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Title: Structural variation in Parkinson's disease : focusing on the role of transposable elements in disease predisposition and pathogenesis
Author: Billingsley, K. J.
ISNI:       0000 0004 8505 6969
Awarding Body: University of Liverpool
Current Institution: University of Liverpool
Date of Award: 2019
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Parkinson’s disease (PD) is a neurodegenerative disorder with a complex aetiology including genetic risk factors, environmental exposure and aging. Recent genome wide association studies have been successful at identifying genetic variation that confers a risk for PD, yet despite this it is predicted that the large majority of the genetic attribution to the disease is still unknown. It is also noted that much of the identified risk loci lie within poorly annotated regions of the genome such as those containing repetitive sequences and transposable elements (TE)s, highlighting the importance of further investigation into such regions. Despite many reports that associate TE insertions with PD no study has comprehensively analysed the role of these elements in the disease. The work presented in this thesis sought to ask three main questions; first, are TE overrepresented at PD risk loci using a haplotype block based genome-wide analysis, second are non-reference TE associated with risk of PD using a newly developed TE detection tool and PD WGS data; and third, are TE differentially regulated in the blood or skin of individuals with PD. This work leveraged genetic and expression datasets to comprehensively address the role of TE in PD. Along with identifying that specific TE are overrepresented at PD risk loci we also show that in the blood, specific repetitive elements (satellite) are differentially expression in PD. Most significantly, we characterised known non-reference TE presence/absence polymorphisms in collaboration with the International Parkinson’s Disease Genomic Consortium (IPDGC) in PD whole genome sequencing data (WGS) from the Parkinson’s Progression Markers Initiative (PPMI) cohort using the TE detection tool MELT. We identify that TE insertions are a heritable and common form of genetic variation that lie within potentially important functional domains of the genome. Not only do many non-reference TE map to PD risk loci, but from our initial study we have identified that non-reference TE’s are in moderate linkage disequilibrium with PD risk variants, and thus a candidate causal variant that warrant further study at these loci. In summary, TE insertions are a major source and often overlooked form of genetic variation in the human genome. Collectively the research presented in this thesis suggests that not only could integrating TE variants be a valuable and critical step forward for furthering our understanding of existing risk PD variants, but it could also be valuable for establishing new risk factors.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral