Jun 04, 2026

National Biobank standard protocol for processing urine samples in Dutch University Medical Centers

This  protocol  is a draft, published without a DOI.
  • Yvonne D. Krom1,2,
  • Jessica C. de Greef3,
  • Ellis Niemantsverdriet4,
  • Jörg Hamann5,6,
  • Wim Timens7,
  • Peggy Manders8,
  • Hilde Brouwers9,
  • Liesbeth Niemans10,
  • Chiel de Theije11,
  • Roger R. Snijder4
  • 1Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands;
  • 2Duchenne Center Netherlands;
  • 3Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands;
  • 4LUMC Biobank Organization, Leiden University Medical Center, Leiden, The Netherlands;
  • 5Department of Experimental Immunology, Amsterdam Institute of Immunology and Infectious Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands;
  • 6Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, the Netherlands;
  • 7Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands;
  • 8Radboud Biobank, Radboud University Medical Center, Nijmegen, The Netherlands;
  • 9Central Biobank Erasmus MC, Erasmus MC, Rotterdam, The Netherlands;
  • 10Central Biobank UMC Utrecht, UMC Utrecht, Utrecht, The Netherlands;
  • 11Central Biobank MUMC+, Department of Central Research Facilities (COV), Maastricht University, Maastricht, the Netherlands
Yvonne D. Krom
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External link: https://openbioresources.metajnl.com/articles/10.5334/ojb.23
Protocol Citation: Yvonne D. Krom, Jessica C. de Greef, Ellis Niemantsverdriet, Jörg Hamann, Wim Timens, Peggy Manders, Hilde Brouwers, Liesbeth Niemans, Chiel de Theije, Roger R. Snijder 2026. National Biobank standard protocol for processing urine samples in Dutch University Medical Centers. protocols.io https://dx.doi.org/
Manuscript citation:
Manniën, J., Ledderhof, T., Verspaget, H.W., Snijder, R.R., Flikkenschild, E.F., van Scherrenburg, N.P.C., Stolk, R.P. and Zielhuis, G.A. 2017 The Parelsnoer Institute: A National Network of Standardized Clinical Biobanks in the Netherlands. Open Journal of Bioresources 4: 3,  DOI: https://doi.org/10.5334/ojb.23
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 04, 2026
Last Modified: June 04, 2026
Protocol  Integer ID: 318516
Keywords: urine, processing urine, processing of urine, processing, standard operating protocol, protocol, biobank of Dutch academic centers, Dutch academic centers, biobank, lumc biobank facility, national biobank standard protocol, urine samples in dutch university medical center, processing urine sample, biobank of all dutch academic center, urine sample, biobank regulation, local biobank, national biobank, clinical data, tissue sample, biobank information management system, store biomaterial, dutch university medical center, lumc it department under supervision, biomarker analysis, downstream data use, potential impact on biomarker analysis, lumc it department, accordance with gdpr, sample processing, national standard, gdpr, lumc, dna, data, human body material, standard protocol, dutch academic center, storage of all material, traceability
Abstract
As of 2007, the 8 Dutch University Medical Centers (UMCs) have agreed to collaborate in, and exchange knowledge regarding, setting up local biobanks, where materials for a wide variety of diseases were collected under the same protocol. These nation-wide protocols are, to a large extent, still in place for most materials collected in the extant 7 UMC biobanks. Materials collected comprise blood derivates, DNA, urine, and tissue samples.
All materials and data are handled in accordance with GDPR (AVG) and Biobank regulations. Researchers may request human body material and/or clinical data.
At LUMC, the protocols to collect and store biomaterials according to national standards have been refined over the years, for example, through automation improvements in sample processing. Registration and storage of all materials is carried out in the Biobank information management system, Sample Navigator. All materials intended for scientific research are assigned a unique code that cannot be traced to the donor without access to Sample Navigator. Access is strictly governed by the LUMC IT department under supervision of the LUMC Biobank Facility.
All pre‑analytical deviations are systematically documented at the sample level to ensure transparency, reproducibility, and high‑quality downstream data use. Deviations are recorded using predefined categories, each accompanied by structured metadata and optional free‑text clarification. This enables traceability, supports FAIR data principles, and allows researchers to assess potential impact on biomarker analyses or clinical interpretation.
This protocol describes the procedure for processing urine samples, used by the Biobank of all Dutch academic centers.
Materials
  • Urine collection tube (Sarstedt)
  • Centrifuge Hettich Rotina 380R or Centrifuge Hettich Rotina 460RS
  • Various adjustable calibrated pipettes
  • Corning pipette tips with filter, sterile, 100-1000 µl
  • Sarstedt tubes
Safety warnings
No hazardous substances are used.
Ethics statement
Sample collection under this protocol may only be performed with prior approval from the user’s Institutional Ethics Board (or equivalent ethics committee) and only when patients have provided informed consent for the specific biobank.
Procedure
10 ml urine is collected in a commercially available urine collection tube.
The urine collection tube is processed within 4 hours after collection.

Before initiating sample processing (and within 4 hours after collection), the urine collection tube is inspected for pre‑analytical deviations. The following deviation categories are captured for the tube, each accompanied by a free‑text field for additional notes:
  • Incorrect storage temperature prior to processing
  • Deviated storage duration prior to processing
The urine collection tube is then spun at 2350 RCF for 10 minutes at 4°C.
Next, the supernatant is collected by pipetting without disturbing the pellet on the bottom of the urine collection tube.
6 aliquots of urine (900 µl each) are distributed in Sarstedt tubes.
The Sarstedt tubes with urine are then stored at -20°C until 5 pm, at which time the tubes are stored in a UHT freezer at -80°C.

After centrifugation and completion of the storage procedure, additional pre‑analytical deviations related to the processing phase are recorded. The following deviation categories are captured for the sample, each with a free‑text field for additional notes:
  • Deviation during centrifugation
  • Storage incident
Protocol references
Manniën, J., Ledderhof, T., Verspaget, H.W., Snijder, R.R., Flikkenschild, E.F., van Scherrenburg, N.P.C., Stolk, R.P. and Zielhuis, G.A. 2017 The Parelsnoer Institute: A National Network of Standardized Clinical Biobanks in the Netherlands. Open Journal of Bioresources 4: 3,  DOI: https://doi.org/10.5334/ojb.23