Clinical guidelines – CUH WGS referrals

Please see NHS England's test selection (opens in a new tab) or the national genomic test directory (opens in a new tab) for up to date guidance.

The commonest indications for WGS are currently:

• Paediatric & Teenage/Young Adult (TYA) tumours (any tumour <25)
• Sarcoma (any site, any age)
• Triple negative breast cancer, glioma, and high grade ovarian carcinoma (any age)
• Failed standard of care for treatment (i.e., refractory to current standard maximal treatment; any tumour type, including carcinoma of unknown primary, any age)
• Failed standard of care for diagnostic testing (i.e., diagnosis not possible using non-WGS techniques; any tumour type, including carcinoma of unknown primary, any age)

The decision to proceed to WGS should ideally be made at MDT in conjunction with radiological, clinical and pathological input, but in certain situations it may be appropriate for the treating clinician to make this decision independently.

Further details on eligibility for molecular tests in cancer can be found in the National Genomic Test Directory.

If the patient has also been consented for a trial involving tissue bank, the tissue bank team should also be informed.

An additional specialised consent process is required for WGS, particularly with reference to the implications of any germline variants that may be discovered.

Consent must be received prior to any biopsy of a tumour for WGS in which tissue (or extra tissue) is taken for the sole purpose of WGS.

The consent process requires completion of a training course “Patient Choice: Discussing Whole Genome Sequencing with Patients” (opens in a new tab).

Each patient’s (and family member where relevant) choices are captured via a nationally standardised Record of Discussion (RoD) form and additional forms where relevant. For WGS to be carried out a RoD must be available to the GLH (see below) for each individual undergoing WGS. The patient choice conversation can be performed remotely and the form submitted without a patient signature – please tick the “Remote consent” section of the RoD form to indicate this.

The completed and signed consent form (record of discussion) can either be e-mailed to the lab (with e-mail subject title “Cancer WGS consent”), posted to the lab with specimen (Cambridge Genomics Laboratory, Box 143), or uploaded to Media on EPIC.

Place an order on Epic for “Histopathology-Routine” for the biopsy.

In order to perform WGS, FRESH TISSUE IS REQUIRED.

This can be taken either:

1) as part of the diagnostic procedure up front (e.g., in paediatric, sarcoma or TYA cases)
2) as part of the treatment (e.g., in a diagnostic/therapeutic resection such as a hysterectomy), or
3) purely to obtain tissue for WGS (e.g., in a case where only formalin fixed tumour is currently available).

To perform WGS, an adequate quantity of tissue is required. To yield adequate quantities of DNA, the following guidelines are offered:

• For core biopsies - tissue totalling ~40mm long (for 16g needle) or 80mm (18g)
• For excisions/excisional biopsies - a fragment of tissue measuring 5 x 5 x 2mm

Please note that these are MINIMUM recommendations.

Please also bear in mind that these recommendations are purely for WGS, and that if routine histopathological diagnosis is also required, ADDITIONAL tissue should be taken for that purpose.

Further guidance on radiological biopsies is available.

Within routine hours (before 16:00)

• The entire specimen should be submitted fresh (in chilled phosphate buffered saline (or equivalent) or simply dry for biopsies, or a dry pot/bucket for resections)
• Fresh samples should be portered to Histopathology laboratory immediately after the biopsy (if there is a delay of over 30 minutes samples can be stored for less than 12h at 4^OC)
• If the specimen has been consented for sampling by Tissue Bank as part of a trial, the specimen should be sent to Tissue Bank (also located in the Histopathology Laboratory).

Out of hours (after 16:00, weekends & bank holidays)

The WGS specimen should be submitted in RNAlater (which preserves nucleic acid at room temperature)

To order RNAlater tubes

Email cuh.add-tr.freshtissuehisto@nhs.net or phone 01223 348213 (ask for Section Leader). Please provide a responsible contact and delivery address. We will send 6 × 5 mL RNAlater universals.

• If this is a combined procedure where routine histopathology and WGS are both required (eg. core biopsies), the specimen must be divided into two separate pots, one containing RNAlater (which preserves nucleic acid but renders the specimen unsuitable for routine histopathology) and one containing formalin (for routine diagnosis).
• Routine diagnosis is always the priority, and at least two good cores should be submitted in formalin, with the remainder submitted in RNAlater.
• If the specimen is a large resection, at least one sample should be taken from the tumour (as per the quantity guidance above) and placed in RNAlater with the remainder placed in formalin as usual.
• An RNAlater/tissue volume ratio of at least 5:1 is required and tissue fragments must be no more than 5mm in thickness to allow sufficient penetration of the fixative.
• Both the formalin and RNAlater specimens can be sent to histopathology at room temperature.

Why we need it

A germline sample provides essential reference point for WGS analysis. The germline sample reflects the patient's healthy genome to compare against the tumour (somatic) genome. Comparing the germline and biopsy samples allows identification of variants that are specific to the tumour, which are relevant to diagnosis, prognosis and treatment. Variants in the germline sample also indicate inherited variants that contribute to cancer risk, and can provide insights into how a patient will respond to certain treatments.

Sample collection

The preferred germline sample is peripheral blood. Required volumes are indicated in the table below. In exceptional circumstances, a saliva sample (using the Oragene collection tube) may be used as a source of germline DNA.

Detailed guidance on germline sampling is available in the “Sample Handling Guidance for Germline Samples” document below.

Internal CUH ordering for WGS is via Order Entry. The oncologist orders the germline sample, and the pathologist places the tumour sample order.

See appendices for EPIC ordering details

Appendix 1 - How to request the germline bloods in EPIC

Appendix 2 - Process of drive through/local blood collection

It is important to ensure that the correct orders are made, so the GLH have visibility of the sample and receive it via our pathway.

Please note, any haematological test directory indications should be ordered as a haem-onc WGS orders, even if the tumour tissue is sampled as a solid sample (i.e., histiocytosis and lymphoma).

Genomics England stipulate that the results of WGS studies should be discussed at a GTAB.

A quorate GTAB will include an Oncologist, a Histopathologist, a Clinical Scientist and if applicable a Clinical Geneticist.

The GLH Clinical Scientist/Molecular Pathology team (which may be based at the Cambridge Hub or in some cases at your local centre) will present the findings to the GTAB colleagues for discussion.

Following the discussion, and the completion of any additional work (e.g., further characterisation or confirmation using an orthogonal test of pertinent variants) a report will be issued.

Further information and guidance is available.