The Leeds Teaching Hospitals NHS Trust

Paediatric Solid Tumours

Types of referrals

A conventional (i.e. G-banding and/or FISH) cytogenetic service is available for the following referrals: 

  • FISH studies on either fresh tissue or formalin fixed paraffin embedded tissue (FFPE)
  • G-banding on cell cultures from fresh tissue

 Please see Molecular Oncology section for information on tumour genotyping and stratified medicine.

 Sample Requirements for cell culture and G-banding

Whilst the great majority of genetic testing in paediatric tumours involves the use of DNA-based tests, a cell culture and karyotyping service is available on fresh tissue for exceptional cases where this may be of clinical benefit.

Cell culture requires living cells. Please ensure that the sample reaches us as quickly as possible (within 24 hours). First class post is satisfactory.

Samples should be placed in sterile containers, containing sterile, fresh (i.e. less than one month since opening) culture medium - this should ideally be Ham’s F10, but any balanced salt solution is acceptable. Transport medium is available from the laboratory on request. On no account should samples be transported in formalin.

Samples from within St James’s Hospital should be sent in sealed plastic bags, with the request card protected from the sample.

Samples from other hospitals should be placed in taped absorbent boxes containing appropriate padding and packing. Request cards should be protected from samples.

Where delays over 24 hours are unavoidable, e.g. for biopsies taken on Saturday afternoon or Sunday, samples should be refrigerated and sent to the laboratory to arrive on the next working day.

Open biopsies from the tumour itself are preferred.

Sample size is important, and the chances of obtaining a successful result increase with biopsies above 5mm in diameter.

Trucut biopsies and fine needle aspirates will also be accepted if no open biopsy is available, although smaller sized samples can result in a higher failure rate.

Where consent for research is available, surplus tumour tissue from paediatric patients will be stored for possible future research or development purposes, in line with the agreed St James’s Hospital Paediatric Oncology tumour storage pathway

Where appropriate, other fluids where tumour infiltration is known or suspected may be sent. These include pleural effusions, cerebro-spinal fluid, bone marrow, blood and cystic fluid.

Cytogenetic analysis of blood or bone marrow may also be undertaken by the molecular oncology team where infiltration into blood or bone marrow is known or suspected.

Sample requirements for FISH studies 

FISH studies can be performed on fresh tissue and on formalin fixed paraffin embedded tissue (FFPE).

Targeted FISH testing on fresh tissue can be performed either on uncultured or cultured cells. The sample requirements are the same as those for G-banding.

Paraffin sections can be used as an alternative to fresh tissue as a targeted test to detect a known specific genetic change. Sections should be 4µm thick on positively charged slides, ideally with an accompanying H&E stained slide with tumour area circled by a histopathologist, and % tumour nuclei within the circled area indicated on the referral form. These can either be cut and marked by the Leeds Histopathology team (if paraffin blocks are sent for testing) or by the referring clinician.

Sample requirements for molecular studies (including tumour genotyping)

For more detail, see the sections on specific tumour types

For a DNA-based test such as Sanger sequencing, pyrosequencing or next generation sequencing, fresh tissue, snap frozen tissue or FFPE (in rolls or in sections) can be used. Requests for such testing should be made directly to the lab.

Sample Transport

When sending samples by post a secure container should be used to conform to current postal regulations, i.e. P650 and UN3373 as applicable. For further information, see here.

For the laboratory address and contact details, see the laboratory contacts page.

Paraffin sections

 Paraffin sections should be packed in suitable slide containers and placed in a taped box containing appropriate padding and packaging.

 Reporting of Results

The clinical significance of cytogenetic input and the urgency with which it is required is highly variable from one case to the next, even within a given disease type, and it will depend to a great extent on the Pathologist’s confidence in the results from other tests such as immunohistochemistry to provide an unequivocal diagnosis.

The European guidelines for cytogenetic investigation in solid tumours published in 2015 include reporting time guidelines.

If the test is known to influence treatment decisions, then all efforts are made to report the results within the timeframe required by the treatment protocol.

In the absence of a specific treatment protocol, where cytogenetics could have a bearing on diagnosis and/or treatment, efforts are made to report all results within 14 days.

Where cytogenetics has no specified bearing on diagnosis and/or treatment, results are reported within 28 days.

Priority can be adjusted in line with clinical urgency and the need to present at MDT.

Some urgent FISH results can be reported with 1-3 days of sample receipt.

The majority of FISH probes used are obtained commercially.

Reports can be e-mailed to an address. Where not available, a secure emailing route can be set up. A paper copy will only be posted if specifically requested.



Hastings RJ et al. Guidelines for cytogenetic investigations in tumours, European Journal of Human Genetics (2015), 1–8