Search Results (1,864)

The rapid evolution of sequencing technologies has profoundly advanced precision oncology. Whole-exome sequencing (WES), whole-genome sequencing (WGS), and whole-transcriptome sequencing (RNA-Seq) enable comprehensive characterization of tumor biology by detecting actionable mutations, gene fusions, splice variants, copy number alterations, and pathway dysregulation. These approaches also provide critical insights into biomarkers such as homologous recombination deficiency (HRD), tumor mutational burden (TMB), and microsatellite instability (MSI), which are increasingly essential for guiding therapeutic decisions. Importantly, comprehensive genomic profiling not only refines patient stratification for targeted therapies but also sheds light on tumor–immune interactions and the tumor microenvironment, paving the way for more effective immunotherapeutic combinations. WGS is considered the gold standard for detecting germline mutations and complex structural variants, while WES remains central for detecting somatic driver mutations that guide targeted therapies. RNA-Seq complements these methods by capturing gene expression dynamics, identifying clinically relevant fusions, and revealing mechanisms of resistance. Together with advances in bioinformatics and artificial intelligence, these tools translate molecular data into actionable strategies for patient care. This review integrates insights from WGS, WES, and RNA-Seq with an overview of FDA- and EMA-approved targeted therapies, organized by tumor type, and highlights the molecular signaling pathways that drive cancer development and treatment. By bridging genomic profiling with regulatory-approved therapies, we outline current advances and future perspectives in delivering personalized cancer care. Full article

African swine fever (ASF), caused by African swine fever virus (ASFV), has inflicted severe economic losses on China’s pig industry. Existing ASFV nucleic acid detection methods struggle to identify infected pigs in the pre-viremic stage, especially for recently emerged recombinant ASFV strains that exhibit delayed clinical symptoms and prolonged virus shedding, posing great challenges to ASF prevention and control. To fit the problem, this study established a TaqMan duplex quantitative polymerase chain reaction (qPCR) assay targeting the ASFV p72 gene and porcine Hp gene for early diagnosis of ASFV infection. The qPCR reaction system (20 μL) and conditions were optimized and showed high sensitivity, with detection limits of 1.42 × 10¹ copies/μL for Hp and 2.23 × 10¹ copies/μL for ASFV, as well as excellent specificity and reproducibility. Serum cDNA samples from pigs infected with virulent or recombinant ASFV strains were tested, and the result showed that Hp was detectable as early as 1 day post-infection (DPI), however ASFV remained undetectable until 3DPI. Then cDNA samples from cohabitation infection were tested and 80% samples were Hp-positive, although ASFV test was negative.In conclusion, this duplex qPCR assay for simultaneous detection of Hp and ASFV enables pre-viremia diagnosis of ASF, providing a valuable tool for early screening of ASFV-infected pigs. Full article

Background/Objectives: Chorionic villus sampling (CVS) is a pivotal diagnostic tool for early prenatal detection of chromosomal and genetic abnormalities; however, the safety and diagnostic efficacy of different CVS approaches remain a subject of clinical interest. This monocentric study compares transcervical (TC-CVS), transabdominal (TA-CVS) and transvaginal (TV-CVS) techniques, focusing on procedure-related fetal loss and diagnostic yield. Methods: In this 15-year, single-operator prospective study, a total of 5500 women underwent CVS between 10 and 14 weeks of gestation at a single center. Sampling was performed via TA-CVS (n = 4500), TC-CVS (n = 850), or TV-CVS (n = 150). Outcomes assessed included fetal loss rates, sample adequacy, early complications and hemodynamic changes measured by Doppler ultrasound. A p-value < 0.05 (two-tailed) was considered statistically significant. Results: Spontaneous abortion rates were significantly lower following TA-CVS (0.18%; 8/4500) compared to TC-CVS (0.6%; 5/850) and TV-CVS (1.3%; 2/150) (χ² = 24.56, p < 0.001). Post hoc pairwise analysis showed significantly lower fetal loss in TA-CVS compared to TC-CVS, but not between TA-CVS and TV-CVS. Cytogenetic abnormalities were detected in 220 cases (4.0%), and clinically significant copy number variants (CNVs) were confirmed in fetuses with major structural malformations. Five-year follow-up showed no diagnosed intellectual disability among assessed children. Optimal tissue weight (10–20 mg) was more frequent with TA-CVS (66.7%) than TC-CVS (35.3%) or TV-CVS (36.7%) (χ² = 350.92, p < 0.001). In a Doppler subset (n = 400), uterine, spiral, and interplacental artery PI changes were non-significant; the umbilical (p = 0.032) and middle cerebral arteries (p < 0.001) showed transient PI reductions after sampling. Conclusions: Transabdominal CVS demonstrated the most favorable balance of safety and diagnostic quality, suggesting it should be the preferred first-line technique in early prenatal diagnosis. Standardized technique and operator training remain critical to optimize outcomes. Full article

Copy number variations (CNVs) affecting the chromosomal region 21q21.3–q22.13 are rare and have been increasingly associated with neurodevelopmental abnormalities and multisystemic manifestations. In this study, we aimed to characterize the clinical, genomic, and genotype–phenotype correlations of a Moroccan child carrying a de novo microdeletion in this region. Whole exome sequencing (WES) was performed using sequencing-by-synthesis technology on the GenoLab M platform, and CNV detection was achieved through the SeqOne platform. Variant interpretation was conducted using the Integrative Genomics Viewer (IGV), and a custom gene–phenotype heatmap was generated in R (ComplexHeatmap and pheatmap) based on OMIM, ClinVar, and DECIPHER databases to prioritize candidate genes within the deleted segment. The patient presented with global developmental delay, microcephaly, psychomotor and staturo-ponderal retardation, facial dysmorphism, epilepsy responsive to treatment, and cerebral anomalies, including passive biventricular hydrocephalus and diffuse cortical atrophy. WES-CNV analysis identified a heterozygous de novo microdeletion of approximately 8.2 Mb in 21q21.3–q22.13, encompassing 124 clinically relevant genes. Integrated analysis confirmed the pathogenicity of the deletion and highlighted genotype–phenotype correlations, particularly implicating dosage-sensitive genes such as SON and RUNX1. This case underlines the clinical utility of combining WES, CNV analysis, and phenotype-based bioinformatic tools for diagnosing complex microdeletion syndromes, contributes to understanding genotype–phenotype relationships in 21q21.3–q22.13 deletions, and supports improved clinical interpretation and patient management. Full article

Cannabis plants are susceptible to microbial contamination, including fungi capable of producing harmful mycotoxins. The presence of these toxins in cannabis products poses serious health risks, especially when used for medical purposes in immunocompromised people. This study evaluated the presence of fungi and mycotoxins in dried cannabis buds following gamma irradiation, using culture-based techniques, PCR/qPCR, and ELISA. Irradiation significantly reduced fungal and bacterial loads, eliminating culturable bacteria but did not achieve complete sterilization. Viable spores of toxigenic fungal genera, such as Aspergillus, Penicillium, and Fusarium, persisted. Sequencing of ITS amplicons revealed dominant mycotoxigenic fungi in non-irradiated (NR), irradiated (IR) and licensed producer (LP) samples, while next-generation sequencing (NGS) revealed additional non-culturable toxigenic species. PCR/qPCR detected biosynthetic genes for aflatoxins, trichothecenes, ochratoxins, and deoxynivalenol across all samples, with gene copy numbers remaining stable post-irradiation, suggesting DNA damage without full degradation. ELISA confirmed aflatoxin, ochratoxin, DON, and T2 toxins in both IR and LP samples at variable concentrations. While LP samples showed lower microbial counts and gene abundance, residual DNA and toxins were still detected. Our study shows that while irradiation decreases microbial loads, it does not completely remove toxigenic fungi or their metabolites. Ensuring the safety of cannabis products necessitates a multifaceted assessment that incorporates cultural, molecular, and immunological techniques, in parallel with more stringent microbial standards during production stage. Full article

Human norovirus (HuNoV), particularly the GII.4 genotype, is a leading cause of acute gastroenteritis worldwide, posing a significant public health and economic burden due to its low infectious dose. To address the need for rapid and sensitive detection, we developed a colorimetric biosensor utilizing a structure-optimized aptamer and gold nanoparticles (AuNPs). Biotin-modified aptamers could protect AuNPs from aggregation in salt solution. Upon specific binding to GII.4 HuNoV virus-like particles (VLPs), this protective effect is disrupted, leading to AuNP aggregation and a measurable color shift quantified by the A620/A520 absorbance ratio. Under optimized conditions, the assay demonstrated a linear response (y = 0.004597x + 0.3277, R² = 0.9922) to GII.4 HuNoV VLP concentrations ranging from 0.1 to 3.0 μg/mL, with the recovery rates between 91.74% and 106.43%. The biosensor exhibited high specificity for GII.4 HuNoV, showing minimal cross-reactivity with other common diarrheal pathogens, and achieved an exceptional detection limit of 27.2 copies/mL in a fecal matrix. Molecular docking and point mutation confirmed the critical roles of specific nucleotide bases (T20, C22, G31, and G44) in the aptamer and the Asn55 residue in the viral capsid for binding. This work establishes a sensitive, rapid, and cost-effective aptamer-based colorimetric platform suitable for the large-scale monitoring of GII.4 HuNoV. Full article

