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Rautila OS, Kaivola K, Rautila H, Hokkanen L, Launes J, Strandberg TE, Laaksovirta H, Palmio J, Tienari PJ. The shared ancestry between the C9orf72 hexanucleotide repeat expansion and intermediate-length alleles using haplotype sharing trees and HAPTK. Am J Hum Genet 2024; 111:383-392. [PMID: 38242117 PMCID: PMC10870140 DOI: 10.1016/j.ajhg.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
The C9orf72 hexanucleotide repeat expansion (HRE) is a common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The inheritance is autosomal dominant, but a high proportion of subjects with the mutation are simplex cases. One possible explanation is de novo expansions of unstable intermediate-length alleles (IAs). Using haplotype sharing trees (HSTs) with the haplotype analysis tool kit (HAPTK), we derived majority-based ancestral haplotypes of HRE samples and discovered that IAs containing ≥18-20 repeats share large haplotypes in common with the HRE. Using HSTs of HRE and IA samples, we demonstrate that the longer IA haplotypes are largely indistinguishable from HRE haplotypes and that several ≥18-20 IA haplotypes share over 5 Mb (>600 markers) haplotypes in common with the HRE haplotypes. These analysis tools allow physical understanding of the haplotype blocks shared with the majority-based ancestral haplotype. Our results demonstrate that the haplotypes with longer IAs belong to the same pool of haplotypes as the HRE and suggest that longer IAs represent potential premutation alleles.
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Affiliation(s)
- Osma S Rautila
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Neurology, Helsinki University Hospital, Helsinki, Finland.
| | - Karri Kaivola
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Harri Rautila
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Laura Hokkanen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Jyrki Launes
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Timo E Strandberg
- University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hannu Laaksovirta
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Johanna Palmio
- Neuromuscular Research Center, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Pentti J Tienari
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Neurology, Helsinki University Hospital, Helsinki, Finland
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Affiliation(s)
- Benedikt Schoser
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Giovanni Meola
- Department of Biomedical Sciences for Health University of Milan, Milan, Italy.,Department of Neurology, IRCCS Policlinico San Donato, Milan, Italy
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