Neurology Genetics

Gross brain findings help guide differential diagnosis, but their diagnostic value across major neurodegenerative diseases remains incompletely characterized. We evaluated whether gross descriptions in autopsy reports could classify cases by final neuropathologic diagnosis. We analyzed 5,613 autopsy cases from the Mayo Clinic Brain Bank collected between 1998 and 2023, including seven diagnostic categories: Alzheimer disease (AD), Lewy body disease (LBD), combined AD and LBD (AD-LBD), frontotemporal lobar degeneration, corticobasal degeneration, progressive supranuclear palsy (PSP), and multiple system atrophy (MSA). A fine-tuned large language model (LLM) converted narrative gross descriptions into semi-quantitative scores for 39 features. Extraction accuracy was 0.95 in 200 manually annotated feature-level test examples. A CatBoost classifier used the extracted scores as input, whereas a second fine-tuned LLM used standardized textual descriptions of the same features. Both classifiers also included age at death, sex, and brain weight. Performance was evaluated in the same held-out test set of 562 cases. CatBoost achieved an accuracy of 0.73, a Cohen's kappa of 0.65, and a macro-average area under the receiver operating characteristic curve of 0.92. The text-based LLM achieved an accuracy of 0.75 and a kappa of 0.68. Macro-average sensitivity was 0.66 for both models. PSP sensitivity was 0.92 with CatBoost and 0.93 with text-based LLM. Corresponding sensitivities were 0.87 and 0.92 for MSA, but only 0.21 and 0.03 for AD-LBD. Feature attribution analysis identified subthalamic nucleus atrophy and putaminal abnormalities as contributors to PSP and MSA predictions, respectively. Narrative gross descriptions contained diagnostic information, particularly for disorders with distinctive macroscopic patterns, whereas combined AD-LBD remained difficult to distinguish.

Background Heterozygous GAA-TTC repeat expansions in the FGF14 gene cause spinocerebellar ataxia 27B (SCA27B), a late-onset cerebellar ataxia (LOCA) increasingly recognized in populations of European ancestry. Objective To characterize the clinical and genetic features of SCA27B and compare its phenotype and progression with those of unexplained idiopathic LOCA (ILOCA) in a large multicenter cohort. Methods We conducted a nationwide multicenter study of patients with unexplained LOCA recruited from 21 Spanish hospitals. FGF14 GAA-TTC repeat expansions were analyzed using a standardized molecular protocol. Clinical, neuroimaging, and longitudinal data were compared between patients with genetically confirmed SCA27B and those with ILOCA. Longitudinal changes in the Scale for the Assessment and Rating of Ataxia (SARA) were analyzed using linear mixed-effects models. Results Among 430 patients with unexplained LOCA, 111 (25.8%) carried FGF14 expansions >250 repeats, and 16 additional patients (3.7%) had intermediate expansions of 200-249 repeats. Including 90 externally recruited genetically confirmed cases, the SCA27B cohort comprised 217 patients. Compared with 283 patients with ILOCA, SCA27B patients had a later age at onset (median 63 vs 55 years, p<0.001), more frequent episodic symptoms (45.2% vs 12.7%), and more frequent oculomotor abnormalities (82.5% vs 71.6%). Downbeat nystagmus was particularly frequent in SCA27B (67.4% vs 32.9%). Conversely, extracerebellar features, including pyramidal and sensory signs, were more common in ILOCA. Among patients receiving 4-aminopyridine (4-AP), subjective improvement was reported more frequently in SCA27B than ILOCA (72.5% vs 36.0%). Longitudinal SARA analysis showed similar rates of progression between groups (SCA27B slope 0.37 vs ILOCA 0.35 points/year; interaction p=0.56). Conclusions SCA27B was a frequent genetic cause of unexplained LOCA in this nationwide Spanish cohort and showed a distinct clinical phenotype characterized by later onset, episodic symptoms, oculomotor abnormalities, and frequent subjective response to 4-AP. Disease progression was similar to that observed in ILOCA. These findings support systematic FGF14 testing in patients with late-onset cerebellar ataxia, particularly those with characteristic clinical features.

Background and Objectives: Deep sequencing of brain tissue in the research setting has established that mosaic variants are a major cause of malformations of cortical development (MCDs) and epilepsy. However, genetic testing in the clinical setting primarily detects germline variants using clinically accessible samples. We aimed to determine the diagnostic yield and clinical utility of deep sequencing in the clinical setting to identify pathogenic mosaic variants for this population. Methods: We performed a retrospective cohort analysis of individuals at Boston Children's Hospital with MCDs with or without epilepsy who received clinical deep sequencing between September 2017 and February 2026. Demographic, clinical, and genetic testing data were abstracted from the medical record. For individuals without systemic features, we classified brain tissue as an affected tissue sample. For individuals with systemic features, we classified brain or relevant non-brain tissue as affected. The primary outcome was the diagnostic yield of clinical deep sequencing performed using affected vs unaffected tissue samples. The secondary outcome was the clinical utility of genetic diagnoses. Results: Our cohort included 37 individuals (19/37 (51%) female, 18/37 (49%) male) with MCDs, of whom 35/37 (95%) had epilepsy (25 with brain tissue samples available from epilepsy surgery) and 8/37 (22%) had systemic features. Most (35/37 (95%)) had dysplasia phenotypes on MRI and 12/27 (44%) with pathology available had Focal Cortical Dysplasia Type I or II. The diagnostic yield was 53% (17/32; 16 mosaic and 1 germline variant) when clinical deep sequencing was performed using an affected tissue sample vs 0% (0/6) using an unaffected tissue sample (p=0.016). Of the diagnosed cases, 13/17 (76%) had testing performed on brain tissue (1 with systemic features) and 4/17 (24%) on non-brain tissue (3 buccal and 1 duodenal tissue, all with systemic features). All but one diagnosis involved the mTOR pathway. All diagnoses had clinical utility. Discussion: Clinical deep sequencing, when performed using an affected tissue sample, has high diagnostic yield and clinical utility for individuals with MCDs, especially dysplasia phenotypes, and epilepsy. Our findings support implementation of clinical deep sequencing for this population, especially as the genetic diagnoses have implications for emerging precision therapies.

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease characterised by progressive motor neuron loss and corticospinal tract degeneration. The genetic landscape of ALS is complex, with increasing recognition of shared genetic and phenotypic features with other neurodegenerative conditions, particularly those involving repeat expansions. Given that repeat expansions in disorders like spinocerebellar ataxia type 27B (SCA27B), caused by an intronic GAA repeat expansion in Fibroblast Growth Factor 14 (FGF14), are recognised to extend beyond cerebellar ataxia with frequent pyramidal signs, we hypothesised that FGF14 repeat expansions might also contribute to ALS and degeneration of corticospinal pathways, and sought to investigate whether repeat length is associated with clinical phenotype. We screened 62 individuals with ALS using PacBio HiFi long-read whole-genome sequencing and compared repeat-size distributions with 256 healthy controls from the Human Pangenome Reference Consortium. Repeat expansions were confirmed using flanking PCR and repeat-primed PCR. We identified pathogenic-range FGF14 GAA [&ge;]250 expansions, the established threshold for SCA27B, in 3/62 ALS cases (4.8%) and none in controls. Further analysis revealed that GAA expansions [&ge;]200 repeats were enriched in ALS compared to controls (8.1% vs 0.4%; p = 0.0013), suggesting a broader pathogenic spectrum for FGF14 GAA repeats in ALS. In contrast, GAAGGA expansions were not significantly associated. Expanded pure GAA alleles were predicted to form triplex (H-DNA) structures, with the repeat-containing isoform (1B) being the predominant FGF14 transcript in motor neurons. These findings demonstrate that FGF14 GAA repeat expansions extend into the motor neuron disease spectrum.

Background Scalable models for Parkinson's disease (PD) genetics in underrepresented populations are needed, as most studies have focused on individuals of European-ancestry, limiting generalisability across ancestral and environmental contexts. Kyrgyzstan has been largely absent from global PD research. Using Kyrgyzstan as a case study, we aimed to develop and evaluate a scalable PD genetics model integrating research and local capacity building. Methods We implemented a stepwise capacity-building framework within a multi-site prospective PD genetics cohort that included participants with PD and controls, with longitudinal follow-up. The framework integrated community engagement, workforce development, specialist clinical services, data governance, clinical phenotyping, biobanking, and genetic data generation. Participants were recruited through a university-affiliated movement disorders clinic and mobile outreach clinics, using a secure electronic data-capture system and Global Parkinson's Genetics Program (GP2)-aligned standards. Feasibility endpoints included recruitment, participation, assessment completeness, and genetic quality-control metrics. Findings Within 20 months, specialist clinical services and a PD registry with biobanking and secure data infrastructure were established, and 1240 participants were enrolled, representing multiple Central Asian ethnicities, including Kyrgyz, Uzbek, Uyghur, Tatar, Kalmyk, and Dungan, and the country's rural-urban distribution. High participation coincided with community engagement and recruitment through mobile clinics and community outreach. Interpretation Embedding capacity building within active research enabled rapid development of neurogenetic and specialist clinical infrastructure in a resource-limited setting. This programme provides a potentially transferable model for equitable inclusion of underrepresented populations in PD genetics and related neurogenetic research in low- and middle-income countries. Funding This project was supported by the Global Parkinson's Genetics Program (GP2; https://gp2.org). GP2 is funded by the Aligning Science Across Parkinson's (ASAP) initiative and implemented by The Michael J. Fox Foundation for Parkinson's Research (MJFF).

Background: The Progressive Supranuclear Palsy Clinical Deficits Scale (PSP-CDS) is a brief rating scale of clinical severity in PSP. However, its longitudinal performance has not been evaluated. We aimed to assess the ability of the PSP-CDS to track disease progression over time and to compare progression across PSP phenotypes in a real-world Asian cohort. Methods: Patients who met the Movement Disorder Society PSP diagnostic criteria and underwent at least 2 PSP-CDS assessments were recruited from movement disorders clinics in Malaysia. Longitudinal progression was evaluated using linear mixed-effects models. Domain-specific progression and subtype-specific trajectories were also analyzed. Associations between annualized changes in PSP-CDS and Barthel Index (BI) scores were examined. Results: 104 patients (including 59 with PSP-Richardson's syndrome [PSP-RS], 28 with predominant parkinsonism [PSP-P], and 14 with progressive gait freezing [PSP-PGF]) contributed 394 PSP-CDS assessments over a median follow-up of 33.2 months (range, 8.7-73.1 months). PSP-CDS scores increased significantly over time ({beta}=0.126 points/month), corresponding to estimated increases of 1.13 points over 9 months and 2.27 points over 18 months. Subtype-specific analyses demonstrated the fastest progression in PSP-RS (0.156 points/month), followed by PSP-PGF (0.081 points/month) and PSP-P (0.077 points/month). Exploratory domain-level analyses showed that finger dexterity, communication, and dysphagia were the most rapidly worsening domains. Annualized PSP-CDS progression correlated significantly with annualized decline in BI scores (Spearman's {rho}=-0.474, P<0.001). Conclusions: The PSP-CDS is sensitive to longitudinal disease progression in PSP and captures clinically-meaningful functional decline. Its brevity and ability to distinguish differential progression across PSP phenotypes support its utility as a pragmatic outcome measure for routine clinical practice and research.

Background and Objectives: Vascular contributions to cognitive impairment and dementia (VCID) represent the second leading cause of dementia and a common comorbidity for reduced functional capacity in many individuals, but clinical management and clinical trial readiness are severely hindered by extreme phenotypic and mechanistic heterogeneity. This study establishes the baseline clinical, functional, and multimodal biomarker characteristics of the first United States (US) cohort of Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL), serving as a single-cause, monogenic small vessel disease model for sporadic VCID. Methods: Cross-sectional analysis of baseline data collected from October 2022 through January 2025 from a longitudinal cohort at 12 US enrollment sites. Adults from families with a documented NOTCH3 variant were recruited through clinical referrals, medical record review, advocacy organizations, and community outreach. Exclusion criteria included other conditions that prevented interpretation of findings and modified Rankin Scale (mRS) scores greater than 3. Central genetic characterization assigned persons with a pathogenic or likely pathogenic NOTCH3 variant to low-, medium-, or high-risk tiers based on epidermal growth factor-like repeat domains. Standardized assessments included clinical histories, exams, objective cognitive and physical assessments, self-reported, companion-reported, and clinician-rated measures, MRI, genetics, and proteomics acquired under harmonized protocols. Group comparisons used Fishers exact and Kruskal-Wallis tests. Multivariable regression used adjustment for age, sex, race, and education. Results: Of 560 participants completing baseline visits, 46 had variants of unknown significance, and 55 had pending genetic analyses. The analytic cohort included 343 persons with a CADASIL-causing NOTCH3 variant and 116 non-carrier family controls. Median age was 47.9 years (IQR 38.7-59.1), median education was 16 years (IQR 14-17), 62.5% were female, and 91.4% were White. Carriers were classified in CADASIL risk tiers: low (7.0%), medium (18.4%), or high (74.6%). Compared with controls, adjusted odds of classification into a more impaired CDR category were higher in all tiers (OR 2.55-5.08, 95% CI 1.22-11.34). Discussion: The US CADASIL Consortium has established a large, genetics-confirmed cohort spanning presymptomatic to moderate disease stages, providing a robust, harmonized platform to define early biomarker signatures and endpoints for targeted VCID therapies.

Importance: With emerging gene-targeted therapies in amyotrophic lateral sclerosis (ALS), gene discoveries and genetic diagnoses provide a crucial path to treatment. Pathogenic variants with moderate effect or incomplete penetrance, however, remain unidentified in genome-wide association studies and can appear sporadic in small modern-day pedigrees. Lack of recognition of familial clustering of ALS, in turn, limits opportunities for gene discovery, genetic diagnosis, risk counseling, and treatment. Objective: To determine the power of automated reconstruction of extended pedigrees, integrating archive records and genetic relatedness, in gene-discovery studies. Design: Retrospective observational study of Dutch ALS patients with the C9orf72 hexanucleotide repeat expansion (HRE), combining clinical family history, civil records, and genome-wide genotyping for relatedness and identity-by-descent (IBD) inference. Setting: National, population-based ALS cohort from the Netherlands and digitized population archives enabling systematic reconstruction of extended pedigrees. Participants: Individuals with ALS and a confirmed C9orf72 HRE. Participants must have provided a clinical family history and traceable Dutch ancestry documented in population archives. Main Outcomes and Measures: The primary outcome was the proportion of C9orf72 HRE carriers with newly identified (distant) relatives with ALS compared with clinical family history. The secondary outcome was the precision of IBD-based methods to fine-map the C9orf72 HRE. Other outcomes included phenotypic similarities between distantly related patients. Results: Among 238 C9orf72 HRE carriers, 91 could be included in one of 39 extended pedigrees dating back to ~1800, with relationships up to the eighth degree of relatedness. Compared with clinical family history alone, our approach increased the number of identified relationships by 2.5-fold. Genome-wide IBD analysis revealed shared haplotypes encompassing the C9orf72 HRE in 94% of pedigrees by [&ge;]7 meioses in 25.7-127.8 centimorgans total IBD shared. Conclusions and Relevance: Large-scale interrogation of archives facilitates reconstruction of extended pedigrees for ALS patients carrying the C9orf72 HRE. This combined genealogical-genetic approach supports the reclassification of apparently sporadic cases, facilitates the discovery of new disease-causing variants in ALS, and is generalizable to other late-onset neurodegenerative diseases. Automated pedigree reconstruction from genealogical data and visualization in an interactive databrowser are implemented in the open-source Mangrove software.

The C9orf72 hexanucleotide repeat expansion (HRE) is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). It follows autosomal dominant inheritance in families, however, a high proportion of cases are sporadic, raising the possibility of parental premutation. We have demonstrated that intermediate-length alleles (IAs) with >18 repeats (allele frequency ~1%) belong to the same pool of haplotypes as the HRE, suggesting shared ancestry. Here, we tested whether alleles with >18 repeats expand in parental transmission. We used two repeat-primed PCR methods to analyze allele lengths in 539 genetically unselected parent-offspring pairs and in 152 pairs known to carry the SNP (rs139185008*C) that tags >18 repeat IAs and the HRE in Finland. We discovered intergenerational repeat length changes only in >20 repeat alleles. A significant (P = 0.0059) sex bias in 6-40 repeat alleles was noted using a logistic regression model. In this allele range, 12 out of 16 expansions were paternally inherited and 6 out of 7 contractions were maternally inherited. The expansion rate of 20-40 repeat alleles was 34 % in paternal and 11 % in maternal transmissions. In the 20-40 repeat range, most intergenerational expansions were 1-4 repeats in size (15/16), but one larger jump, a paternal expansion from 27 to 73 repeats, was observed. These results demonstrate that alleles with >20 repeats have an increased likelihood of instability, that a paternal expansion bias is observed in alleles with 20-40 repeats, and that expansion events are predominantly 1-4 repeats in size.

Familial recurrence of amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD) is the clinical cornerstone for assuming Mendelian, monogenic inheritance which informs genetic testing, counselling and gene-discovery strategies in standard practice. Polygenic inheritance can lead to familial clustering of ALS, while pathogenic variants with reduced penetrance may present sporadically in small, modern-day pedigrees. As both rare genetic variants and polygenic disease contribute to the occurrence of ALS, the accuracy of a positive family history to predict the underlying genetic architecture remains unknown. Using growing knowledge of the genetic architecture of ALS, we designed the APECS simulator: a large-scale pedigree simulator using historical demographic parameters, unifying frameworks for monogenic and polygenic disease models. We simulated 1,000,000 three-generation pedigrees and modelled ALS, FTD, and other dementias under both inheritance models. For index patients with ALS, we examined the performance of proposed familial ALS (fALS) definitions to predict the underlying genetic architecture. Simulation results were benchmarked against real-world population estimates, over a wide range of demographic and genetic parameters. We assessed the phenocopy rate for monogenic index patients, defined as relatives with polygenic ALS or a pathogenic allele from a different ancestor. Finally, we illustrated the value of distant relatedness among apparently sporadic, but monogenic ALS patients. Simulations generated 55.3 million individuals, yielding 5,431 ALS-affected index patients (16.4% monogenic). The proposed criterion for 'definite fALS' (2 or more relatives with ALS among relatives within two degrees) had a 31.1% sensitivity, while falsely classifying 10.0% of 'fALS' as monogenic. The sensitivity of 'definite fALS' was improved to 43.3% when also considering relatives with FTD. Considering any type of dementia raised the false positive rate to 35.9%. In total, 5.3% of monogenic index patients had a phenocopy with ALS in relatives up to the third degree. Of seemingly sporadic monogenic index patients, 83.1% had distant relatives with ALS/FTD up to the fifth degree. A family history provides limited accuracy for inferring genetic architecture in ALS. Considering unspecified dementias in the family history reduces this accuracy, while adding definite FTD improves accuracy. Relying on traditional fALS criteria risks both missing cases for genetic testing and treatments, and falsely alarming families with polygenic ALS. Given the limited value of a family history and risk of phenocopies, routine genetic testing regardless of family history and systematic approaches for detecting distant relatedness will help to find known and novel genetic causes in ALS.

Background: Hereditary spastic paraplegia (HSP) comprises a heterogeneous group of neurodegenerative disorders characterized by progressive lower-extremity weakness and spasticity, with or without additional neurological symptoms. Objectives: To characterize the molecular genetic spectrum, inheritance patterns, molecular finding rate, and clinical characteristics of HSP within a multicenter Canadian cohort. Methods: We investigated 671 patients from 423 families who met clinical criteria for HSP identified through the Canadian HSP (CanHSP) registry from 7 medical centers across Canada. Patients were evaluated using known HSP and HSP mimic gene panels, whereas unsolved and more recent patients underwent whole-exome sequencing (WES). 435 individuals underwent gene-panel testing and 485 underwent WES. Copy-number variants (CNVs) were assessed using ExomeDepth, and candidate CNVs using multiplex ligation-dependent probe amplification (MLPA). Results: Molecular findings were identified in 426 of 671 individuals (63.5%): 351 (52.3%) had HSP-associated findings, 70 (10.4%) HSP-mimicking disorders, and five (0.7%) other molecular findings; 245 (36.5%) remained unresolved. Candidate variants were found in 80 relevant genes, 36 of which were HSP-associated genes. The most frequently implicated genes were SPAST (22.5%), SPG7 (5.7%), ATL1 (5.2%), SPG11 (3.6%), and SPG8 (3.3%). Phenotypically, SPAST, ATL1, and SPG8 w[zg1.1]ere predominantly associated with pure HSP, whereas SPG7 and SPG11 more often showed complicated phenotypes, with prominent cerebellar involvement in SPG7 and cognitive and developmental features in SPG11. Conclusion: Patients in CanHSP present with genetic and phenotypic heterogeneity. Reanalysis and complementary approaches, including whole-genome, RNA, and long-read sequencing, may increase diagnostic yield.

ABSTRACT Introduction: Incomplete penetrance and variable expressivity characterize autosomal dominant neurological disorders, but their genetic determinants remain largely unknown. DYT-TOR1A dystonia provides a model for investigating incomplete penetrance. We aimed to identify modifiers of disease penetrance and severity beyond the known TOR1A c.646G>C modifier. Methods: In a prospective genotype-phenotype association study, we phenotyped Ashkenazi Jewish carriers of TOR1A c.907_909del using a prespecified five-level severity score. The primary analysis compared participants with no or minimal dystonia (scores 0-1) and severe dystonia (scores 3-4), after excluding c.646G>C carriers. Findings were assessed in an independent retrospective cohort. Sanger, exome, and short-read and long-read whole-genome sequencing were used for genotyping. Results: The prospective cohort included 61 carriers: 21 had severe dystonia and 28 had no or minimal dystonia, six of whom carried c.646G>C. Among the 43 participants in the primary analysis, haplotype A was identified in 33 (77%) and haplotype B in eight (19%). All haplotype B carriers had no or minimal dystonia (p=0.003). Haplotype B remained associated with a milder phenotype after including 12 participants with intermediate severity (p=0.006). The retrospective cohort included 147 carriers, 16 of whom carried c.646G>C. After their exclusion, dystonia manifested in 12 (38%) of 32 participants with haplotype B and 63 (64%) of 99 without it (p=0.009). Haplotype B was also associated with lower severity scores (p=0.011). Together, c.646G>C and local haplotype status predicted the phenotype of more than two-thirds of carriers. In silico analyses linked haplotype B to lower TOR1A and higher TOR1B expression in dystonia-relevant brain regions. Conclusion: A common local haplotype in trans to the disease-causing TOR1A variant was strongly associated with reduced penetrance and severity. These findings establish DYT-TOR1A dystonia as a model for investigating how local genetic variation contributes to incomplete penetrance in autosomal dominant neurological disorders.

Background: Parkinson disease (PD) is a genetically complex neurodegenerative disorder, but most genetic discoveries have been derived from populations of European ancestry, limiting the understanding of ancestry-specific genetic risk. Methods: This GWAS included 5,825 East Asian participants (3,043 patients with PD and 2,782 controls). We then combined these results with data from two additional East Asian cohorts through meta-analysis, resulting in a total of 74,716 participants (15,603 patients with PD and 59,113 controls). To our knowledge, this represents the largest genetic study of PD in East Asian populations to date. Findings: We identified two novel loci that were associated with PD in East Asian cohorts and reached genome-wide significance in the cross-ancestry meta-analysis (>1.9 million subjects): TLE4 (lead variant rs10780320, Pmeta_combined = 2.853 x 10^-10) and HLA-V/HLA-G (lead variant rs11751333, Pmeta_combined = 1.031 x 10^-9). Integration of brain eQTL data identified an East Asian-specific intergenic variant at the LRRK2 locus (rs1388594) that was significantly associated with LRRK2 expression in the basal ganglia. This association was replicated across three independent East Asian cohorts (Pgp2_EAS = 8.71 x 10^-4, Psg_EAS = 1.13 x 10^-5, PTPMI_EAS = 4.86 x 10^-4) and reached genome-wide significance in the East Asian meta-analysis (Pmeta_EAS = 5.85 x 10^-10; OR = 1.10, 95% CI: 1.07-1.13). The variant was not associated with PD in populations of European ancestry (P = 0.08). Interpretation: These findings improve our understanding of the genetics of PD across ancestry groups and highlight the importance of including diverse populations in genetic studies to identify ancestry-specific risk variants.

Several polyglutamine-encoding repeat expansions cause spinocerebellar ataxias (SCAs) and other movement disorders. SCAs are genetically heterogeneous with a substantial diagnostic gap. We used genome sequencing data from 266 individuals of European and Asian ancestry and screened genome-wide for repeat expansions using STRling, a dedicated repeat expansion caller. The cohort comprised patients with movement disorders, predominantly dystonia and ataxia, as well as unaffected participants. Further, we screened another 436 individuals with ataxia and 427 ethnically matched controls through fragment analysis of the most promising candidate locus in EP400. We applied targeted long-read sequencing to expansion carriers and one control individual to resolve the sequence structure of the repeat locus. Finally, we used microsatellite markers in chromosome 12q24.32-33 to test for a common founder. A genome-wide outlier analysis in STRling revealed a polyglutamine-encoding repeat expansion (GRCh38 chr12:132,062,525-132,062,590) in the E1A binding protein p400 (EP400) gene in two patients with ataxia. Through screening of additional ataxia patients, we identified in total 18 patients from 14 families with heterozygous repeat expansions in EP400. All expansion carriers were from Serbia. The repeat number in affected individuals ranged from 37 to 55, whereas the longest control allele had 32 repeats. We demonstrated that non-expanded alleles carried a CAA interruption within the 5-prime CAG tract; this interruption was lost in expanded alleles. Expansion carriers have pure SCA with onset mainly in their 40s and 50s. There is an inverse correlation between the number of repeats and age at onset. The EP400-encoded protein plays an essential role in chromatin remodeling, epigenetic regulation and DNA repair. Pathogenic sequence variants in EP400 have previously been implicated in a neurodevelopmental disorder. Our study identifies repeat expansions in EP400 as a novel and frequent cause of ataxia in Serbian patients. This finding further increases the diagnostic yield of ataxia testing and warrants investigation in ataxia patients worldwide. We add EP400 to the growing list of ataxia-associated repeat loci, which warrants inclusion in diagnostic ataxia panels.

Parkinsons disease (PD) arises through disruption of multiple interconnected cellular processes, but the genetic contributions to these processes may differ across ancestries. We investigated functional convergence among genes harboring pathogenic or likely pathogenic (P/LP) variants and variants of uncertain significance (VUS) in a multicenter Indian cohort recruited through the Genetics of Parkinsons Disease in India Young Onset Parkinsons Disease project (GOPI YOPD). The cohort included 668 participants (463 males 69.3%) with a mean age at motor onset of 39.4+/-8.8 years. P/LP variants and VUS identified through previously reported whole-exome or whole genome sequencing were retained as separate evidential categories. The P/LP-associated gene set comprised 11 unique genes and the VUS associated set comprised 40 unique genes. Separate STRING functional-enrichment analyses evaluated Gene Ontology Biological Process, Molecular Function and Cellular Component terms, KEGG pathways, WikiPathways and STRING local network clusters. Terms meeting a Benjamini Hochberg false discovery rate threshold of <0.05 were organized into eight non-mutually-exclusive ontology/pathway categories. Gene to pathway mappings were subsequently projected to individual participants to estimate pathway representation and examine clinical associations. At least one reportable P/LP variant or VUS was identified in 336/668 participants (50.3%): 35 had a P/LP variant alone, 282 had VUS alone and 19 had a P/LP variant together with VUS in one or more additional genes. The most frequently represented categories were mitochondrial organization (247/336, 73.5%), autophagy related processes (228/336, 67.9%) and regulation of synaptic vesicle transport (201/336, 59.8%). PRKN was the most frequent P/LP-associated gene, occurring in 29/54 P/LP carriers, followed by PLA2G6 and PINK1. Lysosomal transport was represented exclusively by VUS-associated genes, particularly GBA1, VPS13C and LRRK2. Among P/LP carriers, additional VUS in distinct genes were not associated with age at onset (P = 0.81) or family history (52.6% versus 31.4%; P = 0.15). No pathway phenotype association remained significant after correction for multiple testing. Genetic findings in this Indian cohort converged across an interconnected mitochondrial autophagic lysosomal vesicular network, with different contributions from P/LP-associated and VUS associated gene sets. This study provides the first pathway resolved South Asian genetic profile and a framework for comparative studies across populations.

Objective: In KCNQ2-related disorders (KCNQ2-RD), neurodevelopmental outcome remains variable despite established genotype-phenotype correlations. Our aim is to improve counselling, by developing and internally validating models predicting neurodevelopmental outcomes based on early clinical and genetic features, universally available to clinicians. Methods: We conducted a multicentric retrospective cohort study including 277 individuals carrying a (likely) pathogenic variant in the KCNQ2 gene, with a minimum follow-up age of three years. Mosaic variants were excluded. The cohort was randomly split into training (70%) and validation (30%) sets. Ten expert selected parameters with minimal missing data were used to train random forest models to predict (i) dichotomous outcomes and (ii) three-category outcomes for cognition, language, and gross motor milestones. Results: Models incorporated seven clinical (neonatal hypotonia, EEG characteristics, age at seizure onset, seizure type, and seizure frequency at onset, prematurity, and sex) and three genetic variables (de novo status, exon localisation, and position within known KCNQ2-developmental and epileptic encephalopathy (DEE) hotspot regions). Dichotomous models showed the highest predictive performance, with accuracies of 0.83 for normal vs. mild-profound intellectual disability (ID), 0.83 for achievement of first words, and 0.86 for achievement of independent walking. Three category models remained clinically informative: accuracies were 0.79 for normal vs. mild vs. moderate-profound ID, 0.70 for first words [&le;]16 months vs. >16 months vs. never, and 0.71 for independent walking [&le;]18 months vs. >18 months vs. never. The strongest predictors for adverse neurodevelopmental outcomes were presence of hypotonia at birth, seizure onset within the first day of life, multiple seizures per day at onset, tonic seizures at onset, a burst-suppression pattern on EEG at onset, the presence of a de novo variant, and variant location within exons 6-7. Significance: These prediction models demonstrate the feasibility of early prognostication in KCNQ2-RD and support future prospective external validation. They enable more accurate individualised counselling by integrating clinical and genetic information readily available at time of genetic diagnosis and provide an objective foundation for early intervention planning and future precision medicine trial stratification.

Amyotrophic lateral sclerosis (ALS) is a genetically and biologically heterogeneous neurodegenerative disease in which distinct pathogenic mechanisms operate across patients while overt molecular pathology is confined to only a subset of cells. Such features would act to dilute disease-associated transcriptomic signals and complicate the identification of reproducible molecular signatures across the growing number of ALS single-nucleus RNA sequencing (snRNA-seq) studies. Here, we systematically assessed cross-study reproducibility across four cortical ALS snRNA-seq datasets comprising 140 donors (87 ALS) and tested whether pathology-defined cell states improve detection of conserved molecular signatures. Cell-type annotations were harmonized prior to comparison of cell-type-specific pseudobulk differential expression using gene-level, pathway-level, gene-ranking and alternative polyadenylation analyses. We further examined nuclei exhibiting TDP-43 pathology, identified by expression of the STMN2 cryptic exon. Conventional ALS-versus-control analyses showed limited reproducibility, with minimal overlap of differentially expressed genes or enriched pathways, while fold-change patterns clustered predominantly by study rather than cell type or brain region. Nevertheless, gene-ranking analyses identified reproducible neuronal transcriptional programs, suggesting that biological signal is present but incompletely resolved by current cohort sizes. In contrast, STMN2 cryptic exon-positive nuclei showed substantially greater concordance, revealing robust TDP-43-associated signatures that partially overlapped independent models of TDP-43 dysfunction while also identifying motor cortex-specific changes, including reduced expression of the recently identified ALS risk gene UNC13C. Reproducible ALS-associated alternative polyadenylation changes were not detected, likely reflecting the higher dimensionality and sparsity of polyadenylation site analyses. Together, our findings demonstrate that pathology-defined cell states provide a more reproducible framework for studying ALS transcriptomic alterations than conventional case-control comparisons. We additionally provide an interactive browser to facilitate exploration and comparison of ALS snRNA-seq datasets.

Background and Objectives: X-linked dystonia-parkinsonism (XDP) is a severe neurodegenerative movement disorder caused by a retrotransposon insertion with a polymorphic hexanucleotide repeat expansion in the TAF1 gene. While the disease predominantly affects males, female carriers may exhibit a variable phenotypic expression. Neurobiological alterations in asymptomatic female mutation carriers (fMC) remain largely unexplored. We aimed to investigate whether fMC exhibit neurodegenerative changes despite the absence of overt clinical manifestations and to assess their clinical, genetic, and longitudinal correlates using multimodal MRI. Methods: In this cross-sectional and longitudinal multimodal study, 103 female relatives of XDP patients underwent clinical, genetic, and MRI assessments. Forty-two were identified as fMC and 61 as healthy controls (HC). Structural T1-weighted MRI was analyzed using voxel-based morphometry and subcortical volumetry, while susceptibility-weighted imaging assessed iron deposition. Clinical evaluation included standardized motor and cognitive testing. Longitudinal follow-up MRI was available for a subset of participants (20 fMC, 13 HC). Results: fMC exhibited significant striatal atrophy compared to HC, with volume reductions in the caudate (-19.4%), putamen (-18.6%), and pallidum (-28.6%) (all p<0.001), despite the absence of overt movement disorders or cognitive deficits, accompanied by relative cerebellar hypertrophy. In fMC striatal volumes decreased with increasing age (putamen: rho=-0.382, p=0.012; caudate: rho=-0.631, p<0.001) and virtual time from genetically determined estimated age at onset (putamen: rho=-0.406, p=0.008; caudate: rho=-0.660, p<0.001). Susceptibility-weighted imaging revealed increased iron deposition in the caudate in fMC, which increased with greater local atrophy (rho=0.718, p<0.001). No significant longitudinal progression was detected over follow-up intervals of up to 25.5 months. Discussion: Asymptomatic female carriers of the XDP-associated TAF1 variant exhibit significant striatal neurodegeneration and iron accumulation, indicating a dominant-negative effect despite X-linked inheritance. Future longitudinal studies should focus on non-motor features and integrate genetic, imaging, and clinical markers to improve risk stratification and identify the subset of female carriers most likely to benefit from future disease-modifying therapies.

Tandem repeat expansions (TREs) cause over 50 neurological conditions, yet their contribution to neurodegenerative disease risk at a population scale remains incompletely characterized. We performed a TRE association study across 6,539 short tandem repeat loci in 276,411 individuals from the UK Biobank and 44,370 individuals from the All of Us Research Program, using two composite neurodegenerative phenotypes to increase statistical power and capture pleiotropic effects. Meta-analysis across the two cohorts identified associations at eight established pathogenic TRE loci, including C9orf72, DMPK, HTT, ATXN2, ATXN3, CACNA1A, CNBP, and PPP2R2B, recovering known disease-associated expansions from short-read sequencing data at biobank scale. We also identified candidate associations at three additional loci. An intronic AATAA expansion in DAPK1 reached significance (q = 0.0045), with fine-mapping and conditional analysis supporting the repeat as the likely variant underlying the association. An intronic ATTTT expansion in ANK3 (q = 0.034) was observed exclusively in individuals of African and Latino/admixed American ancestry, underscoring the importance of ancestrally diverse cohorts for genetic discovery. An exonic polyalanine expansion in RPL14 was also significant (q = 0.039), where longer alleles were consistently associated with reduced RPL14 expression across independent datasets. Together, these findings identify candidate risk loci for neurodegenerative disease that may expand the contribution of TREs to neurodegenerative disease beyond known repeat expansion disorders.

Background and objectives: Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL) is the most common monogenic cerebral small vessel disease. Though neuropsychiatric symptoms (NPS) of CADASIL profoundly impact function and quality of life, these symptoms remain understudied. This analysis characterizes the prevalence, severity, and profile of NPS among individuals with CADASIL-causing NOTCH3 variants and non-carrier biological family controls in the United States CADASIL Consortium (USCC). Methods: This cross-sectional analysis used multimodal baseline data from 12 enrollment sites across the country. Statistical analyses used nonparametric tests and regression models to compare clinical and neuropsychiatric outcomes across CADASIL risk tiers and controls, adjusting for age, sex, race, and education where appropriate. The primary outcome measure was the Neuropsychiatric Inventory Questionnaire (NPI-Q), an informant-reported measure which assesses 12 categories of NPS. NPI-Q item severity and distress were evaluated for individuals with confirmed cysteine-altering NOTCH3 variants and compared with controls. Results: Four hundred fifty-nine USCC participants were included in the analytic cohort: 343 cases [256 high-risk (HR); 63 medium-risk (MR); 24 low-risk (LR)]; and 116 controls. Among participants with available NPI-Q data, at least one neuropsychiatric symptom was reported by 72.6% (n = 228/314) of cases compared with 53.2% (n = 58/109) of controls. Reported symptoms were more common among CADASIL cases than controls, occurring in 75.0%, 71.2%, and 72.7% of participants in the LR, MR, and HR groups, respectively, compared with 53.2% of controls. Compared with controls, participants in the MR group and HR group had higher NPI-Q severity scores. HR participants also had higher NPI-Q distress scores than controls. Discussion: Our findings support the notion that NPS are an important clinical manifestation of CADASIL. Beyond previously reported symptoms, additional neuropsychiatric manifestations were identified. Given the higher burden and variability in the neuropsychiatric presentation of CADASIL, the relationships among neuropsychiatric, neurological, and patient-reported outcomes merit further investigation. The NPS profile may enhance the evaluation of the safety and efficacy of different treatments to target these symptoms for CADASIL patients. Trial Registration Information: The study is registered at ClinicalTrials.gov (NCT05677880, 12/12/2022).