...] Read more.
Background: Microsatellite instability (MSI) is an important biomarker for the diagnosis of Lynch syndrome and for guiding immunotherapy in various solid tumors. Droplet digital PCR (ddPCR) has emerged as a highly sensitive method for detecting MSI, particularly in circulating tumor DNA (ctDNA). This study aimed to evaluate the analytical and clinical performance of a ddPCR assay using three MSI markers (BAT-26, ACVR2A, and DEFB105A/B) in colorectal, gastric, and endometrial cancers. Methods: Formalin-fixed paraffin-embedded (FFPE) samples from 190 patients (83 colorectal, 44 gastric, and 63 endometrial cancers) and 21 plasma samples from patients with metastatic solid tumors were analyzed. MSI status determined by ddPCR was compared with conventional PCR using a pentaplex panel and immunohistochemistry (IHC). Analytical performance, including limit of blank (LoB) and limit of detection (LoD), was evaluated using cell line DNA, and clinical cut-offs were established using receiver operating characteristic analysis. Results: The ddPCR assay demonstrated high analytical sensitivity, with LoD values of 0.075% for BAT-26, 0.1% for ACVR2A, and 0.025% for DEFB105A/B. Using optimized clinical cut-offs, the concordance rate between ddPCR and conventional PCR assays was 98.4% in tissue samples. Marker performance varied by cancer type, with reduced sensitivity observed in endometrial cancer. In plasma samples, MSI-H was detected in 1 of 21 cases (4.8%), and the overall concordance rate with tissue-based MSI status was 94.7%. Conclusions: The ddPCR assay demonstrated high concordance with conventional MSI testing methods and showed potential as a sensitive tool for MSI detection in both tissue and plasma samples. However, optimization of marker panels and establishment of sample-type-specific clinical cut-offs are required, particularly for ctDNA-based analysis. Further large-scale studies are needed to validate the clinical utility of ddPCR for MSI detection and monitoring. Full article
(This article belongs to the Special Issue Advances in Laboratory Markers of Human Disease—2nd Edition)
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14 pages, 1302 KB  
Article
Exosomal CNP and CNP-Related microRNAs: An Open Window into Brugada Syndrome?
by Manuela Cabiati, Federico Vozzi, Elisa Persiani, Marcello Piacenti, Andrea Rossi, Agnese Sgalippa, Antonella Cecchettini, Gianluca Solarino, Giulio Zucchelli, Lorenzo Mazzocchetti, Pasquale Notarstefano, Letizia Guiducci, Maria Aurora Morales and Silvia Del Ry
Biomedicines 2026, 14(5), 1094; https://doi.org/10.3390/biomedicines14051094 - 12 May 2026
Viewed by 504
Abstract
Background: Brugada Syndrome (BrS) is a cardiac arrhythmia associated with an increased risk of ventricular arrhythmias and sudden cardiac arrest. Although the arrhythmic substrate is traditionally localized to the ventricles, atrial fibrillation (AF) is frequently observed, suggesting a shared molecular substrate between atrial [...] Read more.
Background: Brugada Syndrome (BrS) is a cardiac arrhythmia associated with an increased risk of ventricular arrhythmias and sudden cardiac arrest. Although the arrhythmic substrate is traditionally localized to the ventricles, atrial fibrillation (AF) is frequently observed, suggesting a shared molecular substrate between atrial and ventricular arrhythmias. C-type natriuretic peptide (CNP) and related microRNAs (miRNAs) modulate atrial and ventricular physiology, but their roles in exosomes in BrS have not been investigated. Objectives: To investigate alterations in CNP mRNA expression and changes in the expression of selected CNP-associated miRNAs implicated in AF, both analyzed in exosomes isolated from individuals with BrS and from healthy controls. Methods: Exosomes were isolated from the plasma of BrS patients without a history of overt AF and from healthy controls. In silico analyses identified CNP-targeting miRNAs implicated in AF. Exosomal CNP and CNP-related miRNAs were analyzed using Droplet Digital PCR. Results: BrS patients exhibited a significant increase in exosomal CNP mRNA expression levels compared with controls. MiR-138-5p was selectively downregulated, whereas other AF-related CNP-targeting miRNAs (miR-4443, miR-206, miR-142-5p, miR-223-5p) showed comparable levels between groups. A positive correlation between exosomal CNP and miR-223-5p and miR-4443 suggests shared regulatory pathways. Conclusions: these findings indicate that exosomal profiling may provide a more sensitive approach than conventional circulating measurements to detect molecular remodeling in BrS. The observed alterations highlight a potential shared molecular substrate between atrial and ventricular arrhythmias and may inform future studies aimed at refining diagnostics and developing targeted therapeutic strategies. Full article
(This article belongs to the Section Molecular and Translational Medicine)
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19 pages, 6582 KB  
Article
Extracellular Vesicle and Plasma miRNAs as Candidate Biomarkers of Traumatic Brain Injury in the Context of Polytrauma
by Cora Rebecca Schindler, Dirk Henrich, Lena Krämer, Inna Schaible, Jason-Alexander Hörauf, Aileen Ritter, Philipp Störmann, Rald Victor Maria Groven, Markus Huber-Lang, Ingo Marzi and Liudmila Leppik
Int. J. Mol. Sci. 2026, 27(10), 4248; https://doi.org/10.3390/ijms27104248 - 10 May 2026
Viewed by 576
Abstract
Severe traumatic brain injury (TBI) is a leading cause of mortality and long-term disability in polytrauma (PT) patients, and its clinical outcome remains difficult to predict due to clinical heterogeneity and secondary injury mechanisms. Current diagnostic and prognostic approaches based on clinical assessment [...] Read more.
Severe traumatic brain injury (TBI) is a leading cause of mortality and long-term disability in polytrauma (PT) patients, and its clinical outcome remains difficult to predict due to clinical heterogeneity and secondary injury mechanisms. Current diagnostic and prognostic approaches based on clinical assessment and imaging are limited, particularly in PT where neurological evaluation is often impaired. This study aimed to compare plasma- and extracellular vesicle (EV)-associated microRNA (miRNA) signatures in patients with severe TBI and healthy controls to identify their potential as minimally invasive biomarkers and to improve understanding of molecular responses. For profiling circulating miRNAs, blood samples were collected at ≤3 h and at 48 h after admission. In the screening phase, plasma samples of n = 15 patients with severe isolated TBI (Abbreviated Injury Scale [AIS]Head ≥ 4, all other AIS ≤ 1) and n = 15 age- and sex-matched healthy controls were pooled (n = 5/pool) and subjected to next-generation sequencing (NGS). In the following validation phase, n = 25 severely injured trauma patients (Injury Severity Score [ISS] ≥ 16) were enrolled and stratified into PT without TBI (PT; AISHead = 0; n = 13) and isolated TBI (n = 12). Differentially expressed candidate miRNAs identified in the screening phase were validated in individual plasma and EV samples using reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Functional enrichment and pathway analyses were performed using miRNet. NGS identified more differentially expressed miRNAs in plasma (ER: 103; 48 h: 65) than in EVs (Emergency Room [ER]: 14; 48 h: 32). Functional enrichment analysis indicated associations with pathways related to cellular stress, senescence, growth factor signaling, transcriptional regulation, and apoptosis. In validation, 12 of 16 plasma and 10 of 15 EV-miRNAs were confirmed as differentially expressed in TBI patients; among these, three plasma and four EV miRNAs differed between TBI and PT. After adjustment, most plasma miRNAs were associated with injury severity rather than group status. EV miRNA profiles showed heterogeneous patterns, with miR-1469 associated with TBI group status in adjusted analysis, while miR-1237-5p was linked to injury severity and other EV miRNAs showed no consistent group-specific effects. Plasma miRNAs mainly correlated with systemic injury markers, whereas EV miR-1469 showed a moderate association with the Glasgow Coma Scale (GCS). Overall, circulating miRNA profiles after injury appear to be predominantly influenced by systemic trauma severity rather than TBI-specific effects. Plasma miRNAs mainly reflected general injury burden, whereas EV-associated miRNAs showed more heterogeneous patterns, with miR-1469 emerging as a candidate associated with TBI after adjustment for clinical covariates. These findings suggest that EV-derived miRNAs, particularly miR-1469, may provide more targeted signals related to brain injury and warrant further investigation. Full article
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20 pages, 892 KB  
Systematic Review
Evidence Mapping of ctDNA Reporting in Pancreatic Ductal Adenocarcinoma: Toward a Shared Quantitative Language for ctDNA
by Daniel Croagh and Saeed Aslani
Cancers 2026, 18(8), 1318; https://doi.org/10.3390/cancers18081318 - 21 Apr 2026
Viewed by 657
Abstract
Background/Objectives: Circulating tumour DNA (ctDNA) assays enable non-invasive assessment of tumour burden and treatment response in oncology. However, quantitative ctDNA outputs (such as variant allele frequency, tumour fraction, and aggregate burden scores) remain difficult to interpret and compare across platforms. This evidence-mapping [...] Read more.
Background/Objectives: Circulating tumour DNA (ctDNA) assays enable non-invasive assessment of tumour burden and treatment response in oncology. However, quantitative ctDNA outputs (such as variant allele frequency, tumour fraction, and aggregate burden scores) remain difficult to interpret and compare across platforms. This evidence-mapping review evaluates current quantitative reporting approaches in pancreatic ductal adenocarcinoma (PDAC) and examines the potential role of KRAS mutant ctDNA as a biologically grounded reference metric. Methods: A systematic literature search was conducted across PubMed/MEDLINE and Scopus to identify studies reporting quantitative ctDNA metrics in PDAC. Eligible studies included those measuring plasma KRAS mutations and/or reporting variant allele frequency, tumour fraction, or multi-locus aggregate metrics. Additional relevant primary studies identified through broader manual searching of PubMed were assessed against the same prespecified eligibility and classification criteria before inclusion. Data were synthesised narratively, focusing on reporting frameworks, units of measurement, assay characteristics, and the interpretability of quantitative outputs across platforms. Results: Substantial heterogeneity was observed in ctDNA quantification methods and reporting standards. Ratio-based metrics such as variant allele frequency and tumour fraction were commonly used but varied according to assay design, plasma input volume, and background cell-free DNA levels. Few studies reported absolute mutant molecule counts per unit volume. Given that approximately 90–95% of PDACs harbour truncal activating KRAS mutations, plasma KRAS was consistently represented across platforms and demonstrated potential as a shared quantitative anchor. Limited standardisation was noted in distinguishing detectability from quantifiability based on sampling depth and counting statistics. Conclusions: Current ctDNA reporting in PDAC lacks a shared quantitative reference, limiting cross-study comparability. Reporting KRAS mutant molecules per millilitre and adopting an assay-agnostic framework distinguishing detection from quantification may improve interpretability, support harmonisation across platforms, and facilitate cumulative learning in pancreatic cancer ctDNA research. Full article
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15 pages, 1635 KB  
Article
Evaluation of PacBio Long-Read and PCR-Based Short-Read Sequencing for Mitochondrial DNA (mtDNA) Variant Detection, with an Emphasis on Detection and Quantification of mtDNA Deletion
by Tanaya Jadhav, Matthew Aruta, Maria Alejandra Diaz-miranda, Avery Zucco, Laura K. Conlin, Ramakrishnan Rajagopalan and Jing Wang
Int. J. Mol. Sci. 2026, 27(8), 3562; https://doi.org/10.3390/ijms27083562 - 16 Apr 2026
Viewed by 710
Abstract
Accurate detection of all types of mitochondrial DNA (mtDNA) variants, including single large-scale mtDNA deletions (SLSMDs) and multiple mtDNA deletions (MMDs), along with heteroplasmy quantification, is essential for Primary Mitochondrial Disease (PMD) diagnosis. This study compares amplification-free PacBio long-read sequencing (LRS) mtDNA analysis [...] Read more.
