Prioritizing Causative Genomic Variants by Integrating Molecular and Functional Annotations from Multiple Biomedical Ontologies

  • Azza Th. Althagafi

Student thesis: Doctoral Thesis


Whole-exome and genome sequencing are widely used to diagnose individual patients. However, despite its success, this approach leaves many patients undiagnosed. This could be due to the need to discover more disease genes and variants or because disease phenotypes are novel and arise from a combination of variants of multiple known genes related to the disease. Recent rapid increases in available genomic, biomedical, and phenotypic data enable computational analyses, reducing the search space for disease-causing genes or variants and facilitating the prediction of causal variants. Therefore, artificial intelligence, data mining, machine learning, and deep learning are essential tools that have been used to identify biological interactions, including protein-protein interactions, gene-disease predictions, and variant--disease associations. Predicting these biological associations is a critical step in diagnosing patients with rare or complex diseases. In recent years, computational methods have emerged to improve gene-disease prioritization by incorporating phenotype information. These methods evaluate a patient's phenotype against a database of gene-phenotype associations to identify the closest match. However, inadequate knowledge of phenotypes linked with specific genes in humans and model organisms limits the effectiveness of the prediction. Information about gene product functions and anatomical locations of gene expression is accessible for many genes and can be associated with phenotypes through ontologies and machine-learning models. Incorporating this information can enhance gene-disease prioritization methods and more accurately identify potential disease-causing genes. This dissertation aims to address key limitations in gene-disease prediction and variant prioritization by developing computational methods that systematically relate human phenotypes that arise as a consequence of the loss or change of gene function to gene functions and anatomical and cellular locations of activity. To achieve this objective, this work focuses on crucial problems in the causative variant prioritization pipeline and presents novel computational methods that significantly improve prediction performance by leveraging large background knowledge data and integrating multiple techniques. Therefore, this dissertation presents novel approaches that utilize graph-based machine-learning techniques to leverage biomedical ontologies and linked biological data as background knowledge graphs. The methods employ representation learning with knowledge graphs and introduce generic models that address computational problems in gene-disease associations and variant prioritization. I demonstrate that my approach is capable of compensating for incomplete information in public databases and efficiently integrating with other biomedical data for similar prediction tasks. Moreover, my methods outperform other relevant approaches that rely on manually crafted features and laborious pre-processing. I systematically evaluate our methods and illustrate their potential applications for data analytics in biomedicine. Finally, I demonstrate how our prediction tools can be used in the clinic to assist geneticists in decision-making. In summary, this dissertation contributes to the development of more effective methods for predicting disease-causing variants and advancing precision medicine.
Date of AwardJul 20 2023
Original languageEnglish (US)
Awarding Institution
  • Computer, Electrical and Mathematical Sciences and Engineering
SupervisorRobert Hoehndorf (Supervisor)


  • Whole-Exome Sequencing
  • Whole-Genome Sequencing
  • Disease Genes
  • Disease Variants
  • Disease Phenotypes
  • Causal Variants Prediction
  • Causal Genes Prediction
  • Artificial Intelligence
  • Data Mining
  • Machine Learning
  • Deep Learning
  • Data Analytics
  • Biological Interactions
  • Protein-Protein Interactions
  • Gene-Disease Predictions
  • Variant-Disease Associations
  • Rare Diseases
  • Complex Diseases
  • Gene-Phenotype Associations
  • Ontology
  • Gene Product Functions
  • Anatomical Locations
  • Gene Prioritization
  • Variant Prioritization
  • Loss of Gene Function
  • Background Knowledge Data
  • Biological Knowledge Graph
  • Graph-Based Machine Learning
  • Biomedical Ontologies
  • Linked Biological Data
  • Representation Learning
  • Embeddings
  • Data Integration
  • Precision Medicine
  • Decision-Making
  • Biomedicine.

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