Amyotrophic lateral sclerosis onset is influenced by the burden of rare variants in known amyotrophic lateral sclerosis genes
Objective To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to comprehensively sequence 17 known ALS genes in 391 ALS patients from the United States. Methods Targeted pooled‐sample sequencing was used to i...
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| Published in | Annals of neurology Vol. 77; no. 1; pp. 100 - 113 |
|---|---|
| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Blackwell Publishing Ltd
01.01.2015
Wiley Subscription Services, Inc |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0364-5134 1531-8249 1531-8249 |
| DOI | 10.1002/ana.24306 |
Cover
| Abstract | Objective
To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to comprehensively sequence 17 known ALS genes in 391 ALS patients from the United States.
Methods
Targeted pooled‐sample sequencing was used to identify variants in 17 ALS genes. Fragment size analysis was used to define ATXN2 and C9ORF72 expansion sizes. Genotype–phenotype correlations were made with individual variants and total burden of variants. Rare variant associations for risk of ALS were investigated at both the single variant and gene level.
Results
A total of 64.3% of familial and 27.8% of sporadic subjects carried potentially pathogenic novel or rare coding variants identified by sequencing or an expanded repeat in C9ORF72 or ATXN2; 3.8% of subjects had variants in >1 ALS gene, and these individuals had disease onset 10 years earlier (p = 0.0046) than subjects with variants in a single gene. The number of potentially pathogenic coding variants did not influence disease duration or site of onset.
Interpretation
Rare and potentially pathogenic variants in known ALS genes are present in >25% of apparently sporadic and 64% of familial patients, significantly higher than previous reports using less comprehensive sequencing approaches. A significant number of subjects carried variants in >1 gene, which influenced the age of symptom onset and supports oligogenic inheritance as relevant to disease pathogenesis. ANN NEUROL 2015;77:100–113 |
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| AbstractList | To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to comprehensively sequence 17 known ALS genes in 391 ALS patients from the United States.OBJECTIVETo define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to comprehensively sequence 17 known ALS genes in 391 ALS patients from the United States.Targeted pooled-sample sequencing was used to identify variants in 17 ALS genes. Fragment size analysis was used to define ATXN2 and C9ORF72 expansion sizes. Genotype-phenotype correlations were made with individual variants and total burden of variants. Rare variant associations for risk of ALS were investigated at both the single variant and gene level.METHODSTargeted pooled-sample sequencing was used to identify variants in 17 ALS genes. Fragment size analysis was used to define ATXN2 and C9ORF72 expansion sizes. Genotype-phenotype correlations were made with individual variants and total burden of variants. Rare variant associations for risk of ALS were investigated at both the single variant and gene level.A total of 64.3% of familial and 27.8% of sporadic subjects carried potentially pathogenic novel or rare coding variants identified by sequencing or an expanded repeat in C9ORF72 or ATXN2; 3.8% of subjects had variants in >1 ALS gene, and these individuals had disease onset 10 years earlier (p = 0.0046) than subjects with variants in a single gene. The number of potentially pathogenic coding variants did not influence disease duration or site of onset.RESULTSA total of 64.3% of familial and 27.8% of sporadic subjects carried potentially pathogenic novel or rare coding variants identified by sequencing or an expanded repeat in C9ORF72 or ATXN2; 3.8% of subjects had variants in >1 ALS gene, and these individuals had disease onset 10 years earlier (p = 0.0046) than subjects with variants in a single gene. The number of potentially pathogenic coding variants did not influence disease duration or site of onset.Rare and potentially pathogenic variants in known ALS genes are present in >25% of apparently sporadic and 64% of familial patients, significantly higher than previous reports using less comprehensive sequencing approaches. A significant number of subjects carried variants in >1 gene, which influenced the age of symptom onset and supports oligogenic inheritance as relevant to disease pathogenesis.INTERPRETATIONRare and potentially pathogenic variants in known ALS genes are present in >25% of apparently sporadic and 64% of familial patients, significantly higher than previous reports using less comprehensive sequencing approaches. A significant number of subjects