Journal of Medical Genetics

BackgroundHeterozygous c.283+1G>A and c.283G>A variants in the THRB gene, encoding for thyroid hormone receptor (TR){beta}1 and {beta}2, lead to autosomal dominant macular dystrophy (ADMD). We report the detailed clinical characterization of two first-degree relatives with ADMD, heterozygous for THRB c.283+1G>A, and an unrelated ADMD patient with a novel variant, c.283G>C. The genomic and molecular consequences of both variants were studied. MethodsgDNA and mRNA were obtained from leukocytes. Clinical characterization included biochemistry, bone density and body composition, ECG, echocardiography, ultrasound, audiometry and color-vision. In vitro assays investigated TR function and DNA binding. ResultsThe patients manifested no resistance to thyroid hormone beta (RTH{beta}) and had normal FT4 and TSH. Detailed studies in two patients showed no goiter, tachycardia, hypercholesterinemia or hepatic steatosis. Hearing was not impaired. Both had impaired color vision and reduced bone density. RT-PCR from all three patients revealed skipping of exon 4 exclusive to TR{beta}1, producing a deletion of 87 amino acids in the N-terminal domain (TR{beta}1{Delta}NTD). In vitro, DNA-binding affinity of TR{beta}1{Delta}NTD to DR4-TRE with or without RXR was comparable to TR{beta}1WT. Surprisingly, TR{beta}1{Delta}NTD was transcriptionally twice more active than TR{beta}1WT with a similar EC50 for T3, demonstrating gain-of-function of TR{beta}1{Delta}NTD. THRA expression in leukocytes was increased by 3-fold compared to unrelated controls and different from RTH{beta} patients. ConclusionThese THRB splice site variants produce TR{beta}1 exon 4 skipping, resulting in a gain-of-function mutant, TR{beta}1{Delta}NTD. This explains the dominant ADMD phenotype devoid of RTH{beta} and suggests a TR{beta}1 gain-of-function syndrome.

PURPOSE To evaluate cancer risk, age-specific penetrance, and mortality associated with heterozygous pathogenic or likely pathogenic (P/LP) germline PALB2 variants identified through genomic ascertainment and to assess modification by family history of cancer. PATIENTS AND METHODS We conducted a case-control study in two large population-based adult cohorts: the UK Biobank (n=469,580) and Geisinger MyCode (n=167,050). Individuals with heterozygous PALB2 P/LP variants were identified via exome sequencing and compared with non-carriers. Cancer diagnoses and vital status were obtained from linked registry and electronic health record data. We used multivariable logistic regression to estimate odds ratios (ORs) for cancer outcomes and Cox proportional hazards models to estimate hazard ratios (HRs) for all-cause mortality. Age-specific cumulative incidence (penetrance) was estimated using Kaplan-Meier methods. Models were adjusted for birth year, sex (when applicable), smoking status, and body mass index; stratified analyses assessed modification by family history of cancer. RESULTS PALB2 P/LP variant prevalence was 1:571 in UK Biobank and 1:940 in MyCode, with the higher prevalence in the UK cohort driven by the PALB2 p.Trp1038Ter founder variant. Compared with non-carriers, heterozygotes had significantly increased odds of any cancer, female breast cancer, pancreatic cancer, and cancers of ill-defined or secondary sites in both cohorts (P < 0.01). Adjusted hazard ratios for any cancer and female breast cancer ranged from 1.7 to 3.6. All-cause mortality was increased among PALB2-heterozygotes (HR 1.61-1.67), and survival after cancer diagnosis was reduced. Family history further modified cancer risk. CONCLUSION Genomic ascertainment of PALB2-heterozygotes identifies elevated risk for multiple cancers and increased mortality, although risks were lower than estimates from familial ascertainment. These findings inform risk management for individuals identified through genomic screening.

Introduction: Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital malformation with complex etiology involving both genetic and environmental factors. Epigenetic mechanisms may mediate environmental contributions, but separating genetic from environmental effects remains challenging. Methods: We present an epigenome-wide association study with 32 monozygotic and 22 dizygotic twin pairs discordant for NSCL/P on blood and saliva samples. Differential methylation analysis was conducted using linear models to identify CpG sites showing significant methylation differences between affected and unaffected twins followed by functional annotation and pathway enrichment analysis. Results: The top-ranked finding is a differentially methylated region comprising two CpG sites at the CYP26A1 locus, cg12110262 (P = 3.21x10-7) and cg15055355 (P = 1.39x10-3). CYP26A1 is essential for retinoic acid catabolism and craniofacial patterning. The chromatin regulator ANKRD11, which causes KBG syndrome featuring cleft palate was the second best hit. Differentially methylated CpG sites showed significant enrichment in craniofacial enhancers and overlap with multiple GWAS-validated cleft genes including VAX1, PVRL1, SMAD3, and PRDM16. Conclusions: Our findings implicate retinoic acid signaling and chromatin regulation in NSCL/P etiology and demonstrate the value of discordant twin designs for distinguishing environmental from genetic epigenetic contributions to complex malformations.

Abstract Background Understanding the phenotypic spectrum of disease-associated genes is essential for accurate diagnosis and targeted therapy. FRMPD4 (FERM and PDZ Domain Containing 4) has previously been associated with intellectual disability and epilepsy. However, its potential role in non-syndromic hearing loss has not been explored. Methods We performed genetic analysis in two unrelated families presenting with non-syndromic sensorineural hearing loss, identifying maternally inherited missense variants in FRMPD4. Clinical phenotyping included audiological assessment and evaluation for neurodevelopmental involvement. Cross-species expression analyses were conducted in Drosophila, zebrafish, and mouse. Functional characterization included quantitative evaluation of sound-evoked responses in Drosophila nicht gut hoerend (ngh) mutants, assessment of neuronal development and acoustic startle responses in zebrafish loss of function models, and morphological cochlear analyses with auditory brainstem response measurements in knockout mice. Results Three affected males from two unrelated families presented with prelingual, bilaterally symmetrical sensorineural hearing loss, with confirmed congenital onset in one individual and no evidence of neurodevelopmental abnormalities. Cross-species analyses demonstrated evolutionarily conserved expression of FRMPD4 in auditory structures. In Drosophila, quantitative analysis of sound-evoked responses in ngh mutants revealed impaired auditory function. Zebrafish loss of function models exhibited reduced neuronal populations in the otic vesicle and posterior lateral line, abnormal neuromast development, and diminished acoustic startle responses. In mice, Frmpd4 knockout resulted in high-frequency hearing loss and cochlear abnormalities consistent with the human phenotype. Conclusions Our findings expand the phenotypic spectrum of FRMPD4 to include non-syndromic sensorineural hearing loss and establish its evolutionarily conserved role in auditory function. These results have direct implications for genetic diagnosis and variant interpretation in patients with hearing loss.

1.Study questionDo singletons conceived by medically assisted reproduction (MAR) experience an elevated incidence of childhood cancers and are they at a greater risk of such cancers compared to naturally-conceived singletons? Summary answerWe found no strong evidence the adjusted risk of childhood cancers is increased for MAR-conceived singletons. What is known alreadyThere is longstanding concern children conceived via MAR may be at increased risk of childhood cancer. Current epidemiological evidence does not support such a relationship. Study design, size, durationWe conducted a retrospective population-based cohort study of 5,104,121 singletons born in Australia between 1991 and 2019. Median follow-up time varied from 4 to 10 years depending on mode of conception. Participants/materials, setting, methodsWe linked birth records to public medical insurance data of the mother to ascertain MAR conception. We classified treatment as ovulation induction/intrauterine insemination (OI/IUI) or assisted reproductive technology (ART; IVF/ICSI), with ART coded as either fresh embryo transfer or frozen embryo transfer. The cohort included 4,924,354 naturally-conceived singletons and 179,767 singletons conceived via MAR. We calculated standardised incidence ratios (SIRs) to ascertain differences in population incidence of childhood cancer, and generated hazard ratios (HRs) using flexible parametric survival models controlling for key confounders. We report absolute incidence and risk differences for both statistical approaches. Main results and the role of chanceThere was no increase in the incidence or risk of all childhood cancers combined for singletons conceived via MAR, either any MAR or specific MAR types. There was some evidence the incidence of leukemias, myeloproliferative diseases, and myelodysplastic diseases was increased after ART compared to the general population (SIR: 1.32, 95% CI 1.02-1.68; equating to 2.09, 95% CI 0.13-4.44 extra cancers per 100,000 person-years), but no increased risk after adjusting for available confounders (HR: 1.04, 95% CI 0.73-1.46). These cancers showed increased incidence and risk for those conceived via IVF (SIR: 1.54, 95% CI 1.01-2.26; HR: 1.77, 95% CI 1.06-2.95), but not ICSI (SIR: 1.27, 95% CI 0.83-1.85; HR: 0.76, 95% CI 0.48-1.22). Incidence of renal tumours was elevated after IVF (SIR: 2.37, 95% CI 1.02-4.67; equating to 1.83, 95% CI 0.03-3.99 extra cancers per 100,000 person-years) and frozen transfer ART (SIR: 2.52, 95% CI 1.09-4.97; equating to 2.12, 95%CI 0.12-5.53 extra cancers per 100,000 person-years), however risk was not elevated after adjusting for available confounders (HR: 1.06, 95% CI 0.47-2.38; and HR: 1.63, 95% CI 0.73-3.61 respectively). Limitations, reasons for cautionWe did not have information on parental cause of infertility, which could be a confounder for childhood cancer, although we did adjust for parental history of cancer. For many specific cancer types, fewer than 50 cases were observed in total. Given the number of comparisons reported and closeness of the lower-bound confidence interval to 1, we cannot exclude that a significant association between conception via IVF and leukemias, myeloproliferative diseases, and myelodysplastic diseases reflects a type I error. Wider implications of the findingsOur findings align generally with published meta-analyses on the risk of childhood cancers following MAR conception and reinforce the need for very large studies to increase confidence. Parents who have conceived via MAR and their offspring can be reassured there is not strong evidence the treatments increase the overall incidence or risk of childhood cancer. Study funding/competing interest(s)This work was funded by the National Health and Medical Research Council (NHMRC: APP1164852). Dr ARW declares that their involvement in this work was supported by employment at UNSW Sydney. Prof CMV declares payment to their institution from the National Health and Medical Research Council (APP1164852). Prof NH declares payment to their institution from the National Health and Medical Research Council (APP1164852); royalties and licenses for Berek and Hackets Gynecologic Oncology (Walters Kluwer); royalties and licenses for Hacker and Moores Essentials of Obstetrics and Gynecology (Elsevier); consulting fees from Darwin Hospital and Gold Coast University Hospital; support for attending the British Gynaecological Cancer Society meeting in Aberdeen, UK, Jun 2023; support for attending the Symposium on Gynaecological Cancer in Budapest, Hungary, Nov 2023; support for attending the International conference of the Rajiv Gandhi Cancer Centre in Delhi, India, Mar 2025; and membership of the Medical Advisory Committee for TruScreen (Australia and New Zealand). A/Prof SO declares that they received payment to their institution from the National Health and Medical Research Council (APP1164852); they received a grant from the European Society for Human Reproduction and Embryology (Open call 2022) including payment to their institution; and that they are a member of the Advisory Board of the Cervical Screening Program in Norway through The Norwegian Institute of Public Health (NIPH), for which they were reimbursed travel expenses to their institution. Prof MC declares support for Theramex European Society for Human Reproduction and Embryology registration and Fertility Society of Australia and New Zealand registration and accommodation. A/Prof USD declares that her involvement in this work was supported via an Early Career Fellowship from the Cancer Institute NSW (ID: 2020/ECF1163) and employment at UNSW Sydney. A/Prof USD also declares payment to their institution from the National Health and Medical Research Council (APP2035240) and the Medical Research Future Fund (APP2032214; APP2038377), and the Australian Research Council (DP240100072) as well as current grants from NSW Health, Prince of Wales Hospital Foundation, and unpaid involvement as an Associate Editor for the "Journal of Psycho-Oncology Research and Practice". Prof LJ declares payment to their institution from the National Health and Medical Research Council (APP1164852). Prof RJN declares they are the Chair of the Clinical Advisory Committee, Westmead Fertility; External mentor at VinMec hospital; Editorial Editor at the journal "Fertility and Sterility"; and has received funding from the National Health and Medical Research Council (NHMRC) for the NHMRC Centre for Research Excellence in Womens Health in Reproductive Life (CRE WHiRL). A/Prof CS declares stock or stock options associated with CSL Ltd, Sigma Healthcare Ltd, Resmed Inc, Medical Developments International Ltd, Vitrafy Life Sciences Ltd, Intuitive Surgical, and Steris PLC. Prof GMC declares payment to their institution from the National Health and Medical Research Council (APP1164852). Prof CV declares payment to their institution from the National Health and Medical Research Council (APP1164852); research grants receive from Merck KGaA and Ferring; payments for honoraria from Merk Ltd, Merk Sharpe & Dohme, Ferring, Organon, Gedeon-Richter for being an invited lecturer in scientific meetings/conferences on multiple occasions as well as member of advisory boards for these companies who have a commercial portfolio in the field of assisted reproduction technology (ART); and speaking fees from IBSA, Vianex, Sonapharm; travel support for their participation in scientific meetings/conferences both nationally and internationally, usually as an invited speaker for the following companies - Merck Ltd, Merck Sharpe & Dohme, Ferring, Organon, Gedeon-Richter; unpaid involvement as a Board member of the Hellenic Society of Fertility and Sterility, Member of the Editorial Board of the journal "Human Reproduction", Senior Deputy of the Coordination Committee of the Special Interest Group "Reproductive Endocrinology" of the European Society for Human Reproduction and Embryology, Member of the Editorial Board of the journal "F&S Reviews", Member of the Editorial Board of the journal "RBM Online", Member of the Editorial Board of the journal "Reproductive Biology & Endocrinology", Member of the Editorial Board of the journal "Frontiers in Endocrinology", and Member of the Editorial Board of the journal "Reproductive Sciences". SubjectReproductive epidemiology

Objective The decline of the perinatal demise rate is slowing and demises are often unexplained. Significant research has been done regarding diagnostic yield and genetic causes of demise, but little is known about how Geneticist involvement impacts outcomes. The goal of the study was to evaluate post-mortem genetic testing practices and effects of the geneticists involvement. Methods Retrospective data from 111 perinatal demise cases was examined, including rates of prenatal genetic counseling, post-delivery genetics consult, genetic testing, and autopsy investigation. Results In this cohort 54% received genetic testing and 25% received a genetics consult. When compared to those without, cases with genetic specialist involvement were associated with significant increases in testing uptake (p=0.007), diagnostic yield (p<0.001), and patient education (p<0.001). Second trimester stillbirths and those with fewer ultrasound (US) abnormalities were less likely to receive genetic testing (both p values <0.001) and consults (p<0.001, p=0.020). Conclusion Though it was not possible to avoid ascertainment bias, this data demonstrates that geneticist involvement correlates with a higher rate of testing, greater diagnostic yield, and more thorough counseling. These findings underscore the importance of integrating genetics providers into perinatal postmortem healthcare teams.

Introduction Lung cancer is rare before age 45, and its inherited genetic basis remains poorly defined. Methods We performed whole-genome sequencing in 171 predominantly young-onset lung cancer patients and integrated these data with whole-exome sequencing from six major lung cancer consortia, yielding 9,065 patients. After quality control, analyses focused on 6,545 individuals of European ancestry, the largest ancestral group. We compared the prevalence of rare pathogenic and likely pathogenic (P/LP) germline variants between 186 young-onset (age <45 years) and 6,359 older patients at gene and gene-set levels using Fisher's exact test, stratified by histology, sex, and smoking status. Polygenic risk scores (PRS) derived from common variants were also evaluated. Results Young-onset patients carried a higher burden of rare germline P/LP variants in DNA damage response (DDR) genes (including BRIP1, ERCC6, MSH5), and in cilia-related genes, notably GPR161. At the pathway level, DDR genes were significantly enriched (OR=1.66, p=0.007), with the strongest signal in the Fanconi Anemia pathway and among females (OR=1.96, p=0.01). Enrichment was also observed in inborn errors of immunity pathways, with strongest signals in antibody deficiency and the complement system genes. Young-onset patients additionally exhibited higher lung cancer PRS. Conclusion Young-onset lung cancer exhibits a distinct germline genetic architecture, characterized by enrichment of rare P/LP variants in DDR, cilia-related, and immune pathways, and an elevated lung cancer PRS. These findings support a greater role for inherited susceptibility in early-onset disease and have implications for risk stratification, earlier screening, and precision prevention.

Despite autism's prominent genetic etiology and early-life origins, parsing genetic effects contributing to the condition into those that operate directly (via allelic transmission to offspring) vs. indirectly (via influencing prenatal environment) remains challenging. We examined this using a novel design leveraging 3-generation family linkage in Danish national registers. The cohort included all children born in Denmark from 1998-2015 and their relatives identified through 3-generation family linkage. The analytic sample comprised full maternal cousin pairs, including parallel (children of mother's sister) and cross cousins (children of mother's brother). Exposures were diagnoses in the index mother previously associated with offspring autism; the outcome was autism diagnosis in cousins of the index child. We used Cox proportional hazards models to estimate associations separately in parallel and cross cousins, followed by comparisons of these hazard ratios to infer mechanisms. Several maternal diagnoses (e.g., postpartum hemorrhage, personality disorders, epilepsy) were associated with autism in both parallel and cross cousins, consistent with shared direct genetic effects. Other conditions (e.g., false labor, recurrent major depressive disorder, other anxiety disorders, systemic connective tissue involvement) showed stronger associations in parallel than cross cousins, supporting additional indirect genetic effects operating through the prenatal environment. Adjustment for the same diagnosis in the cousin's own mother did not substantially change estimates, providing no evidence for an additional role of non-genetic mechanisms associated with the diagnosis. These findings suggest that both direct and indirect genetic effects contribute to observed links between maternal health and offspring autism, highlighting etiologic heterogeneity and highlighting a registry-based family design to separate these pathways without genetic data.

Loeys-Dietz syndrome (LDS) is an autosomal dominant connective-tissue disorder caused by genetic variants in TGF-{beta} pathway genes, most often TGFBR1/2. While pathogenic TGFBR2 genetic mutations usually cluster in the kinase domain and disrupt SMAD signalling, distinguishing with confidence those with functional impact on TGFBR2 function from rare benign genetic alterations represents one of the most important ongoing challenges for accurate genetic testing. Therefore, there is a pressing need to develop methods that can improve functional variant interpretation. Here, we describe and characterize the functional impact of a novel genetic variant in the TGFBR2 kinase domain (E431K), in a patient with the clinical diagnosis of syndromic genetic aortopathy. We assessed the structural and functional consequences of this variant using AI-driven molecular modelling and in vitro cell-based assays. A high-quality homology-based model of TGFBR2 was generated and computational mutagenesis based on the structural context and evolutionary conservation was used to forecast variant pathogenicity. Relative to wild type, the variant affects protein stability by disrupting intramolecular interactions and likely induces conformational changes that may affect kinase activity and thus TGF-{beta} signalling. This was experimentally confirmed by showing abnormal protein level and alteration of canonical TGF-{beta} pathway activation. Overall, our results establish that the E431K variant leads to aberrant TGF-{beta} signalling and confirm the diagnosis of Loeys-Dietz syndrome type 2 in this patient.

Hormone replacement therapy (HRT) with oestrogen and progestogen is a common medical treatment for alleviating symptoms of menopause. Since 2015, its use has been increasing in the UK. Unscheduled bleeding can be a symptom of endometrial cancer, and guidelines state that women experiencing this should have an urgent referral for suspected endometrial cancer. However, unscheduled bleeding is also common in women taking HRT, particularly in the first few months after starting HRT or if there is a change in regimen. Current guidelines may result in women on HRT receiving referrals that are not necessary and undergoing unpleasant and invasive tests such as hysteroscopy. However, there is a lack of current information to guide recommendations. This protocol describes a cohort study in the ORCHID-e database of anonymised patient records from English primary care. We will use a cohort of women aged over 40 years starting on HRT with oestrogen and progestogen, age matched to women who have not started HRT. Exposure will be a prescription for oestrogen containing HRT with no previous prescription for oestrogen containing HRT in the previous year. Index date in each matched set will be the date of this prescription. Prescriptions for progestogen containing drugs will not be used to define the exposure, but this information will be extracted to describe the study population and for sensitivity analyses. Outcomes will be consultations for unscheduled bleeding, urgent referrals for suspected endometrial cancer, and diagnosis of endometrial cancer. Women will be followed up until they change exposure status or are otherwise censored. Women who start taking HRT in follow-up will re-enter the cohort in the exposed group. We will describe proportions of women with a code for consulting with unscheduled bleeding, proportions of those women referred for further investigation on the pathway for suspected endometrial cancer, and proportions diagnosed with endometrial cancer within one year of referral. We will investigate the diagnostic accuracy of unscheduled bleeding for endometrial cancer separately for women on HRT and those not on HRT. Analyses will be done by 6-month categories of time since index, age, calendar year, sociodemographic variables, risk factors for endometrial cancer, type of HRT.

Background: Facioscapulohumeral muscular dystrophy (FSHD) is a common hereditary neuromuscular disorder. The Russian FSHD Patient Registry was established in 2019 following the development of a PCR-based method for genetic confirmation of the diagnosis. Results: The registry included 470 participants (51% male). Genetic confirmation was obtained for 76% (n=356), the remainder were included based on clinical and anamnestic data. Clinical assessment forms and patient-reported questionnaires were analyzed for 310 and 142 patients, respectively. D4Z4 repeat unit (RU) distribution showed patterns consistent with European cohorts, with a predominance of patients with 3 RUs. A moderate inverse correlation was found between RUs number and clinical severity scales. Periscapular weakness was the most common onset manifestation (46.8%), followed by facial weakness (31.6%) which was often unnoticed by patients. The mean age in the Russian cohort was 37.8 years (range 0-97), indicating a younger cohort compared to international data. A delta-adjusted cluster analysis (n=215) identified three distinct trajectories: a classic phenotype with onset before age 14 and early involvement of various muscle groups (n=177), and two clusters characterized by either facial or periscapular onset with slow progression. Conclusion: The Russian FSHD registry provides a comprehensive characterization of a large national cohort, revealing a predominance of patients with 3 D4Z4 repeats and a younger demographic profile compared to international data. Cluster analysis identified three heterogeneous disease trajectories, offering a framework for improved patient stratification.

The etiology of autism is influenced by genetic and non-genetic factors, with observational studies suggesting associations between early maternal health diagnoses and offspring autism. However, these associations may partly reflect shared familial genetic liability rather than direct causal effects. Using comprehensive national health registers and individual-level genetic data from the iPSYCH cohort (N=117,542), we examined whether maternal health diagnoses are associated with offspring polygenic scores (PGS) for autism. Such associations between maternal health and offspring autism would indicate shared genetic factors and the possibility of genetic confounding in the observational associations. We also tested such associations with PGSs for other neuropsychiatric and neurodevelopmental conditions that are genetically correlated with autism, but with better-powered PGS (due to larger GWAS sample sizes and likely more polygenic genetic architecture), as well as height, a negative control. Several maternal diagnoses were nominally associated with autism PGS in the child, including, e.g., certain obstetric complications, asthma, and obesity. After adjustment for multiple testing, the only statistically significant results included those between maternal diagnoses, predominantly psychiatric, and other neuropsychiatric and neurodevelopmental PGSs in the child. Sensitivity analyses confirmed the robustness of our results across exposure windows, diagnostic settings, and socioeconomic adjustments. These findings indicate that maternal diagnoses associated with autism partially reflect shared genetic liabilities between mothers and their children. However, such genetic effects, as captured by child PGS do not fully explain the observed associations, suggesting additional factors, including e.g., non-genetic familial factors, rare variants, and indirect effects.

