What is it? Why is it important?

Sample processing is the sample-workflow step where collected Biological Material (BM) undergoes additional handling.


The aim is to:

  • Preserve properties of interest by preparing BM for long-term storage (e.g. tissue preservation with FFPE)
  • Extract BM of interest (e.g. blood serum from whole blood through centrifugation)
  • Prepare for multiple downstream analysis by aliquoting collected MB (e.g. aliquot a batch of serum sample into small separate vials)


Standard procedures for BM processing ensure that:

  • BM is of high quality (e.g. cells remain viable, protein degradation is prevented, RNA remains stable)
  • BM aliquots are comparable (e.g. standard thickness of tissue slicing, centrifugation speed and temperature)
  • Analytical results obtained from BM aliquots or different research sites are comparable


BM processing procedures can be based on:

  • Internationally accepted standards, such as ISO 20387 (e.g. internationally validated procedures for the preservation of tissue DNA and RNA). In order to make analytical results comparable:
    • Research sites must comply with given standards
    • Newly established processing methods must be validated
  • A study applicable laboratory manual describing techniques for BM processing. Methods should include validated study specific processing procedures required for the downstream analysis. A reference to the laboratory manual should be made in the study protocol

What do I need to do?

Define sample processing procedures. Based on criteria needed for downstream analysis define the:

  • Timing regarding maximal acceptable delay between BM collection and processing
  • Required number of samples including volume and/or concentration (e.g. an analysis might require a minimum of viable cells)
  • Type of BM (e.g. liquid or tissue sample)
  • BM extract of interest (e.g. plasma, buffy coat, viable or PBMC from whole blood)
  • Needed material and sample storage containers. Include special requirements needed for expected long term storage (e.g. centrifuge, temperature bath, vial type, special coatings, additives, cryopreservation solution, back-up samples)
  • Special labelling requirements (e.g. coding, freezer stable stickers)


Create standardised forms to document:

  • Performed BM processing steps
  • Occurrence of non-conformities (e.g. BM exposure to sub-optimal temperature or conditions, centrifugation was performed at room temperature and not as required 4°C)


Define processing steps in a SOP and/or WI, and ensure staff is properly trained.


In the event BM do not meet acceptance criteria for downstream analysis, a process or reference should be included on how to manage these events (e.g. sample destruction, documentation or report of non-conformity)

Where can I get help?

Your local CTU can support you with experienced staff regarding this topic

The Swiss Biobanking Platform (SBP) can provide you with support on this topic.

SBP Documents

SOPs, Forms and Templates – see in particular

  • Biological Material SOP


ISO 20387:2018 Biotechnology - Biobanking (access liable to cost)- General Requirements for Biobanking – see in particular section

  • 7.6 Preparation and preservation of biological material
  • Specifications for pre-examination processes for frozen tissue
    • Part 1: Isolated RNA (ISO 20184-1:2018)
    • Part 2: Isolated proteins (ISO 20184-2:2018)
    • Part 3: Isolated DNA (ISO 20184-3:2021)
  • Specifications for pre-examinations processes for formalin-fixed and paraffin-embedded (FFPE) tissue
    • Part 1: Isolated RNA (ISO 20166-1:2018)
    • Part 2: Isolated proteins (ISO 20166-2:2018)
    • Part 3: Isolated DNA (ISO 20166-3:2018)
    • Part 4: In situ detection techniques (ISO 20166-4:2021)
  • Specifications for pre-examinations processes for venous whole blood
    • Part 1: Isolated cellular RNA (ISO 20186-1:2019)
    • Part 2: Isolated genomic DNA (ISO 20186-2:2019)
    • Part 3: Isolated circulating cell free DNA from plasma (ISO 20186-3:2019)
  • Specifications for pre-examinations processes in metabolomics
    • Urine, venous blood serum and plasma (ISO 23118:2021)
  • BM – Biological Material
  • CTU – Clinical Trials Unit
  • DNA – Deoxyribonucleic Acid
  • FFPE – Formalin-Fixed Paraffin-Embedded
  • ISO – International Standards Organisation
  • PBMC – Peripheral Blood Mononuclear Cells
  • RNA – Ribonucleic Acid
  • SBP – Swiss Biobanking Platform
  • SOPs – Standard Operating Procedures
  • WI – Work Instruction
Development ↦ Biobanking ↦ Handling of Biological Material ↦ Sample Processing

Provides some background knowledge and basic definitions

Basic Monitoring
Basic Drug or Device

Starts with a study idea

Ends after having assessed and evaluated study feasibility

Concept Drug or Device

Starts with confidence that the study is feasible

Ends after having received ethics and regulatory approval

Development Drug or Device

Starts with ethics and regulatory approval

Ends after successful study initiation

Set-Up Ethics and Laws
Set-Up Quality and Risk
Set-Up Drug or Device

Starts with participant recruitment

Ends after the last participant has completed the last study visit

Conduct Drug or Device

Starts with last study visit completed

Ends after study publication and archiving

Completion Statistics
Completion Drug or Device
Current Path (click to copy): Development ↦ Biobanking ↦ Handling of Biological Material ↦ Sample Processing

Please note: the Easy-GCS tool is currently under construction.