PURPOSE: We set out to develop a publicly available tool that could accurately diagnose spinal muscular atrophy (SMA) in exome, genome, or panel sequencing data sets aligned to a GRCh37, GRCh38, or T2T reference genome. METHODS: The SMA Finder algorithm detects the most common genetic causes of SMA by evaluating reads that overlap the c.840 position of the SMN1 and SMN2 paralogs. It uses these reads to determine whether an individual most likely has 0 functional copies of SMN1. RESULTS: We developed SMA Finder and evaluated it on 16,626 exomes and 3911 genomes from the Broad Institute Center for Mendelian Genomics, 1157 exomes and 8762 panel samples from Tartu University Hospital, and 198,868 exomes and 198,868 genomes from the UK Biobank. SMA Finder's false-positive rate was below 1 in 200,000 samples, its positive predictive value was greater than 96%, and its true-positive rate was 29 out of 29. Most of these SMA diagnoses had initially been clinically misdiagnosed as limb-girdle muscular dystrophy. CONCLUSION: Our extensive evaluation of SMA Finder on exome, genome, and panel sequencing samples found it to have nearly 100% accuracy and demonstrated its ability to reduce diagnostic delays, particularly in individuals with milder subtypes of SMA. Given this accuracy, the common misdiagnoses identified here, the widespread availability of clinical confirmatory testing for SMA, and the existence of treatment options, we propose that it is time to add SMN1 to the American College of Medical Genetics list of genes with reportable secondary findings after genome and exome sequencing.

• MeSH
• algoritmy MeSH
• exom genetika   MeSH
• genom lidský genetika   MeSH
• genomika metody   MeSH
• lidé MeSH
• protein přežití motorických neuronů 1 genetika   MeSH
• protein přežití motorických neuronů 2 genetika   MeSH
• sekvenční analýza DNA metody   MeSH
• sekvenování exomu MeSH
• spinální svalová atrofie * genetika   diagnóza   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Necrotizing enterocolitis (NEC) is one of the most devastating intestinal diseases observed in preterm in the first days of life. Researchers have recently focused on potential predictive biomarkers for early and concomitant diagnoses. Thus, we inquired about the linkage of intestinal dysbiosis, one of the most important factors in NEC development to the gut microbiota. In this study, the systematic differences in the bacterial composition between neonates affected by NEC and healthy newborns were highlighted by metagenomic analysis. The next-generation sequencing of the V3-V4 variable region of the 16S rRNA gene and gene-specific qPCR analyzed the untargeted gut microbiota. Total bacteria, total and fecal coliform loads in stool samples with NEC were higher than control. OTU-level relative abundances of NEC infant was characterized by Firmicutes and Bacteroidetes at phylum levels. At the genus level, NEC stool was identified by the lack of Klebsiella and the presence of Roseburia, Blautia, and Parasutterella. Finally, Clostridium fessum was the predominant species of Clostridium genus in disease and healthy specimens at the species level, whereas Clostridium jeddahitimonense was at NEC diagnosis. Despite a strong relationship between pathophysiology and characterization of gut microbiota at a clinical diagnosis of NEC, our results emphasize the broad difficulty in identifying potential biomarkers.

• MeSH
• Bacteria * klasifikace   genetika   izolace a purifikace   MeSH
• DNA bakterií genetika   MeSH
• dysbióza mikrobiologie   MeSH
• feces * mikrobiologie   MeSH
• lidé MeSH
• metagenomika MeSH
• nekrotizující enterokolitida * mikrobiologie   MeSH
• novorozenec nedonošený MeSH
• novorozenec MeSH
• RNA ribozomální 16S * genetika   MeSH
• střevní mikroflóra * MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• novorozenec MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

Can peripheral blood be used to detect residual disease in acute lymphoblastic leukaemia (ALL) when we increase the sensitivity of the method used? Bendig et al. found that a larger amount of material and the use of next-generation sequencing (NGS) detects MRD in peripheral blood in up to half of patients with B-cell precursor ALL (BCP-ALL) where routine examination was negative. However, a negative result does not exclude the presence of residual disease and thus still limits the use of peripheral blood. Commentary on: Bendig et al. Next-generation sequencing and high DNA input identify previously missed measurable residual disease in peripheral blood of B-cell precursor acute lymphoblastic leukaemia. Br J Haematol 2025; 206:353-356.

