Search Results (749)

Background: Inborn errors of metabolism (IEMs) represent a diverse group of genetic disorders affecting biochemical pathways. Despite advances in diagnostic technologies, comprehensive understanding of their historical evolution, classification systems, and diagnostic approaches remains fragmented. Objectives: This systematic review and meta-analysis aimed to synthesize evidence on the historical development, classification frameworks, and diagnostic modalities for IEMs, diagnostic accuracy, and prevalence estimates, providing a comprehensive resource for clinicians and researchers. Methods: Following PRISMA 2020 guidelines, we conducted a systematic search of seven electronic databases (PubMed/MEDLINE, Embase, Scopus, Web of Science, Google Scholar, SciSpace and ArXiv) from January 2000 to March 2026. Studies addressing historical perspectives, classification systems, or diagnostic approaches for IEMs were included. Two independent reviewers performed screening, data extraction, and quality assessment. Meta-analyses were conducted using random-effects models for diagnostic accuracy and prevalence estimates. Results: From 1342 identified records, 54 studies met the inclusion criteria, encompassing 8,234,567 individuals across 35 countries. Historical analysis revealed 16 major milestones from Garrod’s 1902 “chemical individuality” concept to the current AI-powered diagnostics. Four major classification systems were identified: pathophysiological (intoxication, energy deficiency, complex molecule disorders), biochemical pathway (amino acid, organic acid, urea cycle, carbohydrate, fatty acid oxidation, mitochondrial, peroxisomal, lysosomal disorders), organelle-based, and the integrated Society for the Study of Inborn Errors of Metabolism (SSIEM) nosology. Meta-analysis demonstrated high diagnostic performance of tandem mass spectrometry (MS/MS) with a pooled sensitivity of 99.1% (95% CI: 98.6–99.5) and specificity of 99.8% (95% CI: 99.7–99.9%). The pooled global prevalence of IEMs was 50.9 per 100,000 live births (95% CI 45.2–56.8). Next-generation sequencing achieved a diagnostic yield of 42.8% (95% CI: 38.2–47.5%) in suspected cases. Emerging AI-powered diagnostic tools demonstrated high discrimination performance with area under the curve (AUC) values exceeding 0.95 for specific IEM, though external validation remains limited. Newborn screening expanded from single-disease to comprehensive panels detecting over 50 disorders. Conclusions: This comprehensive review demonstrates that IEMs have evolved from rare curiosities to systematically diagnosable conditions through technological advances. Integration of metabolomics, genomics, proteomics and artificial intelligence promises further diagnostic improvements. Standardized classification systems and evidence-based diagnostic algorithms are essential for optimal patient care. Future directions include artificial intelligence-enhanced diagnostics, expanded screening, and personalized medicine approaches. Full article

Background/Objectives: Advanced hormone receptor-positive (HR+), epidermal growth factor 2-negative (HER2−) breast carcinoma (BC) patients receive frontline therapy with cyclin-dependent tyrosine kinase 4/6 inhibitors + endocrine therapy (ET). At progression, the best management includes mutational analysis for ESR-1, allowing second-line therapy with elacestrant. The aim of this study was to evaluate the efficacy and safety of elacestrant in an Italian real-world setting. Methods: A multicenter, observational study with a mixed retrospective and prospective design was conducted in 13 medical oncology units across Italy. The study population included adult patients with HR+/HER2− locally advanced or metastatic breast cancer with an activating ESR1 mutation documented by liquid biopsy and progressing after at least one line of endocrine therapy containing a CDK4/6 inhibitor. Mutational analysis of plasma was performed using next-generation sequencing with a multigene panel that included ESR1, PIK3CA, AKT, and PTEN. The sample size was calculated according to the two-stage Simon design. Toxicity was classified according to CTCAE version 5.0 criteria. Survival analyses were conducted using the Kaplan–Meier method. Results: At the time of analysis, 39 evaluable patients were enrolled, all female and Caucasian, with a median age of 67 years (range 41–89). The efficacy analysis documented an overall ORR of 28% and a disease control rate of 56%. The median duration of response was 6+ months (95% CL: 3.5–10.6 m). Median overall survival was not reached with a median follow-up of 10 months. The toxicity profile was overall favorable: grade ≥2 asthenia was the most frequent adverse event (23%), followed by gastrointestinal toxicity, which was generally mild. No treatment-related toxicity was reported in 64% of patients. Dose reductions were necessary in 15% of cases, while permanent treatment discontinuation due to toxicity occurred in only 4%. Conclusions: The results of this Italian multicenter observational study confirm the efficacy and tolerability of elacestrant in HR+/HER2− metastatic breast cancer with ESR1 mutation, in a real-world context consistent with the data from the pivotal EMERALD study and with real-world data present in the literature. Full article

Objectives: The aim of this study was to report novel ABCA4 variants detected in a cohort of 259 patients with ABCA4 retinopathy with the intention of improving the diagnostic accuracy for ABCA4 retinopathy and expanding its genetic spectrum. Methods: We retrospectively reviewed 259 patients with ABCA4 retinopathy, comprising 190 patients from the Oxford Cohort and 69 patients from other centres with a clinical diagnosis of ABCA4 retinopathy who were referred for genetic testing. Patients with a phenotype consistent with ABCA4 retinopathy who had a novel ABCA4 variant were included. Phenotyping in the Oxford Cohort included clinical evaluation, retinal imaging, and electrodiagnostic testing. Genetic testing was performed using next-generation sequencing (NGS) and Sanger sequencing. In silico analysis was used to investigate the pathogenicity of novel variants. Results: Eleven novel variants were detected in 12/259 patients, with one variant detected in two unrelated patients. These variants included three missense, four truncating, three splice-site variants, and one exon deletion. The variants were distributed across eight exons and three introns of ABCA4. In silico analysis and phenotype correlation supported the potential pathogenicity of the novel variants. Phenotypes ranged from mild isolated flecks with preserved retinal architecture to extensive chorioretinal degeneration. Conclusions: Despite over 2200 ABCA4 variants being reported to date, a further 11 novel ABCA4 variants were identified in 259 patients using NGS panel-based sequencing and MLPA. The variants were located across the whole ABCA4 gene, emphasising the necessity to sequence the whole gene. Our reporting of these variants expands the known genetic spectrum of ABCA4 retinopathy, contributing to accurate diagnosis in this patient group and the identification of suitable patients for recruitment to potential therapeutic interventions. Full article

Background and Clinical Significance: Biallelic pathogenic variants in the PCARE gene (photoreceptor cilium actin regulator), also known as C2orf71 (chromosome 2 open reading frame 71), are typically associated with retinitis pigmentosa type 54 (RP54) and, less frequently, with cone–rod dystrophy (CORD23). Case Presentation: A 52-year-old man presented with an eight-year history of progressive visual loss, without photophobia or nyctalopia. He underwent a comprehensive ophthalmological evaluation, including multimodal retinal imaging, automated perimetry, and full electrophysiological testing, in accordance with International Society for Clinical Electrophysiology of Vision (ISCEV)’s standards. Genetic testing was performed using next-generation sequencing (NGS) with an inherited retinal dystrophy gene panel, and findings were confirmed by Sanger sequencing. Clinical examination revealed bilateral macular atrophy with minimal foveal sparing and a central scotoma. Optical coherence tomography (OCT) showed disruption of the outer retinal layers and retinal pigment epithelium (RPE) abnormalities. Fundus autofluorescence (FAF) demonstrated central hypoautofluorescence surrounded by a hyperautofluorescent ring. Electrophysiological testing revealed severely reduced rod- and cone- mediated responses on full-field electroretinography (ERG), absent pattern ERG responses, and markedly reduced multifocal ERG responses, indicating widespread retinal dysfunction with significant macular involvement. Genetic analysis identified a homozygous pathogenic nonsense variant in PCARE [c.3289C>T; p.(Gln1097*)], confirming the diagnosis of an autosomal recessive inherited retinal dystrophy. Conclusions: Biallelic PCARE variants can cause late-onset severe retinal dystrophy, with predominant macular involvement and cone–rod dysfunction. Given its phenotypic overlap with other inherited retinal diseases, accurate diagnosis requires the integration of multimodal retinal imaging, electrophysiological testing, and comprehensive genetic analysis. Full article

