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Title: Investigation of the molecular basis of inherited developmental conditions in high risk population isolates
Author: Jones, H.
Awarding Body: University of Exeter
Current Institution: University of Exeter
Date of Award: 2019
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The Amish communities of Ohio (USA) are a distinct group of endogamous, rural-living Anabaptist Christians. An ancestral bottleneck, caused by migratory events in the 17th century and subsequent rapid population expansion, has led to the enrichment of a number of inherited conditions within these communities. This provides significantly enhanced power to identify genes responsible for rare monogenic disorders, as well traits with more complex inheritance patterns. The studies detailed in this thesis aims to provide diagnoses to individuals and their families for the underlying genetic causes responsible for the difficulties they experience and contributes to a long-running, non-profit community clinical-genetic research programme called the Windows of Hope (WoH). Forming part of a wider Amish Hearing Loss Program the studies described in chapter three document the discovery of the genetic causes of hearing loss for eight Amish families. Through a combination of targeted gene sequencing, genome-wide SNP mapping and exome sequencing this study identified a variant in the Gap junction beta-2 (GJB2) gene, not previously reported in the Amish, as the cause of non-syndromic hearing loss in six families. Additionally, one family initially thought to be affected by a neurodevelopment disorder which included syndromic hearing loss, was found to possess two distinct genetic disorders; a 16p11.2 microdeletion, responsible for the developmental delay, and a homozygous GJB2 variant, responsible for the hearing loss. Finally, this chapter proposes two novel hearing loss genes and details the functional work undertaken to assess the pathogenicity of one of these genes (SLC15A5). This work provided important diagnoses for many families and acquired significant information regarding the spectrum and frequency of hearing loss-associated gene variants across distinct Amish communities. Chapter four details work undertaken to define the clinical phenotype and molecular basis of a novel complex autosomal recessive neurological disorder. Work undertaken by one of our collaborators, Dr Zineb Ammous, was instrumental in precisely defining the clinical phenotype of this disorder. A combination of genome-wide SNP mapping and exome sequence identified a sequence variant in Smad Nuclear Interacting Protein 1 (SNIP1), which encodes an evolutionary-conserved transcriptional regulator, as the likely underlying genetic cause. Due to its role as a transcription regulator whole transcriptome sequencing was undertaken to determine the impact of this gene mutation. This work provided important information regarding the specific biological role of SNIP1 and identified gene expression pathways of direct relevance to the clinical phenotype, highlighting therapeutic approaches likely to benefit affected individuals. Additionally, this study determined that SNIP1-associated syndrome is one of the most common conditions across many Amish communities. In recent years the WoH Project has accumulated extensive single nucleotide polymorphisms (SNP) and exome sequencing datasets from patients and individuals from the Amish community. Chapter five outlines a pilot, proof-of-principle study undertaken to explore this data with the aim characterising the architecture of the Amish genome. The interrogation of 26 exomes identified the presence of 12 pathogenic variants known to cause autosomal recessive (AR) diseases that have not yet been reported in the Amish but are likely to be present. Additionally, a PLEXseq sequencing approach was implemented to determine the prevalence of 165 pathogenic variants in 171 unaffected Amish individuals. The findings indicated diverse carrier frequencies within the different Amish communities and contributed to the consolidation of two genes responsible for ultra-rare inherited AR diseases (CEP55, MNS1). By developing approaches to improve knowledge of the specific causes of inherited diseases in the community, this work has laid the foundation for the development of a new genetic-based approach to diagnostic testing in the community. This thesis, and the wider programme of work of Windows of Hope, occupies a privileged positioned at the interface between scientific research and clinical care. The findings described here have made a significant contribution to our understanding of the pathomolecular cause of a number of rare inherited disorders by increasing our knowledge of the nature and spectrum of inherited disease within the Amish laying the foundations to aid the future discovery of new disease genes and improving clinical outcomes by enabling focussed clinical diagnostic and management strategies to be implemented.
Supervisor: Crosby, A. ; Baple, E. ; Chioza, B. Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available