Project

PErsoNal Genome QUery IN clinical practice (PENGQUIN)

Code
1S27825N
Duration
01 November 2024 → 31 October 2028
Funding
Research Foundation - Flanders (FWO)
Research disciplines
  • Medical and health sciences
    • Development of bioinformatics software, tools and databases
  • Engineering and technology
    • Bio-informatics
    • Other computer engineering, information technology and mathematical engineering not elsewhere classified
Keywords
Federated Querying Data Privacy Solid
 
Project description

Medical care is becoming increasingly personalized through the use of patient genetic information. At present, data useful for clinical care, including genomic data, are commonly diffuse, organized arbitrarily, and confined within in data silos. Coupled with stringent privacy regulations, high storage costs, and severely limited data sharing infrastructure, the scalability of personalized clinical strategies is considerably constrained. My proposed Ph.D. aims to improve the connectivity and shareability of genomic data storage(s), while preserving data privacy, to decrease the costs of patient genome data use in clinical practice. I propose a citizen-centric storage framework that integrates insights from various semantic web domains research into a novel, practical solution for clinical use. Specifically, I will (a) store patient geomic data using Solid pods, (b) represent personal genome sequence data using RDF as Linked Data, (c) apply policies to stored data, and (d) optimize link traversal queries for data retrieval using indexing methods. Through this research, I aim to provide a comprehensive framework, complemented by a user-friendly web application, to facilitate practical usage of my proposed framework in clinical settings. Ultimately, this PhD seeks to provide the proof-of-concept for an innovative, streamlined product for clinical genome data storage, paving the way for scalable personalized medicine.