Search Results (444)

Hereditary breast and ovarian cancer (HBOC) syndrome accounts for 5–10% of all breast and ovarian cancers, with BRCA1 and BRCA2 pathogenic variants being the most common genetic alterations. However, additional genes such as BARD1, whose protein product interacts with BRCA1 via its N-terminal RING domain, have been implicated as low-penetrance contributors to cancer risk. This study aimed to investigate the frequency and distribution of the BARD1 variant c.1518_1519delinsCA (p.Val507Met) in a cohort of 920 patients undergoing genetic testing for hereditary cancer predisposition. Next Generation Sequencing (NGS) was performed using a 28-gene panel, and allelic frequencies of BARD1 were analyzed. Among 920 patients, 159 (17.28%) were pure heterozygous for the c.1518_1519delinsCA variant. Notably, c.1519G>A was never observed without c.1518T>C, suggesting a strong linkage between the two variants. The allele frequencies observed (34.51% for A at c.1519 and 77.88% for C at c.1518) challenge current reference genome expectations. Data from the ALFA database confirmed that these frequencies are consistent with population-level variation, not sample bias. Our findings raise the hypothesis that the reference allele at position c.1518 may not reflect the true wild-type sequence. While both c.1518T>C and c.1519G>A are individually classified as benign, their combined occurrence as a dinucleotide substitution (c.1518_1519delinsCA) warrants further investigation. These results underscore the importance of accurate variant annotation and population-specific frequency data for clinical interpretation of NGS findings. Although BARD1 remains a low-frequency contributor to HBOC compared to BRCA1/2, its inclusion in multigene panels is supported by the potential relevance of such complex variants. Full article

Autosomal recessive (AR) disorders represent a significant public health challenge, as asymptomatic carriers are often unaware of their reproductive risks. This study provides the first comprehensive assessment of AR gene variant frequencies and their molecular landscape in a fertile Western Romanian population. Genetic results from 604 unrelated, unaffected Caucasian individuals of reproductive age, tested at a single genetic center between 2020 and 2024, were retrospectively analyzed. Next-generation sequencing (NGS) with a multi-gene panel targeting 300 AR-associated genes was used for molecular profiling. Variants were identified in 156 genes, with 75% of individuals carrying at least one AR variant (mean 1.77 variants/person). A subgroup with >3 pathogenic variants comprised 7.5%, posing a notable risk for future offspring. The most frequent variants were detected in HFE (1:5), CFTR (1:9), BTD (1:16), GJB2 (1:17), and CYP21A2 (1:19). Four variants (HFE, c.187C>G; BTD, c.1330G>C; CFTR, c.1210-34TG[11]T[5]; GALT, c.-119_-116del) were particularly prevalent, each exceeding 3% frequency. Considerable allelic heterogeneity was observed for distrinctive variants in CFTR (14), PAH (12), USH2A (12), and ATP7B (9). Several variants were linked to severe disorders, with CFTR, GALT, ATP7B, and SMN1 identified as “red zone” genes associated with high morbidity and mortality. Low-frequency variants formed a “long tail” (83.9%), reflecting marked population heterogeneity and potential hidden disease risks. The study reveals high allelic diversity and a strong prevalence of AR variants in Western Romania. Variant-based gene classification supports population-level screening, highlighting the public health value of a national program to identify carriers and prevent severe inherited disorders. Full article

Background: Breast and ovarian cancers (BC and OC) are prevalent malignancies in women globally, with germline variants in the BRCA2 gene significantly increasing the risk of developing these cancers. Despite extensive studies, the frequency and impact of BRCA2 variants in women from Jalisco, Mexico, remain underexplored. Objective: The aim of this study was to identify and characterize BRCA2 gene variants in Mexican women diagnosed with BC and OC and to assess their functional and structural consequences using computational analyses. Methodology: Genomic DNA from 140 Mexican women with BC and/or OC, selected based on clinical criteria suggestive of BRCA2 variants, was sequenced using NGS targeting BRCA2 coding regions. Functional effects were predicted with Ensembl VEP, SIFT, and PolyPhen-2. Structural impacts of missense variants were assessed using HOPE and AlphaFold models. Results: BRCA2 variants were identified in 12.86% of patients, with higher frequency in OC (21.05%) than BC (12%). Several mapped to key functional domains, including BRC repeats and the DNA-binding domain. Many were predicted as deleterious or probably damaging, though clinical classifications were often conflicting. Structural analysis indicated potential disruptions in protein stability or interactions for most missense variants. Clinically, BRCA2-positive BC patients were younger at diagnosis and showed a trend toward lower complete response. Conclusion: BRCA2 variants were found in 12.86% of patients, including six VUSs not reported in other populations. Several affected key functional domains with predicted deleterious effects. Findings support the need for genetic panels tailored to the Mexican population. Full article

Background/Objectives: Access to genetic counselling and BRCA1/2 germline testing is standard of care for patients with high-grade serous ovarian carcinoma (HGSOC). While tumour testing reliably detects pathogenic variants in hereditary cancer genes, it cannot distinguish somatic from germline variants. Concurrent testing of non-cancerous (normal) tissue obtained during surgery may improve triage for germline testing and clinical genetics referral. This study evaluated the concordance of inherited variant detection among tumour, normal tissue, and blood to determine whether archived normal tissue can reliably identify germline pathogenic variants. Methods: Patients with HGSOC who had a pathogenic variant identified by targeted Next Generation Sequencing (NGS) tumour testing and underwent germline hereditary cancer gene panel (HCP) testing between April 2019 and November 2020 were included. HCP testing was performed on formalin-fixed, paraffin-embedded normal tissue from the original resection. Variant results were compared across tumour, normal tissue, and germline (blood) samples to determine concordance, false-negative, and false-positive rates. Results: Forty-one patients had confirmed tumour variants in BRCA1/2 or other HCP genes. Of these, 24 harboured a corresponding germline pathogenic variant. Archived normal tissue was available for 23 of these 24 cases, and all germline variants were detected in normal tissue, showing 100% concordance. Among the 17 patients without germline variants, all corresponding normal tissue samples were negative, also demonstrating 100% concordance. No false positives or negatives were identified. Conclusions: NGS testing of normal tissue at surgical resection reliably identifies germline pathogenic variants in patients with HGSOC. Incorporating this approach may help triage patients for clinical genetics assessment. Full article

Background/Objectives: Transient neonatal diabetes mellitus (TNDM) is a form of neonatal diabetes mellitus (NDM) arising in the first weeks of life and remitting in infancy. Epigenetic aberrations at the imprinted 6q24 locus (overexpression of PLAGL1/HYMAI) are the most common causes of TNDM. The aim of this study was a retrospective clinical and genetic analysis of a Polish pediatric cohort, emphasizing the role of methylation-specific MLPA (MS-MLPA) in the diagnosis of TNDM. Methods: We conducted a retrospective analysis of the medical records of 22 patients with diabetes diagnosed at 1 year of age. The molecular studies included an analysis of the NDM gene panel by a targeted NGS and MS-MLPA for the 6q24 imprinting region. Results: 6q24-TNDM was confirmed in five patients, with a median age of diabetes remission of 4 months (IQR: 3–6 months). The MS-MLPA identified paternal UPD6 or isolated maternal hypomethylation of PLAGL1 in three patients, and two had a paternal 6q24 duplication. Conclusions: In our group, changes in the 6q24 region were confirmed in 22.7% of NDM patients, indicating the usefulness of the MS-MLPA technique in the diagnosis and detection of imprinting defects. We acknowledge key limitations, including diagnostic delays and incomplete parental testing, which precluded trio-based confirmation of paternal UPD6 versus epimutation in some cases; future diagnostic workflows should incorporate an early trio-based SNP array or STR confirmation. A methylation analysis should be included early in the NDM genetic diagnosis process to provide genetic counseling and monitor patients for diabetes recurrence. Full article

Congenital eye malformations like microphthalmia–anophthalmia–coloboma (MAC), anterior segment dysgenesis (ASD), primary congenital glaucoma (PCG) and congenital cataracts (CC) are significant causes of childhood visual impairment. Phenotypic heterogeneity often complicates diagnosis. The goal of this study was to optimize the diagnostic strategy for next-generation sequencing (NGS)-based procedures, thereby aiming to identify genetic causes of congenital eye malformations. Forty patients with congenital eye malformations were included. A primary diagnostic testing (PD) of a limited number of genes was followed by multigene panel (MGP) testing, including 186 eye-related genes, and exome sequencing. Causative variants were identified in 17 patients (43%) and clinically relevant variants of uncertain significance (VUS) in 6 patients (15%). PD had a diagnostic yield (DY) of 15%, MGP of 29% and exome sequencing of 4%, leading to a cumulative DY of 43%. Diagnostic rates were highest in CC (75%), bilateral cases (46%), complex ocular phenotypes (78%), patients with extraocular manifestations (55%) and positive family history (70%). Rare and possible new genotype–phenotype correlations and candidate genes (FAT1, POGZ) could be identified. In total, eight (likely) pathogenic variants in six genes (CYP1B1, ADAMTS18, MAB21L2, NHS, MFRP, CRYBB1) were not yet reported. A stepwise genetic testing approach starting with a broad multigene panel followed by exome sequencing provides higher diagnostic yield than limited phenotype-specific testing. Comprehensive genetic diagnosis is essential for prognosis, treatment and genetic counseling, underscoring the need for routine genetic testing and interdisciplinary collaboration in managing congenital eye malformations. Full article

Background: Maturity-onset diabetes of the young (MODY) is a heterogeneous group of monogenic diabetes forms that are frequently misclassified as type 1 or type 2 diabetes due to overlapping phenotypic features. The true prevalence of MODY is likely substantially underestimated. As DNA-based diagnostics become increasingly accessible, an expanding number of novel genetic variants are being identified. Objectives: The aim of this study was to characterize the clinical and genetic features of patients carrying rare variants in the BLK, KLF11, PAX4, PDX1, and CEL genes, with attention to population-specific aspects, family history, and treatment outcomes. Methods: Targeted next-generation sequencing (NGS) using a custom-designed panel covering 27 genes implicated in MODY, neonatal diabetes, and related hereditary syndromes was performed on the Illumina NovaSeq 6000 platform (Illumina). Results: We identified 21 variants in five genes associated with rare MODY subtypes among 24 unrelated patients. MODY9 was diagnosed in two unrelated patients of Russian ethnicity harboring an identical heterozygous missense mutation in exon 5 of the PAX4 gene (HG38, chr7:127615049G>A, c.191C>T, p.Thr64Ile), which has not been previously described in patients with diabetes. MODY11 was diagnosed in a patient carrying the c.773-1G>A variant in the BLK gene. A patient with a de novo c.40_41dupGC (p.Val15Glnfs*41) variant in the KLF11 gene was clinically diagnosed with type 1 diabetes. Conclusion: Our findings expand the current understanding of rare MODY subtypes and contribute to the growing body of evidence on the spectrum and frequency of potentially pathogenic variants in BLK, CEL, KLF11, PDX1, and PAX4 genes across ethnically diverse populations worldwide. Full article

Type 1 Diabetes Mellitus (T1D) is an autoimmune disease characterized by the destruction of pancreatic β-cells, predominantly manifesting in childhood or adolescence. The lack of clearly interpretable biological markers in the early stages, combined with the insidious onset of the disease, poses significant challenges to early diagnosis and the implementation of preventive strategies. The applicability of classic T1D biomarkers for understanding the mechanisms of the autoimmune process, preclinical diagnostics and treatment efficiency is limited. Despite advances in next-generation sequencing (NGS) technologies, which have enabled large-scale genome-wide association studies (GWASs) and the identification of polygenic risk scores (PRSs) associated with T1D predisposition, as well as progress in bioinformatics approaches for assessing dysregulated gene expression, no universally accepted risk assessment model or definitive predictive biomarker has been established. Until now, the use of new promising biomarkers for T1D diagnostics is limited by insufficient evidence base. However, they have great potential for the development of diagnostic methods on their basis, which has been shown in single or serial large-scale studies. This critical review covers both well-known biomarkers widely used in clinical practice, such as HLA-haplotype, non-HLA SNPs, islet antigen autoantibodies, C-peptide, and the promising ones, such as cytokines, cfDNA, microRNA, T1D-specific immune cells, islet-TCR, and T1D-specific vibrational bands. Additionally, we highlight new approaches that have been gaining popularity and have already demonstrated their potential: GWAS, single-cell transcriptomics, identification of antigen-specific T cells using scRNA-seq, and FTIR spectroscopy. Although some of the biomarkers, in our opinion, are still limited to a research context or are far from being implemented in clinical diagnostics of T1D, they have the greatest potential of being applied in clinical practice. When integrated with the monitoring of the classical autoimmune diabetes markers, they would increase the sensitivity and specificity during diagnostics of early and preclinical stages of the disease. This critical review aims to evaluate the current landscape of classical and emerging biomarkers in autoimmune diabetes, with a focus on those enabling early detection—prior to extensive destruction of pancreatic islets. Another goal of the review is to focus the attention of the scientific community on the gaps in early T1D diagnostics, and to help in the selection of markers, targets, and methods for scientific studies on creating novel diagnostic panels. Full article

Autism spectrum disorder (ASD) is a heritable neurodevelopmental condition with a complex genetic architecture. Dissecting the interplay between inherited variants and high-impact de novo variants is critical for understanding its etiology. We conducted a family-based study involving 42 families with ASD (139 individuals). Using a targeted next-generation sequencing (NGS) panel of 236 genes, we identified and characterized rare inherited and de novo variants in affected probands, parents, and unaffected siblings. Our analysis revealed a complex genetic landscape marked by diverse inheritance patterns. De novo variants were predominantly observed in individuals with atypical autism, while biparental (homozygous) inheritance was more common in Asperger syndrome. Maternally inherited variants showed significant enrichment in intronic regions, pointing to a potential regulatory role. We also detected variants in several high-confidence ASD risk genes, including SHANK3, MYT1L, MCPH1, NIPBL, and TSC2, converging on pathways central to synaptic function and neurogenesis. Across the cohort, five variants of uncertain significance (VUS) were identified, comprising two inherited variants in ABCC8 and additional variants in CUL23, TSC2, and MCPH1. Our findings underscore the profound genetic heterogeneity of ASD and suggest that distinct genetic mechanisms and inheritance patterns may contribute to different clinical presentations within the spectrum. This highlights the power of family-based genomic analyses in elucidating the complex interplay of inherited and de novo variants that underlies ASD. Full article

Next-Generation Sequencing (NGS) techniques have become a cornerstone of molecular diagnostics, enabling high-throughput, parallel analysis of multiple disease-associated genes. Their targeted design allows streamlined interpretation and optimised diagnostic yield, especially in disorders with known genetic heterogeneity. In this review, we provide a comprehensive overview of the clinical application of NGS techniques—targeted gene panels, whole exome sequencing (WES) and whole genome sequencing (WGS)—detailing the methodological workflow and the critical steps involved in their implementation. Particular emphasis is placed on the genes identified through NGS that are implicated in neurodevelopmental, neurodegenerative, psychiatric, neuromuscular, cardiovascular, and metabolic disorders. We also compare the advantages and limitations of panel-based diagnostics versus WES and WGS, and discuss future directions, including the integration of long-read sequencing technologies into multidisciplinary clinical practice. Finally, we consider how these advances may ultimately bridge biomedical research and clinical practise to improve the diagnosis and management of multifactorial diseases. Full article