Background/Objectives: Breast cancer (BC) is the most frequently diagnosed malignancy among women worldwide, yet tumor genomic data from Latin American and admixed populations remain limited. This gap affects the interpretation of cancer-associated variants and may limit the representation of these populations in genomic research. This study aimed to characterize the genomic landscape of breast tumors from Ecuadorian women and contextualize variant interpretation through genetic ancestry analysis. Methods: Breast tissue samples from 23 Ecuadorian mestizo women with suspected malignancy were analyzed. After histopathological confirmation, 21 breast tumors were included in the final cohort. Targeted next-generation sequencing was performed using a 94-gene cancer panel. Variants were annotated and classified according to clinical significance. Because matched normal DNA was unavailable, variant allele frequency was used as an exploratory approach to infer putative somatic, putative germline, indeterminate, or putative homozygous germline profiles. Putative germline and indeterminate variants were interpreted using ACMG/AMP criteria, whereas putative somatic variants were evaluated using the AMP/ASCO/CAP framework. Genetic ancestry was inferred using ancestry-informative insertion/deletion markers. Results: Seventy-two unique variants across 40 genes were identified, including 14 pathogenic, 10 likely pathogenic, and 48 variants of uncertain significance. Pathogenic and likely pathogenic alterations were detected in clinically relevant genes, including TP53, BRCA2, PTEN, CDH1, RAD51C, MSH6, NF1, CYLD, and SDHB. Variants of uncertain significance represented 66.7% of all detected variants and affected several cancer-associated and DNA repair genes. The cohort showed a trihybrid ancestry profile, with predominant Native American ancestry, followed by European and African contributions. Conclusions: This study expands BC genomic data from an underrepresented Ecuadorian cohort and highlights the coexistence of clinically relevant alterations with a high burden of variants of uncertain significance. The findings underscore the limitations of tumor-only sequencing and current variant interpretation frameworks in admixed populations. Larger studies integrating matched normal DNA, ancestry-informed analyses, functional validation, and broader sequencing strategies could help improve variant interpretation in Latin American populations. Full article

Background: Lung cancer is a highly heterogeneous disease in which molecular characterization has become essential for guiding personalized therapies. The implementation of next-generation sequencing (NGS) allows for the simultaneous detection of multiple genomic alterations, improving tumor profiling and therapeutic decision-making. This study aimed to characterize the molecular landscape of lung cancer using NGS and to evaluate its association with histological subtypes and programmed death-ligand 1 (PD-L1) expression. Methods: A retrospective observational study was conducted on 96 patients diagnosed with lung cancer between 2023 and 2025. Molecular profiling was performed using the Action OncoKitDx panel. Associations between genetic alterations, histological subtypes, and PD-L1 expression were analyzed using Fisher’s exact test, with p < 0.05 considered statistically significant. Results: Adenocarcinoma was the most common histological subtype (67.7%), followed by squamous cell carcinoma (26%). The most common mutations were KRAS (34.4%), TP53 (29.2%), and EGFR (11.5%). KRAS mutations were significantly associated with adenocarcinoma (p = 0.001), while squamous cell carcinoma showed a higher frequency of cases without molecular alterations detected by the NGS panel (p = 0.002). Co-mutations were identified in 22.9% of cases, with KRAS–TP53 being the most common combination. Tumors harboring EGFR mutations showed a significantly lower frequency of co-mutations (p = 0.012). No significant associations were found between PD-L1 expression and either histological subtypes or the analyzed genetic alterations. Conclusions: Lung cancer exhibits marked molecular heterogeneity, with a predominance of KRAS mutations in adenocarcinoma. The low frequency of co-mutations in EGFR-mutated tumors supports their role as dominant driver alterations. The lack of association between PD-L1 expression and genomic alterations highlights the complexity of its regulation and suggests the involvement of multiple biological factors. These findings reinforce the clinical value of NGS in comprehensive tumor profiling and in the development of precision medicine strategies. Full article

Understanding germline genetic variation is essential for improving human cancer care. Cancer predisposition genetic testing has become a part of the landscape of healthcare. Clinical guidelines have been established to identify individuals with monogenic risk, support variant classification, and guide enhanced cancer surveillance and prevention strategies. However, genetic mechanisms, cancer syndromes, genetic testing, patient education, and high-risk cancer management are often addressed in separate professional domains leading to limited cross-disciplinary understanding and confusion. A review tailored to a broad spectrum of clinicians is necessary to synthesize information, connect key concepts, and clearly define the principles and reasoning underlying recommended practice. Advanced genetic technology identified numerous genes and countless pathogenic variants contributing to a wide range of cancer predispositions. Rapid and accurate next-generation sequencing has enabled the routine use of multi-gene panel testing to stratify cancer risk. In precision cancer therapies, tumor genomic profiling frequently uncovers not only somatic alterations but also germline mutations, revealing additional cancer risk for the patients and their biological relatives. Beyond monogenic risks, the cumulative effect of numerous common polygenic factors can also significantly influence cancer susceptibility. Despite major advances in integrating germline genetic information into cancer care, substantial challenges remain in variant interpretation, precise risk stratification, and implementing personalized screening and prevention strategies. Using several cancer predisposition syndromes as examples, such as breast and ovarian cancer syndrome, Lynch syndrome, and Li-Fraumeni syndrome, the review provides a high-level overview of key concepts, the evolution of knowledge and technology, and the rationale underlying the current clinical management strategies. Full article

Background: The molecular concordance between primary lung adenocarcinoma and metastatic lesions remains incompletely characterized despite its direct implications for precision oncology and biopsy-driven therapeutic decision-making. This prospective monocentric paired-sample study evaluated genomic concordance between primary lung adenocarcinoma and synchronous thoracic metastatic lesions using targeted next-generation sequencing (NGS). Methods: We identified 27 treatment-naïve patients with histologically confirmed lung adenocarcinoma who underwent paired molecular profiling of the primary tumor and a synchronous thoracic metastatic site (pleural or intrapulmonary). DNA and RNA were analyzed using validated institutional NGS platforms. Genomic alterations, including clinically actionable oncogenic drivers consistently covered by the sequencing panel used in each pair, were compared across matched samples. Concordance was assessed using exact binomial confidence intervals, Cohen’s κ statistics, McNemar tests, and paired Wilcoxon signed-rank tests. Results: Actionable driver alterations were identified in 17 of 27 patients (63.0%; 95% CI 42.4–80.6), including EGFR mutations (40.7%), KRAS alterations (18.5%), and one ALK gene rearrangement (3.7%). TP53 concurrent mutations were detected in 14 cases (51.9%). Across all 27 paired samples, driver-level concordance was 100% (95% CI 87.2–100), with perfect agreement for EGFR, KRAS, and ALK alterations (κ = 1.00). TP53 mutations showed high concordance (92.9%; κ = 0.85), while CNVs were concordant in 88.0% of evaluable pairs. Variant allele frequency (VAF) comparisons, adjusted for tumor cellularity, further supported the apparent clonal stability of driver alterations across paired samples. Conclusions: This study demonstrates very high molecular concordance between primary lung adenocarcinomas and their synchronous pleural or intrapulmonary metastases. The observed 100% concordance of actionable driver alterations across paired specimens supports the clinical reliability of thoracic metastatic biopsies for baseline molecular profiling in treatment-naïve disease. Although limited by sample size, these findings support the biological stability of actionable driver alterations during early thoracic metastatic dissemination. Full article

Congenital stationary night blindness (CSNB) is a rare, genetically and clinically heterogeneous group of non-progressive inherited retinal diseases characterized by night blindness, myopia, nystagmus, and decreased visual acuity, for which comprehensive genetic characterization remains essential to enable accurate diagnosis and future gene therapy development. In this study, we performed a clinical and genetic analysis of twenty-one Polish families diagnosed with CSNB using next-generation sequencing (NGS)-based targeted gene panels and, in one case, whole-exome sequencing (WES), complemented by Sanger sequencing for variant validation and segregation analysis. Pathogenic variants were identified in six genes: GPR179 and NYX were the most frequently affected (six families each), followed by CACNA1F (three families), GRM6, TRPM1, and SLC24A1 (two families each). The complete Schubert–Bornschein form predominated in our cohort, in contrast to previous reports indicating higher prevalence of the incomplete form. Notably, ten previously unreported variants were identified in CACNA1F, GRM6, and NYX, expanding the known mutational spectrum of CSNB. Certain variants appear enriched in the Polish population. These findings underscore the value of NGS-based approaches for precise molecular diagnosis of CSNB and contribute to the broader understanding of its genetic architecture. Full article

Inherited retinal diseases (IRDs) are a major cause of visual impairment worldwide, marked by extensive genetic and phenotypic heterogeneity. Recent estimates from the U.S. suggest a prevalence of nearly 1 in 1000 individuals, reflecting both disease burden and improved diagnostic recognition. This review traces the shift from linkage analysis and Sanger sequencing to high-throughput next-generation sequencing, including panel-based, whole-exome, and whole-genome sequencing. Phenotype-driven testing strategies and standardized variant interpretation frameworks, such as the American College of Medical Genetics and Genomics guidelines, have substantially increased diagnostic yield. Copy number and structural variant detection, transcriptomics, and functional assays further help address unresolved cases. Nonetheless, barriers remain regarding cost, access, and the interpretation of variants of uncertain significance. Molecular confirmation has become essential for access to novel gene-directed therapies, exemplified by voretigene neparvovec for biallelic RPE65 variants, and is often a prerequisite for clinical trial participation. The growing role of genetic testing highlights the need for multidisciplinary evaluation and standardized outcome measures. Emerging tools, including artificial intelligence-assisted variant prioritization, image-to-genotype modeling, and multi-omics analyses, bridge molecular diagnoses with clinical phenotypes, accelerating the transition to targeted therapies. Continued progress will depend on increased access, standardized analytical regulations, and the integration of emerging technologies into routine clinical care. Full article

Objectives: To characterize heterozygous pathogenic COCH variants in a French cohort with non-syndromic sensorineural hearing loss (NSHL) and assess genotype–phenotype correlations in autosomal dominant NSHL (DFNA9). Setting: National Reference Center for Genetic Hearing Loss, Necker–Enfants Malades Hospital, Paris, France. Methods: This retrospective observational study included 69 individuals from 20 unrelated families diagnosed with DFNA9 (2005–2025). All individuals underwent clinical and audiological evaluations and genetic testing via targeted COCH Sanger sequencing or next-generation sequencing (NGS) panels. Variants were interpreted according to ACMG guidelines. Audiometric profiles and vestibular data were collected. Results: Seven known pathogenic COCH variants were found in ten families, and ten novel likely pathogenic variants in the others. Variants in vWFA domains were associated with early or late onset, progressive, bilateral and symmetrical hearing loss. Three variants (p.Gln410Arg, p.Ile450Val, p.Cys542Arg) were associated with congenital or prelingual onset, an atypical DFNA9 presentation. Variants in the LCCL domain were associated with later-onset hearing loss and more frequent vestibular dysfunction. Vestibular abnormalities were observed in about half of early-onset cases. Conclusions:COCH-related hearing loss is a rare cause of autosomal dominant NSHL, with only 20 families identified over two decades within the French network. This study expands the mutational spectrum of COCH by reporting ten novel variants and supports a domain-specific genotype–phenotype correlation. These findings improve the understanding of DFNA9 variability and have direct implications for clinical diagnosis, prognosis, and genetic counseling. Full article

Treatment-refractory rectal cancer liver metastasis represents a major therapeutic challenge, particularly in the absence of actionable genomic biomarkers. Functional precision oncology approaches integrating genomic profiling with patient-derived organoid (PDO) drug testing may provide biologically informed therapeutic prioritization. A 50-year-old female patient with KRAS/TP53-mutant, microsatellite-stable (MSS) rectal adenocarcinoma refractory to FOLFIRINOX was enrolled. A liver metastasis from a treatment-refractory rectal cancer patient was processed to establish three-dimensional patient-derived organoids. Histopathological concordance was assessed using H&E and p53 immunohistochemistry. Comprehensive genomic profiling was performed using a 637-gene targeted next-generation sequencing panel, enabling detection of single-nucleotide variants, indels, copy number variations, microsatellite instability, and tumor mutational burden. Functional drug sensitivity profiling was conducted in parallel 2D and 3D platforms using a customized 17-agent panel, followed by exploratory combinatorial validation. The organoids demonstrated high phenotypic and genomic concordance with the parental tumor, preserving key driver alterations (KRAS^A146T, TP53^R175H, APC frameshifts, CCNE1 amplification), microsatellite stability, and low tumor mutational burden (TMB: 6.37 mut/Mb). Functional screening identified selective sensitivity to bevacizumab (IC₅₀: 0.130 μM), doxorubicin (IC₅₀: 0.570 μM), carboplatin (IC₅₀: 0.950 μM), and topotecan (IC₅₀: 1.600 μM) in the 3D organoid model, with consistent cross-platform validation. An exploratory combination assay further supported enhanced viability suppression under bevacizumab-based regimens. Critically, at the time of manuscript preparation, the patient demonstrated radiological disease stabilization under bevacizumab plus trastuzumab deruxtecan, consistent with the organoid-derived response profile. These findings highlight the capacity of integrated genomic and organoid-based profiling to uncover therapeutic vulnerabilities beyond standard biomarker assessment. This proof-of-concept case report study demonstrates the feasibility and translational relevance of an established organoid-based functional precision oncology platform for therapeutic prioritization in metastatic rectal cancer. Full article

