Currently, biobanks at the University Hospital Basel are not centralized. Storage locations are distributed over organizational units, which partly are about to be centrally managed. Biobank inventory management is currently performed in disconnected systems, including Excel lists. There is currently no integrated biobank management software solution in place.
To achieve a professional biobank software solution for a sepsis study at the University Hospital Basel, the Laboratory Medicine team successfully applied for a Swiss National Science Foundation grant (Biolink) grant in January 2017. The call aimed to harmonize IT biobank systems and to establish a biobank management solution (software) in a scientific context.
As a result of a competitive tender process, OpenSpecimen was selected by the Biobanking Committee at University Hospital Basel.
“The OpenSpecimen software solution convinced us with a broad range of technical possibilities and a highly user-friendly interface,” said Prof. Adrian Egli.
Current Research Projects Using OpenSpecimen
Applied Microbiology Research Group
The Applied Microbiology Research Group of Prof. Adrian Egli is involved in a series of clinical and research studies. They aim to analyze host-pathogen interactions and translate their understanding to develop methods of disease diagnostics and prevention.
Currently, they are using OpenSpecimen to manage ~ 20-30 unplanned collection protocols. These protocols involve collecting different types of specimens from the hospitals, which are later utilized for specific studies.
Routine Microbiology Diagnostics
The diagnostic division of Clinical Bacteriology and Mycology of Prof. Adrian Egli uses OpenSpecimen regularly to manage their longitudinal bacterial strain collections from routine diagnostics. This includes e.g., samples for quality measurements or outbreak management. Besides, a series of clinical research trials are also managed by OpenSpecimen e.g.,
- A study exploring the skin microbiome in patients with Graft Versus Host Diseases (GVHD) including swab and skin-tissue samples collection to study skin conditions
- A study to explore community-acquired pneumonia and associated sepsis, which involves the collection of different types of specimens to study changes during severe community-acquired pneumonia and subsequent development of sepsis
University Children’s Hospital Basel Study
The University Children’s Hospital of Both Basel (UKBB), is a University-based hospital committed to healthcare research for children and adolescents. Their primary focus is on disease prevention, diagnostic, and therapeutic research. The research areas involve developmental pediatrics and pneumology, hematology and oncology, immunology and infectiology, and pediatric orthopedics. The UKBB team led by Dr. Stephanie Gros is using OpenSpecimen to manage longitudinal specimen collections from newborns and mothers.
From left to right: Prof. Adrian Egli, Dr. Vladimira Hinic, Swapnil Ingle (OpenSpecimen team), Judith Heckendorn (Team leader of technicians).
The departments of Rheumatology and Clinical Chemistry will start collecting their biospecimen data using OpenSpecimen. The Rheumatology clinical studies are led by Dr. Julia Maurer and Dr. Bettina Bannert. The department of Clinical Chemistry will be processing and temporarily storing the specimens from the external institutes. The specimens will be later distributed as per the requests with the help of the OpenSpecimen’s distribution module. Dr. Sandra Mitrovic, Deputy. Coordinator, Department of Clinical Chemistry, will monitor this study.
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