Artikel
An advanced biomaterial bank interface for clinical studies at the University Medical Center Hamburg-Eppendorf
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Autoren
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Layla Tabea Riemann
- Institute for Applied Medical Informatics (IAM), Center for Experimental Medicine, University Hospital Hamburg-Eppendorf (UKE), Hamburg, Germany
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Michael Brehler
- Institute of Medical Systems Biology, Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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Maximilian Ataian
- Institute for Applied Medical Informatics (IAM), Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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Maksims Fiosins
- Institute of Medical Systems Biology, Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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Hauke Schneiderheinze
- Research IT, University Medical Center Hamburg-Eppendorf, Hamburg (UKE), Hamburg, Germany
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Johnannes Wagner
- Research IT, University Medical Center Hamburg-Eppendorf, Hamburg (UKE), Hamburg, Germany
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Marcus Wurlitzer
- Research IT, University Medical Center Hamburg-Eppendorf, Hamburg (UKE), Hamburg, Germany
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Luis Felipe Barquero Jimenez
- Institute of Medical Systems Biology, Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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Oliver Köckritz
- Research IT, University Medical Center Hamburg-Eppendorf, Hamburg (UKE), Hamburg, Germany
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Jan Erik Gewehr
- Research IT, University Medical Center Hamburg-Eppendorf, Hamburg (UKE), Hamburg, Germany
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Frank Ückert
- Institute for Applied Medical Informatics (IAM), Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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Stefan Bonn
- Institute of Medical Systems Biology, Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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Tobias B. Huber
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany; III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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Maja Lindenmeyer
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany; III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| Veröffentlicht: | 6. September 2024 |
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Gliederung
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Introduction: Using biomaterial banks is important for standardizing and improving the collection of biomaterial samples and patient information, especially for personalized medicine [1] or AI. An advanced biomaterial bank interface (ABBI) is being introduced to facilitate secure data management for biobanking and retrospective register studies. ABBI is introduced as a model for biomaterial banks at the UKE within the kidney biobank with the intent to transcend its application to other medical centers. Biobank here refers to the whole construct and organizational unit, whereas ABBI refers exclusively to the ETL process including the metadata governance, the UI, and the IT-infrastructure.
Methods: Organizationally and ethically, ABBI operates similarly to [2]. ABBI is designed to handle various sample types, e.g., blood, tissue, urine, and PBMC. The biobank has no end date and currently enrolls about 280 patients annually, with ongoing expansion initiatives. Extensive clinical data, including questionnaires, are already collected for each patient, with follow-ups over 10 years. Data from RNA-sequencing,single-cell sequencing,spatial transcriptomics,proteomics,metabolomics,and histology images will be archived with ABBI.
Results: Collecting samples with explicit consent was initiated in 2021, while ABBI was first applied in 01/24. and ABBI functions as a biobank and allows external researchers to use it as follows: After the steering committee accepts a data request and approves the individual research project, the biobank compiles a corresponding dataset. Clinical and sample data of each patient are associated with a patient-specific pseudonym linked to the patient’s real identity in an independent trustee service. The pseudonymized clinical data is registered in REDCap [3], an electronic data capture system, while biospecimen data is stored in OpenSpecimen [4], a biobank management system. The underlying data model is represented in a machine-readable format in a metadata repository. The biomaterial samples are sent to external core facilities for sequencing or proteomic and metabolomic analysis. After sequencing, the data is transferred to the omics data management and analysis tool Semares™. Subsequently, alignment and downstream analyses are performed and lastly, a public API enables the download of the pseudonymized and analyzed data for the researchers that initiated the distinct project. Based on user interviews and a System Usability Scale (SUS [5]), ABBI demonstrates good usability with scores ranging from 72.5 to 77.5 (10 participants:4 researchers, 6 lab employees).
Discussion: Evaluating ABBI's user interface revealed positive feedback on its logical structure and usability, signifying its user-friendly design. The modular concept of ABBI allows flexibility and scalability to utilize the tool for other use cases at UKE and other institutes seeking to establish and grow a biobank. It is planned to obtain the patient data via the data integration center (DIZ), which provides the dataset in a standardized Fast Healthcare Interoperability Resource (FHIR [6]) structure. In the future, AI technologies [1], especially regarding data integration and knowledge discovery as well as data management and analysis will be integrated into ABBI to improve the tool’s usability and accessibility further.
Conclusion: ABBI's design can be adapted for larger data volumes, offering a secure, user-friendly interface for UKE's internal and external researchers. ABBI's components are a valuable reference for institutions planning their biomaterial banks.
The authors declare that they have no competing interests.
The authors declare that a positive ethics committee vote has been obtained.
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