Gene-based therapies are being developed for retinal diseases, including RS1-related X-linked retinoschisis. Therefore it is essential to determine which variants are pathogenic and which are benign when enrolling patients. The Clinical Genome Resource (ClinGen) X-Linked Inherited Retinal Diseases (XLRD) Variant Curation Expert Panel (VCEP) brings together clinician scientists, molecular biologists, and geneticists to apply their expertise and review the clinical, genetic, population, and functional evidence for variants. American College of Medical Genetics (ACMG) guidelines have been modified for RS1 to develop a highly systematic and conservative framework for evaluating variants. The curation process involves applying 28 different codes, each with 4 strength levels (very strong, strong, moderate, supporting) across different domains of phenotype, population data, computational assessment, functional impact, and segregation. With RS1-specific rules, a total of 54 pilot variants were tested. These included 47 variants in ClinVar. Of these 21 variants were re-classified: 2 likely pathogenic variants and one likely benign were changed to variants of uncertain significance and 4 previously unclassified variants were changed to pathogenic, likely pathogenic and likely benign. Other changes resolved conflicts or multiple classifications.
The Argentine population reflects a history of asymmetric admixture, a process particularly evident in uniparental markers. Consequently, the maternal lineage retains a record of the three primary ancestral origins: Native American, Eurasian, and African. The main objective of this study was to conduct an integrated comparative analysis to determine and assess the geographic distribution of mitochondrial haplogroups associated with these three ancestral origins across Argentina. This was achieved through an integrative approach that combined genetic data with census records and published literature. A dataset comprising 7,431 haplogroups analyzed at the provincial level was assembled from the literature. The overall maternal genetic composition obtained for the Argentine was 75
Identifying pathogenic germline variants in men with metastatic prostate cancer is important for therapeutic options and for identifying relatives who may have a high cancer risk. To keep genetic testing costs manageable, it is important to identify which patients should be selected for testing. In this study, we compared expected costs and number of identified pathogenic variants in two scenarios: offering genetic testing to all men with metastatic prostate cancer versus testing only those with additional risk factors linked to a higher likelihood of carrying a pathogenic variant. Costs were evaluated with a mainstream genetic testing pathway, where testing is discussed by a non-genetic healthcare professional. Using Dutch national incidence data, predefined healthcare cost frameworks, and a hypothetical assumption for the acceptance rate of patients, we modelled total costs for the Netherlands and number of identified pathogenic variants for each approach. The costs of genetic testing and post-test counselling decreased threefold when applying selection criteria, compared to the scenario where all metastatic prostate cancer patients are eligible. However, applying selection criteria would result in missing 41
Epilepsy represents a highly prevalent neurological disorder with a significant genetic component, particularly implicating ion channel genes, including SCN1A. In this study, 431 individuals with heterogeneous paediatric-onset epilepsy phenotypes were assessed at the Department of Medical Genetics, University of Pécs between 2018 and 2024. Genetic investigations employed Sanger sequencing, targeted epilepsy gene panels, whole exome sequencing, and multiplex ligation-dependent probe amplification for SCN1A copy number analysis. Thirty-six pathogenic or likely pathogenic SCN1A variants were identified, including 15 variants which have not been reported previously. Furthermore, 9 novel variants were detected in 12 additional epilepsy-associated genes. Diagnostic yield was proportional to the breadth of genomic interrogation. WES analysis revealed 6 novel variants in 19 genes. These findings underscore the considerable genetic heterogeneity of epilepsy and demonstrate the clinical utility of gene panels and WES, particularly in complex phenotypes. The identification of novel variants enhances molecular understanding and facilitates more precise genotype-phenotype correlations, reinforcing the value of comprehensive genomic diagnostics in epilepsy management.
Craniofacial microsomia (CFM) exhibits significant phenotypic variability and degree of severity. While loss-of-function variants in SF3B2 have recently emerged as a genetic etiology, the molecular basis underlying this clinical heterogeneity remains poorly understood. Here, we report two probands harboring novel truncating SF3B2 variants and presenting with distinct clinical phenotypes. Proband 1, with a heterozygous p.(Gln60*) variant, exhibited characteristic CFM features, including mandibular hypoplasia, cleft palate, bilateral tragal abnormalities, microtia, external auditory canal stenosis with hearing impairment, and an epibulbar dermoid. In contrast, Proband 2, carrying a p.(Lys507*) variant, exhibited a milder craniofacial phenotype, although he had hearing loss and developmental delay that could not be explained with certainty by the SF3B2-variant. Western blot analysis demonstrated complete loss of p.(Gln60*) protein, whereas the p.(Lys507*) variant—despite lying outside the predicted nonsense-mediated decay (NMD) escape region—retained 15.5
Human induced pluripotent stem cells (hiPSCs) represent a powerful platform for disease modeling, especially in monogenic diseases as they preserve the donor’s genetic background while enabling directed differentiation into disease-relevant cell types. This makes them highly suitable for studying disease mechanisms in a patient-specific and physiologically relevant context. Although CRISPR/Cas9 is widely applied for genome editing, precise correction of pathogenic variants in hiPSCs remains challenging due to the lack of standardized CRISPR component selection and experimental design. Here, we describe an optimized CRISPR-based strategy for correcting a heterozygous HNF1A frameshift mutation (c.235_236insG; p.Glu79Glyfs*16) in HNF1A-MODY patient-derived hiPSCs. Using electroporation, we efficiently delivered CRISPR components, including a ribonucleoprotein complex of Cas9 and single-guide RNA, along with a single-stranded oligodeoxynucleotide repair template. Corrected hiPSC lines were validated for pluripotency, absence of exogenous reprogramming factors, and off-target effects. Additionally, we discuss key technical challenges encountered during the editing process and provide practical recommendations that may improve the generation of mutation-corrected hiPSC lines. These guidelines could serve as a useful reference for researchers employing CRISPR-based strategies for generation of reliable disease modelling tools.
Congenital microcephaly and lissencephaly spectrum disorders are characterized by disrupted neuronal proliferation and migration, often driven by underlying genetic variants. Here, we identified and characterized of a novel gene (Tetratricopeptide Repeat Domain 14, TTC14) and its homozygous missense variant (c.89 A > G; p.His30Arg (p.H30R)) in a female proband presenting with microcephaly, epileptic spasms, global developmental delay, and neuroimaging features of simplified gyral pattern, focal pachygyria, and corpus callosum thinning. Trio-based whole exome sequencing revealed this variant to be rare and autosomal recessively inherited from both asymptomatic parents. Structural modeling demonstrated that H30 lies at the start of an α-helical region and is evolutionarily conserved. The p.His30Arg substitution caused significant steric clashes and disrupted local folding. Interaction network analysis and molecular dynamics simulations confirmed structural destabilization, increased conformational flexibility, and loss of stability in the mutant protein. While mRNA and protein levels remained unaltered, the TTC14-p.His30Arg protein mislocalized from the nucleus to the cytosol and formed aggregates. Functionally, proband fibroblasts exhibited increased cell death and altered cell cycle progression. TTC14 interacts with RNA splicing and mRNA processing proteins, and gene ontology analysis implicated it in RNA binding and spliceosomal complex assembly in key brain regions including the cerebral cortex, hippocampus, and white matter. These findings collectively suggest that TTC14 plays a crucial role in RNA metabolism during neurodevelopment, and that the p.His30Arg variant impairs its function, possibly leading to a neurodevelopmental disorder within the lissencephaly spectrum. This study identifies TTC14 as a likely pathogenic candidate gene in cortical malformation syndromes.
Melatonin exerts pleiotropic physiological functions and diverse disease associations, but its genetic architecture remains largely uncharacterized. Using low-coverage whole-genome sequencing (lcWGS) in 3,605 Han Chinese adults, we identified four independent loci (P < 1 × 10⁻⁷) associated with circulating melatonin (pg/mL)—located within or near LINC01807, PTPRD, EDIL3/NBPF22P, and LMO1/STK33. Conditional analyses indicated that the STAARpipeline single-variant and sliding-window signals were largely driven by these genome-wide association study (GWAS) lead variants, whereas a gene-centric noncoding aggregation signal in the ZSWIM9 promoter region remained independent. These genes showed tissue-specific expression in neural, vascular, and adrenal tissues (GTEx ). The heritability of serum melatonin was estimated at 21.72
The Mulam people, an ethnic minority group native to southern China, primarily inhabit the Guangxi region. Systematic whole-genome studies on the Mulam population remain limited. In this study, we analyzed genome-wide genotyping data comprising over 700,000 single-nucleotide polymorphisms (SNPs) derived from 107 saliva samples of Mulam individuals in Guangxi, to investigate their genetic origins and relationships with other southern East Asian populations. Based on ancestry inference and population genetic analysis, we identified three major ancestral components in the Mulam genome: ancient Yellow River farmers, indigenous southern East Asian populations, and Austronesian-related groups. These results support historical records indicating that the proto-Mulam were formed through the integration of ancient Yellow River migrants with indigenous southern East Asian communities. Furthermore, shared southern East Asian ancestry reveals a genetic link between the Mulam and Taiwanese indigenous peoples, likely resulting from prehistoric southward population movements. This study emphasizes the complex genetic makeup of the Mulam people and offers new perspectives on population history and dynamics in East Asia.
Weiss-Kruszka syndrome (WSKA; OMIM 618619) is a rare autosomal dominant neurodevelopmental disorder caused by haploinsufficiency of ZNF462, a zinc-finger transcription factor involved in chromatin regulation and early embryonic development. WSKA is characterized by developmental delay, hypotonia, craniofacial dysmorphic features (around 8) and variable congenital anomalies. Genome-wide DNAm profiling was performed on peripheral blood DNA from 9 WSKA cases with (likely) pathogenic ZNF462 variants and matched controls to look for differential methylation. Analysis using the EpiSign™ pipeline identified a robust DNAm pattern, or episignature, specific to WSKA syndrome. Supervised machine-learning classification demonstrated high sensitivity and specificity, with reproducibility confirmed by leave-one-out cross-validation, as well as correctly classifying a validation case with a pathogenic ZNF462 variant. Comparative analysis revealed partial overlap of genome-wide DNA methylation changes between the WSKA episignature and other neurodevelopmental disorders involving chromatin regulators. Functional annotation of differentially methylated probes and regions demonstrated enrichment for pathways related to neurodevelopment, neuron function and cell adhesion. These findings define and validate a distinct DNAm episignature for WSKA, providing a valuable diagnostic biomarker to support variant classification and offering insight into the epigenomic consequences of ZNF462 haploinsufficiency.
Pathogenic variation of SLC26A4 gene causes both Pendred syndrome (PDS) and non-syndromic enlarged vestibular aqueduct (NSEVA/DFNB4), two autosomal recessive disorders. The former accounts for approximately 6
A central challenge in polygenic risk prediction is measuring and controlling for confounding due to population stratification. Standard approaches include adjusting for leading principal components (PCs) of genetic variation and using linear mixed models in genome-wide association studies (GWAS). Evidence of adequate control is typically inferred from reductions in the linkage disequilibrium score regression (LDSC) intercept and the preservation of polygenic risk score (PRS) performance in within-sibling settings. Here, we investigate how the number of PCs included during GWAS/PRS construction relates to the loss of predictive performance when moving from population-based analyses to that of discordant sibling pairs (within-sibling attenuation). This design detects confounding arising from environmental and genetic background effects correlated with population structure. Analyses were performed in the self-identified White subset of the UK Biobank (UKB) for coronary artery disease, type 2 diabetes, breast cancer, and prostate cancer, with educational attainment included as a comparison trait as it is known to exhibit substantial within-sibling attenuation. We find that increasing the number of PCs does not consistently reduce within-sibling attenuation across traits. Furthermore, reductions in attenuation do not closely correspond to decreases in the LDSC intercept, and mixed model-based methods offer little additional improvement in prediction or attenuation. Overall, our results suggest that confounding targeted by PC-adjustment and linear mixed models is either minimal in the UKB, or remains inadequately captured by current methods, reflecting limitations as to how much standard population structure correction improves the causal validity of PRS in the UKB.
A missense variant of adenylate cyclase 7 (AC7), p.Asp439Glu, has been significantly associated with ulcerative colitis (UC) in genome-wide association studies. Previous work suggested that this variant is reduced in expression and exhibits impaired cyclic adenosine-3 ',5 '-monophosphate (cAMP) synthesis, thus skewing T-cell cytokine profiles. Here, we investigated the variant's function measuring dynamic cAMP responses in live HEK293 cells. We show that p.Asp439Glu generates significantly reduced basal cAMP levels despite normal expression. Stimulation with sphingosine-1-phosphate (S1P) and phorbol 12-myristate 13-acetate (PMA) induced a reduced cAMP increase in cells expressing mutant AC7, indicating reduced responsiveness to G-protein-coupled receptor (GPCR) and protein kinase C (PKC) activation. Western blot analysis showed altered downstream phosphorylation of cAMP response element-binding protein (CREB) and cAMP-dependent transcription factor (ATF1) in cells expressing the variant. Higher levels of phosphorylated CREB and ATF1 were observed in cells expressing p.Asp439Glu AC7 under basal conditions while stimulation with S1P had no effect on protein phosphorylation. Our findings provide direct biochemical evidence for strongly impaired AC7 function caused by the variant p.Asp439Glu. These results may pave the way for more causally defined and genotype-specific treatment strategies in UC.
Chromosomal triplications are rare structural variations often associated with complex phenotypes. We report the molecular characterization of a novel intrachromosomal triplication at 18q12.1q21.2 identified in a fetus with ultrasound abnormalities. Conventional karyotyping and array-CGH revealed a partial tetrasomy and a 26 Mb region of loss of homozygosity (LOH), extending from the triplication to the telomere. Long-read sequencing (LRS) identified breakpoint junctions revealing a direct-inverted-direct triplication structure. Breakpoint analysis suggested that this rearrangement arose through a U-type exchange between sister chromatids, likely mediated by microhomology-based mechanisms. This process likely generated a transient dicentric chromosome that subsequently broke during mitosis. The resulting duplicated chromosome may have been stabilized by telomere capture, consistent with the triplicated 18q12.1q21.2 region followed by the 18q21.2q23 LOH. Nine genes within the triplicated region, including SMAD2 and SMAD4, showed high predicted sensitivity to increased dosage, possibly contributing to the clinical phenotype. This study highlights the utility of LRS in defining complex chromosomal rearrangements and emphasizes the importance of molecular breakpoint analysis for understanding pathogenic mechanisms and improving genetic prenatal diagnosis.
While falling costs have expanded access to genomic sequencing, clinical utility is frequently hindered by the challenge of interpreting complex genetic data. Variant analysis for rare disease patients especially requires significant time and expertise, creating a bottleneck that delays diagnostics. Although advances in genetic variant classification have improved diagnostic precision, they have also increased the identification of variants of uncertain significance (VUSs), widening the interpretation gap between data generation and clinical actionability. The high prevalence of VUSs can lead to false reassurance or psychological distress by misinterpretting inconclusive results. We propose that artificial intelligence (AI) is a critical clinical decision-support tool for bridging this gap, offering a scalable framework to optimize variant interpretation and shorten the diagnostic odyssey. While reclassification ultimately requires biological evidence that AI cannot replace, these tools serve as essential aggregators and prioritizers, especially as guidelines transition toward the upcoming quantitative ACMG v4 framework. We advocate integrating AI throughout the genetic diagnostic workflow–from initial phenotyping to variant prioritization–to facilitate data-driven, personalized treatment. We outline current AI-assisted approaches and discuss anticipated challenges in this pursuit, such as privacy, training data bias and quality, model explainability, and the necessity of a total product life cycle for validation. To address these challenges, we provide recommendations for "human-in-the-loop" design and intuitive workflow integration to ensure AI tools meet the highest standards of precision, reproducibility, and transparency to maximize adoption. By standardizing AI across the variant analysis pipeline, we can fast-track the path to genetic diagnoses, effectively bridging the interpretation gap and enabling rapid delivery of personalized medical interventions.
Attention deficit hyperactivity disorder (ADHD) is one of the most prevalent and heritable of neurodevelopmental disorders. To characterize the genetic variants contributing to this heritability, we studied families with members affected by ADHD. Genome-wide array data were obtained on two cohorts: NHGRI Family Cohort (359 nuclear families,1538 individuals) and NCR Family Cohort (25 multigenerational and 132 nuclear families, 631 members). A meta-analysis of family-based association tests (FBAT) of the two cohorts identified three genome-wide significant associations, one upstream from TFRC, and two that were intronic to GSDME and to TRIM31, with the last gene previously implicated in ADHD. Genes associated with ADHD (MAGMA, gene-based association P < 0.05) overlapped with genes implicated in ADHD by prior case/control genome-wide association studies. Meta-analyses of the linkage signals identified one significant linkage region (LOD > 3) on 19p13.2-13.11 that encompassed a genome-wide significant variant in the FBAT of the NHGRI Family Cohort (rs55741253, P = 2.68 × 10− 8). Additionally, two of the five linkage regions that reached a LOD > 2 in our meta-analysis replicated significant linkages from prior studies (prior studies reporting 13 linkages with LOD > 3.0; hypergeometric test of overlapping linkage signals, P < 0.01). Using neuroimaging data from the NCR cohort, we found genes associated with ADHD overlapped with genes associated with the brain’s total surface area and a feature of functional connectivity, reflecting the interaction between the brain’s default mode and task positive networks. Such work begins to delineate the neural substrates of the discovered genetic associations with familial ADHD.
Selective immunoglobulin A deficiency (IgAD) is the most prevalent primary immunodeficiency and frequently coexists with autoimmune diseases (ADs), suggesting a shared genetic etiology. While genome-wide association studies (GWAS) have identified only a few risk loci for IgAD and hundreds for ADs, systematic cross-trait analyses are lacking, leaving the shared genetic architecture and underlying mechanisms poorly understood. In this study, we analyzed summary statistics from large-scale GWAS of IgAD and 10 common ADs. Cross-trait GWAS meta-analysis identified 51 pleiotropic loci significantly associated with IgAD and at least one AD (p < 5×10⁻⁸), 31 of which were novel for IgAD. Colocalization analysis further supported 33 shared loci between IgAD and ADs, including 19 novel IgAD loci, such as those near TNFAIP3, CD28, IRF4, STAT4, SH2B3, APOBR and RAD51B. Gene-level analysis revealed shared pathways involved in T-cell differentiation and the intestinal immune network for IgA production. Tissue heritability analysis identified whole blood and the intestine as critical tissues, while single-cell RNA sequencing (scRNA-seq) highlighted B cell subtypes in the peripheral blood and gut as the most affected cell types in IgAD and ADs. Mendelian randomization further demonstrated bidirectional causal relationships between IgAD and several ADs. Our findings reveal a shared genetic architecture between IgAD and ADs, highlighting common functional mechanisms and providing insights into their biological interplay and potential immune-based therapies.
Pancreatic cancer cell metastasis is a major factor influencing prognosis. A Ras homologue member I (ARHI) was reported to regulate proliferation and apoptosis in pancreatic cancer; however, its role in invasion remains unclear. This study aimed to explore the role and related mechanisms of ARHI in pancreatic cancer metastasis. We revealed that in pancreatic cancer ARHI expression levels were consistent with aggressive cellular phenotypes, and that changes in endogenous ARHI protein expression led to corresponding alterations in epithelial-mesenchymal transition (EMT) markers. Furthermore, ARHI accelerated tumor invasion in pancreatic cancer cells and in a mouse hepatic metastasis model. Notably, this unusual promoting effect of ARHI on EMT and invasion in pancreatic cancer was primarily exerted through the Notch-1 signaling pathway. Collectively, our findings provide insight into the function and molecular mechanisms of ARHI in pancreatic cancer metastasis.
The Sino-Tibetan and Altaic groups have played central roles in shaping the human demographic history of populations at the crossroads of East Asia and Siberia. However, their matrilineal relationships and links to complex cultural interactions remain poorly resolved. Here, we reported 344 newly sequenced complete mitogenomes from representative populations and integrated them with a curated dataset of more than 53,000 reference sequences. We uncovered a highly structured maternal genetic landscape, in which Sino-Tibetan and Altaic groups shared some maternal lineages despite distinct demographic trajectories, including East Asian haplogroups D4 and A. Sino-Tibetan-speaking populations showed elevated frequencies of B4, F1, and M7, whereas Altaic-speaking populations were enriched for C, H, and U. These observed genomic diversity patterns were jointly shaped by linguistic affiliation and geography. High-resolution phylogeographic analyses further showed that Tibeto-Burman groups from the Qinghai-Tibetan Plateau (QTP) carried distinctive maternal components, including region-specific sub-lineages within A, M9, and R32. Phylogenetic reconstructions dated the maternal lineages shared by Sino-Tibetan- and Altaic-speaking populations to 56.87-10.86 thousand years ago (kya), indicating that these early divergences formed the primary genetic foundation of both groups, whereas later Neolithic expansions contributed only modestly. Mongolic groups from the Inner Mongolian Plateau shared some maternal lineages with QTP populations, largely dating to 26.83-12.72 kya, indicating deep maternal connections despite substantial geographic separation.
The baseline heritability of the newly defined metabolic dysfunction-associated steatotic liver disease (MASLD) is unknown. Given that sex and alcohol consumption are well-recognized determinants of fatty liver disease, it is important to understand whether they are also associated with variation in its underlying genetic susceptibility. We aimed to quantify the baseline heritability and investigate these potential effects in a classical twin study of 710 Chinese adults using structural equation modeling. We observed a baseline narrow-sense heritability (A) of 0.57 (95% CI 0.46-0.67) in the lower alcohol intake group. This genetic contribution was not uniform and showed a potential difference by sex, with heritability tending to be higher in females (0.63) than in males (0.30). Furthermore, the genetic architecture appeared to vary across alcohol exposure levels. In contrast to the additive (AE) model observed in lower drinkers, the higher alcohol intake group was better fitted by a dominant/non-additive (DE) model, yielding a broad-sense heritability (D) of 0.60 (95% CI 0.34-0.77). In conclusion, our findings suggest that the genetic architecture of MASLD may vary according to sex and alcohol consumption, highlighting potential gene-environment interactions and the context-dependent nature of genetic susceptibility. These results may have implications for future risk stratification and targeted prevention strategies.
