Whole Genome Sequencing (WGS) for solid tumours and sarcoma

All  current versions of the resources associated with the request process are curated on NHS England Genomic website under the Genomics Resources tab.

Samples for somatic WGS should be collected from patients undergoing diagnostic biopsy or resection for suspected primary or relapsed cancer.

Samples are eligible for WGS following the diagnosis of:

• Children and young people (<25 years of age with any suspected cancer diagnosis)
• CNS/brain tumours
• Adult solid tumour referrals where all other standard of care testing or treatment have been exhausted (where there is a clear, clinical question and where results have expected utility/impact)

This guidance should also be used for patients with a solid haematological cancer, for example lymphoma, where this satisfies the eligibility criteria.

Important

• Samples must contain more that 30% tumour and less than 20% necrosis to be eligible for WGS
• Samples must use fresh or fresh frozen tissue only
• Germline samples (haematology) should be skin or remission samples
• Post-transplant samples are not suitable for WGS

Please see the ‘samples and transport’ section for more details.

Further detail of eligibility is available from the National Genomics Test Directory.

Key guidance – please read

• The WGS service for Haematological Cancer is described in Clinical guideline document: Whole Genome Sequencing for Haematological Cancer.
• Please note however that these solid tumour guidelines should also be followed for solid haematological tumours, for example lymphoma, in children or young people.
• Children in SW England with suspected bone sarcoma are currently referred to the Birmingham sarcoma service and will be eligible for WGS through the Wessex and West Midlands GLH.
• Any Child or Young person up to the age of 25 years is eligible for WGS. Any queries should be discussed with the SWGLH clinical team. (contact email SWGLHexports@nbt.nhs.uk).

Confirmation that discussion about WGS has been completed should be documented with a Record of Discussion (RoD) form and emailed to the SWGLH at SWGLHexports@nbt.nhs.uk. This can be at the same time as completion of the WGS cancer test order form or can occur later, although ideally within one week of the diagnostic biopsy or resection (see section 8.1) as WGS cannot be initiated without this.

Where can I find test order forms?

Please complete the two forms below and send to SWGLHexports@nbt.nhs.uk

NHS Genomic Medicine Service test order form – Cancer

NHS Genomic Medicine Service record of discussion form

Additional forms

All published forms can be found directly on the NHS Genomic Medicine Service Resources website.

For expediency we have directly linked to additional forms that may be required for specific circumstances in the conversation process:

NHS Genomic Medicine Service young persons’ assent form

NHS Genomic Medicine Service genomic consultee declaration (adult requests only)

Below is the form for opt in and out to the National Genomic Research Library as part of the conversation process:

NHS Genomic Medicine Service participation in research form

• WGS results may have broad implications for patients and their family members. For patients with cancer, this includes the potential of WGS to identify information relevant to the patient’s treatment, as well as germline variants associated with a hereditary predisposition to cancer. These should be discussed as appropriate given the clinical context. Patients with a germline finding should be referred to clinical genetics. Patients should also be aware that if they are having a WGS test, their data will be processed through a national system.
• ‘Patient choice’ is a process which enables patients to make an informed decision about having a diagnostic clinical WGS test, as well as make a clear and distinct decision about being part of the National Genomic Research Library (NGRL).
• National policy requires that every patient is given the opportunity to take part in the NGRL, and that this is discussed at some point in their pathway. If a discussion has not taken place when clinical WGS for diagnosis was agreed, or the patient has chosen not to take part, this will not prevent the WGS test.
• The clinical team should ensure that there are robust local measures to ensure adequate discussion with patients and that appropriate documentation is in place, whilst also ensuring that this does not result in unnecessary delay in results.
• Resources about patient choice for clinicians is available here and will be supported by local training.
• Consent for WGS should always be recorded in the patient’s notes in line with local guidance. However, national policy requires that a RoD is also completed and sent to the SWGLH before WGS can be initiated. The RoD reflects the choice the patient has made about joining their genomic data to the National Genomics Research Library.

Please refer to the SWGLH SolidTumour WGS guide v3 for full information.

All patient information leaflets can be found on NHS England National Genomic Services Resource pages and Genomics England Patients and Participants website pages

Direct links here:

Whole genome sequencing for suspected cancer:Information for patients and family members

Information about Whole genome sequencing fir if you think you have cancer – easy read

Genomics England Genomics Research and why it’s important

Please refer to the SWGLH SolidTumour WGS guide v3 for information regarding collection of the somatic WGS sample and next steps.

Important

• Samples must contain more that 30% tumour and less than 20% necrosis to be eligible for WGS
• Samples must use fresh or fresh frozen tissue only
• Germline samples (haematology) should be skin or remission samples. If a suitable germline sample is unavailable then tumour only WGS may be possible

Germline samples

The preferred germline WGS sample is a venous blood sample collected into EDTA (purple top) Vacutainer blood collection tubes:

• Adult: 8 mL (two 4 mL bottles) is desirable, 4 mL (one 4 mL bottle) is the minimum requirement*
• 4 mL (one 4 mL bottle)*
• Blood samples are not suitable if the patient has received a bone marrow transplant.  An alternate tissue, for example skin, may however be suitable; please contact the laboratory for further information

*Where the available sample volume obtained is less than this or if a blood sample cannot be obtained, other agreed sample types or stored DNA may be suitable. please contact the SWGLH laboratory at SWGLHexports@nbt.nhs.uk

Collection of the germline WGS sample by local phlebotomy teams should be ‘requested’ using local electronic systems where possible.

The blood collection tube should be labelled with the patient name, date of birth and NHS number and placed in a sample bag with the form GMS Test Order Form indicating the request is for WGS germline testing.

The germline WGS sample should be sent to the SWGLH (Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, BS10 5NB) at ambient temperature on the next available inter-hospital transport. The sample should arrive within 48 hrs of collection to enable DNA extraction within 72 hrs.

Analysis of the somatic WGS sample cannot occur without parallel analysis of a germline WGS sample. If a peripheral blood sample cannot be obtained, the germline WGS sample may be obtained from other sources such as saliva. In this circumstance please contact the SWGLH for further advice by email at SWGLHexports@nbt.nhs.uk.

Important: please refer to the SWGLH SolidTumour WGS guide v3 for detailed information to support you with this process.

There are many excellent education packages to support your genomic learning journey at Genomics Educational Resources

For more targeted Genomics Education resources to support Whole Genome Sequencing test pathway 

If you require further information regarding genomic testing please contact the laboratory

Tel:0117 4146168 or SWGLHexports@nbt.nhs.uk

If you require support for navigating the pathway including completion of paperwork please contact the Genomic Healthcare Practitioners

email rduh.swgenomicpractitioner@nhs.net