• MeSH
• akutní lymfatická leukemie * krev   diagnóza   genetika   MeSH
• lidé MeSH
• pre-B-buněčná leukemie diagnóza   krev   genetika   MeSH
• reziduální nádor * diagnóza   MeSH
• vysoce účinné nukleotidové sekvenování * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Endometrial carcinomas (EC) of no special molecular profile (NSMP) represent the largest molecular category of EC, comprising a mixture of tumors with different histology and molecular profiles. These facts likely point to different tumor biology, clinical outcomes, and targeted therapy responses within this molecular category. The PIK3CA is currently the only targetable kinase oncoprotein directly implicated in EC carcinogenesis. Investigating a unique single-institution cohort, we attempted to stratify NSMP ECs based on the presence of the PIK3CA pathogenic mutation. Those cases were further analyzed for other well-established-associated oncogenic driver gene mutations. Histological and clinical variables were also correlated in each case. Altogether, 175 ECs were prospectively tested by a limited custom NGS panel containing ARID1A, BCOR, BRCA1, BRCA2, CTNNB1, KRAS, MLH1, MSH2, MSH6, NRAS, PIK3CA, PMS2, POLD1, POLE, PTEN,and TP53 genes. We identified 24 PIK3CA mutated cases in the group of 80 NSMP ECs, with another co-occurring mutation in at least one oncogenic driver gene (CTNNB1, PTEN, ARID1A, KRAS, BCOR, PMS2) in 19 cases. In conclusion, a limited NGS panel can effectively test EC tissue for specific pathogenetically relevant oncogene mutations. The NSMP EC category contains 30% of the PIK3CA mutated cases. Of those, 21% contain the PIK3CA mutation as a sole EC-associated oncogene mutation, while 79% harbor at least one more mutated gene. These findings may inform future healthcare planning and improve the effectiveness of EC patient selection for the PIK3CA-targeted therapy.

• MeSH
• cílená molekulární terapie MeSH
• dospělí MeSH
• fosfatidylinositol-3-kinasy třídy I * genetika   antagonisté a inhibitory   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mutace MeSH
• mutační analýza DNA MeSH
• nádorové biomarkery * genetika   MeSH
• nádory endometria * genetika   patologie   farmakoterapie   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• výběr pacientů MeSH
• vysoce účinné nukleotidové sekvenování * metody   MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Emerging evidence suggests that tumour morphological heterogeneity may influence mutational profiles relevant to therapy response. In this pilot study, we aimed to assess whether mutations identified within specific morphological patterns or at the invasion front correlate with shorter time to progression after anti-EGFR therapy, as compared to whole-tissue analysis. METHODS: We investigated genetic mutations in 142 samples from primary tumours of 39 KRAS wild-type metastatic colorectal cancer (CRC) patients receiving anti-EGFR therapy. Deep next-generation sequencing was performed on whole-tumour sections and six morphology-defined tumour regions. RESULTS: Mutations in genes linked to anti-EGFR therapy response (KRAS, BRAF, NRAS, PTEN and PI3KCA) were found uniquely in the non-responder group, with substantial variability across morphological sub-regions. BRAF mutations were aligned with serrated and mucinous morphologies, while KRAS mutations (p.Lys147Glu and p.Ala146Thr) were associated with mucinous and desmoplastic morphologies. In all cases, the cumulative mutational profile from sub-regions provided more details than that of the whole-tumour profile. CONCLUSION: Our findings highlight that comprehensive analysis, considering morphological heterogeneity, is crucial for personalised CRC treatment strategies.

• MeSH
• chemorezistence * genetika   MeSH
• dospělí MeSH
• erbB receptory antagonisté a inhibitory   MeSH
• fosfohydroláza PTEN genetika   MeSH
• GTP-fosfohydrolasy genetika   MeSH
• inhibitory proteinkinas * terapeutické užití   MeSH
• kolorektální nádory * genetika   farmakoterapie   patologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mutace * MeSH
• mutační analýza DNA MeSH
• pilotní projekty MeSH
• protinádorové látky * terapeutické užití   MeSH
• protoonkogenní proteiny B-Raf genetika   MeSH
• protoonkogenní proteiny p21(ras) genetika   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Global healthcare disparities, stemming from organizational differences in healthcare systems, lead to variable availability and funding, resulting in a gap between recommended and implemented practices for interleukin (IL)-1-mediated autoinflammatory diseases. We aimed to assess diagnostic, treatment and follow-up options for these diseases in Central and Eastern European countries, comparing them with the 2021 recommendations of the European Alliance of Associations for Rheumatology (EULAR)/American College of Rheumatology (ACR). METHODS: In 2023, a structured collaborative effort was organized with representatives from 10 Central and Eastern European countries to address autoinflammatory diseases. The discussion focused on potential strategies to achieve the goals mentioned above. RESULTS: Almost all the participating countries have specialized centers for the diagnosis and treatment of autoinflammatory diseases and the care is provided either by rheumatologists and/or clinical immunologists. Genetic testing is available in all countries, but there is variation in the types of tests offered. Massive parallel sequencing panels for autoinflammatory diseases are available in all countries, with waiting periods for results ranging from 3 to 6 months in most cases. The availability of disease-specific laboratory assessments, such as S100 proteins, is limited. IL-1 inhibitors are available in all countries, but there are differences in practices regarding the licensing and reimbursement of anakinra and canakinumab based on specific indications or diagnoses. The age at which the transition process begins varies, but in most countries, it typically starts around the age of 18 or beyond and in majority of the participating countries there is no structured transition program. CONCLUSIONS: Adherence to the 2021 EULAR/ACR recommendations for IL-1-mediated autoinflammatory diseases is achievable in Central and Eastern European countries. Determining the prevalence and incidence of these diseases in this region remains a persistent challenge for future research efforts, with the overarching goal of identifying new patients with autoinflammatory diseases.

• MeSH
• dědičné zánětlivé autoimunitní nemoci * diagnóza   terapie   farmakoterapie   epidemiologie   MeSH
• humanizované monoklonální protilátky MeSH
• interleukin-1 * antagonisté a inhibitory   MeSH
• lidé MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Evropa MeSH
• východní Evropa MeSH

The ABCB1 gene, encoding the ATP-dependent translocase ABCB1, plays a crucial role in the clearance of amyloid-beta (Aβ) peptides and the transport of cholesterol, implicating it in the pathogenesis of Alzheimer's disease. The study aims to investigate the association between polymorphisms in the ABCB1 gene and cognitive decline in individuals with mild cognitive impairment (MCI), particularly focusing on language function. A longitudinal cohort study involving 1 005 participants from the Czech Brain Aging Study was conducted. Participants included individuals with Alzheimer's disease, amnestic MCI, non-amnestic MCI, subjective cognitive decline, and healthy controls. Next-generation sequencing was utilized to analyze the entire ABCB1 gene. Cognitive performance was assessed using a comprehensive battery of neuropsychological tests, including the Boston Naming Test and the semantic verbal fluency test. Ten ABCB1 polymorphisms (rs55912869, rs56243536, rs10225473, rs10274587, rs2235040, rs12720067, rs12334183, rs10260862, rs201620488, and rs28718458) were significantly associated with cognitive performance, particularly in language decline among amnestic MCI patients. In silico analyses revealed that some of these polymorphisms may affect the binding sites for transcription factors (HNF-3alpha, C/EBPβ, GR-alpha) and the generation of novel exonic splicing enhancers. Additionally, polymorphism rs55912869 was identified as a potential binding site for the microRNA hsa-mir-3163. Our findings highlight the significant role of ABCB1 polymorphisms in cognitive decline, particularly in language function, among individuals with amnestic MCI. These polymorphisms may influence gene expression and function through interactions with miRNAs, transcription factors, and alternative splicing mechanisms.

• MeSH
• Alzheimerova nemoc genetika   MeSH
• jednonukleotidový polymorfismus * MeSH
• kognitivní dysfunkce * genetika   MeSH
• lidé MeSH
• longitudinální studie MeSH
• neuropsychologické testy MeSH
• P-glykoproteiny genetika   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH

Current European/US guidelines recommend that molecular testing in advanced non-small cell lung cancer (aNSCLC) be performed using next-generation sequencing (NGS). However, the global uptake of NGS is limited, largely owing to reimbursement constraints. We compared real-world costs of NGS and single-gene testing (SGT) in nonsquamous aNSCLC. This observational study was conducted across 10 pathology centers in 10 different countries worldwide. Biomarker data collected via structured questionnaires (1 January-31 December 2021) were used to feed micro-costing analyses for three scenarios ['Starting Point' (SP; 2021-2022), 'Current Practice' (CP; 2023-2024), and 'Future Horizons' (FH; 2025-2028)] in both a real-world model, comprising all biomarkers tested by each center, and a standardized model, comprising the same sets of biomarkers across centers. Testing costs (including retesting) encompassed personnel costs, consumables, equipment, and overheads. Overall, 4,491 patients with aNSCLC were evaluated. Mean per-patient costs decreased for NGS relative to SGT over time, with real-world model costs 18% lower for NGS than for SGT in the SP scenario, and 26% lower for NGS than for SGT in the CP scenario. Mean per-biomarker costs also decreased over time for NGS relative to SGT. In the standardized model, the tipping point for the minimum number of biomarkers required for NGS to result in cost savings (per patient) was 10 and 12 in the SP and CP scenarios, respectively. Retesting had a negligible impact on cost analyses, and results were robust to variation in cost parameters. This study provides robust real-world global evidence for cost savings with NGS-based panels over SGT to evaluate predictive biomarkers in nonsquamous aNSCLC when the number of biomarkers to be tested exceeds 10. Widespread adoption of NGS may enable more efficient use of limited healthcare resources.

