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
• Algorithms MeSH
• Exome genetics   MeSH
• Genome, Human genetics   MeSH
• Genomics methods   MeSH
• Humans MeSH
• Survival of Motor Neuron 1 Protein genetics   MeSH
• Survival of Motor Neuron 2 Protein genetics   MeSH
• Sequence Analysis, DNA methods   MeSH
• Exome Sequencing MeSH
• Muscular Atrophy, Spinal * genetics   diagnosis   MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article 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 * classification   genetics   isolation & purification   MeSH
• DNA, Bacterial genetics   MeSH
• Dysbiosis microbiology   MeSH
• Feces * microbiology   MeSH
• Humans MeSH
• Metagenomics MeSH
• Enterocolitis, Necrotizing * microbiology   MeSH
• Infant, Premature MeSH
• Infant, Newborn MeSH
• RNA, Ribosomal, 16S * genetics   MeSH
• Gastrointestinal Microbiome * MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Infant, Newborn MeSH
• Female MeSH
• Publication type
• Journal Article 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
• Precursor Cell Lymphoblastic Leukemia-Lymphoma * blood   diagnosis   genetics   MeSH
• Humans MeSH
• Precursor B-Cell Lymphoblastic Leukemia-Lymphoma diagnosis   blood   genetics   MeSH
• Neoplasm, Residual * diagnosis   MeSH
• High-Throughput Nucleotide Sequencing * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article 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
• Molecular Targeted Therapy MeSH
• Adult MeSH
• Class I Phosphatidylinositol 3-Kinases * genetics   antagonists & inhibitors   MeSH
• Middle Aged MeSH
• Humans MeSH
• Mutation MeSH
• DNA Mutational Analysis MeSH
• Biomarkers, Tumor * genetics   MeSH
• Endometrial Neoplasms * genetics   pathology   drug therapy   MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Patient Selection MeSH
• High-Throughput Nucleotide Sequencing * methods   MeSH
• Check Tag
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article 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
• Drug Resistance, Neoplasm * genetics   MeSH
• Adult MeSH
• ErbB Receptors antagonists & inhibitors   MeSH
• PTEN Phosphohydrolase genetics   MeSH
• GTP Phosphohydrolases genetics   MeSH
• Protein Kinase Inhibitors * therapeutic use   MeSH
• Colorectal Neoplasms * genetics   drug therapy   pathology   MeSH
• Middle Aged MeSH
• Humans MeSH
• Mutation * MeSH
• DNA Mutational Analysis MeSH
• Pilot Projects MeSH
• Antineoplastic Agents * therapeutic use   MeSH
• Proto-Oncogene Proteins B-raf genetics   MeSH
• Proto-Oncogene Proteins p21(ras) genetics   MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH

Patients with cardioembolic ischemic stroke are commonly prescribed direct oral anticoagulants (DOACs), such as dabigatran (a direct thrombin inhibitor) and factor Xa inhibitors (e.g., apixaban and rivaroxaban), or warfarin to reduce the risk of recurrent stroke. A major concern in anticoagulant therapy is the risk of intracerebral hemorrhage, which is associated with a high mortality rate. Cerebral microbleeds (MBs), small asymptomatic brain hemorrhages detectable by susceptibility-weighted imaging (SWI) on magnetic resonance imaging (MRI), are associated with increased hemorrhagic stroke risk. This study evaluated the incidence of new MBs during 1 year of anticoagulation therapy in patients after cardioembolic stroke. Patients indicated for anticoagulant therapy after cardioembolic stroke and monitored in the cerebrovascular outpatient clinic of our department underwent brain MRI at baseline and after 1 year of therapy. The occurrence of new MBs was assessed using SWI sequences. MBs were categorized based on location into 3 groups: deep (dMBs), lobar (lMBs), and infratentorial (iMBs). A total of 79 patients were included, 53 of whom were male (67.1%), with a median age of 71 years (IQR: 64-76). The majority of patients (n = 50, 63.3%) were treated with apixaban, 16 patients (20.3%) with dabigatran, and 13 patients (16.5%) with warfarin. Baseline MRI revealed MBs in 17 patients (21.5%), including dMBs in 2, lMBs in 16, and iMBs in 2 patients. Follow-up MRI showed new MBs in 8 patients (10.1%), with new dMBs in 1, lMBs in 5, and iMBs in 4 patients. No statistically significant differences were observed in MBs the incidence of new MBs between anticoagulant groups (P = .912). Over 1 year of anticoagulant therapy, new MBs were detected in 10.1% of patients, predominantly in lobar and infratentorial regions. No differences in the incidence of new MBs were identified between the different anticoagulant groups.

• MeSH
• Anticoagulants * adverse effects   therapeutic use   MeSH
• Cerebral Hemorrhage * chemically induced   diagnostic imaging   epidemiology   MeSH
• Stroke * prevention & control   MeSH
• Dabigatran adverse effects   therapeutic use   MeSH
• Incidence MeSH
• Middle Aged MeSH
• Humans MeSH
• Magnetic Resonance Imaging methods   MeSH
• Pyrazoles adverse effects   therapeutic use   MeSH
• Pyridones adverse effects   therapeutic use   MeSH
• Secondary Prevention * methods   MeSH
• Aged MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Observational Study 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
• Alzheimer Disease genetics   MeSH
• Polymorphism, Single Nucleotide * MeSH
• Cognitive Dysfunction * genetics   MeSH
• Humans MeSH
• Longitudinal Studies MeSH
• Neuropsychological Tests MeSH
• ATP Binding Cassette Transporter, Subfamily B genetics   MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Czech Republic 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
• Cost-Benefit Analysis MeSH
• Genetic Testing economics   methods   MeSH
• Middle Aged MeSH
• Humans MeSH
• Biomarkers, Tumor * genetics   MeSH
• Lung Neoplasms * genetics   pathology   diagnosis   MeSH
• Health Care Costs MeSH
• Carcinoma, Non-Small-Cell Lung * genetics   diagnosis   pathology   MeSH
• Aged MeSH
• High-Throughput Nucleotide Sequencing * economics   MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Multicenter Study MeSH
• Observational Study MeSH
• Comparative Study 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
• Gene Regulatory Networks MeSH
• Middle Aged MeSH
• Humans MeSH
• RNA, Messenger * genetics   MeSH
• MicroRNAs * genetics   MeSH
• Biomarkers, Tumor genetics   MeSH
• Pancreatic Neoplasms * genetics   pathology   diagnosis   MeSH
• Neuroendocrine Tumors * genetics   pathology   diagnosis   MeSH
• Pancreas * metabolism   pathology   MeSH
• Gene Expression Regulation, Neoplastic MeSH
• Gene Expression Profiling MeSH
• Transcriptome MeSH
• High-Throughput Nucleotide Sequencing methods   MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article 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
• Adult MeSH
• Immunohistochemistry MeSH
• Cyclin-Dependent Kinase Inhibitor p16 MeSH
• Middle Aged MeSH
• Humans MeSH
• Biomarkers, Tumor * genetics   analysis   MeSH
• Uterine Neoplasms * pathology   genetics   MeSH
• Neoplasms, Muscle Tissue * pathology   genetics   MeSH
• Aged MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH