May 22, 2026

National Biobank standard protocol for serum isolation from whole blood 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 serum isolation from whole blood 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: May 18, 2026
Last Modified: May 22, 2026
Protocol  Integer ID: 317251
Keywords: serum from whole blood, processing serum, processing of serum, whole blood sample, serum, whole blood, processing, blood, standard operating protocol, protocol, biobank of Dutch academic centers, Dutch academic centers, biobank, national biobank standard protocol for serum isolation, lumc biobank facility, biobank of all dutch academic center, biobank regulation, local biobank, clinical data, national biobank, whole blood in dutch university medical center, tissue sample, biobank information management system, store biomaterial, serum isolation, serum from whole blood, isolating serum, dutch university medical center, biomarker analysis, lumc it department under supervision, potential impact on biomarker analysis, technology improvements in sample processing, downstream data use, lumc it department, national standard, accordance with gdpr, blood derivate, lumc, gdpr, dna, standard protocol, human body material, dutch academic center, data, donor without access, 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 technology 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 isolating serum from whole blood, used by the Biobank of all Dutch academic centers.
Materials
  • CAT tube
  • 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
Treat all blood samples as potentially infectious. 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
Whole blood is collected in a commercially available CAT tube. If the donor is over 12 years of age, a standard 10 ml tube is used; otherwise, a 4 ml tube is used.
The CAT tube is processed within 4 hours after collection.

Before initiating sample processing (and within 4 hours after collection), the CAT 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:
  • Hemolytic material
  • Lipemic material
  • Icteric material
  • Incorrect tube type used
  • Incorrect storage temperature prior to processing
  • Deviated storage duration prior to processing
The CAT tube is then spun at 2350 RCF for 10 minutes at 20°C to remove cells and platelets.
Next, the supernatant is collected by pipetting without disturbing the red pellet on the bottom of the CAT tube.
2-3 aliquots (from 4 ml tube) or 5 aliquots (from 10 ml tube) of serum (500 µl each) are distributed in Sarstedt tubes.
The Sarstedt tubes with serum 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