Clinical guidelines – Non CUH WGS referrals

1. Eligibility for Whole Genome Sequencing (WGS)

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 treatment or diagnostic testing (ie. refractory to current standard maximal treatment or 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.

2. Consent

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 received by the GLH 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”) or posted to the lab with specimen (see address below).

3. Sampling the tumour tissue

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.

Detailed guidance on tissue sampling is available via the FutureNHS (opens in a new tab) ‘NHS Genomic Medicine Service’ workspace (see “Sample Handling Guidance for Whole Genome Sequencing of Solid Tumour Samples”, videos are also available (opens in a new tab).

The specimen must be received fresh in the histopathology laboratory as soon as possible (ideally within 30 minutes), in chilled PBS (or similar isotonic solution) and handled by an appropriately trained laboratory staff member. If there is any delay in delivering the specimen, it should be placed in a 4oC refrigerator temporarily.

4. Handling the specimen in Histopathology

Key steps are summarised as follows:

PLEASE NOTE In the absence of an onsite histopathology department, the cores should be placed in an appropriate isotonic solution (see above) and transported to the centre that routinely reports their histopathology for handling. The tissue should be kept at 4^oC throughout the transport chain, either in a refrigerator or on (wet) ice. Ideally these biopsies should be taken in the morning, and must be transported, handled and frozen on the same day as the biopsy. The receiving laboratory must be notified in advance.

On reception in the histopathology laboratory:

• If material is also required for histopathological diagnosis, this should be separated from the fresh specimen, fixed and processed separately.
• The fresh specimen should then be frozen, ideally into at least two separate vials.

The next step is histopathological assessment:

• Frozen sections should be cut and histologically assessed
• Tumour sampling should be confirmed
• The tumour specimen submitted should be at least 30% tumour cellularity, with <20% necrosis*
• It is acceptable to submit multiple vials of the same tumour to increase yield

* On occasions, it may be appropriate to submit specimens not meeting these criteria, please contact the laboratory to discuss such cases.

See “Sample Handling Guidance for Whole Genome Sequencing of Solid Tumour Samples” available via the FutureNHS (opens in a new tab) NHS Genomic Medicine Service workspace for further details.

5. Germline sample collection

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

The germline sample should be taken at the same time as the biopsy/surgery and sent to Histopathology with the tumour sample.

Detailed guidance on germline sampling is available via the FutureNHS (opens in a new tab) NHS Genomic Medicine Service workspace at (see “GLH Sample Handling Guidance for Germline Samples” and “Guidance for Whole Genome Sequencing of Haematological Malignancies”)

6. Requesting Whole Genome Sequencing

The WGS requesting form (opens in a new tab) is available (see Appendix for details on navigating the auto populated form).

A blank form (“NHS Genomic Medicine Service test order form – Cancer” (opens in a new tab)) is also available.

Please complete all fields. We will not be able to submit the sample without the required details.

If there is more than one tumour (distinct tissue mass) to be tested, please complete separate referral forms for each tumour and provide a different identifying description to distinguish them (e.g., 3 o`clock and 12 o`clock).

7. Submitting the sample for WGS

Please send the 1/ tumour sample, 2/germline sample, 3/ request form, 4/ Record of Discussion (if not already sent electronically) and 5/ a copy of the related histopathology report if available to the Genomic Laboratory Hub:

East Genomic Laboratory Hub,
Box 143, Level 6 Addenbrooke's Treatment Centre,
Cambridge University Hospital NHS Foundation Trust,
Hills Road, Cambridge, CB2 0QQ

Please note that the tumour specimen must be kept frozen during transport, ideally on dry ice.

Blood samples should ideally be sent at 4^oC but it is acceptable to send samples at ambient temperature if the total time from collection to extraction does not exceed 72 hours.

When sending a sample, please let us know the patient details, and what sample (germline or tumour) is being sent, and details of the courier by e-mail (with e-mail subject title including “Cancer WGS”).

8. Checklist for submitters

• Test request form (cancer WGS-specific form)
  • The GLH is unable to order WGS if mandatory information is missing
• Record of Discussion form (WGS-specific)
  • Data is not returned to the GLH without a completed and signed RoD
• Germline sample
  • Peripheral blood in EDTA tube, transport chilled (not frozen)
• Tumour sample
  • Fresh-frozen only, transport frozen (dry ice ideally)

9. Report and discussion at Genomic Tumour Advisory Board meeting (GTAB)

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 on our website.

If a standard discussion pathway has not been established previously, the GLH will e-mail the responsible clinician inviting them to a suitable GTAB forum for discussion of results.

Appendix – auto-populated test request form

Go to NHS England test selection page (opens in a new tab).

Search and select relevant clinical indication

If patient is eligible, click Yes, start referral

Click Use the PDF order form

Search and select site requesting WGS (sites served by the East-GLH are listed here.

Continue and then Download referral form

Complete form. Mandatory information must be provided (highlighted in screenshot below).

The GLH cannot order WGS without it:

1. Requesting organisation (auto populated)
2. Patient demographics
3. Test directory clinical indication code (auto populated)
4. Presentation status
5. Solid tumour requests
   1. Indicate if Primary, Metastatic, Unknown, Lymphoma
   2. Histopathology Lab ID
   3. Date of the Diagnosis
6. Indicate tumour/germline sample type
7. Tumour purity
8. Submitter contact details

Print form and send with sample to the the East-GLH laboratory address indicated on the GMS page.