Equipment & Technologies

ART

All CFMPB activities are supported by an in house developed web application ‘Application and Request Tool’ (ART). ART is the online tool for e.g. study registration (human biospecimens IRBm and human data IRBd, or combi IRBdm and IRBb for biobanks), Institutional Review Board (IRB) review, lab logistics, track and trace of biospecimens and cost recovery. All the user activities (histology & digital pathology, immunohistochemistry, molecular genetics) are stored in the ART database and by doing so, information about the applications, biospecimen identifiers, succeeding actions and derivatives accumulates and this enriches the data already available.

Histology & digital pathology

The CFMPB provides a comprehensive histology and digital pathology service, including FFPE (single and multiple tissue slide) and fresh frozen (FF) tissue sectioning, histochemical staining (H&E), micro- and macrodissection , tissue microarray (TMA) construction, slide digitization and digital image management. Digital slide logistics are supported by automated slide scanners; the 3DHISTECH P1000 slide scanner, the PhenoImager  (Vectra Polaris), the PhenoCycler-fusion and Axio scanner (Bioimaging Facility). All digital images are securely archived in the Azure cloud.  SlideScore serves as the central platform for digital pathology workflows, enabling slide sharing, scoring, TMA grid management and collaboration with both internal and external users. The platform is fully integrated with ART.  We have two cryostats for frozen sectioning. For very small frozen tissue specimens, such as needle biopsies, the 4FME protocol in combination with the PrestoCHILL system is used to preserve tissue morphology and optimize section quality (also in collaboration with HMF).

TMAs are generated using the TMA GrandMaster. When older FFPE blocks are incompatible with the instrument, manual TMA construction is available. In general, TMAs are generated from resection specimens. The use of biopsy material is discouraged because of the limited amount of donor tissue, resulting in unstable cores with limited tissue representation. Only in exceptional cases will biopsy material be used after consultation with the requesting investigator and pathologist. Using the microtome high quality paraffin sectioning can be offered, varying from whole resection ribbon till multiple tissue slides on standard or special purpose glass. The newly developed Tissue Transfer Tool offers a TMA  design without creating a TMA block.  For dissection of tissue for isolation purposes we offer micro and macro dissection. For very small tumor areas to obtain highly enriched tumor tissue, the CFMPB has a laser microdissection (LMD) system from Leica (LMD6500). The stereo microscope can also be used to obtain specific small tissue from slides when it is not possible to scratch it off without a microscope. 

 

Histology equipment list:

• Microtome (Leica)
• Discussion microscope (Leica)
• Glass printer Tissue-Tek auto write (Axlab)
• Multistainer (Sakura)
• Coverslipping Instrument (Sakura)
• P1000 3D Histec scanner Sysmex (see below)

• 2x Cryostates (1xLeica, 1xThermo Scientific)
• Prestochill Cryo-embedding system Prestochill (Milestone Medical)
• Laser Microdissection System (LMD6500, Leica)
• Grand Master TMA arrayer Sysmex (see below)

Immunohistochemistry

The CFMPB has a fully equipped and dedicated immunohistochemistry (IHC) lab.  All IHC, routine and newly designed,  is performed using the BenchMark Ultra (Ventana, Roche) automated stainers, in close collaboration with the Diagnostic Pathology department (>300 antibody protocols available). All IHC slides are evaluated and scored by an experienced pathologist (mandatory).  Additionally we have 3 Discovery Ultra (Ventana, Roche) automated stainers available for new IHC assay development and protocol optimization, multiplexing (chromogenic and fluorescent) staining, RNA scope and FISH. The PhenoImager (Vectra Polaris) (Akoya/Quantrix) is used for digital pathology multi spectral imaging. The PhenoImager is a microscope/scanner enabling detection of up to 8 different markers in situ. Multiplex immunofluorescence (MPIF) enables simultaneous visualization of multiple cell populations within the tumor microenvironment. Several validated antibody panels are available, while additional application-specific panels are continuously being developed and optimized.

Both the Akoya Codex Phenocycler Open and Fusion are available for highplex IF image analysis. Up to approximately 50 barcoded Antibodies can be analyzed simultaneously (antibody information available on request). Antibody conjugation is performed in collaboration with the Protein Facility.

Digital image analysis is performed using HALO and the open-source software QuPath, in close collaboration with the BioImaging Facility. 

Ample experience is available for the development of new antibody staining protocols. Elaboration and optimization of staining protocols is performed in close collaboration with the requesting scientist and the involved pathologist.

 

IHC equipment list:

• PhenoImager (Akoya/Quanterix)
• Codex Phenocycler Open (Akoya/Quanterix)
• Codex Phenocycler Fusion (Akoya/Quanterix)
• 3x Discovery Ultra, Ventana stainer (Roche)
• 2x Benchmark Ultra, Ventana stainer (Roche) (see below)

Molecular genetics

To ensure consistent high-quality results, all DNA and RNA isolations from NKI biobank samples are performed by, or under the supervision of, CFMPB technicians. All derived samples are handled and stored in the dedicated lab (pre-PCR, QC conditions) under supervision of the coordinating technicians according to standardized protocols tailored to the requirements of each project. Six QIAcube instruments are available for automated DNA and RNA isolation, primarily using the QIAGEN AllPrep DNA/RNA kits for both FFPE and fresh frozen tissue.  The Clinical Chemistry Department (AKL) carries out all isolations of samples from the serum biobank and Blood biobank using the Qiasymphony. Quality control includes NanoDrop spectrophotometry, Qubit fluorometry and TapeStation analysis for DNA integrity (DIN) and RNA integrity (RIN).

A variety of molecular analysis techniques are offered, in close collaboration with (and in the lab of) the diagnostic Molecular Pathology team (Sequenom, PCR, HPV, MLPA, Ampliseq, Nanostring).

All samples are registered in a Lab Management System and in the CFMPB database system ART-CFMPB. All samples, derived materials and generated data (type (IHC slides and scores, DNA, RNA), quality and transition are registered. All DNA and RNA samples are coded with a unique (barcoded) core-study number before distribution for further use. The decoding key will be kept in ART (and will be accessible depending on the governance model, study design and consent). The material and manpower (including pathologist time) costs are reimbursed through ART by the financial department.

 

Molecular genetics equipment list:

• Tapestation (Agilent)
• Nanodrop 2000 (Isogen lifescience)
• Quantas Fluorometer (Promega)
• Qubit 2.0 Fluorometer (Invitrogen)
• Nanostring Flex Analysis system (Nanostring)
• 6x Qiacube DNA/RNA isolation robot (Qiagen) (see below)

In collaboration with and on location of the Pathology department:

• Sequenom (Agena Bioscience)
• Rotorgene (HPV)

In collaboration with and on location of the General clinical laboratory (AKL) department:

• Qia-Symphony (Qiagen)

All studies will be carried out by the CFMPB technicians, in consultation technical support can be provided by the applicant.

 

Workflow management

New laboratory requests are submitted through ART and automatically received in the CFMPB request mailbox. Requests are reviewed for completeness, feasibility, planning, ethical approval and consent requirements and discussed with the relevant CFMPB staff. Following prioritization, projects are scheduled and executed in consultation with the applicant, the study team and, where applicable, the responsible pathologist.

Together, these integrated workflows provide researchers with end-to-end support for histopathology, digital pathology, molecular analyses, and spatial biology. By combining technical expertise, pathology oversight, advanced instrumentation, and standardized quality-controlled procedures, the CFMPB enables high-quality translational cancer research from tissue acquisition to data generation.