Hans Prydz Guest Lecture by Imre Västrik

Imre Västrik, Research Coordinator in the Bioinformatics Team at the Institute for Molecular Medicine Finland (FIMM) will give a talk titled, "TheDB - a smart integrated IT systemfor managing and analysing precision medicine data"

Photo of Imre Västrik

Imre Västrik


We have developed a secure, scalable and extendable solution for management, collection and analysis of most of the health and lifestyle related data - including but not limited to genomic and research data, diagnoses, treatments, clinical lab results, vital signs, questionnaires and answers to them, biological sample storage, cancer somatic mutations, germline variants, gene expression, drug sensitivities - within the same system. The system enables:

  • Storing and managing structured as well as unstructured data with easy-to-use and flexible tools for controlling access to the data.
  • Controlled access to the data: every user access only the data that s/he or his/her role has the right to access, access is logged and changes leave audit trail.
  • Fast, intuitive, web-based queries over potentially massive and complex biomedical data, e.g. how many diagnosis stage myeloma patients with biobanked samples and mutation in K-RAS gene there has been in 2017, who are the people with elevated genetic risk for the Alzheimer's disease, etc.
  • Multicenter/collaborative studies where each party nevertheless may have or want to keep some of the data only to themselves.
  • Queries over aggregate data to assess the data availability, e.g. how many patients matching certain criteria there are, without providing access to the individual level data.
  • Graphical visualisation on data.
  • Management of referrals, requests for sample analysis and data on storage of samples aliquots.
  • Easy processing, QC and reporting of the drug sensitivity testing data.

For example, the haematological samples sent to FIMM for molecular profiling analyses are registered in the system which is then used to store all the data on and derived from the samples.The system has integrate functionality for processing drug sensitivity testing data all the way from plate reader output files to the reports sent back to the clinician who commissioned the analysis.

During my presentation I will give you a walk-through of the system demonstrating some of its most pertinent capabilities.

Published Nov. 6, 2017 3:12 PM - Last modified Nov. 6, 2017 3:13 PM