Identification and functional analysis of biallelic loss-of-function variants of WNT7B in a Chinese family affected with PDAC syndrome.

Exome and genome sequencing enable opportunistic screening for secondary findings (SFs). We report on exome analysis for a broad range of medically relevant SFs in the setting of the Incidental Genomics randomized clinical trial (NCT03597165). Participants had exome sequencing and were randomized to receive only primary cancer findings (control) or cancer findings and a choice of SFs (intervention). Across 279 participants, there were 4441 unique variants in SF genes: 5.0% (221) were reportable pathogenic/likely pathogenic variants, and 81.4% (3615) were nonreportable variants of uncertain significance (VUS). Intervention arm participants had on average 2.6 (SD 1.66, range 0-9) pathogenic/likely pathogenic variants and 29.5 VUS (SD 13.2, range 2-74). SFs for monogenic disease risk were reported in 35.3% (49/139) of participants (American College of Medical Genetics and Genomics non-cancer subset in 1.4%) and carrier status in 89.3% (117/131). In the intervention arm, variant filtration was 7.7 times longer per case (95% CI 5.3 to 11.3, P < .0001), variant classification was 13.3 times longer (95% CI 10.6 to 16.5, P < .0001), and report preparation was 3.3 times longer (95% CI 2.6 to 4.1, P < .0001). Although the yield of reportable SFs was high, this was accompanied by many nonreportable VUS and increased efforts for exome analysis.

HLA-G encodes an immune checkpoint molecule with restricted expression in immune-privileged tissues and pathological conditions. It exhibits limited coding diversity but substantial regulatory-region variation influencing expression levels. Strong linkage disequilibrium across HLA-G creates a structured genetic architecture in which regulatory and coding variants co-segregate into well-defined haplotypes, enabling the imputation of complete HLA-G haplotypes from partial genomic data. We developed imputation models to predict HLA-G 4-field alleles, promoter, and 3'UTR haplotypes from whole-exome sequencing and SNP array data using HIBAG. Multi-ethnic reference panels were constructed from 5,347 individuals from three diverse cohorts (1000 Genomes, Human Genome Diversity Project, and Brazilian SABE cohort). Models were validated through cross-validation and independent datasets. Exome-based imputation achieved high accuracy (>99%) for common alleles (frequency>1%), with mean posterior probabilities exceeding 0.95. SNP array-based models showed slightly lower but still robust performance (>95% accuracy). Our approach enables simultaneous prediction of coding and regulatory sequences, providing comprehensive functional information from datasets that do not capture the complete HLA-G diversity. These models facilitate HLA-G analysis in widely available genomic datasets lacking introns and regulatory regions (tumor exomes, SNP arrays), enabling investigation of HLA-G's role in immune regulation, transplantation, cancer, and pregnancy complications without full-gene sequencing.

Introduction: Nitric Oxide Synthase 1 (NOS1) has been implicated in Parkinson’s Disease (PD) pathogenesis through its role in neuronal signaling and oxidative stress. However, evidence of specific genetic contributions in Indian populations remains limited. Aim: The present study aimed to examine whether genetic variations in exon 18 of the NOS1 gene are associated with PD in a South Indian cohort. Materials and Methods: The present observational crosssectional study was conducted between March 2022 and May 2023 at a Tertiary Care Hospital, Karnataka, India. One hundred clinically diagnosed PD patients underwent detailed neurological assessment and 1 mL venous blood collection. Deoxyribonucleic Acid (DNA) was extracted and exon 18 of NOS1 (chromosome no 12 ) was amplified by PCR and sequenced using Sanger sequencing. Variants were analysed and verified using bioinformatics tools and reference sequences. Results: The cohort comprised 65 males and 35 females, with 64 cases classified as sporadic, 34 idiopathic, and 2 familial. Demographic data showed that 67% were urban residents. Sequencing of exon 18 detected a synonymous single nucleotide variant (g.119313C&gt;T, rs1047735) in three patients: two heterozygous and one homozygous. This variant (c.2706C&gt;T) results in p.His902=, without amino acid change. Conclusion: Only synonymous variants were found. Although these variants do not change the amino acid sequence, they may influence NOS1 regulation at the RNA level. Larger casecontrol studies with functional analyses and broader genomic approaches such as whole-exome sequencing are necessary to clarify whether NOS1 exon 18 variants contribute to PD susceptibility.

Genetic Diversity in Early Infantile Epileptic Encephalopathy: A Three-Year Cohort Study.

We aimed to broaden the understanding of autosomal recessive neurodevelopmental disorders caused by VARS1 by describing new clinical and molecular findings and assessing the predicted structural impact of identified variants. We clinically evaluated 13 affected individuals from 10 unrelated families presenting with a neurodevelopmental disorder. We used exome sequencing and cosegregation analyses to identify disease-causing variants, followed by three-dimensional in silico analyses and molecular dynamics simulations to assess the likely functional consequences of both previously reported and novel variants. In all affected individuals who presented with a neurodevelopmental syndrome with progressive microcephaly, seizures, and intellectual disability, we identified biallelic disease-causing variants in VARS1. Two variants were predicted to induce premature protein truncation leading to loss of VARS1 function. The remaining 13 detected missense variants were located in the catalytic and aminoacylation domains, and in silico analysis of the affected residues showed that such substitutions can disrupt local protein dynamics, RNA-interaction surfaces, or catalytic geometry, thereby affecting ligand recognition, substrate specificity, and tRNA interaction. Together with prior reports, our results provide strong additional evidence supporting VARS1 as a recurrent cause of autosomal recessive neurodevelopmental disorders and expand the known clinical and allelic spectrum. While in silico analyses provide mechanistic plausibility for novel variants, functional studies will be important to confirm variant-specific effects and disease mechanisms.

Pathogenic variants in myosin heavy chain 9 (MYH9), encoding the heavy chain of nonmuscle myosin IIA (NMMIIA), cause autosomal-dominant MYH9-related disease that may include proteinuric kidney disease, macrothrombocytopenia, cataract, sensorineural deafness, and elevated liver enzymes. Whole exome sequencing and segregation analysis were performed in a patient with end-stage renal disease. Histology of kidney and liver biopsies was assessed and blood smears were examined for the presence of Döhle-like bodies. Deformability cytometry and monocyte migration assays were performed. Immortalized podocytes and primary skin fibroblasts of 1 patient were transfected with plasmids containing MYH9 wild type (WT) or the p.(Arg424Gly) variant. Biochemical studies using recombinantly produced proteins were conducted to assess the variant's impact on adenosine triphosphate (ATP) turnover and motor function. We identified the likely pathogenic heterozygous MYH9 variant c.1270C>G, p.(Arg424Gly) in all affected members of a nonconsanguineous family. Typical microscopic findings, such as Döhle-like bodies or NMMIIA conglomerates were absent. Nonetheless, all patients presented with proteinuric kidney disease, elevated liver enzymes, and intermittent thrombocytopenia. The altered protein showed increased ATP turnover in the presence of actin and enhanced motor activity under both unloaded and loaded conditions. We identified a novel fully segregating MYH9 variant causing MYH9-related disease. Based on biochemical findings, we report the first gain-of-function variant of MYH9. We propose that the enhanced intrinsic motor activity of the p.(Arg424Gly) variant is a key contributor to the disease mechanism. Incorporation of the p.(Arg424Gly) variant into nonmuscle myosin IIA filaments and higher-order actomyosin assemblies may, in principle, affect actomyosin dynamics.

Osteogenesis imperfecta (OI) is a genetically heterogeneous connective tissue disorder marked by bone fragility and deformities. This study aimed to define the clinical and molecular characteristics of 21 OI patients from 15 unrelated Egyptian families. Most probands were analyzed by exome sequencing. In three consanguineous cases, variants were identified through SNP array-based homozygosity mapping followed by direct sequencing of a candidate gene. Genotype-phenotype correlations were additionally explored. Parental consanguinity was documented in 66.7% (10/15) of the total cohort and in 100% (8/8) of the families with autosomal recessive OI. Pathogenic or likely pathogenic variants were identified in 14 families, five of which were novel. A variant of uncertain significance was identified in the remaining family. COL1A1 and COL1A2 (n = 7) were the most commonly mutated genes, followed by CRTAP (n = 4), while variants in P3H1, WNT1, CREB3L1, and SEC24D were each identified in a single patient. The present study highlights the molecular heterogeneity of OI. In total, 15 distinct variants in seven OI-related genes were identified. We also report a particularly high number of OI lethal forms affecting 10 patients out of 21. The study adds further evidence for the utility of ES in the genetic diagnosis of OI, which facilitates counseling and personalized care.

Clinical and Genetic Characterization of CAPN3-Related Limb-Girdle Muscular Dystrophies in an Egyptian Cohort.

Essential tremor: Family-based sequencing suggests involvement of neuronal and metabolic pathways.

Prenatal Exome Sequencing (pES) increases the diagnostic rate for genetic disorders in pregnancies with structural abnormalities and substantially impacts parental decision-making regarding pregnancy continuation or termination. Previous qualitative research on parental experiences of pES has typically been performed several months after results were returned to parents. Moreover, parental experiences of pES might be dependent on cultural aspects and country-specific healthcare systems. This research therefore prospectively explores experiences of families undergoing pES in the Netherlands. Expectant parents undergoing pES because of ultrasound anomalies were invited to participate with two interviews: interview T1 after counseling for genetic testing but prior to return of results and interview T2 six months after return of results. We translated a previously designed Australian interview script, used in similar research, to Dutch, including four open-end and two multiple-choice questions in addition to demographic details. An inductive content analysis approach was used for coding and analysis. Twelve families were interviewed at T1, of which five participants agreed to T2 follow-up interviews. We constructed six content categories of importance: (1) Prenatal feelings of fear, uncertainty, guilt, and anxiety; (2) conflicting feelings in the face of (un)certainty; (3) overall satisfaction with genetic counseling; (4) decision-making influenced by desire for information about their child's quality of life; (5) decision-making influenced by reproductive options and family planning; and (6) importance of empathy, kindness, and clear communication from friends, family, and healthcare professionals. Many content categories show overlap to previous research. However, families in this cohort did not explicitly express negative opinions about waiting on results which is possibly explained by concurrently running multiple genetic testing modalities. Moreover, all participants mentioned positive experiences of the provided healthcare, partly because of swift multidisciplinary collaboration. This study highlights the value of pre-test counseling by clinical geneticists and shows the need for close collaboration between feto-maternal specialists, clinical geneticists, and laboratory specialists.

Early Exome Sequencing for an Infant With Paroxysmal Eye Movements Reveals a Monogenic Etiology for Spasmus Nutans.

The clinical application of prenatal exome sequencing (pES) for fetal structural anomalies is relatively new. Although a prenatal genetic diagnosis has been shown to have high clinical and personal utility for families, nearly 70% of pregnancies undergoing pES will receive nondiagnostic results. Currently, there is little literature on postnatal outcomes following a nondiagnostic pES result in fetuses with structural anomalies, making it difficult to interpret the postnatal significance of the nondiagnostic result and tailor anticipatory guidance for expectant parents. This retrospective chart review identified trends in clinical outcomes following nondiagnostic pES results for 63 pregnancies and the resulting 61 liveborn children at a specialized maternal and newborn tertiary care hospital. Postnatal clinical outcome measures, including premature delivery (54%), NICU admissions (85%), hospitalizations (52%), surgical interventions (62%), and deaths (20%), highlight the complex care needs of the children in this cohort. However, the clinical outcomes were predominantly predictable, with 69% of the children having clinical care needs as expected based on what was counseled to parents prenatally. The results of this study affirm the assumptions that nondiagnostic pES does not equate to less medical complexity for children with prenatally identified structural anomalies, and that nondiagnostic pES results should not be interpreted as broadly reassuring. Comprehensive post-test counseling is essential and should address the residual risk related to the severity of the identified anomaly or anomalies, the potential for unanticipated or complex clinical outcomes, and the limitations of antenatal ultrasound in capturing the full phenotypic spectrum.

Hemophagocytic lymphohistiocytosis secondary to isolated bronchial infection caused by Mycobacterium marseillense in a patient with GATA2 missense mutation: A rare case report.

To determine the genetic causes of miscarriage by analyzing products of conception (POC). Chromosomal microarray (CMA) using the Affymetrix Cytoscan HD array was performed in 172 POC specimens from women experiencing spontaneous miscarriage before 20weeks of gestation to detect aneuploidies, copy number variants (CNVs), and loss of heterozygosity (LOH). Whole exome sequencing (WES) with Roche KAPA HyperExome V2 probes was used for cases where CMA results were normal. Common clinical indications included recurrent pregnancy loss, first-time miscarriage, absence of cardiac activity, intrauterine death, and fetal growth restriction (FGR), making up 72.55 % of cases. CMA identified chromosomal abnormalities in 38.37 % of samples, with numerical anomalies in 16.86 % and structural anomalies in 21.51 %. Turner syndrome (5.8 %) and various trisomies (5.8 %) were frequent numerical anomalies. Mosaicism and LOH were observed in 11.04 and 2.91 % of cases. WES detected pathogenic or likely pathogenic mutations in 21 genes (e.g., KCNQ1, KCNE1, COL1A2, ROBO1) in 18 cases, adding a 10.46 % diagnostic yield. K-means clustering grouped 17 of these genes into three pathways: chondrocyte differentiation, fibrin clot formation, and Ehlers-Danlos syndrome. Combining CMA and WES provides a diagnostic yield of 48.83 %, offering a powerful approach to uncover genetic causes of pregnancy loss and guide clinicalcare.

The broad genetic heterogeneity of neurodevelopmental disorders (NDDs) makes their molecular diagnosis particularly challenging. In this context, Whole-Exome Sequencing (WES), specifically in a trio-based design, is a powerful strategy due to its ability to detect de novo variants, which are a major contributor to NDDs. However, its clinical implementation is often limited by its associated cost. In this study, we applied a sequential diagnostic workflow to a cohort of 221 individuals with syndromic NDDs and prior negative results from targeted sequencing. The workflow integrates initial solo-WES, followed by a second-tier trio-WES using pooled parental DNA (trio pooled-WES). Overall, this workflow achieved a diagnostic yield of 20.98% and led to the identification of 13 novel candidate genes. The pooling strategy was optimized and validated, demonstrating that trio pooled-WES retains the main advantages of conventional trio-WES while substantially reducing sequencing costs. These results support its implementation as a clinically applicable approach for the genetic diagnosis of NDDs.

Epilepsy is a common neurological disorder with a strong genetic basis, most frequently arising from ion channel dysfunction. Although multiple inwardly rectifying potassium (Kir) channels have been implicated in epileptogenesis, the contribution of KCNJ4, which encodes the Kir2.3 channel, has not previously been established in human epilepsy. The present study aimed to identify pathogenic KCNJ4 variants and to elucidate their functional consequences in the context of epilepsy. Trio whole exome sequencing was performed in four unrelated individuals with refractory epilepsy and neurodevelopmental abnormalities. Identified KCNJ4 variants were evaluated for rarity and inheritance patterns. Functional consequences were assessed using two-electrode voltage-clamp recordings in Xenopus laevis oocytes coexpressing wild-type or mutant Kir2.3 together with Kir2.1. Protein expression levels were examined by Western blot analysis to exclude effects attributable to altered channel expression or trafficking. We identified four rare heterozygous missense variants in KCNJ4 (Gly136Ser, Val206Met, Met293Lys, and Glu384Lys), all of which were absent from public population databases. Clinically, affected individuals exhibited a broad phenotypic spectrum ranging from isolated epilepsy to severe developmental and epileptic encephalopathy. Electrophysiological analyses revealed variant-specific functional alterations; the Gly136Ser and Glu384Lys variants significantly increased inwardly rectifying potassium currents, consistent with gain-of-function effects, whereas the Val206Met and Met293Lys variants markedly reduced current amplitudes, indicating loss of function. These functional changes were independent of channel protein expression levels. Our findings establish KCNJ4 as a novel epilepsy-associated gene and demonstrate that both gain- and loss-of-function mechanisms of Kir2.3 can contribute to epileptogenesis. This study expands the genetic landscape of epilepsy and highlights the critical role of inward-rectifier potassium channel regulation in neuronal excitability, with potential implications for mechanism-based therapeutic strategies.

Multicystic mesothelioma (MCM) is a rare disease and there is debate about it's neoplastic nature with a spectrum of disease behaviour and little known about the genomic profile. In contrast, the genomic profile of malignant peritoneal mesothelioma (MPeM) is characterised. We characterized 24 MCM and 18 MPeM cases across a panel of cancer related regions and expanded to whole-exome sequencing for 11 MCMs. Validation by amplicon sequencing and functional assessment by molecular dynamic simulation were carried out. Kaplan-Meier analysis was carried out to assess recurrence-free survival. Few mutations were identified in MCMs across the panel. Exome sequencing revealed 28 genes mutated in >1 MCM case. We saw significant overrepresentation of mutations in the cohesin complex in SMC3, SMC1A, and STAG3. Multiple mutations in SMC3 at codon p.E1144 indicated a mutational hotspot. Molecular dynamics simulations showed mutation at this site impacts the protein function. Amplicon sequencing confirmed hotspot mutations in further MCMs. We observed a significant association (p = 0.0302) of mutation in SMC3 or SMC1A with disease recurrence. We see recurrent somatic mutations in MCMs particularly at a novel mutational hotspot in SMC3, consistent with a neoplastic process. Mutations in cohesin complex genes are associated with disease recurrence.

Heterozygous variants in SLC12A6 have recently been shown to cause dominant Charcot-Marie-Tooth disease (CMT). We aim to characterise the phenotype of patients with previously reported and novel heterozygous variants in the gene and understand any genotype-phenotype correlation. Patients were clinically and genetically assessed in sites from Europe, Australia, Brazil and the USA. All patients underwent whole exome or whole genome sequencing. Variants were classified using American College of Medical Genetics and Genomics criteria. Twenty-three individuals from 13 families carried nine variants classified either as pathogenic/likely pathogenic or variants of uncertain significance segregating in multiple family members, including five novel variants. Forty-eight percent (11/23) were male with a mean age of disease onset of 15.7 years (range 1-45 years). Clinical phenotype varied dramatically with genotype; Arg207His and Ser647Pro caused a severe childhood-onset, sensory and motor, conduction-slowing neuropathy, whereas Gly552Asp caused a mild, adult-onset, sensory-predominant neuropathy, Thr991Ala an infantile-onset motor neuropathy, and the Met282Lys/Gly286Cys locus a complex, axonal neuropathy. Heterozygous variants in SLC12A6 can cause CMT of all clinical phenotypes, severity and age of onset, depending on the genotype. Such phenotypic diversity has not been described for any other CMT gene, and more work is needed to understand disease mechanisms to guide future therapeutic options.

Colon cancer is genetically heterogeneous, necessitating standardized genomic analyses for cross-cohort comparisons. While The Cancer Genome Atlas (TCGA)-colon adenocarcinoma (COAD) is a widely used dataset, its comparability to other ethnically different populations remains unclear. This study systematically compares the genomic characteristics of TCGA-COAD and ChangKang, a Chinese colon cancer cohort, using an identical data-processing pipeline to minimize methodological biases. Whole-exome sequencing data from both cohorts were uniformly processed to analyze five key genomic features: tumor mutation burden (TMB), microsatellite instability (MSI), significantly mutated genes, mutational signatures, and copy number variation (CNV). Samples were classified into hypermutated and non-hypermutated subgroups for further comparisons. The TCGA-COAD cohort exhibited a higher overall TMB, driven by a greater proportion of hypermutated samples. However, the hypermutated subgroup of the ChangKang cohort included more ultramutated cases with POLE exonuclease domain mutations, leading to a higher subgroup TMB. MSI was more prevalent in TCGA-COAD, while significantly mutated gene frequencies varied, with lower APC and ACVR2A mutation rates in the ChangKang cohort. CNV patterns were largely similar, though CNV frequencies were higher in TCGA-COAD. Despite differences in subgroup distributions and mutation frequencies, the overall genomic characteristics of colon cancer remain consistent between these ethnically different cohorts. This suggests that cross-population analyses are feasible when standardized processing methods are applied. This study provides a systematic, unbiased comparison of TCGA-COAD and the Chinese ChangKang cohort, demonstrating that the genomic characteristics remain largely consistent across ethnically distinct populations.