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Malignancy - other tissue types

Sample requirements

Full clinical information including suspected or confirmed diagnosis and tumour load are required for the accurate interpretation of the cytogenetic result.

Karyotype and/or FISH investigation

  • Lymph node tissue collected either in sterile medium (contact the laboratory if required) or in sterile isotonic saline.
  • Fluid (e.g. cerebrospinal fluid where neoplastic involvement suspected) in a sterile container.


FISH investigation only

  • Paraffin embedded tumour tissue (4 micron) sections on poly-l-lysine coated slides (2 slides per FISH test required) with H&E slide

  • Tumour smears or touch preps - fixed, on poly-l-lysine coated slides.
  • Unless sections comprise all tumour tissue (please indicate if all tissue is representative) please ring/mark abnormal area on the reverse of slides to allow targeting of analysis.

Fresh samples should ideally be sent to the Cytogenetics Department on the same day (result may be compromised if the sample is delayed). Where a delay is inevitable (such as over weekends) please store the sample in a refrigerator before sending on the next working day. For paraffin embedded tissues transit time is not an issue. For sample labelling and completion of referral form criteria please see referral requirements.


Acceptance and rejection criteria

Lymph node

Whilst some samples that do not meet our criteria can be rejected, due to the unrepeatable nature of these samples, all lymph nodes are usually attempted. Samples from patients with suspected TB cannot be processed. Please see high risk samples.


PET slides

If known upon receipt, PET slides will be rejected if there is insufficent material to process on the slides or if the tumour load is <10%. Please see below for further information on limitations of PET FISH studies.


Referral Categories

We receive and process samples from a wide range of paediatric and adult tumours.Tumour tissue may be referred at diagnosis, for monitoring, at disease progression or at relapse.


Tests available


The department offers karyotype analysis from fresh samples only.



We have a large number of FISH probes available in line with the test directory published on the NHS England website. Please see our Tumour FISH probe list. We are able to FISH preparations from paraffin embedded/frozen tissue. Please contact the Cytogenetics Department to discuss your requirements and the availability of FISH probes.

FISH image 1

FISH on paraffin embedded tissue sections. Positive MDM2 amplification.

FISH image 2

FISH on paraffin embedded tissue sections. Positive EWSR1 rearrangement.

FISH image 3

FISH on paraffin embedded tissue sections. Positive ALK rearrangement.

Reporting times

Please see our Target Reporting Times.

Limitations of tests

The success and accuracy of FISH studies on paraffin embedded tissue slides depends on the tumour load within the tissue on the slides and the amount of tissue itself. Generally at least 100 good quality interphase cells are analysed. A slide with a very small amount of tissue may therefore not be sufficient to obtain a full result. If the tumour load is low, the neoplastic clone may not be represented within the cells analysed. If the tissue has been damaged or crushed during the preservation process this may also compromise the result.

In addition please see our malignancy samples limitations below:


Storage and further testing

Fixed material from all solid tumour, lymph node, cerebrospinal fluid referrals is stored after reporting for 10 years for possible future testing. Paraffin embedded tissue slides (after FISH testing) are stored for 2 years. Any spare/unused paraffin embedded tissue slides are kept for 4 months from receipt and are either returned to the referring centre or discarded, depending on the request of the centre. All H+E slides are returned to the referring centres usually 4 months after receipt.

Page last updated 30/09/2021 by MC. Please note that if printed, the information is only valid on the day of printing.