• MeSH
• analýza nákladů a výnosů MeSH
• genetické testování ekonomika   metody   MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádorové biomarkery * genetika   MeSH
• nádory plic * genetika   patologie   diagnóza   MeSH
• náklady na zdravotní péči MeSH
• nemalobuněčný karcinom plic * genetika   diagnóza   patologie   MeSH
• senioři MeSH
• vysoce účinné nukleotidové sekvenování * ekonomika   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• multicentrická studie MeSH
• pozorovací studie MeSH
• srovnávací studie MeSH

BACKGROUND: Only a limited number of biomarkers guide personalized management of pancreatic neuroendocrine tumors (PanNETs). Transcriptome profiling of microRNA (miRs) and mRNA has shown value in segregating PanNETs and identifying patients more likely to respond to treatment. Because miRs are key regulators of mRNA expression, we sought to integrate expression data from both RNA species into miR-mRNA interaction networks to advance our understanding of PanNET biology. METHODS: We used deep miR/mRNA sequencing on six low-grade/high-risk, well-differentiated PanNETs compared with seven non-diseased tissues to identify differentially expressed miRs/mRNAs. Then we crossed a list of differentially expressed mRNAs with a list of in silico predicted mRNA targets of the most and least abundant miRs to generate high probability miR-mRNA interaction networks. RESULTS: Gene ontology and pathway analyses revealed several miR-mRNA pairs implicated in cellular processes and pathways suggesting perturbed neuroendocrine function (miR-7 and Reg family genes), cell adhesion (miR-216 family and NLGN1, NCAM1, and CNTN1; miR-670 and the claudins, CLDN1 and CLDN2), and metabolic processes (miR-670 and BCAT1/MPST; miR-129 and CTH). CONCLUSION: These novel miR-mRNA interaction networks identified dysregulated pathways not observed when assessing mRNA alone and provide a foundation for further investigation of their utility as diagnostic and predictive biomarkers.

• MeSH
• genové regulační sítě MeSH
• lidé středního věku MeSH
• lidé MeSH
• messenger RNA * genetika   MeSH
• mikro RNA * genetika   MeSH
• nádorové biomarkery genetika   MeSH
• nádory slinivky břišní * genetika   patologie   diagnóza   MeSH
• neuroendokrinní nádory * genetika   patologie   diagnóza   MeSH
• pankreas * metabolismus   patologie   MeSH
• regulace genové exprese u nádorů MeSH
• stanovení celkové genové exprese MeSH
• transkriptom MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

Assessing the biological behavior of uterine inflammatory myofibroblastic tumors (IMTs) remains challenging. This study evaluated previously proposed risk schemes and features in 9 IMTs (6 indolent, 3 aggressive) by integrating clinicopathological features, immunohistochemistry, and next-generation sequencing (NGS). High-risk features (necrosis, infiltrative growth, nuclear atypia) were present in both groups, with LVSI in 1/3 of aggressive IMTs. Aberrant p16 expression and CDKN2A/2B deletions were noted in 2/3 aggressive cases. All cases harbored ALK fusions, wild-type p53, and lacked pathogenic gene mutations. Aggressive cases harbored arm-level and segmental copy number gains/losses at chr 1, 2, X, and had significantly reduced AR expression. The clinicopathological risk stratification score (CRSS) predicted the biological behavior correctly in cases with complete clinicopathological data (size, mitoses, age, infiltrative growth). Two morcellated cases (one indolent and one aggressive) would have been predicted as low risk based solely on the absence of pathogenic mutations. Hereby, the reliability of the proposed CRSS was confirmed. Aberrant p16 expression predicted malignant behavior in 2/3 aggressive cases. Absence of pathogenic mutations or presence of large scale CNVs does not seem to be a predictor of clinical behavior. Additional studies and NGS analyses of more cases may improve risk stratification for patients with incomplete clinicopathological information and may reveal additional risk stratifiers (such as the suggested large-scale CNVs or AR downregulation) for IMTs.

• MeSH
• dospělí MeSH
• imunohistochemie MeSH
• inhibitor p16 cyklin-dependentní kinasy MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádorové biomarkery * genetika   analýza   MeSH
• nádory dělohy * patologie   genetika   MeSH
• nádory ze svalové tkáně * patologie   genetika   MeSH
• senioři MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH