Neurology Genetics

Background: PD GENEration (NCT04057794, NCT04994015), sponsored by the Parkinson's Foundation in partnership with Aligning Science Across Parkinson's (ASAP) through the Global Parkinson's Genetics Program (GP2), is an international, observational, clinical research study that offers genetic testing and counseling to people living with Parkinson's disease (PwP) at no cost. PD GENEration has aimed to empower PwP and their clinicians with knowledge of their genetic status, to accelerate recruitment into precision medicine trials, and to advance research through data sharing. Since its launch in 2019, the study has expanded to enroll over 32,000 PwP (as of March 31, 2026), from 10 countries across North, Central, and South America, the Caribbean, and Israel. Methods: Over the course of 6 years, PD GENEration has evolved to accommodate the growing scientific and research needs of the Parkinson's community while also increasing the ability to return genetic test results to PwP at a greater scale. Participants with a diagnosis of Parkinson's disease (PD) may enroll in-person or virtually where informed consent and blood sample collection can occur. Samples are analyzed at a College of American Pathologists/Clinical Laboratory Improvement Amendments (CAP/CLIA)-certified laboratory using whole genome sequencing, with variants curated for a primary panel of seven PD-associated genes. Results are disclosed during a genetic counseling visit, where further testing is offered for two optional additional gene panels. Those who consent undergo analysis of additional genes, and results are returned during a genetic counseling visit for those that test positive for a variant. In addition to returning genetic results to PwP, a central pillar of the study design has been the open sharing of genomic data to advance discovery in PD research in partnership with ASAP and GP2. Discussion: PD GENEration applies a flexible framework, allowing for country specific considerations and the integration of multiple site models, evolving based on participant needs and the prioritization of equity and accessibility. We summarize PD GENEration's implementation and scaling, highlight key accomplishments and lessons learned, and provide guidance for those interested in implementing large-scale clinical genetic testing studies across other diseases and therapeutic domains.

BackgroundHuntington disease (HD) is a neurological disorder caused by an aberrant CAG expansion in the HTT gene, producing a mutant protein (mHTT). Although HD is classically characterized by adult-onset cortical and striatal degeneration, accumulating evidence suggests that altered cortical development may also contribute to disease pathogenesis. ObjectiveWe sought to investigate the impact of mHTT on neocortical patterning, which is a largely unexplored aspect of HD. MethodsUsing the HdhQ140 HD knock-in mouse model, we performed immunofluorescence and in situ hybridization to analyze the patterning of the cortex from embryonic day 10 to postnatal day 7. ResultsDuring embryogenesis, HTT expression exhibited a high medial-to-low lateral gradient in the neocortex, like that observed for key transcription factors involved in cortical patterning. Notably, HTT expression was absent from the cortical hem, a critical patterning center. In HD, the protein gradient remained unchanged whereas the expression in medial pallium seemed increased. During the early development of the cerebral hemispheres, the expression of morphogens and signaling pathways, including Shh, Fgf8, and Wnt/BMP genes, were disrupted in organizing centers, leading to altered expression of major neocortical transcription factors. At postnatal stages, the motor and somatosensory cortical areas were misplaced. These developmental alterations were associated with postnatal sensorimotor deficits relevant to HD. ConclusionsOur findings demonstrate that HD-related neurodevelopmental alterations arise as early as embryonic day 10 in mice. This supports previous work suggesting that defects in brain development contribute to HD pathogenesis prior to clinical onset.

CLN3 disease is an inherited neurodegenerative disease, typically with childhood onset, and characterized by vision loss, seizures, cognitive decline, and difficulties. The CLN3 Staging System (CLN3SS) characterizes disease progression. Our aim was to assess differences in cognitive test scores in relation to CLN3SS among individuals with CLN3 disease. We evaluated the relationship between cognitive test performance and the CLN3SS in individuals with genetically confirmed CLN3 disease. Participants completed tasks of verbal reasoning, vocabulary knowledge, attention, fund of information, and ability to recite the alphabet. One-way ANOVA testing assessed differences in mean cognitive test score among CLN3SS score groups, and Chi-square testing was used to compare the proportion in each CLN3SS group that could recite the alphabet. Data were evaluated from a sample of 85 individuals with a total 245 CLN3SS assessments conducted within 6 months of their cognitive testing, A significant decrease in test scores was found between CLN3SS Stages 1 (vision loss present) and 2 (vision loss and seizures present) for each of the cognitive tests. The proportion of participants able to recite the alphabet also decreased from Stage 1 to Stage 2 (X2=12.1, p<.01). Cognitive ability declines with advanced disease severity in CLN3 disease, though motor disability in Stage 3 likely contributes to difficulty participating in cognitive assessment at this later disease stage. Understanding the relationship between cognition and CLN3 disease stage may help guide decision making, i.e., determining who could or should undergo cognitive assessment for clinical care or for group stratification in disease modifying clinical trials.

BackgroundClassification of central nervous system (CNS) tumors has become increasingly complex over the past decade, raising concerns about the availability, feasibility and sustainability of comprehensive molecular diagnostics. We have evaluated nanopore whole genome sequencing (nWGS) as a single workflow to replace multiple diagnostic assays. MethodsWe performed nWGS on DNA extracted from 90 adult CNS tumor samples (58 retrospective, 32 prospective) and compared the results to findings from standard of care (SoC) diagnostic work-up. Analysis was done through an automated workflow that consolidated diagnostically and therapeutically relevant genomic alterations, including copy-number variation, structural, and single-nucleotide variants, chromosomal aberrations, gene fusions and methylation-based classification. ResultsNanopore WGS enabled final diagnostic classification in all samples with >15% tumor cell content, requiring [~]3 hours of hands-on library preparation, parallel sample processing, and sequencing times within 72 hours. Methylation-based classification was available within 1 hour and was concordant with the integrated final diagnosis in 89% of cases (80/90). All diagnostically relevant copy-number variations, single-nucleotide variants, and gene fusions were concordant with standard-of-care testing, and MGMT promoter methylation status matched in 94% of cases. In addition, nWGS identified prognostic and potentially actionable variants that were not reported or covered by SoC. ConclusionsNanopore WGS delivers comprehensive genetic and epigenetic results with a fast turn-around compared to standard methods. This enables efficient, accurate, and scalable molecular diagnostics of CNS tumors using a single platform. Its broad applicability supports its implementation in routine clinical practice and may be extended to other cancer types requiring complex genomic profiling.

BackgroundPhenoconversion to Parkinsons disease (PD) or dementia with Lewy bodies (DLB) currently relies on established clinical diagnostic criteria. Availability of in vivo biomarkers--CSF -synuclein seed amplification assay (CSFaSynSAA) and dopamine transporter (DAT) imaging--offer the opportunity to investigate congruency between clinical phenoconversion and biologically defined disease. MethodsWe analyzed Parkinso[n]s Progression Markers Initiative participants who phenoconverted to PD, DLB, multiple system atrophy (MSA), Alzheimers disease (AD) or other dementias from prodromal and non-manifesting genetic carrier (NMC) groups and controls. Site investigators determined phenoconversion based on established diagnostic criteria. All phenoconverters with [&ge;]1 annual follow-up visit, with available biomarkers and persistent clinically defined diagnosis at last observation were included. Neuronal alpha-Synuclein Disease Integrated Staging System (NSD-ISS) staging was applied. ResultsAmong 121 phenoconverters, 103 had evaluable CSFaSynSAA and DAT data and were included in analysis: 92 PD, 7 DLB, 2 MSA, 2 AD/other dementias. Phenoconversion annual rates varied widely across groups: iRBD 7.9%, hyposmia 4.2%, GBA1 0.3%, LRRK2 1.3%, LRRK2+GBA1 0.9%, and controls 0.5%. Median time from baseline to phenoconversion ranged from 13-14 months in iRBD and hyposmia to 36-85 months in NMCs. The expected biomarker profile (CSFaSynSAA+/DAT+) for clinically-diagnosed synucleinopathy occurred in 74 (71.8%) participants. Biological alignment (CSFaSynSAA+/DAT+) was present in 87% hyposmics and 72% iRBD phenoconverters. CSFaSynSAA negativity was high among LRRK2 phenoconverters (67%), who also were more likely to have a preserved sense of smell (83%). Phenoconversion occurred later than onset of functional impairment: 15/47 (31.9%) iRBDs and 7/38 (18.4%) hyposmics were already NSD-ISS stage [&ge;]4 at time of phenoconversion. ConclusionsClinical phenoconversion did not necessarily align with biological evidence of synucleinopathy or dopaminergic loss and can be delayed compared to onset of meaningful functional impairment. Longitudinal follow up on converters without biological evidence of PD is required to confirm conversion diagnosis and evaluate for a later occurrence of biomarker positivity.

IntroductionSleep-dependent memory consolidation differs by sex and maybe disrupted by Alzheimers disease (AD) risk. Whether sex moderates associations between apolipoprotein E {varepsilon}4 (APOE {varepsilon}4) status, non-rapid eye movement (NREM) sleep, and memory remains unclear. MethodsEighty cognitively unimpaired older adults completed a word-pair memory task with encoding and immediate testing occurring prior to overnight polysomnography with high-density electroencephalography (hdEEG) and delayed recall occurring after sleep. Sleep-memory associations were examined as a function of sex and APOE {varepsilon}4 status. ResultsIn this sample, a sexxAPOE {varepsilon}4 interaction was associated with overnight memory retention, with female carriers exhibiting less overnight forgetting than female non-carriers and male {varepsilon}4 carriers. NREM sleep differed by sex and APOE {varepsilon}4 status and was associated with memory retention in{varepsilon} 4 carriers. DiscussionThese findings indicate sex-specific, sleep-dependent memory mechanisms associated with genetic AD risk, highlighting sleep as a potential early target for intervention, pending replication in larger samples.

BackgroundRett Syndrome (RTT) is a severe neurodevelopmental disorder affecting approximately 1 in 10,000 live female births worldwide. The Rett Syndrome Behaviour Questionnaire (RSBQ), remains one of the most widely used standardized behavioral assessment tools for RTT. However, the RSBQ was originally validated only in British English, limiting its applicability for Spanish-speaking caregivers and clinical centers across Latin America and Spain. ObjectiveThe primary aim of this study was to develop and validate the comprehension of the Spanish translation of the RSBQ to ensure cultural and linguistic equivalence, enhance data reliability, and facilitate earlier, more accurate clinical assessments among Spanish-speaking RTT populations. MethodsSurveys were administered in two phases to Spanish-speaking caregivers between November 2023 and September 2025. Phase I consisted of 12 guided survey administrations with participants being able to ask clarifying questions and offer linguistic modifications of RSBQ questions. Phase II consisted of independent online administration of the refined Spanish RSBQ and a retest at least 7 days later. Participants were recruited through direct outreach and supported virtually during questionnaire completion. ResultsFollowing data cleaning and quality control, a total of 51 caregivers successfully completed both surveys. The Spanish RSBQ demonstrated high caregiver comprehension and strong engagement across multiple Latin American countries, including Argentina, Mexico, and Peru. Responses were highly correlated between test and retest timepoints, and no question showed biased response distributions. A slight effect of response interval on test-retest correlation was observed, potentially indicating the impact of natural disease progression confounding retest evaluation for long (>80 day) intervals; however this effect did not impact the overall linguistic validation results as analysis of only <21 day test-retest responders confirmed the findings. ConclusionsThis linguistic validation study represents the first formal step toward the clinical validation of the Spanish RSBQ, enabling broader inclusion of Spanish-speaking populations in RTT research. The collaborative, bilingual data collection strategy proved both feasible and effective, paving the way for multinational trials and expanding therapeutic accessibility through localized, patient-centered innovation.

BackgroundParkinsons disease (PD) genetics research has predominantly focused on populations of European ancestry, limiting understanding of disease mechanisms across diverse populations. African-Caribbean communities harbor complex genetic admixture and exhibit distinct clinical features, yet remain underrepresented in PD genetic studies. We investigated ancestry-specific molecular signatures underlying PD using rare variant burden analysis in geographically and genetically distinct cohorts. MethodsUsing a discovery cohort design and gene-based rare-variant aggregation testing, we performed RNA-sequencing on peripheral blood mononuclear cells from 33 participants: Montreal, Canada (n=16; 8 PD, 8 controls) and Guadeloupe, French West Indies (n=17; 9 PD, 8 controls). We conducted gene-based rare variant burden testing, protein-protein interaction network analysis, pathway enrichment, and linkage disequilibrium (LD) profiling. Clinical assessments included MDS-UPDRS, Hoehn & Yahr staging, and evaluation of prodromal and autonomic features. ResultsPrincipal component analysis revealed distinct population structure, with Montreal participants forming a homogeneous cluster and Guadeloupe participants displaying greater variance consistent with African-European admixture. Ancestry-stratified burden analysis identified divergent immune pathway enrichments: IL-17 signaling predominated in PD patients from Montreal (FDR=0.04), while MHC class II antigen presentation and interferon-{gamma} pathways characterized PD patients from Guadeloupe (FDR=1.59x10-). A NOD2 frameshift variant (rs2066847) was identified in 3/8 Montreal patients, providing a mechanistic link to IL-17 pathway dysregulation. LD analysis revealed ancestry-specific haplotype structures, with 14 African-admixed American-specific LD pairs exclusive to Guadeloupe participants and 11 European-specific pairs present in both populations, demonstrating distinct haplotype architectures shaped by ancestry. Clinical differences aligned with molecular findings: Montreal patients showed higher prevalence of REM sleep behavior disorder (71.4% vs 37.5%) and hyposmia (54.3% vs 22.5%), while Guadeloupe patients showed more autonomic symptoms. Control-only comparison showed no pathway enrichments, validating that PD findings reflect disease-associated mechanisms rather than population stratification. ConclusionsTogether, these findings provide evidence for ancestry-specific immune signatures in PD, challenging a one-size-fits-all paradigm in neurodegenerative disease genetics. The identification of distinct molecular pathways underlying clinically overlapping phenotypes suggests PD may encompass multiple molecular entities converging on shared symptoms. These findings emphasize the necessity of ancestry-inclusive research for advancing mechanistic understanding and achieving equity in precision medicine for neurodegenerative disorders.

BackgroundVariants in GBA1 are important genetic risk factors for synucleinopathies, including Parkinsons disease (PD). While several GBA1 variants are established risk or severity modifiers, the role of the p.E427K variant remains unclear. ObjectiveTo determine whether the GBA1 p.E427K variant is associated with risk of synucleinopathies. MethodsWe performed a meta-analysis of case-control studies reporting the frequency of GBA1 p.E427K (p.E388K) in PD and related synucleinopathies. Data were obtained from published studies, open-access resources, and large cohorts, including in-house datasets. Odds ratios (ORs) were calculated for each cohort and pooled using a random-effects model. ResultsAcross 67,484 patients and 124,079 controls, GBA1 p.E427K was associated with increased disease risk (pooled OR = 1.87, 95% CI 1.28-2.72, P = 0.001). Enzymatic data showed reduced glucocerebrosidase activity in carriers. ConclusionsThe GBA1 p.E427K variant is a risk factor for synucleinopathies and should be considered in genetic studies and clinical trials.

BackgroundQuantitative genome-wide association studies (GWAS) primarily rely on additive linear models that compare average phenotypic differences between genotype groups. While effective for detecting common variants of moderate effect in large sample sizes, such approaches inherently reduce high-resolution phenotypic data to summary statistics (group averages), potentially limiting the detection of subtle genotype-phenotype relationships. Genomic Informational Field Theory (GIFT) is a recently developed methodology that preserves the fine-grained informational structure of quantitative traits by analysing ranked phenotypic configurations rather than relying solely on mean differences. MethodsWe applied GIFT to genetic and neuropathological data from the Brains for Dementia Research cohort, a well characterised dataset of 563 individuals, and compared its performance with conventional GWAS. Principal component analysis (PCA) derived matrix was used to derive independent quantitative traits linked to from Alzheimers disease (AD) neuropathology measures (CERAD, Thal, Braak staging), with and without inclusion of age at death. Principal component analyses were performed using GWAS and GIFT frameworks on the same filtered genotype dataset. ResultsBoth GWAS and GIFT identified genome-wide significant associations (pvalue<10-6) within the APOE locus (NECTIN2-TOMM40-APOE-APOC1), demonstrating concordance with established AD genetic variants. However, GIFT detected additional significant 19 SNPs beyond those identified by GWAS. Variants associated with AD pathology implicated genes involved in amyloid processing, neuronal apoptosis, synaptic function, neuroinflammation, and metabolic regulation. Notably, GIFT identified 29 loci associated with age at death-related variation that were not detected by GWAS, highlighting genes linked to lipophagy, mitochondrial quality control, sphingolipid metabolism, frailty, and aging-related processes. ConclusionsGIFT recapitulates canonical GWAS findings while uncovering additional biologically relevant associations. By preserving the fine-grained structure of phenotypic data distributions and detecting non-random genotype segregation across ranked trait values, GIFT enables the identification of associations that remained undetected by traditional average-based GWAS approaches. These results demonstrate that rethinking analytical representation, rather than solely increasing sample size, can expand discovery potential of genetic association studies, offering a transparent and complementary framework for quantitative genomics in deeply phenotyped datasets.

ImportanceAccurate diagnosis of neurodegenerative movement disorders is challenging because of a lack of in vivo biomarkers, overlapping clinical features and a delay in the emergence of pathognomonic features. ObjectiveTo evaluate clinicopathological correlation, diagnostic accuracy, genetic association with pathology, and ancestry-related differences in a multi-ancestry brain bank cohort. DesignMulticentre retrospective autopsy cohort study on donors enrolled between 1985 - 2024. Setting11 academic brain banks in the UK, US and Australia ParticipantsBrain donors identified from participating brain banks with available brain tissue and a clinical diagnosis of Parkinsons disease, Parkinsons disease dementia, dementia with Lewy bodies, progressive supranuclear palsy, corticobasal syndrome, multiple system atrophy, or neurologically normal controls. ExposureGenetic variant carrier status and clinical diagnostic category. Main outcomeClinical diagnostic accuracy; Lewy body and Alzheimers disease pathology burden; survival; association with genetic variants and genetically inferred ancestry. ResultsWe studied 3,353 brain donors (1281 [38.2%] female, mean [SD] age at death, 76.8 [10.6] years). Misdiagnosis rates for movement disorders ranged approximately from 10% - 20%. Clinical diagnoses of dementia with parkinsonism (PDD/DLB) were more strongly associated with Lewy body pathology than Parkinsons disease without dementia (OR = 1{middle dot}96, 95% CI = 1{middle dot}30 - 3{middle dot}04, p = 7{middle dot}2e-04). Lewy pathology was identified in 4% of neurologically normal controls. Alzheimers disease co-pathology was present in 40% of cases with Lewy body disease. GBA1 variant carriers exhibited greater Lewy body burden compared with noncarriers (OR = 1{middle dot}94, 95% CI = 1{middle dot}24 - 3{middle dot}03, p = 0{middle dot}01) or LRRK2 carriers (OR = 7{middle dot}44, 95% CI = 2{middle dot}16 - 25{middle dot}64, p = 0{middle dot}01). Pathological diagnoses differed by ancestry, with South Asian donors more likely to have progressive supranuclear palsy pathology and Ashkenazi Jewish donors more likely to have Lewy body disease (p < 0.0001), independent of GBA1 and LRRK2 mutation status. Conclusion and RelevanceOur findings highlight the value of integrating genetic and pathological data to improve diagnostic accuracy. The high prevalence of Alzheimers disease co-pathology and ancestry-related differences in pathology point to the need for biologically informed diagnostic tools. These results support the integration of genetically and pathologically stratified approaches, correlating pathology with in vivo biomarkers, for future therapeutic trials. FundingMedical Research Council, Global Parkinsons Genetic Program/Aligning Science Across Parkinsons Key PointsO_ST_ABSQuestionC_ST_ABSHow do genetic variants and neuropathology influence clinical features and diagnostic accuracy in movement disorders? FindingsIn this multi-ancestry brain bank series including over 3000 individuals, clinical misdiagnosis was common. Dementia with parkinsonism was more strongly associated with Lewy body (LB) pathology than Parkinsons disease without dementia, and Alzheimers disease co-pathology was frequent. Genetic variation was associated with pathological differences. GBA1 carriers had greater LB burden, while LRRK2 pathogenic variant carriers had a lower LB burden and longer survival. Pathological diagnosis differed by ancestry. MeaningIntegrating genetics and neuropathology may improve diagnosis and support pathology-informed therapeutic trials.

ImportanceDementia is common in Parkinsons disease (PD), causing greater disability than other symptoms, but varies in timing. Although visual deficits are linked with PD dementia, how these interact with genetic factors to predict PD dementia has not been characterised. ObjectiveTo investigate whether visual deficits and genetic factors predict PD dementia. DesignLarge prospective longitudinal case-control study, mean follow-up 32.7 (SD=12.3) months. SettingCases were recruited between 2017-2020 at 35 UK PD clinics. ParticipantsPeople with PD without dementia at baseline were included. Main outcomes and measuresVisual function was measured using a web-based platform. The main outcome measure was global cognition, measured as the Montreal Cognitive Assessment (MoCA). Blood samples were collected for genetics. Results450 patients with PD were included. Mean age of PD patients was 71.7 (SD=7.8), 68% male. Mean baseline MoCA was 27.7 (SD=1.7). 263 patients with PD were classed as poor-vision based on baseline visual tests: mean age 74.4 (SD=6.8) compared to 69.7 (SD=7.5) with good-vision. Poor-vision PD patients had higher rates of progression to mild cognitive impairment (PD-MCI) (HR=2.34, CI=1.58-3.48, pFDR=0.00062, age- and sex-corrected). The combination of genetic factors together with vision influenced outcomes. In good-vision PD patients, high-risk GBA1 gene variants were linked with greater progression to PD-MCI (HR=4.61, CI=1.73-12.28, pFDR=0.0068). Polygenic Risk Score (PRS) for both PD and Alzheimers disease (AD) also modified cognitive survival when combined with vision status. High PD-PRS was associated with greater progression to PD-MCI in good-vision patients (HR=2.66, CI=1.21-5.81, pFDR=0.0381); and high AD-PRS with greater progression to PD-MCI in poor-vision PD patients (HR=1.91, CI=1.10-3.32, pFDR=0.04999). Combining high PD- and AD-PRS, compared to low PD- and AD-PRS in good-vision PD showed even higher progression to PD-MCI (HR=6.14, CI=1.36-27.83, pFDR=0.046). Simulations showed that adding visual and genetic stratification reduced sample size from n=705 to n=160 for clinical trials. Conclusions and relevancePoor vision in PD predicts progression to PD-MCI and dementia. This combines with the effects of genetic factors including GBA risk variants and PD- and AD-PRS. These findings can enable enrichment of clinical trials for patients at higher risk of PD dementia, for more efficient trial design for interventions to slow progression. Key pointsO_ST_ABSQuestionC_ST_ABSDo clinical factors, measured by performance on visual tests, and genetic factors help predict which patients are more likely to develop cognitive involvement in Parkinsons disease? FindingsThis prospective longitudinal study of 450 Parkinsons patients, based in Parkinsons clinics, with mean follow-up 32.7 months, found that Parkinsons patients with poor vision are more likely to develop cognitive impairment; and that genetic factors in combination with poor vision further predict poor prognostic groups for Parkinsons dementia. MeaningThese data could enable selection of Parkinsons patients at highest risk of dementia for clinical trials aimed at slowing Parkinsons dementia.

Background and objectivesA pathogenic GGC repeat expansion in the zinc finger homeobox 3 (ZFHX3) gene, encoding a pure polyglycine tract, is the cause of spinocerebellar ataxia type 4 (SCA4). Intermediate expansions of other SCA loci contribute to the risk of amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease involving the progressive loss of motor neurons. There is increasing awareness of the role of short tandem repeat (STR) motif composition and configuration in disease pathogenicity. Given the genetic pleiotropy between ALS and SCA, this study aimed to evaluate whether ZFHX3 GGC expansions were associated with ALS and to characterise repeat motif composition. MethodsExpansionHunter v5 was used to genotype ZFHX3 GGC repeat sizes in short-read whole genome sequencing data from people with ALS and healthy controls of European ancestry. Repeat sizes were visually inspected using REViewer v2. Repeat motif configurations of Australian ALS cases were manually derived from REViewer images. Receiver operating characteristic (ROC) curve analysis and Youdens J statistic were performed to find a candidate repeat size threshold for association testing using Fishers exact test. ResultsAnalysis of 5,785 people with ALS and 7,982 healthy controls found no association between ZFHX3 GGC repeat expansions and disease risk. However, more than 30 unique repeat motif compositions were identified across 802 people with ALS. Of these, seven distinct configurations coded a pure polyglycine tract which, when expanded, is canonical to SCA4. DiscussionAlthough no association was observed between ZFHX3 GGC repeat expansions and ALS, this study established the dynamic nature of ZFHX3 repeat motif composition and configuration. Unique motif compositions were identified both within and between repeat sizes, including the presence of pure polyglycine repeats in ALS. Consideration of repeat motif composition and configuration, in addition to repeat allele length, may be important for assessing neurodegenerative disease risk.

PurposeAlthough most developmental and epileptic encephalopathies (DEEs) have a monogenic aetiology, routine clinical genetic testing is negative for 50% of patients. We hypothesized that the diagnostic yield could be increased in a large cohort of individuals with unsolved DEEs by applying genome sequencing along with enhanced variant analyses outside of coding regions. MethodsWe performed genome sequencing for 242 participants with DEEs negative on prior genetic testing. We interrogated single nucleotide variants (SNVs), indels, and structural variants in both established and candidate DEE genes. All variants of interest were reviewed, classified, and validated by a multidisciplinary team. ResultsA molecular diagnosis was discovered for 36/242 (15%) participants. The pathogenic or likely pathogenic variants comprised 26 SNVs and indels within coding regions, 9 structural variants, and 5 SNVs and indels in introns or non-coding genes. Variants of uncertain significance were detected in a further 10/242 (4%) participants. ConclusionGenetic diagnostic yield for individuals with unsolved DEEs improves with genome sequencing analysis. This increase reflects both the identification of structural and non-coding variants not detectable on exome or gene panel analysis, and the detection of variants in genes newly associated with DEEs.

Abstract Background Gene dosage disorders impact cognition and psychopathology, but outcomes vary widely amongst carriers of the same variant. Recent work has sought to better predict proband outcomes using measures of corresponding traits in family members. However, family-based models have not yet been prospectively quantified across several traits in different genetic disorders, nor evaluated for the precision they afford: both crucial issues for clinical implementation. Methods In a first test case for these questions, we apply regression analyses to quantify and compare family-based prediction of 12 traits (including IQ, autism- and ADHD-related traits) in 433 individuals from families including a proband with XXY or XYY syndrome (N=93 and 58, respectively). Results The 12 traits vary substantially in their proband-family associations (0.001<|r|<0.55) - with differences emerging between XXY and XYY syndrome. Only two traits also show significant and similar proband-family associations in both aneuploidies, with the greatest concordance found for IQ. A family-based model for IQ prediction in male sex chromosome trisomies significantly reduces error vs. a group mean IQ model (F = 7.4, p = 0.006), but only in 65% of probands, and with mean error reduction of ~2 IQ points. Conclusions Family-based prediction of neuropsychiatric traits in genetic syndromes likely requires trait- and syndrome- specific models. Family models can significantly improve outcome prediction for IQ, but to variable degrees across individuals and with a small mean improvement. By mapping and quantifying these limits, our work helps draft a roadmap for refinement of family-based prediction of proband outcomes in gene dosage disorders.

Background: The Alzheimer's Disease Sequencing Project Gene Verification Committee developed a systematic framework to adjudicate genetic evidence for AD and related dementias, addressing wide variation in association quality. Methods: Phase 1 established tiered criteria by evaluating 23 nominated loci across study designs. Phase 2 applied this framework to 29 large-scale genome-wide studies published since 2015, tiering 163 unique loci. Results: Phase 1 yielded 17 high-confidence loci (12 linked to specific genes), and Phase 2 identified 111 high-confidence loci/genes with replicated associations across ancestries and convergent single-variant/variant-set evidence. Prioritized loci highlight APP processing, microglial immunity, and lipid metabolism pathways, including genes not captured by existing resources like Agora or Open Targets. Summarized results can be viewed at https://topgenes.niagads.org/. Conclusion: This rigorously adjudicated catalog represents the most comprehensive AD/ADRD genetics resource to date, providing a foundation for functional validation and therapeutic discovery with broad applicability to complex diseases.

BackgroundTandem repeat expansions (TREs) cause over 60 known neurological, neuromuscular, and developmental disorders. Detecting these expansions genome-wide is challenging due to their size, sequence complexity (including interruptions), and population variation. While long-read sequencing is an emerging technology that can fully resolve many TREs, no methods have been described for genome-wide identification and prioritization of candidate pathogenic TREs with this technology. MethodsUsing a newly developed pipeline called TRoLR (Tandem Repeat outliers identified with Long Reads), we analyzed haplotype-resolved long-read genome assemblies from 471 ancestrally diverse individuals to define population distributions for over three million tandem repeat loci, capturing clinically relevant interruptions. Outlier expansions were identified relative to these distributions and prioritized by genomic location and comparison to known pathogenic loci. The framework was applied to 47 cases from the Undiagnosed Diseases Network. ResultsPopulation stratification of repeat metrics was observed at 7% of loci, with highest variability among individuals of African ancestry. Outlier analysis confirmed known pathogenic CNBP and ATXN8OS expansions, detected carrier-range alleles at RFC1, CSTB, and FXN, and revealed a novel CGG expansion in the 5 UTR of PCMTD2 exhibiting hypermethylation and intergenerational instability. Genome-wide screening also identified intronic pentanucleotide expansions at IQCB1 and MAP3K15 in controls composed of motifs that have been associated with pathogenicity at other disease loci. ConclusionsQuantifying the longest uninterrupted repeat segment in long-read assemblies enables detection of clinically relevant repeat expansions and loss of stabilizing interruptions. This approach enhances both diagnostic confirmation and discovery of candidate pathogenic expansions, with implications for clinical interpretation and research into complex repeat-mediated disorders.

In the Global Parkinson's Genetics Program (GP2) we aim to advance precision medicine by integrating large-scale clinico-genetic data from diverse populations worldwide. We investigated potentially trial-eligible carriers of pathogenic and high-risk GBA1 and LRRK2 variants and conducted a global precision-medicine survey across GP2 sites. Among 65,509 individuals with Parkinson's disease, we identified 9,019 (13.8%) potentially trial-eligible genetic variant carriers, including 6,789 GBA1, 2,084 LRRK2, and 146 dual GBA1-LRRK2 carriers. Individuals were distributed across multiple global regions, many of which currently lack active gene-targeted trials, highlighting a global disparity between relevant variant carriers and the availability of disease modifying treatment trials. GP2's unified framework supports equitable recruitment for gene-targeted therapeutic studies and helps address critical gaps in Parkinson's disease genetics and future therapeutic development.

Mitochondrial diseases (MDs) are genetically and phenotypically diverse and can be difficult to diagnose. Prevalence estimates derive largely from diagnosed cases and may underestimate population MD risk. Population-based studies are limited in scope and number but indicate MD variants are common. As genomic sequencing advances have made comprehensive population-based evaluation feasible, we sought to evaluate nuclear MD variation in a population cohort to understand variant prevalence and differences in MD risk estimates We identified disease-associated nuclear gene variants in 270 nuclear MD genes across 2,845 healthy older individuals in the Medical Genome Reference Bank. From Pathogenic or Likely Pathogenic Variants (PLPVs) we estimated autosomal recessive (AR) and autosomal dominant (AD) MD risk for individual genes and all nuclear variant-associated MDs. We identified 554 PLPV alleles representing 357 unique variants in 145 genes. Combined AR MD risk was estimated at 25.8 per 100,000 (95% CI 18.7 to 32.9), or 1 in 3,880 individuals. SPG7 (12.65 per 100,000; 95% CI 7.52-20.6) and POLG (4.23 per 100,000; 95% CI 2.10-8.01) contributed the greatest single gene AR MD risks and OPA1 variants posed the greatest AD MD risk. We observed a high rate of MD-associated nuclear gene variation in this healthy older cohort. The estimated lifetime AR MD risk was higher than commonly quoted prevalence estimates for all MDs, and the presence of common AD variants suggests variant penetrance may be lower than previously understood. These data help contextualise population MD risk and may inform clinical counselling and care.

BackgroundWhole-genome sequencing (WGS) has improved the diagnosis of rare genetic disorders, yet interpretation of non-coding variants that affect splicing remains challenging. In silico predictions alone are insufficient, and short-read RNA sequencing may fail to capture complex or low-abundance splicing events. Targeted amplicon-based long-read RNA sequencing (Amp-LRS) offers a cost-effective approach for functional validation of candidate splice-altering variants. MethodsWe applied Amp-LRS to five patients with neurological disorders (central nervous system, peripheral nervous system, or muscle) harbouring candidate non-coding variants predicted to alter splicing. RNA was extracted from fibroblasts or peripheral blood, and full-length transcript amplicons were sequenced using Oxford Nanopore Technologies. Nonsense-mediated decay (NMD) inhibition was performed on fibroblast cultures using cycloheximide. ResultsAmp-LRS validated all five candidate variants, including intronic and UTR variants in POLR3A, OPA1, PYROXD1, GDAP1, and SPG11. Aberrant splicing events included exon skipping, intron retention, cryptic splice site activation, and pseudoexon inclusion, often resulting in frameshifts and premature termination codons. For POLR3A and OPA1, multiple abnormal isoforms arose from single variants, highlighting the complexity of splicing disruption. Some pathogenic effects were detectable only in a minority of reads and variably enriched by NMD inhibition, consistent with being hypomorphic. The approach was successfully applied using accessible tissues and enabled multiplexed sequencing at low per-sample cost. ConclusionsAmp-LRS is a sensitive, versatile, and cost-effective method for functional assessment of non-coding splice-altering variants identified by WGS. By enabling full-length transcript analysis from accessible tissues, this approach improves interpretation of variants of uncertain significance and could enhance molecular diagnosis in rare neurological diseases.