Identifying and characterising novel genomic variants and disease mechanisms in patients with rare and novel diseases

  • John Harkness

Student thesis: Phd


Rare diseases are individually uncommon, but cumulatively affect 1 in 17 people. Development of next generation sequencing technologies including whole genome sequencing (WGS) and whole exome sequencing (WES), and associated data analysis algorithms allow the identification of rare and novel genetic variants that underly rare inherited diseases. However, for many patients diagnosis is challenging due to the complexity involved in predicting effect of novel variants in non-coding regions and genes that are poorly described. The aim of this work is to identify novel genomic variants which contribute to monogenic disease in patients with rare diseases, and to characterise any novel mechanisms of disease. We carried out analysis of WGS or WES data from several individuals affected by different rare diseases. In an individual with atypical urofacial syndrome WES analysis identified a variant in EBF3, which causes hypotonia, ataxia, and developmental delay syndrome, within which urological phenotypes are common. WGS analysis was carried out for a cohort of foetuses with urorectal septum malformation sequence following detailed foetal autopsy. WGS was not diagnostic in this cohort, but did identify candidate variants in HOXD9, NALCN, SLIT6, TMEM132A, implying an oligogenic model of disease. WGS data were reanalysed from a family with a variable occipital horn syndrome phenotype, leading to identification of a novel deep intronic ATP7A variant. Analysis of splicing in a minigene assay and patient RNA revealed a leaky splicing effect predictive of protein truncation. Autozygosity mapping and WES analysis of a consanguineous family with several children affected by acute necrotising encephalopathy secondary to febrile infection identified a novel homozygous variant in RCC1. Further patients were identified though reverse phenotyping. Enzymatic and stability assays using recombinantly expressed protein refuted a hypothesis of thermolability. Immunofluorescent imaging suggests delocalisation of Rcc1 from chromatin, prompting further investigation into the involvement of nucleocytoplasmic transport dysfunction. This work displays the value offered by undertaking genomic analysis of patients in a research setting and highlights the challenges that remain in detecting genomic variants in patients with complex phenotypes.
Date of Award1 Aug 2023
Original languageEnglish
Awarding Institution
  • The University of Manchester
SupervisorSimon Hubbard (Supervisor), William Newman (Supervisor) & Siddharth Banka (Supervisor)


  • ATP7A
  • Urorectal Septum Malformation Sequence
  • RCC1
  • Occipital Horn Syndrome
  • Fever-Associated Axonal Neuropathy
  • Urofacial Syndrome
  • NGS
  • Missing Heritability
  • Rare Disease
  • Genomics
  • EBF3

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