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The South West Genomic Laboratory Hub (SWGLH) offers a number of genomic tests for patients with solid tumours, neurological tumours, sarcoma and tumours in children and young adults.

How do I know which test to request?

The best place to check what test you need is the National Genomic Test Directory. These directories provide information on the most appropriate test for clinical indications, who is eligible for testing, who can request tests and which technology will be used for testing.

Where can I find forms, documents and guidance?

  • Whole genome sequencing for any solid tumour in children and young adults or sarcoma (please see the WGS section below)
  • ctDNA testing (please see the ctDNA page here).
  • Gene panels, FISH and direct mutation tests for solid tumours, neurological tumours, sarcoma and tumours in children and young adults , including lymphoma (please follow the sequential steps at the bottom of this page.)

Whole Genome Sequencing

When you request a genetic test for cancer, you may or may not be aware that some of these tests are run using whole genome sequencing (WGS).  If your test is run using WGS technology, you will need additional forms. These can be found in the drop-down boxes below.

Test order forms and additional documents for Whole Genome Sequencing

To request a whole genome sequencing test for rare disease, you will need to download and complete the NHS Genomic Medicine Service test order form – Cancer

Please also complete the NHS Genomic Medicine Service Record of Discussion form

You will need to send these to: SWGLHexports@nbt.nhs.uk

What additional forms are needed?

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

For example, these additional forms 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

Resources for patients (Whole Genome Sequencing)

Resources for healthcare professionals (Whole Genome Sequencing)

One page pathway guide for the request process for Whole Genome Sequencing in Rare Disease can be accessed here: WGS Sarcoma Short Guide v3 PDF

Pathway guide for WGS requests in Paediatric Oncology (non- neuro): WGS Paeds Onc Short Guide v1.2

Pathway guide for WGS requests in Paediatric Neurology Oncology: WGS Paeds Onc Neuro Short Guide v1.2

Clinical guidance document: Whole genome sequencing for solid tumours: SWGLH SolidTumour WGS guide v3

The HEE resource for guidance on elements of the consent conversation can be found here: Guide to requesting WGS in cancer

More resources

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 

Support for Whole Genome Sequencing

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

Step by step instructions for all tests

Eligibility

Eligible tumours and the available tests are shown in the National Genomic Test Directory for Cancer (NGTD) Only tests specified by the National Genomic Test Directory are funded, please note the M-code for the required investigation.

Genomic testing for tumours is rapidly advancing. The SWGLH is implementing new technologies such as a large gene panel test that detect single nucleotide changes, copy number changes, and gene fusions. The strategy aims to provide timely results for multiple tumour types that are relevant for clinical care and entry into trials.

Consent

An appropriate discussion of genomic testing and the possible implications for a patient and their family members must take place before testing is requested.

It is the referring clinician’s responsibility to ensure that the patient/carer knows the purpose of the test and that the sample may be stored for future diagnostic testing. In submitting a sample with a request form, the clinician confirms that informed consent has been obtained for (a) testing and storage (indefinitely) (b) the use of this sample and the information generated from it to be shared with members of the donor’s family and their health professionals (if appropriate). The patient should be advised that the samples may be used anonymously for quality assurance and training purposes.

If stated as a requirement for a specific test, a record of this discussion must be retained within the patient record when a genomic test is ordered.

For more information please view the Consent and Confidentiality in Genomic Medicine guidelines from the Joint Committee on Medical Genetics.

Test order form

Important information

The M-code should be included to identify which test is required.

The request form should clearly state who the report should be sent to. Reports will be issued by email. Multiple email addresses may be included (e.g. the referring clinician, pathologist, and MDT coordinator)

The request should be sent to your local Pathology lab to activate the preparation of samples for genomic testing.

Whole Genome Sequencing

Please note, if the test you are requesting uses Whole Genome sequencing, you will need to use additional forms, these can be found in the WGS drop-down section at the top of the page, or in the related links section to your right.

Samples and transport

  • Gene panel and direct mutation tests will be performed on FFPE samples obtained at biopsy or surgical resection, or from cytology samples
  • Samples should be prepared by the local Pathology lab and forwarded to the SWGLH with minimal delay.
  • The Pathologist’s assessment of neoplastic cell content of the sample is essential to ensure suitability for genomic testing.
  • Sample requirements as follows:
    • For DNA or RNA extraction only
      • Sample with >20% neoplastic cells: send one tube (Eppendorf or Universal): containing 5 x 10µm sections (curls/scrolls)
      • OR Sample with <20% neoplastic cells: send 10 x 5µm slide mounted sections along with H&E with regions of >20% neoplastic cells highlighted.
    • For DNA and RNA extraction
      • Sample with >20% neoplastic cells: send two tubes (Eppendorf or Universal): each containing 5 x 10µm sections (curls/scrolls)
      • Sample with <20% neoplastic cells: send 20 x 5µm slide mounted sections along with H&E with regions of >20% neoplastic cells highlighted.
    • For FISH
      • Please send 2 x 4µm and 2 x 2µm sections on ‘APES’ or ‘sticky’ slides per test required with an accompanying H&E slide with the appropriate tumour rich area(s) marked.
  • Indication M4.5 Blood samples for circulating tumour DNA analysis should be sent directly by the referring clinician to the Bristol Genetics Laboratory.

For further guidance, please see the guidance at the bottom of the page.

For a full list of sample requirements and transport guidance, please visit the samples and transport page of the website. 

Results and turnaround times

We aim to report gene panel tests within 7-10 working days of sample receipt at the SWGLH to help ensure that results available to clinicians to guide selection of treatment for cancer.

When special circumstances require a more urgent result, a rapid single gene test may be performed instead of a gene panel. Clinicians or Pathologists should contact the Bristol Genetics laboratory directly to access this service.

Visit the results and turnaround page for more information.

Guidance for healthcare professionals

The following guides have been guided to help you:

SWGLH SolidTumor_pathologists guide_FINAL

SWGLH SolidTumour_clinicans guide_FINAL