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Baumgartner D, Mušová Z, Zídková J, Hedvičáková P, Vlčková E, Joppeková L, Kramářová T, Fajkusová L, Stránecký V, Geryk J, Votýpka P, Mazanec R. Genetic Landscape of Amyotrophic Lateral Sclerosis in Czech Patients. J Neuromuscul Dis 2024:JND230236. [PMID: 39058450 DOI: 10.3233/jnd-230236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Background Genetic factors are involved in the pathogenesis of familial and sporadic amyotrophic lateral sclerosis (ALS) and constitute a link to its association with frontotemporal dementia (FTD). Gene-targeted therapies for some forms of ALS (C9orf72, SOD1) have recently gained momentum. Genetic architecture in Czech ALS patients has not been comprehensively assessed so far. Objective We aimed to deliver pilot data on the genetic landscape of ALS in our country. Methods A cohort of patients with ALS (n = 88), recruited from two Czech Neuromuscular Centers, was assessed for hexanucleotide repeat expansion (HRE) in C9orf72 and also for genetic variations in other 36 ALS-linked genes via next-generation sequencing (NGS). Nine patients (10.1%) had a familial ALS. Further, we analyzed two subgroups of sporadic patients - with concomitant FTD (n = 7) and with young-onset of the disease (n = 22). Results We detected the pathogenic HRE in C9orf72 in 12 patients (13.5%) and three other pathogenic variants in FUS, TARDBP and TBK1, each in one patient. Additional 7 novel and 9 rare known variants with uncertain causal significance have been detected in 15 patients. Three sporadic patients with FTD (42.9%) were harbouring a pathogenic variant (all HRE in C9orf72). Surprisingly, none of the young-onset sporadic patients harboured a pathogenic variant and we detected no pathogenic SOD1 variant in our cohort. Conclusion Our findings resemble those from other European populations, with the highest prevalence of HRE in the C9orf72 gene. Further, our findings suggest a possibility of a missing genetic variability among young-onset patients.
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Affiliation(s)
- Daniel Baumgartner
- Department of Neurology, Neuromuscular Center, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Zuzana Mušová
- Department of Biology and Medical Genetics, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jana Zídková
- Center for Molecular Biology and Genetics, Internal Haematology and Oncology Clinic, University Hospital Brno and Faculty of Medicine, Masaryk University Brno, Czech Republic
| | - Petra Hedvičáková
- Department of Biology and Medical Genetics, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Eva Vlčková
- Department of Neurology, Neuromuscular Center, University Hospital Brno and Faculty of Medicine, Masaryk University Brno, Czech Republic
| | - Lubica Joppeková
- Department of Neurology, Neuromuscular Center, University Hospital Brno and Faculty of Medicine, Masaryk University Brno, Czech Republic
| | - Tereza Kramářová
- Center for Molecular Biology and Genetics, Internal Haematology and Oncology Clinic, University Hospital Brno and Faculty of Medicine, Masaryk University Brno, Czech Republic
| | - Lenka Fajkusová
- Center for Molecular Biology and Genetics, Internal Haematology and Oncology Clinic, University Hospital Brno and Faculty of Medicine, Masaryk University Brno, Czech Republic
| | - Viktor Stránecký
- Department of Pediatrics and Inherited Metabolic Disorders, Research Unit for Rare Diseases, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Jan Geryk
- Department of Biology and Medical Genetics, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Pavel Votýpka
- Department of Biology and Medical Genetics, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Radim Mazanec
- Department of Neurology, Neuromuscular Center, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
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Ross JP, Akçimen F, Liao C, Kwan K, Phillips DE, Schmilovich Z, Spiegelman D, Genge A, Dupré N, Dion PA, Farhan SMK, Rouleau GA. Rare-variant and polygenic analyses of amyotrophic lateral sclerosis in the French-Canadian genome. Genet Med 2024; 26:100967. [PMID: 37638500 DOI: 10.1016/j.gim.2023.100967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023] Open
Abstract
PURPOSE The genetic etiology of amyotrophic lateral sclerosis (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. METHODS 335 ALS cases and 356 controls from Québec, Canada were concurrently tested by microarray genotyping and targeted sequencing of ALS genes known at the time of study inception. ALS genome-wide association studies summary statistics were used to estimate an ALS polygenic risk score (PRS). Cases and controls were subdivided into rare-variant heterozygotes and non-heterozygotes. RESULTS Risk for ALS was significantly associated with PRS and rare variants independently in a logistic regression model. Although ALS PRS predicted a small amount of ALS risk overall, the effect was most pronounced between ALS cases and controls that were not heterozygous for a rare variant in the ALS genes surveyed. CONCLUSION Both PRS and rare variants in ALS genes impact risk for ALS. PRS for ALS is most informative when rare variants are not observed in ALS genes.
