Search Results (1,899)

Hereditary breast cancer (BC) remains unexplained in a substantial proportion of families who test negative for BRCA1/2 and other known susceptibility genes. To contribute to the genomic characterization of these unresolved cases, we generated a whole-genome sequencing (WGS) dataset from six women belonging to two unrelated high-risk families, each comprising three sisters diagnosed with BC. All participants had previously received negative results in conventional multigene panel testing. WGS was performed on peripheral blood DNA using the Illumina NovaSeq platform, followed by variant calling against GRCh38 and the comprehensive annotation of single-nucleotide variants, indels, and structural variants. For each family, we identified shared ClinVar-annotated variants, rare exonic or splice-site alterations, and intronic variants located within a curated set of 286 cancer-related genes. The dataset includes per-patient VCF files, copy number variation annotations, and family-level variant summaries. Raw and processed data are publicly available through the Sequence Read Archive and Zenodo. This resource supports variant reinterpretation, exploration of regulatory and intronic regions, and methodological benchmarking in the study of familial BC beyond established susceptibility genes. Full article

Large genomic rearrangements (LGRs), occurring as copy number alterations (CNAs), represent a clinically relevant class of pathogenic or likely pathogenic variants (P LPVs) in BRCA1/2 (BRCA) genes in ovarian cancer (OC). We evaluated the performance of a high-resolution algorithm integrated into a commercial homologous recombination deficiency (HRD) assay to improve the identification of clinically actionable CNAs in BRCA genes by formalin-fixed paraffin-embedded (FFPE) samples. A total of 760 OC samples were analyzed using a commercial HRD assay incorporating a bioinformatics algorithm for CNA detection. The algorithm was additionally applied to additional homologous recombination repair (HRR) genes, and associations between CNA events and genomic instability (GI) were evaluated. The algorithm demonstrated high sensitivity for both gene and exon-level CNA. The high correlation between CNA positivity cases and GI, in the absence of P/LPVs BRCA single-nucleotide or indels variants, emphasizes the value of integrating CNA detection into routine HRD testing workflows. The extended analysis of additional HRR genes enabled broader characterization of clinically relevant CNAs. This study enables reliable identification of clinically relevant BRCA LGRs from FFPE within HRD testing, supporting a tumor-first diagnostic strategy. This approach may expand the identification of OC patients potentially eligible for PARP inhibitor therapy. Full article

Background/Objectives: Coronary artery disease (CAD) remains the leading cause of mortality worldwide, with South Asia bearing a disproportionately high and rising burden, particularly at younger ages. The present study aimed to investigate genetic variants associated with premature coronary artery disease (PCAD) using whole-genome sequencing (WGS). Methods: WGS was conducted on 12 people (five PCAD cases, seven matched controls) to assess feasibility and methodology for future large-scale research. High-quality genomic DNA was sequenced at a minimum read depth of 10× with a quality threshold of Q30. Variant calling with stringent quality control identified single-nucleotide polymorphisms (SNPs), followed by annotation against gnomAD for allele frequencies and ClinVar for pathogenicity. Protein-coding variants were filtered, and candidate genes were prioritized for comparative analysis between cases and controls. Results: An average of over 8.8 million SNPs per individual was identified, with comparable overall variant distributions between cases and controls. Initial analyses revealed 120 SNPs exclusively present in PCAD cases. All protein-coding variants were rare (allele frequency < 0.0001), and none were previously classified as pathogenic in ClinVar. After filtration, 87 candidate genes were prioritized. Enriched or unique variants in PCAD cases are mapped to genes involved in lipid metabolism, endothelial dysfunction, inflammatory signaling, immune regulation, thrombosis, vascular remodeling, and metabolic processes. Additional variants were identified in genes related to smooth muscle proliferation, oxidative stress, and other biological pathways. Conclusions: This WGS pilot study provides an initial overview of the genomic landscape of PCAD in a South Asian cohort, highlighting rare variants across multiple biological pathways implicated in atherosclerosis that need validation in a large-scale study. Full article

Acute myeloid leukemia (AML) is a heterogeneous malignancy, with clonal complexity and somatic mutations critically influencing prognosis and treatment. While global genomic profiling efforts have revolutionized AML classification and risk stratification, the molecular landscape in Pakistani patients remains underexplored. Our aim is to perform targeted next-generation sequencing (NGS) for somatic mutational profiling of newly diagnosed AML patients in Pakistan. This prospective study was conducted at the Armed Forces Institute of Pathology, Pakistan, from January 2021 to January 2026. Among 104 patients, 204 somatic variants were identified (mean: 1.96 variants/patient), predominantly single-nucleotide variants (49.5%). Missense mutations (38.2%) were most common, with enriched transitions (Ti/Tv: 1.27:1). Frequently mutated genes included TP53 (22.1%), KIT (9.8%), CEBPA (8.8%), and NRAS (5.9%). Cell-signaling genes (30.4%) and tumor suppressor genes (27.0%) were the most affected functional groups. Co-mutation analysis showed clustering led by DNMT3A–IDH1 co-occurrence (ρ ≈ 0.43). DNA-methylation alterations frequently co-occurred with tumor suppressors (OR ≈ 4.6, p = 0.007), transcription factors (OR ≈ 3.9, p = 0.023), and NPM1 (ρ = 0.32). This study provides the first comprehensive genomic map of Pakistani AML patients, revealing unique mutational signatures. The findings lay the groundwork for population-specific precision oncology in low- and middle-income countries. Full article

Agricultural pests can rapidly adapt to chemical pressures, and expression-based surveys of chemosensory genes may not fully capture the associated genomic variation. We hypothesized that the molecular profiles of chemosensory and detoxification genes in the mulberry thrips Pseudodendrothrips mori Niwa (Thysanoptera: Thripidae) are associated with local genomic variability and methylation context alongside transcript abundance. To explore this, we integrated PacBio HiFi-derived single-nucleotide polymorphisms (SNPs), structural variants (SVs), DNA methylation, and RNA-seq data on a chromosome-level reference genome. We analyzed 179 focal genes from six families, applying a consensus prioritization framework—based on weighted percentiles of feature values, principal component distances, and anomaly-detection scores—to rank the candidates. The integrated priority score correlated positively with SNP (r = 0.603) and SV burden (r = 0.632) and negatively with local methylation (r = −0.524), whereas its correlation with expression was weaker (r = 0.427). Three OBPs—PSMOgene01223, PSMOgene012530, and PSMOgene012982—emerged among the highest-priority candidates, exhibiting favorable in silico docking scores (−5.038 to −6.792 kcal/mol) with (Z)-octadec-11-enyl acetate and a long-chain oxygenated acetate. These findings indicate potential linkages between multi-omics plasticity and chemosensory gene variation. Furthermore, these computationally prioritized OBPs suggest potential targets for exploring semiochemical-based management tools. Full article

A growing body of epidemiological and toxicological evidence indicates that exposure to toxic elements (TEs), including As, Cd, Cr(VI), Pb, and Hg, is associated with a wide range of adverse health outcomes, including cancer, neurological and cardiovascular diseases. Given their widespread presence and toxicity, understanding the factors underlying inter-individual differences in susceptibility is essential, as not all exposed individuals develop the same health effects. Genetic variability, particularly single-nucleotide polymorphisms (SNPs), is increasingly recognized as a key determinant of individual responses to TE exposure. Variants in genes involved in metal transport, detoxification, and DNA repair, including DMT1, GSTP1, MT2A, hOGG1, and XRCC1, may influence internal dose and biological effects and have been proposed as potential susceptibility markers. However, current evidence remains inconsistent due to small sample sizes, heterogeneous exposure assessments, and limited considerations of ethnic diversity and gene–environment interactions. Future research should prioritize large and well-characterized populations integrating detailed exposure and lifestyle data. This review focuses on genetic susceptibility and gene–environment interactions in TE exposure, with particular emphasis on SNPs as key modulators of individual risk. It summarizes major toxic metals, reviews epidemiological evidence of the associated health risks, and highlights the role of genetic background in modulating TE-induced toxicity. Full article

Alzheimer’s disease (AD), the most common cause of dementia, is characterized by progressive memory and cognitive decline. Conventional genome-wide association studies (GWAS) comparing AD cases and controls may miss genetic influences that act along a continuum of cognitive function. Using data from 3007 participants in the National Institute on Aging Late-Onset Alzheimer’s Disease Family Study (NIA-LOAD GWAS), we conducted a family-based GWAS of eight quantitative cognitive phenotypes encompassing episodic memory (Logical Memory IA and IIA), working memory (Digit Span Forward, Backward, and Ordering), and semantic fluency (Animal, Fruit and Vegetable, and Vegetable Fluency). Family-based association testing in PLINK v1.9 identified numerous single nucleotide polymorphisms (SNPs) associated with cognitive phenotypes at genome-wide significant (p < 5 × 10⁻⁸) levels. Notably, genome-wide significant variants with cognatic functions were localized to genes implicated in synaptic function, neurodevelopment, and neurodegeneration, including TOMM40 (rs2075650), ERBB4 (rs1521543), APLP2 (rs12281267, rs959354), PTPRD (rs1353983, rs970347, rs1392511), NCAM2 (rs2826728), GRM7 (rs6788201), PAX5 (rs2988003, rs2381595), NRG1 (rs16875655), and NRG3 (rs1937957). Furthermore, the TOMM40 (rs2075650) was significantly associated with AD as a binary outcome (p = 4.60 × 10⁻²⁴) and APLP2 (rs12281267, rs959354), APOE (rs405509), PTPRD (rs1353983, rs970347, rs1392511) were associated with AD (p < 0.001). Additionally, several pathways including the ERBB4 signaling pathway (adjusted p = 2.82 × 10⁻³), driven by ERBB4, NRG1, and NRG3 may contribute to cognitive impairments. This study provides a comprehensive resource of cognitive endophenotype associations in AD families, advancing understanding of the genetic architecture underlying memory, executive function, and cognitive aging, and highlights new therapeutic targets for replication and functional follow-up. Full article

Background/Objectives: TCIRG1-associated infantile osteopetrosis is a severe hereditary disorder caused by impaired osteoclast function, leading to osteosclerosis, hematological abnormalities, neurological complications, and early mortality. Early diagnosis and intervention are critical. Methods: A literature-based analysis was performed on clinical manifestations, outcomes of allogeneic hematopoietic stem cell transplantation (HSCT), immunomodulatory therapy, and experimental gene therapy and cell-based approaches, including lentiviral vectors and patient-derived induced pluripotent stem cells (iPSCs). Results: Allogeneic HSCT is the only established curative therapy, restoring osteoclast function and preventing severe complications. Early transplantation with HLA-matched donors and myeloablative conditioning provides optimal outcomes. Interferon γ1b can transiently enhance osteoclast activity but is not curative and shows variable efficacy. Preclinical studies demonstrate that lentiviral TCIRG1 delivery and transgenic correction in patient-derived iPSCs restore osteoclast function and bone resorption, with stable gene expression and minimal toxicity. Base and prime editing approaches offer potential for precise correction of single-nucleotide TCIRG1 variants, minimizing risks associated with double-strand DNA breaks. Conclusions: Allogeneic HSCT remains the standard therapy for TCIRG1-associated infantile osteopetrosis. Gene therapy and cell-based strategies represent promising adjuncts or alternatives, potentially avoiding immune-related complications and expanding therapeutic options. Further studies are needed to ensure safety, stable engraftment, and long-term efficacy, supporting translation of gene therapy into clinical practice. Full article

Background/Objectives: Understanding the genetic basis of food consumption is a key step toward precision nutrition, viewed as a long-term future perspective. This study aimed to investigate genetic variants associated with grapefruit (Citrus paradisi) intake and to evaluate their potential relationship with obesity risk. Methods: A genome-wide association study (GWAS) was conducted on 19,653 European-ancestry participants from two prospective cohorts, the Nurses’ Health Study (NHS) and the Health Professionals Follow-Up Study (HPFS). We employed a functional annotation strategy to select a suggestive locus for follow-up analysis, and computationally derived molecular docking simulations explored a plausible functional link between grapefruit’s bioactive compounds and the candidate gene product. Results: Although falling short of the conventional threshold for genome-wide significance, a suggestive locus was prioritized on chromosome 14, with the lead single nucleotide polymorphism (SNP), rs2124 (p < 5 × 10⁻⁶), located within the metabolic gene ADCK1 (aarF domain containing kinase 1). Molecular docking simulations supported a plausible mechanistic hypothesis, indicating that key bioactive compounds in grapefruit could bind with high affinity to the ADCK1 protein. Consistent with the GWAS finding, individuals with the CC genotype reported lower mean grapefruit intake. This genotype was also associated with other lifestyle factors, notably, lower physical activity in women. In age- and multivariate-adjusted models, the CC genotype was associated with a modestly increased risk of incident obesity in females, but not in males. Conclusions: Our exploratory findings suggest a prioritized candidate locus associated with grapefruit intake, and its link to obesity risk may be mediated by the metabolic gene ADCK1. However, given the lack of genome-wide significance and independent replication, these findings should be considered preliminary and exploratory. These hypothesis-generating results support the integration of genetics and dietary habits, warranting further mechanistic validation. Full article

Genetic diversity and antifungal susceptibility profiles of Aspergillus fumigatus are critical for understanding the evolution of resistance in clinical and environmental settings. We performed comprehensive genomic characterization of A. fumigatus isolates using whole-genome sequencing combined with phenotypic susceptibility assays. SnpEff-based variant annotation identified 76,079 single-nucleotide polymorphisms, revealing a high proportion of mutations (78.8%) in upstream and downstream regulatory regions, whereas high-impact coding variants remained rare (0.083%). Several key mutations were identified, including the well-established cyp51A M220V and HMG1 S212P/Y564H mutations. Moreover, a diverse array of peripheral cyp51A polymorphisms (M39I, E402D, N248K, and K372N) was detected, although these variants did not correlate with the resistant phenotypes. Our comparative genomic analysis identified a novel A586T substitution in the FKS1 gene in an isolate with an elevated minimum effective concentration of caspofungin, suggesting its possible association with reduced susceptibility, although functional validation is required. In isolates lacking canonical target-site mutations, the high frequency of regulatory-region variants indicated the involvement of non–target-site mechanisms. This study provides a detailed map of the genomic landscape of A. fumigatus and identifies candidate loci for future functional validation. Our results demonstrate the utility of high-throughput genomic surveillance for monitoring emerging resistance trends and characterizing the genetic background of clinical fungal pathogens. Full article

Background: Familial hemiplegic migraine (FHM) is a rare and severe form of migraine disorder featuring aura symptoms that include hemiplegia during attacks. While pathogenic missense variants in CACNA1A, ATP1A2, and SCN1A can cause FHM or its sporadic form, they explain less than 20% of suspected hemiplegic migraine cases, suggesting the involvement of other genes or genetic variations, potentially including copy number variations (CNVs). PPRT2 gene variants including CNVs have also been implicated in hemiplegic migraine. Methods: Multiplex ligation-dependent probe amplification (MLPA) assays were used to investigate the presence of CNVs in the CACNA1A, SCN1A, ATP1A2, and PRRT2 genes in a cohort of 170 unrelated probands suspected to have FHM who had tested negative for pathogenic missense or small indel variants within these genes. Potential CNVs were subsequently confirmed using quantitative PCR. Results: In 15 patients referred for FHM genetic testing, various CNVs in the target genes were detected by MLPA and subsequently validated by quantitative PCR. CACNA1A exon duplications were identified in six patients and deletions found in two. Two patients had ATP1A2 exon deletions, while one had a duplication. For SCN1A, exon deletions were found in three patients and a duplication in one. PRRT2 exon deletions were detected in five patients, with a single nucleotide polymorphism (SNP) array confirming a deletion spanning PRRT2 and neighbouring loci including 26 genes in one of those. Three patients had CNVs in more than one FHM gene. Conclusions: Our study demonstrates the presence of CNVs in FHM genes in a subset of hemiplegic migraine cases (~9%), suggesting a likely role in the disorder and highlighting the need to explore structural variation in addition to the commonly interrogated genetic mutation points. These findings contribute to further understanding of genetic mechanisms that underlie hemiplegic migraine and may inform improved diagnostic and therapeutic strategies. Full article

Background: Breast cancer (BC) is a leading cause of cancer-related mortality worldwide and a major public health concern in Mexico. Regulatory variants in KRAS, particularly within the 3′UTR and intronic regions, may influence gene expression through microRNA binding and transcriptional regulation. Methods: Five regulatory single-nucleotide variants (SNVs) in KRAS (rs12228277, rs1137196, rs8720, rs12587, and rs12245) were genotyped in BC patients and cancer-free controls. Associations were evaluated using odds ratios (ORs) with 95% confidence intervals (CIs), adjusting for age, alcohol, and tobacco use. Multiple testing was corrected using the Benjamini–Hochberg false discovery rate (FDR). Linkage disequilibrium (LD), multilocus combinations, and in silico functional analyses were also performed. Results: Variants rs12228277, rs1137196, rs8720, and rs12245 showed significant genotype-level associations with BC susceptibility, all remaining significant after FDR correction (pFDR < 0.05). No clinicopathological associations remained significant after correction in single-variant analyses. Multilocus analysis identified specific high-risk combinations (e.g., involving rs12228277, rs1137196, and rs8720) associated with increased BC susceptibility. At the nominal level, these combinations showed associations with clinicopathological features, including hormone receptor–positive status (PR and ER), proliferation markers, and Luminal B subtype; however, none remained significant after FDR correction. LD analysis indicated weak linkage among variants. In silico analyses suggested potential regulatory effects on microRNA binding and KRAS expression. Conclusions: Regulatory variants in KRAS are associated with BC susceptibility through independent effects and potential combinatorial patterns. These findings support the relevance of non-coding variation in cancer risk and warrant further functional and replication studies. Full article

Basal blood pressure (BP) is partly determined by systemic vascular resistance, which is modulated by vasoactive pathways, including gaseous messengers. Carbon monoxide (CO), continuously generated by the constitutive enzyme heme oxygenase-2 (HO-2) encoded by HMOX2, promotes vascular smooth muscle relaxation and may contribute to interindividual variability in resting BP. The functional single-nucleotide polymorphism rs4786504_T>C has been associated with higher HMOX2 expression in C-allele carriers, providing a plausible biological link between genetic variation in the HO-2/CO pathway and vascular redox signaling. We investigated this association in forty young, healthy, normotensive adults studied under controlled laboratory conditions during a 4-day sleep deprivation protocol, with repeated standardized daytime BP measurements (478 observations). Linear mixed-effects models were adjusted for major physiological and behavioral covariates. T-allele carriers (C/T + T/T) exhibited higher diastolic BP (β = +6.08 mmHg, 95%CI [1.32–10.84], p = 0.017) and mean arterial pressure (β = +5.28 mmHg, 95%CI [0.28–10.29], p = 0.046) than C/C homozygotes, with no effect on systolic BP or heart rate. The association remained consistent across sensitivity and additive genetic models. This hypothesis-generating study provides preliminary evidence in humans, albeit limited by sample size, of a link between a functional HMOX2 variant and resting BP, consistent with a possible contribution of constitutive HO-2 activity to BP regulation. Full article

Background/Objectives: Population-specific genomic data are essential for understanding hepatocellular carcinoma (HCC) biology, particularly in underrepresented regions. This study aimed to perform exploratory single-nucleotide polymorphism (SNP)-array-based profiling of HCC tumor samples from Indonesian patients and to prioritize candidate functional variants using a systematic in silico framework. Methods: This retrospective cross-sectional study included 15 resected HCC cases with available formalin-fixed paraffin-embedded (FFPE) tumor tissue. Genome-wide SNP genotyping was performed using the Illumina Asian Screening Array. Following quality control and filtering, variants were annotated using the Ensembl Variant Effect Predictor. A case-only functional prioritization approach incorporating multiple in silico prediction tools was applied, followed by gene-level burden aggregation. Results: After multistep filtering, 11 samples and 104 prioritized variants were retained for analysis. Variants consisted predominantly of splice-region, missense, and regulatory changes. Gene-level burden analysis identified Nuclear Autoantigenic Sperm Protein (NASP, rs775916096) as the highest-ranked candidate gene, while G protein-coupled receptor 78 (GPR78, rs558447540) emerged as a secondary candidate with predicted functional annotations but currently limited biological evidence in HCC. Given the tumor-only design without matched normal tissue, the prioritized variants cannot be distinguished from rare germline variants. Conclusions: This exploratory SNP-array study provides a hypothesis-generating framework for functional variant prioritization in Indonesian HCC. NASP and GPR78 represent preliminary candidates that require validation in larger cohorts with matched normal tissue and sequencing-based confirmation. Full article

Prenatal whole-genome sequencing (WGS) is a comprehensive genetic test for fetal anomalies, enabling simultaneous detection of aneuploidies, copy number variants (CNVs), single-nucleotide variants (SNVs), small insertions/deletions, structural variants, and regions of absence of heterozygosity. However, its clinical performance, optimal sequencing strategies, and implementation challenges remain incompletely defined. We conducted a narrative review of PubMed-indexed studies (1966–December 2025) evaluating prenatal WGS in fetuses with structural anomalies. Across 29 studies, diagnostic yield ranged from approximately 20% to 40%, influenced by phenotype complexity, sequencing depth, and study design. Low-coverage WGS (≤5×) reliably detected large chromosomal abnormalities with a performance comparable to chromosomal microarray analysis. Moderate-coverage WGS (20–40×) additionally enabled detection of SNVs and structural variants, providing up to 30% incremental diagnostic yield after uninformative standard testing. Turnaround times were typically 14–21 days. Higher sequencing depth increases detection of variants of uncertain significance (0.6% to 35.7%) and secondary/incidental findings (1.6–30.8%). Prenatal WGS offers meaningful diagnostic value but requires careful patient selection, multidisciplinary expertise, and structured pre- and post-test genetic counseling to ensure responsible integration into routine clinical practice, with careful consideration of clinical benefit and economic feasibility. Full article