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Journal article
The landscape of non-reference SINE-VNTR-Alus in amyotrophic lateral sclerosis
Experimental biology and medicine (Maywood, N.J.), Vol.250, 10600
2025
Abstract
The fatal neurodegenerative disease, amyotrophic lateral sclerosis (ALS), leads to the degeneration of motor neurons in the brain and spinal cord. Many different genetic variants are known to increase the risk of developing ALS, however much of the disease heritability is still to be identified. To identify novel genetic factors, we characterised SINE-VNTR-Alu (SVA) presence/absence variation in 4403 genomes from the New York Genome Center (NYGC) ALS consortium. SVAs are a type of retrotransposon able to mobilise in the human genome generating new insertions that can modulate gene expression and mRNA splicing and to date 33 insertions are known to cause a range of genetic diseases. In the NYGC ALS consortium sequence data 2831 non-reference genome SVAs were identified and 95% of these insertions were rare with an insertion allele frequency of less than 0.01. Association analysis of the common SVAs with ALS risk, age at onset and survival did not identify any SVAs that survived correction for multiple testing. However, there were three different rare SVA insertions in the ALS associated gene NEK1 identified in four different individuals with ALS. The frequency of these rare insertions in NEK1 was significantly higher in the individuals with ALS from the NYGC ALS consortium compared to the gnomAD SV non-neuro controls (p = 0.0002). This study was the first to characterise non-reference SVA presence/absence variation in a large cohort of ALS individuals identifying insertions as potential candidates involved in disease development for further investigation.
Details
- Title
- The landscape of non-reference SINE-VNTR-Alus in amyotrophic lateral sclerosis
- Authors/Creators
- Abigail L. Pfaff - Murdoch UniversityVivien J. Bubb - University of LiverpoolJohn P. Quinn - University of LiverpoolSulev Kõks - Perron Institute for Neurological and Translational Science
- Publication Details
- Experimental biology and medicine (Maywood, N.J.), Vol.250, 10600
- Publisher
- Frontiers Media S.A.
- Number of pages
- 9
- Identifiers
- 991005783431407891
- Copyright
- © 2025 Pfaff et al.
- Murdoch Affiliation
- Personalised Medicine Centre; Genomics Core Research Facility
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 1 Clinical & Life Sciences
- 1.54 Molecular & Cell Biology - Genetics
- 1.54.1122 Transposable Elements
- Web Of Science research areas
- Medicine, Research & Experimental
- ESI research areas
- Clinical Medicine