Accurate detection of all types of mitochondrial DNA (mtDNA) variants, including single large-scale mtDNA deletions (SLSMDs) and multiple mtDNA deletions (MMDs), along with heteroplasmy quantification, is essential for Primary Mitochondrial Disease (PMD) diagnosis. This study compares amplification-free PacBio long-read sequencing (LRS) mtDNA analysis with long-range PCR-based targeted mtDNA sequencing by short-read sequencing (SRS) in terms of detection sensitivity and accuracy. In total, 17 samples, including 4 SLSMD cases (3 blood, 1 muscle), 9 MMD muscle samples, and 4 deletion-negative controls (1 blood, 3 muscle), were sequenced using the PacBio Sequel IIe. Our findings demonstrate LRS’s efficacy in detecting single nucleotide variants (SNVs) and large mtDNA deletions with precise breakpoints. LRS can accurately detect and distinguish SLSMD from MMD, providing deletion heteroplasmy without the need for a second methodology. Deletion heteroplasmy computed from LRS was highly correlated with the Droplet Digital PCR (ddPCR) estimates (Pearson’s r2 = 0.95). While LRS can detect SNVs with approximately 5% heteroplasmy, only variants exceeding 10% heteroplasmy can attain 100% sensitivity, specificity, and precision when compared to those previously identified through clinical testing. In conclusion, our findings establish PacBio LRS as a robust tool for comprehensive mtDNA analysis capable of accurately detecting and quantifying heteroplasmic mtDNA variants and complex deletions. Full article
(This article belongs to the Special Issue Mitochondrial Dysfunction and Oxidative Stress in Human Diseases)
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19 pages, 1420 KB  
Article
A Species-Specific Assay for Salmo cf. trutta and Its Application in eDNA-Based Spawning Activity Monitoring
by Andrea Novaković, Jovana Jovanović Marić, Stoimir Kolarević, Lucija Markulin, Teja Petra Muha, Irena Todorović, Jelena Stanković Ristić, Tamara Mitić, Stefan Andjus, Jelena Čanak Atlagić, Ana Marić and Margareta Kračun-Kolarević
Fishes 2026, 11(4), 219; https://doi.org/10.3390/fishes11040219 - 6 Apr 2026
Viewed by 778
Abstract
Understanding salmonid spawning dynamics is critical for conserving cold-water river ecosystems amid increasing human and climate pressures. This study developed and validated a species-specific eDNA (Salmo cf. trutta and Thymallus thymallus) and evaluated its performance for seasonal spawning activity monitoring using [...] Read more.
Understanding salmonid spawning dynamics is critical for conserving cold-water river ecosystems amid increasing human and climate pressures. This study developed and validated a species-specific eDNA (Salmo cf. trutta and Thymallus thymallus) and evaluated its performance for seasonal spawning activity monitoring using droplet digital PCR (ddPCR). Species-specific primers and probes targeting mitochondrial nd5 (S. trutta) and cytb (T. thymallus) genes were designed and optimized as a duplex assay. Performance assessments included in vitro validation, cross-amplification testing, and determining the LOB, LOD, and LOQ. Field validation over a year at two spawning sites in the Gradac River, Serbia, involved seasonal eDNA sampling, filtration, extraction, and ddPCR analysis. Fish community composition was also assessed with electrofishing and metabarcoding. The assay showed high specificity and sensitivity, with LODs of 0.14 cp/µL and LOQs of 0.99 and 1.25 cpµL for S. trutta and T. thymallus. S. trutta eDNA peaked in late autumn during spawning, while T. thymallus remained at or below detection limits, reflecting its lower abundance and different spawning season. Filter type affected filtration efficiency but not eDNA yield. These findings confirm ddPCR-based eDNA as a powerful, non-invasive tool for monitoring salmonid spawning and seasonal changes, supporting adaptive fisheries management and conservation amid environmental changes. Full article
(This article belongs to the Section Biology and Ecology)
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17 pages, 8460 KB  
Review
Advances of Digital Detection for Foodborne Pathogens
by Ruonan He, Diming Hua, Wenwen Wu, Mojun Shi, Xuejiao Huang, Xuhan Xia and Ruijie Deng
Foods 2026, 15(7), 1250; https://doi.org/10.3390/foods15071250 - 6 Apr 2026
Cited by 1 | Viewed by 828
Abstract
The implementation of stringent regulatory policies for foodborne pathogens necessitates ultra-sensitive analytical methods. Digital detection, characterized by absolute quantification and tolerance to complex matrices, serves as a robust approach for food safety monitoring. This review summarizes recent advances in digital detection for foodborne [...] Read more.
The implementation of stringent regulatory policies for foodborne pathogens necessitates ultra-sensitive analytical methods. Digital detection, characterized by absolute quantification and tolerance to complex matrices, serves as a robust approach for food safety monitoring. This review summarizes recent advances in digital detection for foodborne pathogens, including nucleic acid amplification-based platforms such as droplet digital PCR and digital isothermal amplification, as well as emerging preamplification-free approaches based on enzyme-mediated signal conversion, functional nanomaterials, and microfluidic devices. We also profile the applications of digital detection technologies for achieving highly specific and accurate detection of foodborne pathogens and discuss their capabilities in viable bacteria quantification, antimicrobial resistance analysis, and multiplex detection. We finally discuss emerging trends, including partition-free digital detection and artificial intelligence-assisted analysis. These advances are expected to promote the development of intelligent and data-driven food safety surveillance strategies. Full article
(This article belongs to the Special Issue Advanced Detection and Control Techniques for Foodborne Pathogens)
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25 pages, 799 KB  
Review
HPV Detection in Oropharyngeal Cancer: A Narrative Review of Diagnostic and Emerging Molecular Approaches
by Fernando López, Remco de Bree, M. P. Sreeram, Sandra Nuyts, Juan Pablo Rodrigo, Karthik N. Rao, Nabil F. Saba, Carol Bradford, Arlene Forastiere, Luiz P. Kowalski, Anna Luíza Damaceno Araújo, Carlos Suarez and Alfio Ferlito
Diagnostics 2026, 16(7), 1010; https://doi.org/10.3390/diagnostics16071010 - 27 Mar 2026
Viewed by 1142
Abstract
Human papillomavirus (HPV)-driven oropharyngeal squamous cell carcinoma (OPSCC) has emerged as a biologically distinct entity, typically affecting younger, non-smoking patients and showing improved survival compared to HPV-negative tumors. Accurate HPV status determination is essential for correct staging, prognostic assessment, and treatment de-escalation. Despite [...] Read more.
Human papillomavirus (HPV)-driven oropharyngeal squamous cell carcinoma (OPSCC) has emerged as a biologically distinct entity, typically affecting younger, non-smoking patients and showing improved survival compared to HPV-negative tumors. Accurate HPV status determination is essential for correct staging, prognostic assessment, and treatment de-escalation. Despite advances, substantial variability persists among diagnostic methods and clinical workflows. A narrative review of PubMed, Scopus, and Web of Science databases was conducted up to July 2025. Studies addressing HPV detection techniques in OPSCC—including p16^INK4a^ immunohistochemistry (IHC), HPV DNA and RNA assays, liquid biopsy approaches, and computational surrogates—were critically analyzed regarding diagnostic accuracy, clinical applicability, and emerging innovations. Tissue-based assays remain the diagnostic reference standard. p16 IHC provides high sensitivity but limited specificity and should be confirmed with nucleic acid-based methods such as DNA PCR, in situ hybridization (ISH), or E6/E7 mRNA detection. Combined or “orthogonal” testing minimizes discordance and refines risk stratification. Liquid biopsy detection of circulating HPV DNA using droplet digital PCR or next-generation sequencing has shown high sensitivity and specificity in cohorts of patients with HPV-associated OPSCC, supporting its potential role as a complementary biomarker for treatment monitoring and surveillance. However, circulating HPV DNA alone does not unequivocally identify the anatomic source of HPV DNA and should be interpreted together with clinical, radiologic, and tissue-based findings. Oral rinse and saliva assays show moderate diagnostic performance, while artificial intelligence-based radiomic and histopathologic models are emerging as complementary tools. Reliable HPV attribution in OPSCC requires a multimodal diagnostic strategy integrating p16 IHC, molecular confirmation, and ctHPV-DNA monitoring. Methodological standardization and prospective validation are essential to implement precision-guided, cost-effective workflows in routine clinical practice. Full article
(This article belongs to the Special Issue Clinical Diagnosis of Otorhinolaryngology)
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13 pages, 1084 KB  
Article
Circulating Plasma Cells as a Minimally Invasive Adjunct to Bone Marrow Aspirates for Genetic Analysis of ER Stress and Autophagy in Multiple Myeloma: A Feasibility Study
by A.-M. Joëlle Marivel, Therese M. Becker, Alexander James, Yafeng Ma, Nirupama D. Verma, Tara L. Roberts and Silvia Ling
Biomedicines 2026, 14(4), 737; https://doi.org/10.3390/biomedicines14040737 - 24 Mar 2026
Viewed by 568
Abstract
Background: Multiple myeloma (MM) is characterised by clonal expansion of plasma cells (PCs) in the bone marrow (BM). Disease assessment and monitoring typically rely on invasive, single-site procedures, such as BM biopsies (BMBs), which may inadequately capture intra- and extra-medullary spatial heterogeneity. Circulating [...] Read more.
Background: Multiple myeloma (MM) is characterised by clonal expansion of plasma cells (PCs) in the bone marrow (BM). Disease assessment and monitoring typically rely on invasive, single-site procedures, such as BM biopsies (BMBs), which may inadequately capture intra- and extra-medullary spatial heterogeneity. Circulating plasma cells (CPCs), enriched from peripheral blood (PB), may represent a minimally invasive alternative or adjunct for molecular profiling. Objectives: This study aimed to evaluate the feasibility of using CPCs, enriched from PB, for mRNA analysis in plasma cell dyscrasia, including MM. A secondary objective was to assess whether mRNA expression levels of the endoplasmic reticulum (ER) stress sensors X-box-binding protein 1 (uXBP1) and activating transcription factor 6 (ATF6), and the chaperone-mediated autophagy marker Lysosomal-Associated Membrane Protein 2 (LAMP2A) by droplet digital PCR (ddPCR), were associated with resistance to the second-generation proteasome inhibitor (PI) carfilzomib (Cfz). Methods: Multiple myeloma (MM) cell lines (H929 and U266) and their carfilzomib-adapted derivatives were used to establish and validate droplet digital PCR (ddPCR) assays targeting ER stress (uXBP1, ATF6) and autophagy-related (LAMP2A) transcripts. Solid tumour cell lines, including serum-starved HeLa cells, served as biological controls to support assay specificity and sensitivity. Total RNA was extracted and reverse-transcribed to complementary DNA prior to analysis. Transcript levels were normalised to those of β-actin or GAPDH, as appropriate. ddPCR was performed using the BioRad QX200 system, with results reported as the normalised transcript copy number per microlitre of reaction. Matched bone marrow aspirate (BMA) and peripheral blood (PB) samples were collected at a single clinical time point from adults undergoing investigation for plasma cell dyscrasia between January 2021 and December 2023. Samples were obtained as part of standard clinical care and/or during treatment with Bortezomib (Btz) or Cfz. Mononuclear cells were isolated by density gradient centrifugation, and CD138+ plasma cells were enriched by fluorescence-activated cell sorting. Enrichment purity was assessed qualitatively by immunofluorescence microscopy using CD138 and CD117 markers. Samples yielding fewer than 1000 CD138+ plasma cells were excluded, resulting in 10 evaluable matched patient pairs. Results: Carfilzomib-adapted MM cell lines demonstrated reduced levels of uXBP1, ATF6, and LAMP2A mRNA compared to treatment-naïve cells. In matched BM and PB samples, uXBP1 mRNA levels were consistently lower in circulating PCs than in BM-derived PCs, whereas ATF6 mRNA levels were concordant between compartments. LAMP2A mRNA levels exhibited marked inter-patient heterogeneity. Conclusions: This study demonstrates the feasibility of using CPCs as a minimally invasive source for mRNA-based biomarker assessment and highlights ddPCR as a sensitive platform for quantifying ER stress and chaperone-mediated autophagy related transcripts in CPCs. Cfz adaptation was associated with reduced levels of uXBP1 and LAMP2A mRNA in MM cell lines. Future prospective studies evaluating the clinical utility of ER stress and chaperone-mediated autophagy associated transcripts in CPCs as predictors of resistance to PI are warranted. Full article
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12 pages, 702 KB  
Article
Circulating microRNAs as Early Biomarkers of Breast Cancer: A Nested Case-Control Study Within a Prospective Cohort in Italy
by Lisa Padroni, Giorgia Marmiroli, Laura De Marco, Valentina Fiano, Saverio Caini, Claudia Agnoli, Claudia Vener, Vittorio Simeon, Salvatore Panico, Luca Manfredi, Lorenzo Milani, Fulvio Ricceri and Carlotta Sacerdote
Int. J. Mol. Sci. 2026, 27(6), 2706; https://doi.org/10.3390/ijms27062706 - 16 Mar 2026
Viewed by 517
Abstract
Circulating microRNAs (miRNAs) are promising minimally invasive biomarkers for cancer risk assessment, yet prospective evidence for breast cancer (BC) remains limited. We conducted a nested case–control study within a prospective cohort to examine whether pre-diagnostic circulating miRNAs are associated with subsequent BC risk [...] Read more.
Circulating microRNAs (miRNAs) are promising minimally invasive biomarkers for cancer risk assessment, yet prospective evidence for breast cancer (BC) remains limited. We conducted a nested case–control study within a prospective cohort to examine whether pre-diagnostic circulating miRNAs are associated with subsequent BC risk and to explore their potential relevance in prospective population-based settings. Baseline serum from 160 women (80 incident BC cases; 80 matched controls) was analyzed, with a median time to diagnosis of 8.9 years. Eight candidate miRNAs were quantified by droplet digital PCR (ddPCR) and normalized to miR-484. Group differences were evaluated by non-parametric tests, and odds ratios for BC were estimated using logistic regression models adjusted for established risk factors, with Bonferroni correction for multiple testing. Cases and controls were comparable at baseline. Among the candidates, lower circulating miR-181 levels showed a suggestive inverse association with BC risk in fully adjusted models, while lower Let7 levels showed only a non-significant, hypothesis-generating inverse trend that did not survive Bonferroni correction. No other miRNA displayed clear associations with BC risk. These findings, while preliminary, support further large-scale prospective investigations specifically designed to assess predictive performance and external validation. employing standardized pre-analytical and analytical protocols, repeated sampling, and independent replication/external validation to clarify the etiologic relevance and potential risk-prediction value of circulating miRNAs for BC. Full article
(This article belongs to the Section Molecular Oncology)
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11 pages, 614 KB  
Article
Examining Epigenetic Age in Women with Different Obesity Conditions Using DNA Methylation at the FHL2 Gene
by Licínio Manco, Helena Correia Dias and Lara Palmeira
Methods Protoc. 2026, 9(2), 47; https://doi.org/10.3390/mps9020047 - 12 Mar 2026
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Abstract
DNA methylation (DNAm) age estimation is one of the hottest topics in forensic contexts. However, there is growing evidence that DNAm can be affected by several factors, including many clinical conditions. In this study, we analyzed the methylation levels within the FHL2 gene [...] Read more.
DNA methylation (DNAm) age estimation is one of the hottest topics in forensic contexts. However, there is growing evidence that DNAm can be affected by several factors, including many clinical conditions. In this study, we analyzed the methylation levels within the FHL2 gene in Portuguese women using the droplet digital PCR (ddPCR) methodology to develop age prediction models (APMs). We hypothesized that obesity could affect the accuracy of APMs and would be associated with the advancement in epigenetic aging. We collected blood samples from 62 women (aged 21–58 years old) with overweight and obesity. DNA extracts were subjected to bisulfite conversion followed by ddPCR using dual-labeled probes targeting the methylated and unmethylated FHL2 CpG site cg06639320. The developed APM yielded a mean absolute deviation (MAD) of 4.72 years between predicted and chronological ages in the total sample. When applying the developed APM to women classified as overweight, the MAD was 3.64 years, while, for those with obesity class 1, it was 3.93 years, and, for those with obesity class 2, 6.29 years. The same pattern of accuracy was observed when we developed APMs specifically for the groups categorized by overweight and obesity, obtaining MAD values of 3.75 years (overweight), 3.69 years (obesity class 1) and 6.24 years (obesity class 2). Our study indicates that severe obesity may impact the accuracy of DNA methylation-based age estimators. We did not find evidence of an association between BMI and accelerated epigenetic aging. However, we found signals of epigenetic age acceleration in younger subjects and epigenetic age deceleration in the older participants. Full article
(This article belongs to the Section Biomedical Sciences and Physiology)
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17 pages, 1330 KB  
Article
Clonal Dynamics of FLT3-ITD from Diagnosis to Relapse: Ultra-Sensitive Patient-Specific Monitoring by ddPCR
by Alessandro Ferrando, Johanna Umurungi, Alice Costanza Danzero, Antonio Frolli, Rita Vacca, Arianna Savi, Giovanni Fornari, Valentina Gaidano, Alessandro Cignetti, Beatrice Sani, Simone Rocco, Barbara Pergolizzi, Carmen Fava, Cristina Panuzzo, Jessica Petiti and Daniela Cilloni
Int. J. Mol. Sci. 2026, 27(5), 2481; https://doi.org/10.3390/ijms27052481 - 8 Mar 2026
Viewed by 729
Abstract
The FLT3-ITD mutation is a critical prognostic marker in acute myeloid leukemia (AML) and recent clinical trials demonstrate that FLT3-based measurable residual disease (MRD) is both prognostic and predictive, guiding therapeutic interventions in intensive and post-transplant settings. Conventional detection methods lack the sensitivity [...] Read more.
The FLT3-ITD mutation is a critical prognostic marker in acute myeloid leukemia (AML) and recent clinical trials demonstrate that FLT3-based measurable residual disease (MRD) is both prognostic and predictive, guiding therapeutic interventions in intensive and post-transplant settings. Conventional detection methods lack the sensitivity required for effective MRD monitoring. We developed a patient-specific droplet digital PCR (ddPCR) approach achieving analytical sensitivity of 10−5 (0.001%) for FLT3-ITD quantification. In our cohort, ddPCR enabled longitudinal monitoring of clonal dynamics, allowing the detection of re-emerging FLT3-ITD clones months before hematologic relapse and earlier than standard capillary electrophoresis. Notably, 25% of patients who relapsed as FLT3-ITD positive despite being classified as FLT3-negative at diagnosis harbored detectable microclones when retrospectively analyzed by ddPCR, suggesting that FLT3-ITD-positive relapse frequently originates from pre-existing subclones below conventional detection thresholds. These findings challenge current diagnostic classification and may influence risk stratification and treatment decisions, particularly regarding FLT3 inhibitor eligibility. While ddPCR is limited to tracking known dominant clones, it represents a practical, cost-effective solution for high-sensitivity MRD surveillance. In the era of targeted FLT3 therapies, integrating sensitive molecular monitoring into routine AML management may enable timely therapeutic adjustments and improve patient outcomes. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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