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Affiliation(s)
- Jay P Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Fulya Akçimen
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Calwing Liao
- Department of Medicine, Harvard Medical School, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA
| | - Karina Kwan
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, QC, Canada
| | - Daniel E Phillips
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Biology, McGill University, Montréal, QC, Canada
| | - Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Dan Spiegelman
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Angela Genge
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Nicolas Dupré
- Division of Neurosciences, CHU de Québec, Université Laval, Québec City, QC, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Québec City, QC, Canada
| | - Patrick A Dion
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Sali M K Farhan
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada.
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Roggenbuck J, Eubank BHF, Wright J, Harms MB, Kolb SJ. Evidence-based consensus guidelines for ALS genetic testing and counseling. Ann Clin Transl Neurol 2023; 10:2074-2091. [PMID: 37691292 PMCID: PMC10646996 DOI: 10.1002/acn3.51895] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 08/12/2023] [Indexed: 09/12/2023] Open
Abstract
OBJECTIVE Advances in amyotrophic lateral sclerosis (ALS) gene discovery, ongoing gene therapy trials, and patient demand have driven increased use of ALS genetic testing. Despite this progress, the offer of genetic testing to persons with ALS is not yet "standard of care." Our primary goal is to develop clinical ALS genetic counseling and testing guidelines to improve and standardize genetic counseling and testing practice among neurologists, genetic counselors or any provider caring for persons with ALS. METHODS Core clinical questions were identified and a rapid review performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA-P) 2015 method. Guideline recommendations were drafted and the strength of evidence for each recommendation was assessed by combining two systems: the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) System and the Evaluation of Genomic Applications in Practice and Prevention (EGAPP). A modified Delphi approach was used to reach consensus among a group of content experts for each guideline statement. RESULTS A total of 35 guideline statements were developed. In summary, all persons with ALS should be offered single-step genetic testing, consisting of a C9orf72 assay, along with sequencing of SOD1, FUS, and TARDBP, at a minimum. The key education and genetic risk assessments that should be provided before and after testing are delineated. Specific guidance regarding testing methods and reporting for C9orf72 and other genes is provided for commercial laboratories. INTERPRETATION These evidence-based, consensus guidelines will support all stakeholders in the ALS community in navigating benefits and challenges of genetic testing.
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Affiliation(s)
- Jennifer Roggenbuck
- Division of Human Genetics, Department of Internal MedicineThe Ohio State University Wexner Medical CenterColumbusOhioUSA
- Department of NeurologyThe Ohio State University Wexner Medical CenterColumbusOhioUSA
| | - Breda H. F. Eubank
- Health & Physical Education Department, Faculty of Health, Community, & EducationMount Royal University4825 Mount Royal Gate SWCalgaryAlbertaCanada
| | - Joshua Wright
- Department of NeurologyThe Ohio State University Wexner Medical CenterColumbusOhioUSA
| | - Matthew B. Harms
- Department of NeurologyColumbia University Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Stephen J. Kolb
- Department of NeurologyThe Ohio State University Wexner Medical CenterColumbusOhioUSA
- Department of Biological Chemistry & PharmacologyThe Ohio State University Wexner Medical CenterColumbusOhioUSA
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Dong S, Yin X, Wang K, Yang W, Li J, Wang Y, Zhou Y, Liu X, Wang J, Chen X. Presence of Rare Variants is Associated with Poorer Survival in Chinese Patients with Amyotrophic Lateral Sclerosis. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:167-181. [PMID: 37197644 PMCID: PMC10110782 DOI: 10.1007/s43657-022-00093-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 05/19/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder with phenotypic and genetic heterogeneity. Recent studies have suggested an oligogenic basis of ALS, in which the co-occurrence of two or more genetic variants has additive or synergistic deleterious effects. To assess the contribution of possible oligogenic inheritance, we profiled a panel of 43 relevant genes in 57 sporadic ALS (sALS) patients and eight familial ALS (fALS) patients from five pedigrees in east China. We filtered rare variants using the combination of the Exome Aggregation Consortium, the 1000 Genomes and the HuaBiao Project. We analyzed patients with multiple rare variants in 43 known ALS causative genes and the genotype-phenotype correlation. Overall, we detected 30 rare variants in 16 different genes and found that 16 of the sALS patients and all the fALS patients examined harbored at least one variant in the investigated genes, among which two sALS and four fALS patients harbored two or more variants. Of note, the sALS patients with one or more variants in ALS genes had worse survival than the patients with no variants. Typically, in one fALS pedigree with three variants, the family member with three variants (Superoxide dismutase 1 (SOD1) p.V48A, Optineurin (OPTN) p.A433V and TANK binding kinase 1 (TBK1) p.R573H) exhibited much more severe disease phenotype than the member carrying one variant (TBK1 p.R573H). Our findings suggest that rare variants could exert a negative prognostic effect, thereby supporting the oligogenic inheritance of ALS.
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Affiliation(s)
- Siqi Dong
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040 China
- National Center for Neurological Disorders, Shanghai, 200040 China
| | - Xianhong Yin
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Human Phenome Institute, Fudan University, Shanghai, 200433 China
| | - Kun Wang
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Wenbo Yang
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040 China
- National Center for Neurological Disorders, Shanghai, 200040 China
| | - Jiatong Li
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040 China
- National Center for Neurological Disorders, Shanghai, 200040 China
| | - Yi Wang
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Human Phenome Institute, Fudan University, Shanghai, 200433 China
| | - Yanni Zhou
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Xiaoni Liu
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040 China
- National Center for Neurological Disorders, Shanghai, 200040 China
| | - Jiucun Wang
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Human Phenome Institute, Fudan University, Shanghai, 200433 China
| | - Xiangjun Chen
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040 China
- National Center for Neurological Disorders, Shanghai, 200040 China
- Human Phenome Institute, Fudan University, Shanghai, 200433 China
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5
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Genotype-phenotype correlation in Tunisian patients with Amyotrophic Lateral Sclerosis. Neurobiol Aging 2022; 120:27-33. [DOI: 10.1016/j.neurobiolaging.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/31/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022]
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Riva N, Pozzi L, Russo T, Pipitone GB, Schito P, Domi T, Agosta F, Quattrini A, Carrera P, Filippi M. NEK1 Variants in a Cohort of Italian Patients With Amyotrophic Lateral Sclerosis. Front Neurosci 2022; 16:833051. [PMID: 35495032 PMCID: PMC9048593 DOI: 10.3389/fnins.2022.833051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction In the last few years, different studies highlighted a significant enrichment of NEK1 loss of function (LoF) variants in amyotrophic lateral sclerosis (ALS), and an additional role for the p.Arg261His missense variant in the disease susceptibility. Several other missense variants have been described so far, whose pathogenic relevance remains however unclear since many of them have been reported in both patients and controls. This study aimed to investigate the presence of NEK1 variants and their correlation with phenotype in a cohort of Italian patients with ALS. Methods We sequenced a cohort of 350 unrelated Italian patients with ALS by next-generation sequencing (NGS) and then we analyzed the clinical features of NEK1 carriers. Results We detected 20 different NEK1 rare variants (four LoF and 16 missense) in 33 unrelated patients with sporadic ALS (sALS). The four LoF variants (two frameshift and two splice-site variants) were all novel. The p.Arg261His missense variant was enriched in the patients’ cohort (p < 0.001). Excluding this variant from counting, the difference in the frequency of NEK1 rare missense variants between patients and controls was not statistically significant. NEK1 carriers had a higher frequency of flail arm (FA) phenotype compared with the other patients of the cohort (29.2% vs. 6.4%). Nine NEK1 carriers (37.5%) also harbored variants in other ALS-related genes. Conclusion This study confirms that NEK1 LoF and p.Arg261. His missense variants are associated with ALS in an Italian ALS cohort and suggests a correlation between the presence of NEK1 variants and FA phenotype.
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Affiliation(s)
- Nilo Riva
- Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE), San Raffaele Scientific Institute, Milan, Italy
- Neurology Unit, San Raffaele Scientific Institute, Milan, Italy
- Neurorehabilitation Unit, San Raffaele Scientific Institute, Milan, Italy
- *Correspondence: Nilo Riva,
| | - Laura Pozzi
- Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE), San Raffaele Scientific Institute, Milan, Italy
| | - Tommaso Russo
- Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE), San Raffaele Scientific Institute, Milan, Italy
- Neurology Unit, San Raffaele Scientific Institute, Milan, Italy
| | | | - Paride Schito
- Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE), San Raffaele Scientific Institute, Milan, Italy
- Neurology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Teuta Domi
- Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE), San Raffaele Scientific Institute, Milan, Italy
| | - Federica Agosta
- Neuroimaging Research Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE), San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Angelo Quattrini
- Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE), San Raffaele Scientific Institute, Milan, Italy
| | - Paola Carrera
- Unit of Genomics for Human Disease Diagnosis, San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Filippi
- Neurology Unit, San Raffaele Scientific Institute, Milan, Italy
- Neurorehabilitation Unit, San Raffaele Scientific Institute, Milan, Italy
- Neuroimaging Research Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE), San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Neurophysiology Service, San Raffaele Scientific Institute, Milan, Italy
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Ratti A, Peverelli S, D'Adda E, Colombrita C, Gennuso M, Prelle A, Silani V. Genetic and epigenetic disease modifiers in an Italian C9orf72 family expressing ALS, FTD or PD clinical phenotypes. Amyotroph Lateral Scler Frontotemporal Degener 2021; 23:292-298. [PMID: 34382491 DOI: 10.1080/21678421.2021.1962355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Objective: The presence of the hexanucleotide repeat expansion (HRE) in C9orf72 gene is associated to the ALS/FTD spectrum, but also to parkinsonisms. We here describe an Italian family with the father diagnosed with Parkinson disease (PD) at the age of 67 and the two daughters developing FTD and ALS at 45 years of age. We searched for C9orf72 HRE with possible genetic and epigenetic modifiers to account for the intrafamilial phenotypic variability. Methods: C9orf72 mutational analysis was performed by fragment length analysis, Repeat-primed PCR and Southern blot. Targeted next generation sequencing was used to analyze 48 genes associated to neurodegenerative diseases. Promoter methylation was analyzed by bisulfite sequencing. Results: Genetic analysis identified C9orf72 HRE in all the affected members with a similar repeat expansion size. Both the father and the FTD daughter also carried the heterozygous p.Ile946Phe variant in ATP13A2 gene, associated to PD. In addition, the father also showed a heterozygous EIF4G1 variant (p.Ala13Pro), that might increase his susceptibility to develop PD. The DNA methylation analysis showed that all the 26 CpG sites within C9orf72 promoter were unmethylated in all family members. Conclusions: Neither C9orf72 HRE size nor promoter methylation act as disease modifiers within this family, at least in blood, not excluding HRE mosaicism and a different methylation pattern in the brain. However, the presence of rare genetic variants in PD genes suggests that they may influence the clinical manifestation in the father. Other genetic and/or epigenetic modifiers must be responsible for disease variability in this C9orf72 family case.
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Affiliation(s)
- Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milano, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milano, Italy
| | - Silvia Peverelli
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | | | - Claudia Colombrita
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | | | - Alessandro Prelle
- U.O.C. of Neurology - Stroke Unit, ASST Ovest milanese, Legnano, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milano, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milano, Italy
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Roggenbuck J, Rich KA, Vicini L, Palettas M, Schroeder J, Zaleski C, Lincoln T, Drury L, Glass JD. Amyotrophic Lateral Sclerosis Genetic Access Program: Paving the Way for Genetic Characterization of ALS in the Clinic. NEUROLOGY-GENETICS 2021; 7:e615. [PMID: 34386583 PMCID: PMC8356701 DOI: 10.1212/nxg.0000000000000615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022]
Abstract
Objective To report the frequency of amyotrophic lateral sclerosis (ALS) genetic variants in a nationwide cohort of clinic-based patients with ALS with a family history of ALS (fALS), dementia (dALS), or both ALS and dementia (fALS/dALS). Methods A multicenter, prospective cohort of 573 patients with fALS, dALS, or fALS/dALS, underwent genetic testing in the ALS Genetic Access Program (ALS GAP), a clinical program for clinics of the Northeast ALS Consortium. Patients with dALS underwent C9orf72 hexanucleotide repeat expansion (HRE) testing; those with fALS or fALS/dALS underwent C9orf72 HRE testing, followed by sequencing of SOD1, FUS, TARDBP, TBK1, and VCP. Results A pathogenic (P) or likely pathogenic (LP) variant was identified in 171/573 (30%) of program participants. About half of patients with fALS or fALS/dALS (138/301, 45.8%) had either a C9orf72 HRE or a P or LP variant identified in SOD1, FUS, TARDBP, TBK1, or VCP. The use of a targeted, 5-gene sequencing panel resulted in far fewer uncertain test outcomes in familial cases compared with larger panels used in other in clinic-based cohorts. Among dALS cases 11.8% (32/270) were found to have the C9orf72 HRE. Patients of non-Caucasian geoancestry were less likely to test positive for the C9orf72 HRE, but were more likely to test positive on panel testing, compared with those of Caucasian ancestry. Conclusions The ALS GAP program provided a genetic diagnosis to ∼1 in 3 participants and may serve as a model for clinical genetic testing in ALS.
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Affiliation(s)
- Jennifer Roggenbuck
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Kelly A Rich
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Leah Vicini
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Marilly Palettas
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Joceyln Schroeder
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Christina Zaleski
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Tara Lincoln
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Luke Drury
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Jonathan D Glass
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
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Roggenbuck J. C9orf72 and the Care of the Patient With ALS or FTD: Progress and Recommendations After 10 Years. NEUROLOGY-GENETICS 2020; 7:e542. [PMID: 33575483 PMCID: PMC7862089 DOI: 10.1212/nxg.0000000000000542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022]
Abstract
The 2011 discovery of the pathogenic hexanucleotide repeat expansion (HRE) in C9orf72, the leading genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), marked a breakthrough in the effort to unravel the etiology of these conditions. Ten years later, clinicians are still working to integrate the implications of this discovery into the care of individuals with ALS and/or FTD. Consensus management guidelines for ALS do not comprehensively address the issue of genetic testing, and questions remain about whom to test, what counseling should be provided before and after testing, laboratory methods, and test interpretation. These challenges have contributed to inconsistent clinical practices and present barriers to patients wishing to access testing. This review summarizes the clinical impact of the discovery of the C9orf72 HRE, outlines ongoing challenges, and provides recommendations for C9orf72 testing, counseling, and research.