Importance: NGLY1 (N-Glycanase 1) Deficiency is an ultra-rare autosomal recessive disorder affecting ~165 patients worldwide, characterized by developmental delay, hyperkinetic movement disorders, and shortened life expectancy. Despite its severe neurological manifestations, comprehensive neuroimaging characterization has been limited to case reports and small descriptive studies. Objective: To investigate alterations in brain morphology in patients with NGLY1 Deficiency and determine whether these metrics associate with clinical phenotypes. Design, Setting, and Participants: This case series analyzed real-world MRI scans performed on 11 patients with NGLY1 Deficiency between 1999-2023 at sites across the globe. Ages ranged from 2 to 19 years at scan time (5 female, 6 male). Exposure: Molecular diagnosis of NGLY1 Deficiency. Main Outcomes and Measures: Cortical and subcortical morphology, including subcortical volume, and cortical thickness, surface area, volume, and curvature, were measured with 3-dimensional T1-weighted magnetic resonance imaging (MRI) scans. Z-scores were calculated using normative models from CentileBrain for patients >3 years old or custom models for patients <3 years old. Clinical phenotypes were matched to Human Phenotype Ontology codes. Results: 16 scans from 11 patients met quality criteria for analysis. Both age groups (under and over 3 years old) showed significantly reduced subcortical volumes, particularly in bilateral thalamus and putamen. Younger patients demonstrated widespread reductions in cortical surface area, volume, and curvature, indicating altered gyrification patterns. Older patients showed thinner dorsal and thicker ventral cortical regions with limited surface area reductions. Thalamic volume reduction in older patients correlated with gait disturbance, dysphagia, and EEG abnormalities, with additional cortical associations with sleep and hearing abnormalities. Seizure presence in younger patients correlated with altered cortical thickness, surface area, and curvature patterns. Conclusions and Relevance: NGLY1 Deficiency is associated with pervasive alterations in brain development affecting both subcortical and cortical morphology. Age-dependent patterns of cortical alterations indicate disrupted neurodevelopmental trajectories that may reflect impaired neuronal migration and/or altered synaptic pruning. Correlations with clinical variables suggest that these measures may serve as useful biomarkers for tracking disease progression and/or treatment efficacy. These findings provide a comprehensive neuroimaging characterization of NGLY1 Deficiency and establish a foundation for understanding brain structure-function relationships in this ultra-rare disorder.

Background: Diagnosing the over 700 known rare bone diseases (RBDs) is inherently challenging and often requires extensive time and multiple clinical visits. Effective treatment, particularly for RBDs with approved therapies, depends on early and precise identification of the specific RBD type. Image recognition artificial intelligence (AI) has the potential to significantly enhance diagnostic processes and improve patient outcomes. Many of these disorders cause characteristic skeletal changes, especially in the hands, and are associated with growth abnormalities. Consequently, affected children routinely undergo hand radiographs for bone age assessment, making these images a widely available yet underutilized diagnostic resource. Materials and Methods: We retrospectively compiled 5,623 multi-institutional hand radiographs from 2,471 patients with 45 different RBDs and 1,382 unaffected controls. We trained two deep learning models: a binary classifier to differentiate between RBD and non-RBD hand radiographs, and a multi-class classifier covering ten RBDs (or RBD groups), using 5-fold cross-validation. Preprocessing included masking, normalization, and data augmentation. Additionally, we applied occlusion sensitivity mapping to visualize class-specific features and evaluated the learned representations through cosine-based retrieval and UMAP projections of the feature space. Results: The affected versus unaffected classifier achieved a balanced accuracy of 85.5% on the test dataset. The ten-class classifier reached a balanced (top-1) accuracy of 76.6%, with top-3 accuracy exceeding 90%. Disorders with highly distinctive phenotypes, such as achondroplasia, achieved accuracies above 95%, whereas phenotypically overlapping disorders, such as ACAN- and SHOX-related short stature, were more frequently confused. Feature space analysis showed that validation samples clustered closely with their respective training distributions, supporting the consistency and generalizability of the learned embeddings. Conclusion: This manuscript presents a proof of principle for the development of Bone2Gene, a next-generation phenotyping (NGP) tool for the detection and differential diagnosis of RBDs, currently based on hand radiographs. Ongoing efforts focus on expanding the dataset to include additional RBDs or RBD groups in the current multi-class classifier for differential diagnosis and to further evaluate its generalizability. The Bone2Gene study is open to collaboration.

Background: Despite strong evidence from controlled trials, uncertainty remains about the real-world use of 0.05% atropine in patients with lighter irises due to tolerability concerns, and predictors of treatment response are poorly understood. Here, we evaluated the effectiveness, tolerability, and early biometric response to 0.05% atropine in clinical practice among patients with predominantly light irises. Methods: This prospective cohort study included 33 patients treated with 0.05% atropine (82% with light irises). Cycloplegic spherical equivalent refraction (SER) was measured at baseline and 3-month intervals. Axial length (AL), photopic pupil diameter, accommodation amplitude, and subjective side effects were monitored more frequently initially. Results: Median age at treatment initiation was 11.97 years, SER -5.38 D, and AL 25.42 mm. Over 12 months, SER changed by -0.078 {+/-} 0.349 D (mean {+/-} SD), and AL increased by 0.052 {+/-} 0.115 mm. Eighty-eight percent of participants had a SER change of <0.5 D, and 91% had axial elongation of <0.2 mm, indicating clinically limited myopia progression. Photopic pupil diameter was larger, and accommodation amplitude was reduced throughout follow-up. Early in treatment, side effects, including photophobia and near-work difficulties, were common but minimally disruptive. Their incidence decreased rapidly and rarely required treatment modification. In exploratory analyses, early AL changes predicted 12-month AL outcomes, with associations detectable as early as 1 week and strengthening over time. Conclusions: 0.05% atropine was well tolerated and effective in this population with light irises. Early AL changes may predict 12-month treatment response. These findings support the implementation of 0.05% atropine in routine clinical practice in populations with light irises and highlight the potential for early AL monitoring to guide timely treatment adjustments.

Background: Saudi Arabia bears a disproportionate burden of autosomal recessive genetic disorders, driven by consanguineous marriage rates of 50 to 58% and elevated carrier frequencies for conditions such as sickle cell disease (carrier rate up to 25%), betathalassemia (12%), and spinal muscular atrophy (6%). The existing premarital screening program screens for only two conditions. We developed SafeGene, a computational platform that expands predictive genetic screening to 50+ conditions using region specific population genetics. Methods: SafeGene integrates five risk calculation engines: (1) Mendelian inheritance models for AR, AD, XR, and XD conditions; (2) Hardy Weinberg equilibrium based carrier probability estimation using Saudi, Gulf, and global databases; (3) a six level consanguinity coefficient calculator (F = 0 to 1/8) with risk amplification multipliers; (4) multifactorial polygenic risk models for 12 complex diseases; and (5) maternal age dependent trisomy risk curves. Built using React.js, Node.js/Express, and MongoDB with bilingual Arabic/English support. Results: The platform encompasses 50 genetic conditions across 12 categories. Validation against published Saudi data demonstrated concordance with observed disease frequencies. Economic modeling projects that expanding screening could prevent 2,800 to 4,200 affected births annually, yielding savings of SAR 1.2 to 2.8 billion ($320 to 746 million USD) per year. Conclusions: SafeGene represents a scalable, evidence-based digital health solution for comprehensive genetic screening addressing the unique population genetics of consanguineous Gulf societies. The platform is protected under pending patent applications in South Africa (CIPC) and Saudi Arabia (SAIP).

Genetic counselling outcome measures are increasingly adapted for diverse clinical contexts. While the Genetic Counselling Outcome Scale (GCOS-24) is available in Swedish, no autism-specific version has been developed. Therefore, we adapted the Swedish GCOS-24 using the English version of the modified GCOS-24 (mGCSOS-24) to create a Swedish autism-specific mGCOS-24. Thereafter, we evaluated both the Swedish autism mGCOS-24 and the Swedish general GCOS-24 using Rasch analysis to assess their psychometric properties. Both instruments exhibited structural challenges, including multidimensionality, disordered thresholds, local item dependence, and invariance issues. For the Swedish autism mGCOS-24, we were able to identify subscales with acceptable measurement properties. However, applying the same structure to the Swedish general GCOS-24 did not resolve its broader limitations. This study introduces the first Swedish autism-specific mGCOS-24 and represents the first Rasch-based evaluation of any GCOS-24 or mGCOS-24 in Swedish. Our findings highlight important opportunities for measure refinement but also indicate that new or more substantially adapted tools may be needed to capture outcomes of genetic counselling in autistic populations.

Background: Idiopathic pulmonary fibrosis (IPF) is a rare disease with a poor prognosis. Disease risk involves rare and common genetic variants. However, an inverse association have been described between them. Accordingly, IPF patients with a higher polygenic risk score (PRS) for IPF are less likely to carry rare deleterious variants and vice versa. Here, we evaluate weather PRS of IPF could serve as an additional criterion to patient prioritisation for rare variant discovery. Methods: We identified carriers based on the presence of rare qualifying variants (QVs) in genes linked to monogenic forms of pulmonary fibrosis in 888 IPF patients from the Pulmonary Fibrosis Foundation Patient Registry (PFF-PR). Genome-wide association study (GWAS) summary statistics from independent cohorts were used to construct a whole-genome PRS (WG-PRS) using a clumping and thresholding method (C+T) and a Bayesian method (SBayesRC). PRS were also derived from 19 known common sentinel IPF variants (Sentinel-PRS). Logistic regression models were used to evaluate associations between PRS and carrier status. Discriminatory performance was evaluated using area under the curve (AUC) analysis, and comparisons were made with DeLong test. Validation was performed in 472 IPF individuals from the UK PROFILE cohort. Results: IPF-PRS were strongly associated with the QVs carrier status: Odds Ratio [OR] 0.65 (95% Confidence Interval [CI] 0.53-0.79) for WG-PRSC+T, OR 0.71 (95% CI 0.59-0.86) for WG-PRSSBayesRC, and OR 0.77 (95% CI 0.63-0.94) for Sentinel-PRS. Adding WG-PRS to the patient personal clinical history improved the prediction of QVs carriers: AUC=0.62 for the clinical model, AUC=0.68 for WG-PRSC+T (DeLong test, p=9.54x10-4) and AUC=0.66 for WG-PRSSBayesRC (DeLong test, p=0.02). Adding of IPF-PRS to clinical variables correctly reclassified 22.8% of carriers when using WG-PRSC+T, 20.8% when using Sentinel-PRS, and 16.7% for WG-PRSSBayesRC. WG-PRSSBayesRC and the Sentinel-PRS also demonstrated improved prediction of QVs carriers in telomere-related genes in PROFILE. Conclusions: Incorporating IPF-PRS into a model based on the patient clinical history improves the identification of QVs carriers. Although the overall discriminatory power was moderate, these findings raise de the possibility of using WG-PRS as useful criterion for rare variant discovery in patients with IPF and enhance decision-making.

AimAutistic children have a high but varied prevalence of internalizing and externalizing problems. This study aimed to identify the subtypes of internalizing and externalizing problems among autistic preschool children in Japan, examine their temporal stability, and investigate differences in participation in daily life and family outcomes across these subtypes. MethodsA prospective cohort study was conducted with 275 caregivers of autistic children aged 51-75 months. Internalizing and externalizing problems were assessed using the Strengths and Difficulties Questionnaire. ResultsLatent transition analysis identified five subtypes: Low-symptom, High-emotional, Externalizing, Comorbid, and Peer-difficulty groups. Membership in the High-emotional and Externalizing groups was relatively stable over time, whereas the Peer-difficulty group showed frequent transitions to subtypes with higher levels of internalizing or externalizing problems. Significant differences in participation in daily life and family outcomes were observed across subtypes, but these patterns were inconsistent with a simple gradient of symptom levels. ConclusionsThe novel findings that the temporal stability of subtype membership varied and that differences in participation in daily life and family outcomes were observed across the subtypes suggest that the heterogeneity of internalizing and externalizing problems may be associated with variations in childrens participation in daily life and family outcomes over time. Plain Language SummaryAutistic preschool children often experience emotional and behavioral difficulties, but the way these difficulties manifest varies widely across individuals. This study aimed to identify the patterns of these difficulties, examine how they change over time, and investigate how participation in daily life and family outcomes differ across autistic preschool children. We conducted a study with 275 caregivers of autistic children aged 4-6 years in Japan. From caregiver reports of childrens emotional and behavioral difficulties, five distinct patterns were identified: a group with mainly emotional difficulties, a group with mainly behavioral difficulties, a group with both types of difficulties, a group with relatively low levels of difficulties, and a group characterized primarily by peer-related difficulties. Our findings suggest that different patterns of emotional and behavioral difficulties are associated with differences in childrens participation in daily life and family outcomes. These differences could not be explained simply by the overall severity of difficulties but rather reflect distinct patterns based on the type of difficulty. The results indicate that autistic children face diverse difficulties that change over time.

Genotype-phenotype databases are essential for variant interpretation and disease gene discovery. Genetic variation differs among human populations, mainly in allele frequencies and haplotype patterns shaped by ancestry and demographic history. Population-specific genotypes can influence traits and disease risk; this makes population specific characterization important. Most existing resources focus on the characterization of a population's genetic background, but do not represent the resulting phenotypes. We have developed PAVS (Phenotype-Associated Variants in Saudi Arabia), a curated, publicly accessible database that integrates 5,132 Saudi clinical cases from four Saudi cohorts and 522 cases from analysis of a mixed-population cohort, together with 1,856 cases from the Deciphering Developmental Disorders study (DDD) and 9,588 literature phenopackets. Each case record describes patient-level phenotypes, encoded with the Human Phenotype Ontology (HPO), and links them to genomic variants, gene identifiers, zygosity, pathogenicity classifications, and disease diagnoses mapped to standardized disease terminologies. The data is represented in Phenopackets format and as a knowledge graph in RDF. Additionally, a web interface provides phenotype-based similarity search, gene and variant browsers, and an HPO hierarchy explorer. We evaluate the utility of the phenotype annotations for gene prioritization using semantic similarity. While there are clear differences to global literature-curated databases, phenotypes in PAVS can successfully rank the correct gene at high rank (ROCAUC: 0.89). PAVS addresses a gap in population-specific genotype-phenotype resources and provides a benchmark for phenotype-driven variant prioritization in under-represented populations.