Respiratory disease remains one of the mostly costly challenges in the U.S. swine industry and is frequently associated with polymicrobial infections. Routine qPCR assays are highly sensitive but are limited in multiplexing capacity and generally do not provide sequencing information for pathogen characterization. We hypothesized that a target next-generation sequencing (tNGS) panel could provide the broad, simultaneous detection of swine respiratory pathogens while preserving clinically relevant sensitivity. A multiplex Ion Torrent tNGS panel was developed and analytically validated using 20 serially diluted qPCR-positive clinical samples and synthetic gBlock controls, followed by diagnostic validation with 25 qPCR positive and 25 qPCR negative respiratory samples. Most targets were detected across clinically relevant pathogens concentrations. Actinobacillus suis primers showed nonspecific amplification, streptococcus suis serotyping was not consistently achievable in clinical samples, and porcine reproductive and respiratory syndrome virus typing was limited to distinguishing North American and European genotypes. Diagnostic agreement with routine qPCR was high (Cohen’s κ = 0.84), although sensitivity decreased for low-abundance targets. The assay detected mixed infections and additional organisms outside routine qPCR panels. These findings support tNGS as a complementary diagnostic and surveillance tool for swine respiratory disease. Full article

The undesired prognosis of biliary tract cancer is mainly attributed to the difficulty in detecting cancer lesions, including intraepithelial neoplasia, and other hurdles in procuring sufficient pathological samples by forceps biopsy and brushing, or even their combination. However, the transpapillary approach under endoscopic retrograde cholangiopancreatography (ERCP) is the mainstream approach for the work-up and treatment of biliary tract diseases, especially biliary tract cancers, because the ERCP-guided approach efficiently enables simultaneous biliary drainage for the treatment of cholangitis/jaundice and specimen acquisition for the diagnosis of biliary tract lesions. To improve diagnostic accuracy, several studies have been conducted on the feasibility and efficacy of genomic analysis of endoscopic specimens, namely, brushing samples, forceps biopsy samples, and aspiration samples such as bile with sensitivities ranging from 47 to 100%, with specificities ranging from 69 to 100%. Clinical use of genomic analysis remains heterogeneous due to the panel and next-generation sequencing system. For the efficient and precise treatment of patients with biliary tract cancer, future diagnosis and treatment should be based on molecular and genetic analyses. In this article, we review and summarize the comprehensive gene panel analyses of transpapillary brushing/biopsy/aspiration specimens for biliary tract cancer using next-generation sequencing, promoting effective clinical practice and providing a basis for future studies. Full article

Minimal residual disease (MRD) is the most robust independent prognostic biomarker for pediatric acute lymphoblastic leukemia (ALL). Conventional MRD detection assays suffer from insufficient sensitivity and inherent technical limitations, failing to identify ultra-low-level leukemic blasts and thereby contributing to disease relapse. Next-generation sequencing (NGS)-based MRD detection (NGS-MRD) overcomes these drawbacks by targeting immunoglobulin (Ig)/T-cell receptor (TCR) gene rearrangements and enabling the precise quantification of residual leukemic clones. In recent years, NGS-MRD has undergone extensive technological optimization in target panel design, result interpretation and sample type expansion, and has been validated for its clinical utility in therapeutic threshold definition, prognostic stratification, post-therapy monitoring and treatment adjustments in pediatric ALL. This review synthesizes the latest technological refinements and clinical applications of NGS-MRD in pediatric ALL, critically discusses the current challenges that limit its routine clinical use, and proposes future research directions to address these issues. Full article