Neuroblastoma (NB) is an aggressive childhood cancer requiring intensive multimodal therapies in high-risk (HRNB) patients. Currently, invasive surgical biopsies are required to classify NB risk group and assign treatment based on the tumour genetic profile. Circulating tumour DNA (ctDNA) obtained from blood samples can be used to identify tumour biomarkers. Here we applied targeted next-generation sequencing (tNGS) using a panel of 42 genes to analyse 32 NB ctDNA samples for the presence of single-nucleotide variants and copy number changes from 28 patients in all NB risk groups. In two additional ctDNA samples, droplet digital PCR was used to detect hotspot ALK variants. Pathogenic mutations with a variant allele frequency (VAF) > 1% were identified in 13/32 (41%) ctDNA samples. ALK and PTPN11 were the most frequent, each being detected in 4/32 (13%) samples, together with oncogene amplifications. Targeted NGS of ctDNA detected actionable variants, including those absent in the diagnostic primary tumour due to spatial and temporal heterogeneity. Our findings confirm the usefulness of ctDNA in detecting genetic abnormalities in NB. Full article

Introduction: For pregnant women with a history of fetal and neonatal alloimmune thrombocytopenia (FNAIT) or hemolytic disease of the fetus and newborn (HDFN), prenatal intervention in subsequent pregnancies may be necessary to prevent complications for the fetus. A non-invasive prenatal diagnostic procedure (NIPD) is recommended for fetal blood group genotyping. RT-PCR is used for fetal RHD determination as a reliable screening method with high sensitivity and specificity. For other antigens with variants involving single-base substitutions, droplet digital PCR (ddPCR) and next-generation sequencing (NGS) are recommended to reduce the risk of false-negative results. Only NGS offers the possibility of determining the cell-free fetal DNA (cffDNA) fraction in maternal plasma by sequencing additional gene fragments in parallel, but no standard exists for assay validation. Material and Methods: A custom-made primer panel was designed to target the common platelet and red cell antigens involved in fetal red cell and platelet incompatibilities, as well as additional anonymous single-nucleotide polymorphism (SNP) targets for use as an internal control. Amplicon-based NGS was carried out using semiconductor sequencing. For HPA-1a (HPA*1A, ITGB3) and K (KEL*01.01, KEL) assay validation, the limit of detection (LOD) and limit of quantification (LOQ) were estimated, as were false-positive antithetic alleles, linearity, and inter-assay variation, using cell-free DNA (cfDNA) extracted from the blood samples of healthy blood donors. An additional analysis was performed using 23 diagnostic samples from 21 pregnant women. Results: Regression analysis of dilution series using HPA-1a- and K-positive cell-free plasma samples in antigen-negative donor plasma showed that recovery is definitely feasible up to an HPA*1A and KEL*01.01 allele frequency of 1%. Base calls of false-positive antithetic alleles were detected with a maximum of 0.25% using 21 healthy blood donors. The LOD was estimated to be 0.2057% (mean + 3 SD) for HPA*1A with a LOQ of 0.6298% (mean + 10 SD). For KEL*01.01, the LOD was 0.1706% (mean + 3 SD) and the LOQ was 0.5314% (mean + 10 SD). The analysis of 15 of 21 cases with diagnostic samples from pregnant women with neonatal blood available for confirmatory testing resulted in 100% concordant results. The fetal fraction of these samples was calculated with a median of 11.03% (95% CI: 8.89, 13.20). Conclusions: NGS for non-invasive fetal blood group genotyping is an accurate and reliable method. In-house validation of the used assays can be performed using healthy donors to determine the LOD, LOQ and sensitivity. The threshold for paternally inherited fetal HPA*1A and KEL*01.01 alleles could be set at 1% (i.e., 2% fetal fraction) to obtain reliable test results. Internal controls for assessing the fetal fraction are essential to avoid false-negative test results. Full article

Background: The TWNK gene encodes a protein that colocalizes with mitochondrial DNA (mtDNA) in mitochondrial nucleoids. It acts as mtDNA helicase during replication, thus playing a pivotal role in the replication and maintenance of mtDNA stability. TWNK mutations are associated with a wide spectrum of clinical phenotypes and a marked heterogeneity. However, heterozygous nonsense variants in the gene have never been described in association with disease. Methods: We analyzed a next-generation sequencing (NGS) targeted gene panel in a cohort including 40 patients with high clinical suspicion of mitochondrial disorders. Selected patients underwent a complete neurological examination, electrophysiology tests, and muscle biopsy. Segregation analysis was performed in available family members. The 3D structure of twinkle was visualized and analyzed using Swiss Model and Pymol version 3.1.6.1. Results: We found four TWNK-mutated subjects from two unrelated families. They exhibited a variable clinical spectrum, ranging from asymptomatic individuals to subjects with psychiatric disorder, chronic progressive external ophthalmoplegia (CPEO), and CPEO-plus. All the subjects shared the heterozygous TWNK p.Glu665Ter variant. Discussion and Conclusions: We describe the clinical phenotype and muscle biopsy findings associated with the first reported heterozygous nonsense TWNK variant, thus expanding the current knowledge of Twinkle-related disorders. Our findings are in line with the high intrafamilial clinical variability associated with TWNK mutations. Although PEO and skeletal muscle involvement remain hallmarks of the disease, extra-muscular features should be carefully assessed. Full article

Background and Objectives: Severe combined immunodeficiency (SCID) represents a group of rare and potentially fatal monogenic disorders arising from pathogenic variants in a broad spectrum of genes. Diagnostic delays beyond the first few months of life have been associated with poor overall survival and hematopoietic stem cell transplantation (HSCT) outcomes. Therefore, the aim of our study was to apply an NGS assay enabling the rapid and reliable diagnosis of SCID. Materials and Methods: We developed a targeted NGS panel of 30 genes implicated in the pathogenesis of most SCID cases and we applied it to three Greek infants with suspected SCID. Results: Each patient displayed a distinct immunophenotype—T⁻B⁻NK⁻, T⁻B⁻NK⁺ and T⁻B⁺NK⁻, respectively—and was found to harbor pathogenic or likely pathogenic variants in the analyzed SCID-related genes. In particular, patient 1 carried two heterozygous ADA variants (c.58G>A, p.Gly20Arg and c.956_960del, p.Glu319Glyfs); patient 2 harbored two discrete pathogenic variants in the DCLRE1C gene (a large deletion of exons 1–3 and the nonsense mutation c.241C>T, p.Arg81*), causing Artemis deficiency; and patient 3 carried a hemizygous IL2RG missense variant (c.437T>C, p.Leu146Pro), associated with X-linked SCID. All variants were confirmed by Sanger sequencing. Conclusions: Our method successfully identified the underlying genetic defects in all patients, thereby establishing a molecular diagnosis of SCID. These findings highlight the potential of targeted NGS assays for achieving rapid and accurate molecular diagnosis of SCID, which is crucial for the timely treatment of life-threatening conditions in affected children. Full article

Alpha-thalassemia is most often caused by large deletions within the α-globin gene cluster which reduce or abolish α-globin chain synthesis. Several common deletions are well described, but atypical structural variants remain underdiagnosed. In this study, we report three novel large heterozygous deletions of the α-globin cluster. The variants were identified in unrelated patients who presented with persistent microcytosis and hypochromia in the absence of iron deficiency or structural hemoglobin variants. A stepwise molecular diagnostic approach was applied. It combined commercial deletion screening assays, Sanger sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA), and targeted Next-Generation Sequencing (NGS) with the Devyser Thalassemia panel. MLPA detected three deletions ranging from ~17 kb to ~360 kb. All involved the critical HS-40 regulatory region and both HBA1 and HBA2 structural genes, consistent with α⁰-thalassemia alleles. Next-Generation Sequencing confirmed the extent of each deletion and refined their genomic boundaries. Comparative genomic mapping showed that these deletions are distinct from classical variants such as --SEA or --MED, indicating novel structural configurations. Clinically, all patients displayed a carrier phenotype, with normal HbF levels (<1%) and normal or slightly reduced HbA2 values. This study broadens the mutational spectrum of α⁰-thalassemia and demonstrates the diagnostic value of combining MLPA and NGS in patients with unexplained microcytosis. By enabling accurate distinction from iron-deficiency anemia and other microcytic disorders, these findings have direct translational implications for improving diagnostic precision and genetic counseling in clinical practice. Full article