Background/Objectives: Human adenovirus 55 (HAdV55) is a notable pathogen causing community-acquired pneumonia; outbreaks occur frequently in military camps, hospitals, and schools, thereby posing a threat to public health security. This study aimed to develop a method for detecting HAdV55 nucleic acid by targeting the conserved region of the Hexon gene. The sequence was amplified using enzymatic recombination isothermal amplification (ERA) technology, in conjunction with CRISPR-Cas12a technology, to enhance the amplification signal. Methods: Optimized primer and crRNA sequences were selected through ERA isothermal amplification testing. The ERA-CRISPR/Cas12a detection method was completed within 30 min at a constant temperature of 42 °C. Results: Sensitivity was assessed by detecting standard plasmids and live strains at various dilution concentrations. The detection limits were determined to be 9 copies/reaction for standard plasmids and 2.5 copies/reaction for cultured HAdV55 strains. Specificity tests were conducted on positive samples for five common respiratory pathogens and five other adenovirus subtypes, all of which showed no cross-reactivity. Conclusions: A rapid ERA-CRISPR/Cas12a nucleic acid detection method for HAdV55 has been successfully developed, demonstrating high sensitivity and specificity without the need for expensive or complex instruments. This method holds promise for on-site pathogen screening and detection. Full article

Background: Acute lymphoblastic leukemia (ALL) is a genetically heterogeneous malignancy driven by structural variants (SVs) that impact diagnosis, prognosis, and treatment. Traditional methods such as karyotyping, FISH, and PCR often fail to detect cryptic or complex rearrangements, which are critical for accurate risk stratification. Methods: Optical Genome Mapping (OGM) is a technology that directly analyzes ultra-high-molecular-weight DNA, enabling the identification of balanced and unbalanced SVs, copy number variations (CNVs), and gene fusions with high resolution. This review compares the advantages and limitations of OGM versus standard techniques in ALL. Results: OGM improves ALL diagnosis by detecting clinically relevant alterations such as IKZF1 deletions, cryptic KMT2A rearrangements, and kinase fusions, especially in cases with normal or uninformative karyotypes. It reduces artifacts by eliminating cell culture and shortens reporting times. OGM resolves complex events like intrachromosomal amplifications and chromothripsis, enhancing classification and therapy decisions. Limitations include reduced sensitivity in repetitive regions, challenges in detecting Robertsonian translocations, difficulties with complex ploidies, and lower sensitivity for low-frequency subclones. Conclusions: Integrating OGM with next-generation sequencing (NGS) allows comprehensive genomic profiling, improving diagnosis, prognosis, and personalized treatment in ALL. Future advancements promise to further enhance the clinical utility of OGM. Full article

Omsk hemorrhagic fever is an acute zoonotic disease caused by Omsk hemorrhagic fever virus, a member of the genus Flavivirus (family Flaviviridae), with a reported case-fatality rate of approximately 3%. Historically confined to southwestern Siberia, ecological changes raise concerns about possible spread to non-endemic regions. Although no Omsk hemorrhagic fever cases have been reported in the Republic of Korea, the risk of accidental importation highlights the importance of establishing a reliable diagnostic protocol. We established and validated an institutionally developed diagnostic protocol employing real-time reverse transcription polymerase chain reaction targeting the NS2A and C genes of Omsk hemorrhagic fever virus. Primers and probes were designed from all available genomes to ensure broad strain coverage. Human ribonuclease P was used as an internal control to verify nucleic acid extraction and amplification. Using synthetic deoxyribonucleic acid fragments and in vitro-transcribed ribonucleic acid, assay performance was optimized, and analytical sensitivity was determined using probit analysis. The limits of detection were 74.50 copies/µL (threshold cycle 32.99) for NS2A and 70.41 copies/µL (threshold cycle 35.38) for C. Specificity testing using representative flaviviruses (West Nile virus, Yellow fever virus, Zika virus, St. Louis encephalitis virus, and Tick-borne encephalitis virus) and an alphavirus (Venezuelan equine encephalitis virus) demonstrated no cross-reactivity. The assay demonstrated high sensitivity, specificity, and reproducibility, supporting its potential application in national and international Omsk hemorrhagic fever virus surveillance systems. Full article

Background: Wilson’s disease (WD) is a rare autosomal recessive disorder caused by mutations in the ATP7B gene, leading to copper accumulation in the liver and brain. Given the clinical heterogeneity of the disease, this study aimed to characterize the mutational spectrum of ATP7B and explore genotype–phenotype correlations in Turkish patients. Methods: Whole-exome sequencing (WES) was performed in 17 Turkish patients clinically diagnosed with WD. Variants were annotated and evaluated using five in silico prediction tools (REVEL, CADD, PolyPhen, SIFT, MutationTaster). Copy number variation (CNV) analysis was conducted using the CLC Genomics Server (Version 22.0.2). Results: A total of 14 distinct ATP7B variants were identified, comprising 12 missense, 1 nonsense, and 1 frameshift mutation. Variant distribution showed some phenotype-specific patterns: four variants were found more frequently in hepatic cases and three in neurological cases, although no statistically significant or consistent correlation between genotype and clinical presentation could be established. The most frequent mutation was p.His1069Gln, present in both phenotypes. All missense variants were predicted to be pathogenic by at least three computational tools, with high concordance among platforms. No pathogenic CNVs were detected. Conclusions: This study expands the mutational landscape of ATP7B in Turkish patients with WD and supports the utility of WES combined with in silico tools for accurate variant classification. The results emphasize the genetic heterogeneity of WD and suggest possible associations between certain mutations and clinical phenotypes. Full article

Autophagy (cellular self-eating) is a tightly regulated catabolic process of eukaryotic cells during which parts of the cytoplasm are sequestered and subsequently delivered into lysosomes for degradation by acidic hydrolases. This process is central to maintaining cellular homeostasis, the removal of aged or damaged organelles, and the elimination of intracellular pathogens. The nematode Caenorhabditis elegans has proven to be a powerful genetic model for investigating the regulation and mechanism of autophagy. To date, the fluorescent autophagy reporters developed in this organism have predominantly relied on multi-copy, randomly integrated transgenes. As a result, the interpretation of autophagy dynamics in these models has required considerable caution due to possible overexpression artifacts and positional effects. In addition, starvation-induced autophagy has not been characterized in detail using these reporters. Here, we describe the development of two endogenous autophagy reporters, gfp::mCherry::lgg-1/atg-8 and gfp::atg-5, both inserted precisely into their endogenous genomic loci. We demonstrate that these single-copy reporters reliably track distinct stages of the autophagic process. Using these tools, we reveal that (i) the transition from the earliest phagophore to the mature autolysosome is an exceptionally rapid event because the vast majority of the detected fluorescent signals are autolysosome-specific, (ii) starvation triggers autophagy only after a measurable lag phase rather than immediately, and (iii) the regulation of starvation-induced autophagy depends on the actual life stage, and prevents excessive flux that could otherwise compromise cellular survival. We anticipate that these newly developed reporter strains will provide refined opportunities to further dissect the physiological and pathological roles of autophagy in vivo. Full article

Newborn screening (NBS) for spinal muscular atrophy (SMA) and severe combined immunodeficiency (SCID) faces challenges. Accurate and precise SMN1 and SMN2 copy number determination, confirmed by two orthogonal methods, are vital for SMA prognostication and treatment. Single SMN1 copy detection also enables the further feasibility to screen for compound heterozygotes. In SCID, low-level T-cell receptor excision circle (TREC) quantification by quantitative PCR is imprecise, necessitating replicates for reliable results. An assay with enhanced accuracy, precision, and high throughput is warranted for NBS SMA and SCID. False positive of SMN1 deletions due to allele dropout are also a potential pitfall in PCR-based methods. We evaluated a first-tier fully automated quadruplex droplet digital PCR (ddPCR) assay detecting SMN1, SMN2, TREC, and RPP30 using dried blood spots together with a second-tier Sanger sequencing to exclude SMN1 allele dropout. Five proficiency test samples and six patient samples with known SMN1 and SMN2 copy numbers confirmed by multiplex ligation-dependent probe amplification were used for accuracy evaluation with full concordance. The ddPCR assay showed high precision for SMN1 and SMN2 (<7% coefficient of variation (CV) for ≥0 copy) and TREC (14.6% CV at 37 copies/µL blood). Second-tier Sanger sequencing identified all SMA cases with homozygous deletions. Accuracy for TREC classification was concordant with 10 proficiency samples. The reference interval of TREC concentration was established for newborns ≥ 34 weeks (n = 1812) and the 2.5th percentile was 57 copies/µL blood. A two-tiered approach with fully automated quadruplex ddPCR and Sanger sequencing delivers accurate and precise quantitation for NBS SMA and SCID, enabling early treatment and counseling. Full article

Background/Objectives: Lyme disease diagnosis remains challenging due to the limitations of current methods. While PCR-based assays are widely used, their sensitivity can be affected by sample type and the inhibition of host DNA. This study aimed to evaluate the feasibility and sensitivity of a CRISPR/Cas12-based detection system for Borrelia burgdorferi sensu lato, comparing its performance with real-time PCR. Methods: DNA from three Borrelia genospecies (B. burgdorferi, B. garinii, and B. afzelii) was amplified targeting the OspA gene. Detection was performed using a Cas12/crRNA system with a fluorescent ssDNA reporter. Sensitivity assays were conducted on serial dilutions of Borrelia DNA, with and without human genomic DNA, and results were compared with qPCR. Results: Direct detection of Borrelia DNA without amplification was not feasible. However, when combined with PCR, the Cas12/crRNA system reliably detected as few as 5 genome copies per reaction. End-point PCR extended to 60 cycles improved detection robustness for B. garinii and B. afzelii, although sensitivity decreased in the presence of human genomic DNA. Conclusions: The Cas12/crRNA-based system offers a sensitive and accessible alternative to qPCR, especially in settings lacking real-time PCR instrumentation. Future developments may include integration with isothermal amplification and microfluidic platforms to enhance direct detection capabilities. Full article

Background/Objectives: Legionella micdadei is a clinically significant species within the Legionella genus, requiring accurate detection methods, surveillance, and precise clinical diagnosis. Our objective was to develop a sensitive polymerase chain reaction (PCR) assay specific for L. micdadei to detect its presence in environmental specimens. Methods: We targeted the 23S–5S intergenic spacer region, which can differentiate Legionella spp. We tested the detection of L. micdadei with 20 strains and determined the limit of detection with 2 strains. We verified assay specificity with 17 strains of other Legionella spp., 62 strains of other bacterial and fungal genera, and three human DNA specimens. We evaluated intra- and inter-run precision. We tested 15 environmental specimens (water, swabs of water faucets, mulch, and soil) by PCR. Results: The PCR assay demonstrated 100% analytical specificity (no cross-reactivity with non-targeted species), 100% inclusivity (detection of all L. micdadei strains), and high precision, with a coefficient of variation ≤ 2% across replicates. The limit of detection was estimated at 5 genomic DNA copies per reaction. We detected L. micdadei in environmental specimens. Conclusions: This PCR assay enables accurate detection of L. micdadei and is not subject to competition with other Legionella spp., thereby addressing limitations of current broad-spectrum Legionella approaches. The evaluation supports its application in environmental detection for surveillance. Full article

Avian reovirus (ARV), a highly pathogenic agent in poultry, causes severe economic losses through immunosuppression and secondary infections. Traditional diagnostic methods like reverse transcription quantitative PCR (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA) face limitations in resource-limited settings due to equipment dependency and prolonged processing. To address this, we developed a rapid, portable detection method integrating reverse transcription–recombinase-aided amplification (RT-RAA) with CRISPR/Cas12a. By targeting the conserved P17-coding region of the ARV S1 gene, this assay amplifies viral RNA isothermally (37 °C) within 20 min, followed by Cas12a-mediated collateral cleavage of fluorescent or lateral flow reporters for visual readout. The method achieved a sensitivity of 1 copy/μL, surpassing RT-qPCR (10 copies/μL), and completed detection in 40 min. Specificity tests against non-target pathogens confirmed zero cross-reactivity. Utilizing a portable incubator and low-cost visual tools, this platform eliminates reliance on thermocyclers and skilled personnel. Its field-deployable design enables on-site diagnosis, facilitating early ARV detection to mitigate outbreaks and economic losses in poultry farming. This study provides a paradigm shift in avian pathogen surveillance, combining speed, sensitivity, and accessibility for global agricultural and public health applications. Full article