carried variants in >1 gene, which influenced the age of symptom onset and supports oligogenic inheritance as relevant to disease pathogenesis. Objective To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to comprehensively sequence 17 known ALS genes in 391 ALS patients from the United States. Methods Targeted pooled-sample sequencing was used to identify variants in 17 ALS genes. Fragment size analysis was used to define ATXN2 and C9ORF72 expansion sizes. Genotype-phenotype correlations were made with individual variants and total burden of variants. Rare variant associations for risk of ALS were investigated at both the single variant and gene level. Results A total of 64.3% of familial and 27.8% of sporadic subjects carried potentially pathogenic novel or rare coding variants identified by sequencing or an expanded repeat in C9ORF72 or ATXN2; 3.8% of subjects had variants in >1 ALS gene, and these individuals had disease onset 10 years earlier (p=0.0046) than subjects with variants in a single gene. The number of potentially pathogenic coding variants did not influence disease duration or site of onset. Interpretation Rare and potentially pathogenic variants in known ALS genes are present in >25% of apparently sporadic and 64% of familial patients, significantly higher than previous reports using less comprehensive sequencing approaches. A significant number of subjects carried variants in >1 gene, which influenced the age of symptom onset and supports oligogenic inheritance as relevant to disease pathogenesis. ANN NEUROL 2015; 77:100-113 To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to comprehensively sequence 17 known ALS genes in 391 ALS patients from the United States. Targeted pooled-sample sequencing was used to identify variants in 17 ALS genes. Fragment size analysis was used to define ATXN2 and C9ORF72 expansion sizes. Genotype-phenotype correlations were made with individual variants and total burden of variants. Rare variant associations for risk of ALS were investigated at both the single variant and gene level. A total of 64.3% of familial and 27.8% of sporadic subjects carried potentially pathogenic novel or rare coding variants identified by sequencing or an expanded repeat in C9ORF72 or ATXN2; 3.8% of subjects had variants in >1 ALS gene, and these individuals had disease onset 10 years earlier (p = 0.0046) than subjects with variants in a single gene. The number of potentially pathogenic coding variants did not influence disease duration or site of onset. Rare and potentially pathogenic variants in known ALS genes are present in >25% of apparently sporadic and 64% of familial patients, significantly higher than previous reports using less comprehensive sequencing approaches. A significant number of subjects carried variants in >1 gene, which influenced the age of symptom onset and supports oligogenic inheritance as relevant to disease pathogenesis. Objective To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to comprehensively sequence 17 known ALS genes in 391 ALS patients from the United States. Methods Targeted pooled‐sample sequencing was used to identify variants in 17 ALS genes. Fragment size analysis was used to define ATXN2 and C9ORF72 expansion sizes. Genotype–phenotype correlations were made with individual variants and total burden of variants. Rare variant associations for risk of ALS were investigated at both the single variant and gene level. Results A total of 64.3% of familial and 27.8% of sporadic subjects carried potentially pathogenic novel or rare coding variants identified by sequencing or an expanded repeat in C9ORF72 or ATXN2; 3.8% of subjects had variants in >1 ALS gene, and these individuals had disease onset 10 years earlier (p = 0.0046) than subjects with variants in a single gene. The number of potentially pathogenic coding variants did not influence disease duration or site of onset. Interpretation Rare and potentially pathogenic variants in known ALS genes are present in >25% of apparently sporadic and 64% of familial patients, significantly higher than previous reports using less comprehensive sequencing approaches. A significant number of subjects carried variants in >1 gene, which influenced the age of symptom onset and supports oligogenic inheritance as relevant to disease pathogenesis. ANN NEUROL 2015;77:100–113 |
| Author | Miller, Timothy M. Harms, Matthew B. Goate, Alison Baloh, Robert H. Cady, Janet Ravits, John Bali, Taha Pestronk, Alan Allred, Peggy Mitra, Robi D. |
