Neurology Genetics

FGF14 (GAA)n repeat expansions are a common cause of idiopathic late-onset ataxia (SCA27B). The cerebellar form of multiple system atrophy (MSA) has comparable clinical features, albeit faster progression. Hence, we performed an analysis of FGF14 genomic variability in a South Korean cohort of 199 patients with probable MSA, compared with 1,048 ethnically-matched controls. All whole genome sequences (WGS) are depicted on a computational genome analysis platform, CGAP, to enable storage, visualization and analysis for partners of the International MSA Coalition. The size of the FGF14 (GAA)n repeat was also assessed by genomic PCR, and by interrogating WGS data using Expansion Hunter (EH) with an extensive catalogue of potential repeats. However, MSA samples were not significantly different to matched Korean controls, and only three MSA patients showed possible abnormal FGF14 (GAA)n expansions >300bp. Nevertheless, as PCR and EH findings were often discordant, a subset of samples with expansions was validated by long-read sequencing. Some intermediate expansions (>150 bp) were found in 6.9% (27/392) of controls compared to 13.4% (46/344) in MSA, though overall our results suggest FGF14 (GAA)n repeat expansions do not influence susceptibility to MSA in Korean patients and highlight challenges inherent in this genetic testing.

ObjectiveTo better understand the pathology of amyotrophic lateral sclerosis, we used sequence data from patients seen at the University of Utah to identify novel disease-associated loci. We utilized both in vitro and in vivo studies to determine the biological effect of patient mutations in MFN2. MethodSequence data for a total of 140 patients were run through VAAST and Phevor to determine genes that were more burdened with rare, nonsynonymous variants compared to control longevity cohort. Variants identified in MFN2 were expressed in Mfn2 knockout cells to determine if mutant MFN2 could rescue mitochondrial morphology defects. We identified additional rare, nonsynonymous variants in MFN2 in ALSdb that were expressed in knockout mouse embryonic fibroblasts (MEFs). Membrane potential was measured to quantify mitochondrial health upon mutant MFN2 expression. mfn2 knockout zebrafish were used to examine movement compared to wildtype and protein aggregation in brain. ResultsMFN2 mutations identified in ALS patients from our University of Utah cohort and ALSdb were defective in rescuing morphological defects in Mfn2 knockout MEFs. Selected mutants showed decreased membrane potential compared to wildtype MFN2 expression. Zebrafish heterozygous and homozygous for loss of mfn2 showed increased TDP-43 levels in their hindbrain and cerebellum. ConclusionIn total, 21 rare, deleterious mutations in MFN2 were tested in Mfn2 knockout MEFs. Mutant MFN2 expression was not able to rescue the knockout phenotype, though at differing degrees of severity. Decreased membrane potential also argues for inhibited mitochondrial function. Increased TDP-43 levels in mutant zebrafish illustrates MFN2s function in ALS pathology. MFN2 variants influence ALS pathology and highlight the importance of mitochondria in neurodegeneration.

BackgroundTrinucleotide repeat expansions are an emerging class of genetic variants associated with several movement disorders. Unbiased genome-wide analyses can reveal novel genotype-phenotype associations and provide a diagnosis for patients and families. ObjectivesTo identify the genetic cause of a severe progressive movement disorder phenotype in two affected brothers. MethodsA family of two affected brothers and unaffected parents had extensive phenotyping and natural history followed since birth. Whole-genome and long-read sequencing methods were used to characterize genetic variants and methylation status. Results: We describe a CGG repeat expansion in the 5-untranslated region of DIP2B in two affected male siblings presenting with a novel DIP2B phenotype including neurodevelopmental disability, dysmorphic traits, and a severe progressive movement disorder (prominent chorea, dystonia, and ataxia). ConclusionsThis is the first report of a severe progressive movement disorder phenotype attributed to a CGG repeat expansion in the DIP2B 5-UTR.

Frontotemporal lobar degeneration-TDP Type C (TDP-C) is a unique neurodegenerative disease that starts by attacking the anterior temporal lobe leading to language and/or behavioral syndromes. Current literature on the genetic associations of TDP-C, which we have reviewed here, is uneven and lacks a discernible corpus of robust findings. In our study, we completed genome wide hypothesis-free analyses utilizing artificial Intelligence (AI) to identify rare and common variants associated with TDP-C. We then investigated ANXA11 and TARDBP in a hypothesis-driven analysis, since it was recently shown that TDP-43 and Annexin A11 co-aggregate in all TDP-C cases. 1) Whole genome sequencing was completed to identify pathogenic rare variants prioritized with Illuminas AI-based Emedgene software on 37 confirmed or probable TDP-C cases from the Northwestern-University Cohort. 2) A genome wide association study was then completed to identify common variants associated with TDP-C cases vs 290 controls. 3) Next, common and rare variants in TARDBP, and ANXA11 were investigated in TDP-C vs controls. These analyses identified novel genetic associations between FIG4, UBQLN2, INPP5A, and ANXA11 with TDP-C. Of these FIG4, UBQLN2 and ANXA11 have been associated previously with Amyotrophic lateral sclerosis (ALS). To further assess the observed potential genetic overlap between ALS and TDP-C, we leveraged Mendelian randomization (MR) to assess if the ALS genetic load is associated with TDP-C risk, and found evidence supporting this association. The genetic association of ANXA11 with TDP-C is particularly interesting in view of the recently discovered role of Annexin A11 in forming heterodimers with TDP-43 in all abnormal precipitates, a feature not found in TDP-A or TDP-B, which have no similar predilection for the anterior temporal lobe. In addition to the observed overlap between ALS genetics/ genetic load and TDP-C, it is worth mentioning that FIG4, INPP5A and ANXA11 have been implicated in the inositol metabolism pathway, a feature that remains to be elucidated mechanistically. Our TDP-C genetic literature review identified a surprising paucity of neuropathologically confirmed cases in published investigations. Nonetheless, the literature offers support for some of our findings and reemphasizes the absence of dominant or major pathogenic genes for TDP-C, another feature that sets this neuropathologic entity apart from TDP-A and TDP-B.

BackgroundAmyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting over 30,000 people in the United States. It is characterized by the progressive decline of the nervous system that leads to the weakening of muscles which impacts physical function. Approximately, 15% of individuals diagnosed with ALS have a known genetic variant that contributes to their disease. As therapies that slow or prevent symptoms, such as antisense oligonucleotides, continue to develop, it is important to discover novel genes that could be targets for treatment. Additionally, as cohorts continue to grow, performing analyses in ALS subtypes, such as primary lateral sclerosis (PLS), becomes possible due to an increase in power. These analyses could highlight novel pathways in disease manifestation. MethodsBuilding on our previous discoveries using rare variant association analyses, we conducted rare variant burden testing on a substantially larger cohort of 6,970 ALS patients from a large multi-ethnic cohort as well as 166 PLS patients, and 22,524 controls. We used intolerant domain percentiles based on sub-region Residual Variation Intolerance Score (subRVIS) that have been described previously in conjunction with gene based collapsing approaches to conduct burden testing to identify genes that associate with ALS and PLS. ResultsA gene based collapsing model showed significant associations with SOD1, TARDBP, and TBK1 (OR=19.18, p = 3.67 x 10-39; OR=4.73, p = 2 x 10-10; OR=2.3, p = 7.49 x 10-9, respectively). These genes have been previously associated with ALS. Additionally, a significant novel control enriched gene, ALKBH3 (p = 4.88 x 10-7), was protective for ALS in this model. An intolerant domain based collapsing model showed a significant improvement in identifying regions in TARDBP that associated with ALS (OR=10.08, p = 3.62 x 10-16). Our PLS protein truncating variant collapsing analysis demonstrated significant case enrichment in ANTXR2 (p=8.38 x 10-6). ConclusionsIn a large multi-ethnic cohort of 6,970 ALS patients, rare variant burden testing validated known ALS genes and identified a novel potentially protective gene, ALKBH3. A first-ever analysis in 166 patients with PLS found a candidate association with loss-of-function mutations in ANTXR2.

Mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE) is a recently discovered histopathological lesion entity. Approximately half of affected individuals carry a pathogenic brain mosaicism in the X-linked SLC35A2 gene, and all suffer from epilepsy. In this work, we extended the search for genetic alterations of MOGHE by investigating sex chromosome copy number alterations in 29 brain tissue samples from 19 males and 10 females with histopathologically confirmed MOGHE. Twenty individuals carried pathogenic SLC35A2 variants, while no genetic alteration was identified in nine individuals using targeted deep panel sequencing. Interestingly, DNA methylation-derived copy number variation (CNV) plots revealed significant gains of the Y chromosome in 16/19 males (84.2%) and in 5/10 females (50%). These findings were validated by chromogenic and fluorescent in situ hybridisation (ISH), PCR amplification of Y-specific sequences, and microscopic localisation of cells with Y-chromosomal gain in clusters of oligodendroglial hyperplasia. PCR and ISH demonstrated lesion-restricted Y-chromosome gains, absent in the overlying non-lesional neocortex. Together with pathogenic variants in the X-chromosomal SLC35A2 gene, Y-chromosomal sequences detected in phenotypic females and mosaic Y chromosome gains in males provide a genomic correlate for all cases of MOGHE. Based on SLC35A2 mutational status and Y-chromosome copy number changes, we stratified the cohort into three subgroups: SLC35A2-mutant without Y gain (SLC+/Y-, n = 8), SLC35A2-mutant with Y gain (SLC+/Y+, n = 12), and SLC35A2-wild type with Y gain (SLC-/Y+, n = 9). These genetically defined subgroups also differed in their clinical presentation, with individuals from group 2 having the earliest disease onset and the largest lesion volume on MRI. These findings expand the genetic spectrum of epileptogenic cortical malformations and highlight a potentially overlooked role of sex chromosome biology in this focal epilepsy.

Repeat expansion diseases, particularly those involving GC-rich motifs, have been increasingly recognized as contributors to neurological and neuromuscular disorders. Amyotrophic lateral sclerosis (ALS) has been linked to several such expansions, including intermediate-length repeats in genes implicated in oculopharyngodistal myopathy (OPDM). To investigate the possible involvement of CGG repeat expansions in ALS, 424 ALS patients and 312 controls of Japanese descent were screened for expansions in five genes associated with repeat expansion disorders, namely GIPC1, RILPL1, FMR1, AFF2, and NUTM2BAS1. Repeat-primed PCR and fragment analysis revealed that four ALS patients exhibited abnormal CGG expansions in GIPC1 (33-55 repeats), whereas two control individuals harbored expanded alleles (67 and 83 repeats). No expansions in the other genes were detected. Long-read sequencing confirmed repeat sizes and showed sequence instability. Histopathological analysis of ALS patients with GIPC1 expansion demonstrated classical ALS pathology, including phosphorylated TDP-43-positive inclusions. RNA fluorescence in situ hybridization revealed nuclear foci containing GIPC1 repeat RNA exclusively in ALS patients with GIPC1 expansions, suggesting RNA-mediated toxicity. These findings indicate that a subset of ALS patients present with intermediate CGG expansions in GIPC1, which may represent a novel pathogenic mechanism analogous to other noncoding repeat disorders. Given that GIPC1 full expansions are associated with OPDM, these results support the hypothesis of a pathological continuum between neurodegeneration and myopathy driven by repeat length and sequence context. Nonetheless, further investigations into the potential of GIPC1 CGG expansions as genetic risk factors or modifiers in ALS are warranted.

BackgroundParkinsons disease (PD) is a genetically heterogeneous condition; both single nucleotide variants (SNVs) and copy number variants (CNVs) are important genetic risk factors. We examined the utility of combining exome sequencing and genome-wide array-based comparative genomic hybridization (aCGH) for identification of PD genetic risk factors. MethodsWe performed exome sequencing on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated exome sequencing and array comparative genomic hybridization data for pathogenic SNVs and CNVs at Mendelian PD gene loci. SNVs were confirmed via Sanger sequencing. CNVs were confirmed with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing. ResultsUsing exome sequencing, we discovered individuals with known pathogenic single nucleotide variants in GBA (p.E365K, p.T408M, p.N409S, p.L483P) and LRRK2 (p.R1441G and p.G2019S). Two subjects were each double heterozygotes for variants in GBA and LRRK2. Based on aCGH, we additionally discovered cases with an SNCA duplication and heterozygous intragenic GBA deletion. Five additional subjects harbored both SNVs (p.N52fs, p.T240M, p.P437L, p.W453*) and likely disrupting CNVs at the PARK2 locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors. ConclusionsIntegrated exome sequencing and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for SNCA and PARK2 CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder with limited therapeutic options. Riluzole remains the only widely available treatment in ALS, yet its benefits are modest and highly variable across patients. Genetic variation in cytochrome P450 2D6 (CYP2D6), a major enzyme in drug metabolism, detoxification of environmental toxins, and biotransformation of endogenous transmitters, has been implicated as a risk factor in neurodegenerative diseases. It has been observed to play a role in the development of both Parkinsons disease and Alzheimers disease, but its role in ALS has not been established. Using whole-genome sequencing data from more than 6000 individuals in the multinational Project MinE consortium, we examined whether CYP2D6 variants and genotype-inferred metaboliser phenotypes influence ALS risk and survival. We used both multivariable logistic regression and multivariable Cox proportional hazards regression for the analyses, controlling for important clinical covariates. Reduced CYP2D6 activity, driven by the common loss-of-function CYP2D6*4 and other *-alleles causing either decrease or loss of the enzyme function, was associated with increased risk of ALS. Although CYP2D6 variation had no overall effect on survival, in patients receiving Riluzole we observed a protective association, with poor metabolisers showing the greatest survival advantage compared with normal metabolisers. These findings suggest that variation in CYP2D6 contributes to ALS susceptibility and can modify treatment response. Incorporating CYP2D6 genetic profiling into ALS clinical trials could reduce pharmacokinetic variability and improve detection of therapeutic effects. More broadly, this work provides a rationale for integrating pharmacogenomics into ALS research and care as a step towards precision medicine in neurodegeneration.

BackgroundMen with fragile X-associated tremor/ataxia syndrome (FXTAS) often develop executive dysfunction, characterized by disinhibition, frontal dyscontrol of movement, and working memory and attention changes. Although cross-sectional studies have suggested that earlier executive function changes may precede FXTAS, the lack of longitudinal studies have made it difficult to address this hypothesis. MethodsThis study included 66 FMR1 premutation carriers (PC) ranging from 40-78 years (Mean=59.5) and 31 well-matched healthy controls (HC) ages 40-75 (Mean 57.7) at baseline. Eighty-four participants returned for 2-5 follow up visits over a duration of 1 to 9 years (Mean=4.6); 28 of the PC developed FXTAS. The Behavior Rating Inventory of Executive Function-Adult Version (BRIEF-A) was completed by participants and their spouses/partners at each visit. ResultsLongitudinal mixed model regression analyses showed a greater decline with age in PC compared to HC on the Metacognition Index (MI; self-initiation, working memory, organization, task monitoring). Conversion to FXTAS was associated with worsening MI and Behavioral Regulation Index (BRI; inhibition, flexibility, emotion modulation). For spouse/partner report, FXTAS conversion was associated with worsening MI. Finally, BRIEF-A executive function problems at baseline significantly predicted later development of FXTAS. ConclusionsThese findings suggest that executive function changes represent a prodrome of the later movement disorder.

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.

ImportanceThe chromosome 17q21.31 region, containing a 900 Kb inversion that defines H1 and H2 haplotypes, represents the strongest genetic risk locus in progressive supranuclear palsy (PSP). In addition to H1 and H2, various structural forms of 17q21.31, characterized by the copy number of , {beta}, and {gamma} duplications, have been identified. However, the specific effect of each structural form on the risk of PSP has never been evaluated in a large cohort study. ObjectiveTo assess the association of different structural forms of 17q.21.31, defined by the copy numbers of , {beta}, and {gamma} duplications, with the risk of PSP and MAPT sub-haplotypes. Design, setting, and participantsUtilizing whole genome sequencing data of 1,684 (1,386 autopsy confirmed) individuals with PSP and 2,392 control subjects, a case-control study was conducted to investigate the association of copy numbers of , {beta}, and {gamma} duplications and structural forms of 17q21.31 with the risk of PSP. All study subjects were selected from the Alzheimers Disease Sequencing Project (ADSP) Umbrella NG00067.v7. Data were analyzed between March 2022 and November 2023. Main outcomes and measuresThe main outcomes were the risk (odds ratios [ORs]) for PSP with 95% CIs. Risks for PSP were evaluated by logistic regression models. ResultsThe copy numbers of and {beta} were associated with the risk of PSP only due to their correlation with H1 and H2, while the copy number of {gamma} was independently associated with the increased risk of PSP. Each additional duplication of {gamma} was associated with 1.10 (95% CI, 1.04-1.17; P = 0.0018) fold of increased risk of PSP when conditioning H1 and H2. For the H1 haplotype, addition {gamma} duplications displayed a higher odds ratio for PSP: the odds ratio increases from 1.21 (95%CI 1.10-1.33, P = 5.47 x 10-5) for H1{beta}1{gamma}1 to 1.29 (95%CI 1.16-1.43, P = 1.35 x 10-6) for H1{beta}1{gamma}2, 1.45 (95%CI 1.27-1.65, P = 3.94 x 10-8) for H1{beta}1{gamma}3, and 1.57 (95%CI 1.10-2.26, P = 1.35 x 10-2) for H1{beta}1{gamma}4. Moreover, H1{beta}1{gamma}3 is in linkage disequilibrium with H1c (R2 = 0.31), a widely recognized MAPT sub-haplotype associated with increased risk of PSP. The proportion of MAPT sub-haplotypes associated with increased risk of PSP (i.e., H1c, H1d, H1g, H1o, and H1h) increased from 34% in H1{beta}1{gamma}1 to 77% in H1{beta}1{gamma}4. Conclusions and relevanceThis study revealed that the copy number of {gamma} was associated with the risk of PSP independently from H1 and H2. The H1 haplotype with more {gamma} duplications showed a higher odds ratio for PSP and were associated with MAPT sub-haplotypes with increased risk of PSP. These findings expand our understanding of how the complex structure at 17q21.31 affect the risk of PSP. Key PointsO_ST_ABSQuestionC_ST_ABSDo large copy number variations (i.e., , {beta}, and {gamma}) inside 17q21.31 contribute to the risk of progressive supranuclear palsy (PSP) independently from the H1 and H2 haplotypes? Do structural forms of 17q21.31, characterized by combinations of , {beta}, and {gamma}, present divergent risk to the development of PSP? Are structural forms of 17q21.31 associated with MAPT sub-haplotypes, such as H1c? FindingsIn this case-control study of 1,684 individuals with PSP and 2,392 control subjects, the copy number of {gamma} duplication was independently associated with the risk of the disease. H1 haplotypes with more {gamma} duplications (H1{beta}1{gamma}2, H1{beta}1{gamma}3, and H1{beta}1{gamma}4) displayed a higher odds ratio for PSP when compared to H1{beta}1{gamma}1. Notably, H1{beta}1{gamma}3 was observed to be in linkage disequilibrium with H1c, a widely recognized MAPT sub-haplotype associated with PSP. MeaningThe association between the H1 and H2 haplotypes and PSP involves multiple contributing factors, including the copy number of {gamma} duplication.

Parkinsons disease is a complex neurodegenerative disorder, affecting approximately one million individuals in the USA alone. A significant proportion of risk for Parkinsons disease is driven by genetics. Despite this, the majority of the common genetic variation that contributes to disease risk is unknown, in-part because previous genetic studies have focussed solely on the contribution of single nucleotide variants. Structural variants represent a significant source of genetic variation in the human genome. However, because assay of this variability is challenging, structural variants have not been cataloged on a genome-wide scale, and their contribution to the risk of Parkinsons disease remains unknown. In this study, we 1) leveraged the GATK-SV pipeline to detect and genotype structural variants in 7,772 short-read sequencing data and 2) generated a subset of matched whole-genome Oxford Nanopore Technologies long-read sequencing data from the PPMI cohort to allow for comprehensive structural variant confirmation. We detected, genotyped, and tested 3,154 "high-confidence" common structural variant loci, representing over 412 million nucleotides of non-reference genetic variation. Using the long-read sequencing data, we validated three structural variants that may drive the association signals at known Parkinsons disease risk loci, including a 2kb intronic deletion within the gene LRRN4. Further, we confirm that the majority of structural variants in the human genome cannot be detected using short-read sequencing alone, encompassing on average around 4 million nucleotides of inaccessible sequence per genome. Therefore, although these data provide the most comprehensive survey of the contribution of structural variants to the genetic risk of Parkinsons disease to date, this study highlights the need for large-scale long-read datasets to fully elucidate the role of structural variants in Parkinsons disease.

The genetic etiology of ALS includes few rare, large-effect variants and potentially many common, small-effect variants per case. The genetic risk liability for ALS might require a threshold comprised of a certain amount of variants. Here, we tested the degree to which risk for ALS was affected by rare variants in ALS genes, polygenic risk score, or both. 335 ALS cases and 356 controls from Quebec, Canada were concurrently tested by SNP-chip genotyping and targeted sequencing of known ALS genes. ALS GWAS summary statistics were used to estimate an ALS PRS. Cases and controls were subdivided into rare variant carriers and non-carriers. Risk for ALS was significantly associated with PRS and rare variants independently, but the interaction was not significant. ALS PRS affected risk only in those not carrying a rare variant, suggesting that rare variants in ALS genes are generally sufficient for disease risk. Rather than modifying the penetrance of rare variants, ALS PRS is most informative in the absence of these variants.

BackgroundThe ancestral genetic heterogeneity (admixture) of Caribbean Hispanics makes studies of this population critical to the discovery of ancestry-specific genetic factors in Alzheimer disease. In this study, we performed whole genome sequencing in multiplex Caribbean Hispanic Puerto Rican families to identify rare causal variants influencing Alzheimer disease through linkage and segregation-based approaches. MethodsAs part of the Puerto Rican Alzheimer Disease Initiative, whole genome sequencing data were generated for 100 individuals (61 affected) from 23 Puerto Rican families. To identify the genetic loci likely to carry risk variants, we performed a parametric multipoint affected individuals-only linkage analysis using MERLIN software. Following the linkage analysis, we identified the consensus region (heterogeneity logarithm of the odds score (HLOD) > 5.1), annotated variants using Ensembl Variant Effect Predictor, and combined annotation dependent depletion score (CADD). Finally, we prioritized variants according to allele frequency (< 0.01), function (CADD > 10), and complete segregation among affected individuals. ResultsA locus at 9p21 produced a linkage HLOD score of 5.1 in the parametric affecteds-only multipoint affected individuals-only model supported by 9 families. Through the prioritization step, we selected 36 variants (22 genic variants). Candidate genes in the regions include C9orf72, UNC13B, and ELAVL2. ConclusionsLinkage analysis of Caribbean Hispanics Puerto Rican families confirmed previously reported linkage to 9p21 in non-Hispanic White and Israeli-Arap families. Our results suggest several candidates in the region as conferring AD risk. Identified putative damaging rare variants in multiplex families indicates the critical role of rare variation in Alzheimer disease etiology.

Pantothenate kinase-associated neurodegeneration (PKAN) is a rare, autosomal recessive neurological disorder characterized by the progressive degeneration of specific regions in the brain and is invariably fatal. Several individuals in families affected by PKAN were known to live in an isolated region in a southwestern province of the Dominican Republic and had been previously studied. Forty-six individuals with PKAN in 34 families were evaluated for disease manifestations using the PKAN-Disease Rating Scale and the Leiter-3 Cognitive and Neuropsychological assessment. We completed whole genome sequencing in the 46 affected individuals and their 80 unaffected relatives. Haplotype analysis was used to identify shared genetic patterns among individuals with the mutation to identify common ancestral and founder effects. The classical form of PKAN was observed in 22 individuals with moderate to severe oromandibular dystonia and limb dystonia and onset in early childhood. The atypical form was observed in 24 individuals with parkinsonism, dystonia, and cognitive impairment and later onset of disease. A PANK2 variant, chr20:3907977: A:G (c.680A>G, p.Y227C), was homozygous among 42 affected individuals equally divided by disease form. There were 59 heterozygous carriers of this variant among parents and relatives of the affected individuals. Four individuals from two families were compound heterozygotes for c.680A>G and chr20:3918728: C:T (c.1594C>T). Haplotype analyses revealed shared patterns across families and of African origin consistent with founder effects for c.680A>G and c.1594C>T, likely introduced to the island 25 to 35 generations earlier. The frequency of heterozygous carriers of c.680A>G allele among individuals of Dominican ancestry living in New York was 0.18% but was 0.8% among individuals living in the Dominican Republic, significantly higher than the reported frequency for all causal PANK2 mutations worldwide. This investigation confirmed likely founder mutations in PANK2 associated with the classical and atypical forms of PKAN in 34 families in an isolated region of the Dominican Republic. Compound heterozygosity was observed in four individuals from two families. The heterozygous frequency of c.680A>G was exceptionally high in the Dominican population compared with worldwide data. Founder mutations in such communities offer a unique opportunity to set up relevant, affordable and accessible genetic counseling and screening.

In frontotemporal degeneration (FTD) and amyotrophic lateral sclerosis (ALS), subsequent motor or cognitive-behavioral features, respectively, are associated with shorter survival. However, factors influencing subsequent feature development remain largely unexplored. In this study, we examined whether the presence of a C9orf72 expansion or the initial clinical syndrome was associated with increased risk of subsequent feature development in individuals with ALS and FTD. We performed a retrospective evaluation of the entire disease course of individuals with ALS and FTD who had neuropathological confirmation of TDP-43 proteinopathy at autopsy or a C9orf72 hexanucleotide repeat expansion. We examined the odds and hazard of subsequent feature development and assessed whether each was modified by the presence of a C9orf72 expansion or initial clinical syndrome. At autopsy, we evaluated the association between TDP-43 pathology burden in characteristic brain regions and features across the FTD-ALS spectrum. For individuals with ALS (n=168) and FTD (n=73), binary logistic regression revealed increased odds (OR=3.49[95% CI 1.64-7.80], p=0.002) for developing subsequent features in those with a C9orf72 expansion compared to those without and decreased odds (OR=0.25[95% CI 0.12-0.53], p<0.001) for developing subsequent features in those with an initial ALS clinical syndrome compared to those with an initial FTD clinical syndrome. Cox proportional hazard analyses revealed an increased hazard (HR=3.78[95% CI 1.86-7.65], p<0.001) for developing subsequent features in those with a C9orf72 expansion compared to those without. We observed a 94-month difference in the time after symptom onset of the initial clinical syndrome that a given person without a C9orf72 expansion reached the highest probability of developing subsequent features (0.12[95% CI (0.03-0.19], 113.00 months) and a person with a C9orf72 expansion surpassed that probability (0.13[95% CI 0.06-0.19], 19.00 months). Beyond C9orf72 expansion status, cox proportional hazard analyses revealed a decreased hazard (HR=0.48[95% CI 0.25-0.95], p=0.03) for developing subsequent features in those with an initial ALS clinical syndrome compared to those with an initial FTD clinical syndrome. Age at symptom onset and sex were not associated with development of subsequent features. The distribution of TDP-43 pathology across characteristic brain regions reflected both the initial clinical syndrome and subsequent features, with relatively preserved spinal cord only in FTD cases without subsequent motor features (p<0.0001) and relatively preserved neocortical regions only in ALS cases without subsequent cognitive-behavioral features (p<0.0001). These data highlight the need for clinician vigilance to detect the onset of subsequent motor and cognitive-behavioral features in patients carrying a C9orf72 expansion, regardless of initial clinical syndrome. C9orf72 clinical care can be enhanced through coordination between cognitive and neuromuscular clinics. Abbreviated SummarySpencer et al. demonstrated both the presence of a C9orf72 expansion and the initial clinical syndrome modify risk of subsequent feature development in frontotemporal degeneration and amyotrophic lateral sclerosis, highlighting the need for clinician vigilance to detect the onset of subsequent motor and cognitive-behavioral features in this disease spectrum.

Amyotrophic lateral sclerosis (ALS) is a progressive nervous system disease that causes loss of muscle control. Over 30 mutated genes are associated with ASL. However, 90-95% of ASL cases have been found without a family history. Here, we have analyzed RNA-Seq data of NYGC ALS Consortium and identified fusion transcripts from ASL patients and non-neurologic controls (NNC). In this study, we combined previously-curated 1180 monozygotic (MZ) hereditary fusion genes (HFGs), and 204 HFGs discovered from NNC to analyze ASL fusion transcripts and identified 348 HFGs. Comparative analysis between ASL and GTEx shows that 139 HFGs are associated with ASL and ranged from 10.4% to 98.7% of 77 ASL patients. The most recurrent HFG is ZNF528-ZNF880, detected in 98.7% of 77 ASL patients and 4.5% of 133 GTEx brain cortexes. Alignments of HFG transcripts from ASL with fusion transcripts from mesial temporal lobe epilepsy (MTLE) and Alzheimers disease (AD) showed that 43.9% and 11.6% of the ASL HFGs were present in MTLE and AD, respectively. The most recurrent and common HFG among ASL, MTLE, and AD was ADAMTSL3-SH3GL3, which behaves like ubiquitously-expressed SH3GL3-ADAMTSL3 epigenetic fusion gene (EFG) and shows that ADAMTSL3-SH3GL3 is a potential dormant or differentially-expressed HFG (dHFG), suggesting that they have common pathophysiological mechanisms. These HFGs associated with ASL have shown that HFGs are the missing genetic heritability and provide novel therapeutic targets for more efficient therapeutic drugs and methods to treat and cure many neurological diseases.

ATXN2 expansions of [&ge;]33 CAG-repeats are associated with spinocerebellar ataxia type 2, while "intermediate" length expansions have been associated with amyotrophic lateral sclerosis (ALS). Yet, no consensus is established regarding the lengths that define a true association with ALS risk, with recent studies debating between a lower limit of [&ge;]29 or [&ge;]31 repeats. Here, we assessed the risk of ALS imparted by various ATXN2 repeat lengths to establish an accepted lower limit of repeats that impart risk of disease in the largest meta-analysis to-date. We identified 19 studies with carrier counts of expansions ranging from 24 to [&ge;]34 repeats in cohorts of individuals with ALS and controls that we meta-analysed with the ATXN2 repeat lengths of the large-scale Project MinE ALS Consortium dataset (total individuals with ALS = 19202; total controls = 22177) and determined a lower limit of 30 repeats defining significant ALS risk. These findings were validated with a secondary assessment of the individuals with ALS captured within the meta-analysis using the gnomAD short tandem repeat dataset as a proxy control cohort. We also applied our defined ATXN2 repeat risk threshold to explore relationships with ALS clinical outcomes. While we did not observe a significant relationship between ATXN2 repeat lengths and age of ALS onset, we did identify a significant inverse correlation between ATXN2 repeat lengths as a continuous metric and duration of disease and found that individuals with ALS carrying the risk variant allele of [&ge;]30 repeats had significantly shorter times to diagnosis than those without the repeat expansion. Our comprehensive analyses propose a lower-limit threshold of [&ge;]30 ATXN2 trinucleotide repeats in length defining true ALS risk. These findings are imperative for allowing improved accuracy in risk interpretation and guidance for patients and their families, particularly as clinical genetic testing efforts continue to expand and there becomes increased need for guiding targeted clinical trial inclusion criteria. Our results may also aid in future analyses assessing ATXN2 pathogenic mechanisms and therapeutic strategies.

SOD1 is the second most mutated gene in European amyotrophic lateral sclerosis (ALS) patients, after C9orf72 expansion. Given the recent authorisation of SOD1-directed antisense oligonucleotide for use in SOD1-ALS patients, prompt screening for SOD1 mutations in ALS patients is highly recommended. Large-scale genomic analysis could inform on the population-based prevalence of SOD1 mutation carriers, who would potentially benefit from treatment. We aim to determine the number of people with pathogenic SOD1 variants in the UK Biobank (UKB), to address a critical gap between clinical and genetic prevalence of SOD1-ALS, with important implications for early therapeutic intervention in presymptomatic carriers. We analysed variants in the SOD1 gene within exome sequencing data from 470,000 individuals over 40 years old at the time of recruitment. We evaluated their pathogenic role using referenced databases and according to ACMG guidelines. Leveraging the carrier frequency in UKB and age at onset distribution data, we estimated the disease prevalence of SOD1-ALS. We identified 122 individuals with monoallelic SOD1 coding variants. 93.4% of them were asymptomatic at enrollment. In addition, the low penetrance disease allele p.Asp91Ala was observed in heterozygosis in 535 subjects, while it was never found in homozygosis. Based on this data, the expected number of people developing SOD1-ALS in the UK population, excluding the p.Asp91Ala allele, is 1.1:100,000, four times higher than the prevalence derived from clinical data. Incomplete and age-related penetrance and heterogeneous phenotypic expression likely account for the reduced number of symptomatic patients identified. Our findings highlight the need for systematic genetic screening in the general population, which could dramatically expand the pool of individuals who might benefit from novel molecular-silencing therapies presymptomatically. Given the existence of a therapeutic option, an in-depth follow-up of these subjects is highly recommended.