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Affiliation(s)
- Jennifer Roggenbuck
- Departments of Neurology and Internal Medicine, The Ohio State University Wexner Medical Center, Columbus
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Shatunov A, Al-Chalabi A. The genetic architecture of ALS. Neurobiol Dis 2020; 147:105156. [PMID: 33130222 DOI: 10.1016/j.nbd.2020.105156] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Aleksey Shatunov
- Department of Basic & Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9RX, UK
| | - Ammar Al-Chalabi
- Department of Basic & Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9RX, UK; Department of Neurology, King's College Hospital, London SE5 9RS, UK.
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Lattante S, Marangi G, Doronzio PN, Conte A, Bisogni G, Zollino M, Sabatelli M. High-Throughput Genetic Testing in ALS: The Challenging Path of Variant Classification Considering the ACMG Guidelines. Genes (Basel) 2020; 11:genes11101123. [PMID: 32987860 PMCID: PMC7600768 DOI: 10.3390/genes11101123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
The development of high-throughput sequencing technologies and screening of big patient cohorts with familial and sporadic amyotrophic lateral sclerosis (ALS) led to the identification of a significant number of genetic variants, which are sometimes difficult to interpret. The American College of Medical Genetics and Genomics (ACMG) provided guidelines to help molecular geneticists and pathologists to interpret variants found in laboratory testing. We assessed the application of the ACMG criteria to ALS-related variants, combining data from literature with our experience. We analyzed a cohort of 498 ALS patients using massive parallel sequencing of ALS-associated genes and identified 280 variants with a minor allele frequency < 1%. Examining all variants using the ACMG criteria, thus considering the type of variant, inheritance, familial segregation, and possible functional studies, we classified 20 variants as “pathogenic”. In conclusion, ALS’s genetic complexity, such as oligogenic inheritance, presence of genes acting as risk factors, and reduced penetrance, needs to be considered when interpreting variants. The goal of this work is to provide helpful suggestions to geneticists and clinicians dealing with ALS.
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Affiliation(s)
- Serena Lattante
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Roma, Italy; (S.L.); (P.N.D.); (M.Z.)
- Complex Operational Unit of Medical Genetics, Department of Laboratory and Infectious Disease Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy
| | - Giuseppe Marangi
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Roma, Italy; (S.L.); (P.N.D.); (M.Z.)
- Complex Operational Unit of Medical Genetics, Department of Laboratory and Infectious Disease Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy
- Correspondence: ; Tel.: +39-0630154606
| | - Paolo Niccolò Doronzio
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Roma, Italy; (S.L.); (P.N.D.); (M.Z.)
- Complex Operational Unit of Medical Genetics, Department of Laboratory and Infectious Disease Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy
| | - Amelia Conte
- Adult NEMO Clinical Center, Complex Operational Unit of Neurology, Department of Aging, Neurological, Orthopedic and Head-Neck Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy; (A.C.); (G.B.); (M.S.)
| | - Giulia Bisogni
- Adult NEMO Clinical Center, Complex Operational Unit of Neurology, Department of Aging, Neurological, Orthopedic and Head-Neck Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy; (A.C.); (G.B.); (M.S.)
| | - Marcella Zollino
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Roma, Italy; (S.L.); (P.N.D.); (M.Z.)
- Complex Operational Unit of Medical Genetics, Department of Laboratory and Infectious Disease Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy
| | - Mario Sabatelli
- Adult NEMO Clinical Center, Complex Operational Unit of Neurology, Department of Aging, Neurological, Orthopedic and Head-Neck Sciences, A. Gemelli University Hospital Foundation IRCCS, 00168 Roma, Italy; (A.C.); (G.B.); (M.S.)
- Section of Neurology, Department of Neuroscience, Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Roma, Italy
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