| Author_xml | – sequence: 1 givenname: Janet surname: Cady fullname: Cady, Janet organization: Department of Neurology, Washington University, MO, St, Louis – sequence: 2 givenname: Peggy surname: Allred fullname: Allred, Peggy organization: Department of Neurology, Cedars Sinai Medical Center, CA, Los Angeles – sequence: 3 givenname: Taha surname: Bali fullname: Bali, Taha organization: Department of Neurology, Washington University, MO, St, Louis – sequence: 4 givenname: Alan surname: Pestronk fullname: Pestronk, Alan organization: Department of Neurology, Washington University, MO, St, Louis – sequence: 5 givenname: Alison surname: Goate fullname: Goate, Alison organization: Department of Neurology, Washington University, St, Louis, MO – sequence: 6 givenname: Timothy M. surname: Miller fullname: Miller, Timothy M. organization: Department of Neurology, Washington University, St, Louis, MO – sequence: 7 givenname: Robi D. surname: Mitra fullname: Mitra, Robi D. organization: Department of Genetics, Washington University, MO, St Louis – sequence: 8 givenname: John surname: Ravits fullname: Ravits, John organization: Department of Neurosciences, University of California, San Diego, CA, La Jolla – sequence: 9 givenname: Matthew B. surname: Harms fullname: Harms, Matthew B. email: harmsm@neuro.wustl.edu organization: Department of Neurology, Washington University, St, Louis, MO – sequence: 10 givenname: Robert H. surname: Baloh fullname: Baloh, Robert H. email: harmsm@neuro.wustl.edu organization: Department of Neurology, Cedars Sinai Medical Center, CA, Los Angeles |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25382069$$D View this record in MEDLINE/PubMed |
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| Copyright | 2014 American Neurological Association 2014 American Neurological Association. 2015 American Neurological Association |
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| Notes | Genetics Epidemiology Training - No. 5-T32-HL-83822-5 ArticleID:ANA24306 NIH - No. R01-NS069669 ark:/67375/WNG-WKG5WFN7-X istex:C44974017E6964F18DADDF8DB385CBC4BB6834A8 NIH National Institute of Neurological Disorders and Stroke - No. K08-NS075094 NIH National Institute on Aging - No. 5P50 AG005681-29; No. 5P01 AG03991-30; No. 5R01 AG035083-04 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 |
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| PublicationTitle | Annals of neurology |
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MacArthur DG, Manolio TA, Dimmock DP, et al. Guidelines for investigating causality of sequence variants in human disease. Nature 2014;508:469-476. Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 2012;14:178-192. Al-Chalabi A, Fang F, Hanby MF, et al. An estimate of amyotrophic lateral sclerosis heritability using twin data. J Neurol Neurosurg Psychiatry 2010;81:1324-1326. Chiò A, Calvo A, Mazzini L, et al. Extensive genetics of ALS: a population-based study in Italy. Neurology 2012;79:1983-1989. Kurland LT, Mulder DW. Epidemiologic investigations of amyotrophic lateral sclerosis. 2. Familial aggregations indicative of dominant inheritance. I. Neurology 1955;5:182-196. Harms MB, Baloh RH. Clinical neurogenetics: amyotrophic lateral sclerosis. Neurol Clin 2013;31:929-950. Wu C-H, Fallini C, Ticozzi N, et al. Mutations in the profilin 1 gene cause familial amyotrophic lateral sclerosis. Nature 2012;488:499-503. Vallania FLM, Druley TE, Ramos E, et al. High-throughput discovery of rare insertions and deletions in large cohorts. Genome Res 2010;20:1711-1718. Harms MB, Cady J, Zaidman C, et al. Lack of C9ORF72 coding mutations supports a gain of function for repeat expansions in amyotrophic lateral sclerosis. Neurobiol Aging 2013;34:2234.e13-2234.e19. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinforma Oxf Engl 2009;25:2078-2079. Elden AC, Kim H-J, Hart MP, et al. Ataxin-2 intermediate-length polyglutamine expansions are associated with increased risk for ALS. Nature 2010;466:1069-1075. 1000 Genomes Project Consortium, Abecasis GR, Auton A, et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491:56-65. Kwon M-J, Baek W, Ki C-S, et al. 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| References_xml | – reference: Kwon M-J, Baek W, Ki C-S, et al. Screening of the SOD1, FUS, TARDBP, ANG, and OPTN mutations in Korean patients with familial and sporadic ALS. Neurobiol Aging 2012;33:1017.e17-1017.e23. – reference: Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 2012;14:178-192. – reference: Druley TE, Vallania FLM, Wegner DJ, et al. Quantification of rare allelic variants from pooled genomic DNA. Nat Methods 2009;6:263-265. – reference: Renton AE, Chiò A, Traynor BJ. State of play in amyotrophic lateral sclerosis genetics. Nat Neurosci 2014;17:17-23. – reference: Gros-Louis F, Gaspar C, Rouleau GA. Genetics of familial and sporadic amyotrophic lateral sclerosis. Biochim Biophys Acta 2006;1762:956-972. – reference: Xue Y, Chen Y, Ayub Q, et al. Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am J Hum Genet 2012;91:1022-1032. – reference: DeJesus-Hernandez M, Mackenzie IR, Boeve BF, et al. Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 2011;72:245-256. – reference: Van Blitterswijk M, van Es MA, Hennekam EAM, et al. Evidence for an oligogenic basis of amyotrophic lateral sclerosis. Hum Mol Genet 2012;21:3776-3784. – reference: 1000 Genomes Project Consortium, Abecasis GR, Auton A, et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491:56-65. – reference: Kurland LT, Mulder DW. Epidemiologic investigations of amyotrophic lateral sclerosis. 2. Familial aggregations indicative of dominant inheritance. II. Neurology 1955;5:249-268. – reference: Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinforma Oxf Engl 2009;25:2078-2079. – reference: Harms MB, Baloh RH. Clinical neurogenetics: amyotrophic lateral sclerosis. Neurol Clin 2013;31:929-950. – reference: Van Damme P, Veldink JH, van Blitterswijk M, et al. Expanded ATXN2 CAG repeat size in ALS identifies genetic overlap between ALS and SCA2. Neurology 2011;76:2066-2072. – reference: Kurland LT, Mulder DW. Epidemiologic investigations of amyotrophic lateral sclerosis. 2. Familial aggregations indicative of dominant inheritance. I. Neurology 1955;5:182-196. – reference: Mehta P, Antao V, Kaye W, et al. Prevalence of amyotrophic lateral sclerosis - United States, 2010-2011. Morb Mortal Wkly Rep Surveill Summ 2014;63(suppl 7):1-14. – reference: Andersen PM, Al-Chalabi A. Clinical genetics of amyotrophic lateral sclerosis: what do we really know? Nat Rev Neurol 2011;7:603-615. – reference: Flanagan SE, Patch A-M, Ellard S. 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Amyotroph Lateral Scler 2011;12:157-159. – reference: Abhinav K, Stanton B, Johnston C, et al. Amyotrophic lateral sclerosis in South-East England: a population-based study. The South-East England register for amyotrophic lateral sclerosis (SEALS Registry). Neuroepidemiology 2007;29:44-48. – reference: Vallania FLM, Druley TE, Ramos E, et al. High-throughput discovery of rare insertions and deletions in large cohorts. Genome Res 2010;20:1711-1718. – reference: Robinson JT, Thorvaldsdóttir H, Winckler W, et al. Integrative genomics viewer. Nat Biotechnol 2011;29:24-26. – reference: Al-Chalabi A, Fang F, Hanby MF, et al. An estimate of amyotrophic lateral sclerosis heritability using twin data. J Neurol Neurosurg Psychiatry 2010;81:1324-1326. – reference: Brooks BR. El Escorial World Federation of Neurology criteria for the diagnosis of amyotrophic lateral sclerosis. 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Am J Hum Genet 2013;92:345-353. – volume: 31 start-page: 929 year: 2013 end-page: 950 article-title: Clinical neurogenetics: amyotrophic lateral sclerosis publication-title: Neurol Clin – volume: 89 start-page: 82 year: 2011 end-page: 93 article-title: Rare‐variant association testing for sequencing data with the sequence kernel association test publication-title: Am J Hum Genet – volume: 29 start-page: 24 year: 2011 end-page: 26 article-title: Integrative genomics viewer publication-title: Nat Biotechnol – volume: 466 start-page: 1069 year: 2010 end-page: 1075 article-title: Ataxin‐2 intermediate‐length polyglutamine expansions are associated with increased risk for ALS publication-title: Nature – volume: 108 start-page: 20881 year: 2011 end-page: 20890 article-title: A yeast functional screen predicts new candidate ALS disease genes publication-title: Proc Natl Acad Sci U S A – volume: 83 start-page: 1201 year: 2012 end-page: 1203 article-title: Classification of familial amyotrophic lateral sclerosis by family history: effects on frequency of genes mutation publication-title: J Neurol Neurosurg Psychiatry – volume: 20 start-page: 1711 year: 2010 end-page: 1718 article-title: High‐throughput discovery of rare insertions and deletions in large cohorts publication-title: Genome Res – volume: 491 start-page: 56 year: 2012 end-page: 65 article-title: An integrated map of genetic variation from 1,092 human genomes publication-title: Nature – volume: 17 start-page: 17 year: 2014 end-page: 23 article-title: State of play in amyotrophic lateral sclerosis genetics publication-title: Nat Neurosci – volume: 14 start-page: 178 year: 2012 end-page: 192 article-title: Integrative Genomics Viewer (IGV): high‐performance genomics data visualization and exploration publication-title: Brief Bioinform – volume: 32 start-page: 358 year: 2011 end-page: 368 article-title: Performance of mutation pathogenicity prediction methods on missense variants publication-title: Hum Mutat – volume: 6 start-page: 263 year: 2009 end-page: 265 article-title: Quantification of rare allelic variants from pooled genomic DNA publication-title: Nat Methods – volume: 23 start-page: 2220 year: 2014 end-page: 2231 article-title: A genome‐wide association meta‐analysis identifies a novel locus at 17q11.2 associated with sporadic amyotrophic lateral sclerosis publication-title: Hum Mol Genet – volume: 63 start-page: 1 issue: suppl 7 year: 2014 end-page: 14 article-title: Prevalence of amyotrophic lateral sclerosis ‐ United States, 2010–2011 publication-title: Morb Mortal Wkly Rep Surveill Summ – volume: 12 start-page: 157 year: 2011 end-page: 159 article-title: Proposed criteria for familial amyotrophic lateral sclerosis publication-title: Amyotroph Lateral Scler – volume: 25 start-page: 2078 year: 2009 end-page: 2079 article-title: The Sequence Alignment/Map format and SAMtools publication-title: Bioinforma Oxf Engl – volume: 50 start-page: 776 year: 2013 end-page: 783 article-title: Delineating the genetic heterogeneity of ALS using targeted high‐throughput sequencing publication-title: J Med Genet – volume: 71 start-page: 1123 year: 2014 article-title: Genome‐wide analysis of the heritability of amyotrophic lateral sclerosis publication-title: JAMA Neurol – volume: 72 start-page: 245 year: 2011 end-page: 256 article-title: Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p‐linked FTD and ALS publication-title: Neuron – volume: 13 start-page: 217 year: 2012 end-page: 222 article-title: SOD1, ANG, TARDBP and FUS mutations in amyotrophic lateral sclerosis: a United States clinical testing lab experience publication-title: Amyotroph Lateral Scler – volume: 76 start-page: 2066 year: 2011 end-page: 2072 article-title: Expanded ATXN2 CAG repeat size in ALS identifies genetic overlap between ALS and SCA2 publication-title: Neurology – volume: 33 start-page: 1017.e17 year: 2012 end-page: 1017.e23 article-title: Screening of the SOD1, FUS, TARDBP, ANG, and OPTN mutations in Korean patients with familial and sporadic ALS publication-title: Neurobiol Aging – volume: 91 start-page: 1022 year: 2012 end-page: 1032 article-title: Deleterious‐ and disease‐allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population‐scale resequencing publication-title: Am J Hum Genet – volume: 488 start-page: 499 year: 2012 end-page: 503 article-title: Mutations in the profilin 1 gene cause familial amyotrophic lateral sclerosis publication-title: Nature – volume: 21 start-page: 3776 year: 2012 end-page: 3784 article-title: Evidence for an oligogenic basis of amyotrophic lateral sclerosis publication-title: Hum Mol Genet – volume: 5 start-page: 249 year: 1955 end-page: 268 article-title: Epidemiologic investigations of amyotrophic lateral sclerosis. 2. 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Subcommittee on Motor Neuron Diseases/Amyotrophic Lateral Sclerosis of the World Federation of Neurology Research Group on Neuromuscular Diseases and the El Escorial “Clinical limits of amyotrophic lateral sclerosis” workshop contributors publication-title: J Neurol Sci – volume: 81 start-page: 1324 year: 2010 end-page: 1326 article-title: An estimate of amyotrophic lateral sclerosis heritability using twin data publication-title: J Neurol Neurosurg Psychiatry – volume: 14 start-page: 533 year: 2010 end-page: 537 article-title: Using SIFT and PolyPhen to predict loss‐of‐function and gain‐of‐function mutations publication-title: Genet Test Mol Biomark – volume: 1762 start-page: 956 year: 2006 end-page: 972 article-title: Genetics of familial and sporadic amyotrophic lateral sclerosis publication-title: Biochim Biophys Acta – volume: 34 start-page: 2234.e13 year: 2013 end-page: 2234.e19 article-title: Lack of C9ORF72 coding mutations supports a gain of function for repeat expansions in amyotrophic lateral sclerosis publication-title: Neurobiol Aging – volume: 92 start-page: 345 year: 2013 end-page: 353 article-title: Large C9orf72 hexanucleotide repeat expansions are seen in multiple neurodegenerative syndromes and are more frequent than expected in the UK population publication-title: Am J Hum Genet – volume: 5 start-page: 182 year: 1955 end-page: 196 article-title: Epidemiologic investigations of amyotrophic lateral sclerosis. 2. 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To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to... To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to... Objective To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to... |
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| SubjectTerms | Adolescent Adult Age of Onset Aged Aged, 80 and over Amyotrophic lateral sclerosis Amyotrophic Lateral Sclerosis - genetics Ataxins C9orf72 Protein Computational Biology Female Genes Genetic Association Studies Genetic Variation - genetics Genotype Humans Longitudinal Studies Male Middle Aged Nerve Tissue Proteins - genetics Phenotype Proteins - genetics United States Young Adult |
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| Title | Amyotrophic lateral sclerosis onset is influenced by the burden of rare variants in known amyotrophic lateral sclerosis genes |
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