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Investigating the role of rare genetic variants in the aetiology of haemostasis disorders


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Type

Thesis

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Authors

Abstract

High throughput sequencing and publicly accessible genomic resources increased the diagnostic yields for inherited conditions, and, nowadays, the genetic bases for thousands of Mendelian disorders have been identified. However, providing a molecular diagnosis for these conditions remains challenging, and a considerable portion of patients with inherited conditions still lack a genetic diagnosis. In clinical genomics, identifying the aetiological variants remains a significant hurdle because they are hidden amongst thousands of rare variants present in the genome of each person. Furthermore, historically only the coding portion of the genome, or so-called exome, has been explored to identify causal variants. It is reasonable to assume that, for a fraction of patients with unexplained inherited diseases, the answer lies in the non-coding portion of the genome. To date, the ability to interpret the functional consequences of variants in the non-coding space remains limited. My thesis uses large-scale genomics studies and functional genomic techniques to investigate the role of genetic variants in the aetiology of haemostatic diseases. To explore the contribution of rare coding variants to the different phenotypes, I selected all the pathogenic and likely pathogenic variants from a few well-curated resources. Then, I identified carriers of these variants in the UK Biobank cohort and explored their phenotypes. This approach allowed me to estimate the effect sizes of this class of rare variants on the haemostatic phenotypes and investigate their interplay with common ones. I then expanded my investigation to non-coding regions. I performed experiments to define the most detailed cell type-specific maps of interactions between promoters and regulatory elements for the 93 diagnostic-grade genes for haemostatic diseases. To obtain these interaction landscapes, I differentiated human induced pluripotent stem cells from the principal cell types functionally implicated in haemostasis. I also generated chromatin conformation maps for the relevant genes using a capture Hi-C approach. Finally, I characterised the captured sequences by annotating them with cell type-specific epigenomic features, and I experimentally examined the regulatory potential of some of the defined regions. These validation experiments were based on two independent approaches: (I) reporter assays (II) perturbation of the epigenetic state for a few identified regions. Furthermore, I assessed the impact of rare genetic variants found in the NIHR BioResource Rare Disease participants, 10% of whom have haemostatic diseases. The aim of my PhD project was: (i) to investigate the contribution of rare coding variants to different phenotypes, (ii) to improve the annotation of the non-coding space of a set of well-characterised rare diseases genes and, (iii) to improve our ability to provide an accurate molecular diagnosis for individuals with unexplained inherited haemostatic diseases.

Description

Date

2021-09-30

Advisors

Ouwehand, Willem
Frontini, Mattia

Keywords

genomics, non-coding DNA, Haematology, bleeding disorders, platelet disorders

Qualification

Doctor of Philosophy (PhD)

Awarding Institution

University of Cambridge
Sponsorship
British Heart Foundation (RE/18/1/34212)
British Heart Foundation Cambridge Centre for Research Excellence (RE/18/1/34212)
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