Journal article
Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis
Gene, Vol.843, Art. 146799
2022
Abstract
The genetics of an individual is a crucial factor in understanding the risk of developing the neurodegenerative disease amyotrophic lateral sclerosis (ALS). There is still a large proportion of the heritability of ALS, particularly in sporadic cases, to be understood. Among others, active transposable elements drive inter-individual variability, and in humans long interspersed element 1 (LINE1, L1), Alu and SINE-VNTR-Alu (SVA) retrotransposons are a source of polymorphic insertions in the population. We undertook a pilot study to characterise the landscape of non-reference retrotransposon insertion polymorphisms (non-ref RIPs) in 15 control and 15 ALS individuals’ whole genomes from Project MinE, an international project to identify potential genetic causes of ALS. The combination of two bioinformatics tools (mobile element locator tool (MELT) and TEBreak) identified on average 1250 Alu, 232 L1 and 77 SVA non-ref RIPs per genome across the 30 analysed. Further PCR validation of individual polymorphic retrotransposon insertions showed a similar level of accuracy for MELT and TEBreak. Our preliminary study did not identify a specific RIP or a significant difference in the total number of non-ref RIPs in ALS compared to control genomes. The use of multiple bioinformatic tools improved the accuracy of non-ref RIP detection and our study highlights the potential importance of studying these elements further in ALS.
Details
- Title
- Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis
- Authors/Creators
- A.L. Savage (Author/Creator) - University of LiverpoolA. Iacoangeli (Author/Creator) - King's College LondonG.G. Schumann (Author/Creator) - Paul Ehrlich InstitutA. Rubio-Roldan (Author/Creator) - Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological ResearchJ.L. Garcia-Perez (Author/Creator) - University of EdinburghA. Al Khleifat (Author/Creator) - King's College LondonS. Kõks (Author/Creator) - Perron Institute for Neurological and Translational ScienceV.J. Bubb (Author/Creator) - University of LiverpoolA. Al-Chalabi (Author/Creator) - King's College LondonJ.P. Quinn (Author/Creator) - University of Liverpool
- Publication Details
- Gene, Vol.843, Art. 146799
- Publisher
- Elsevier BV
- Identifiers
- 991005542317607891
- Copyright
- © 2022 The Authors.
- Murdoch Affiliation
- Centre for Molecular Medicine and Innovative Therapeutics
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 1 Clinical & Life Sciences
- 1.54 Molecular & Cell Biology - Genetics
- 1.54.1122 Transposable Elements
- Web Of Science research areas
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics