Professionals FAQ
All of your questions answered
Whole Genome Sequencing sequences a person’s complete DNA. Whole-genome sequencing entails sequencing all coding (exons) and non-coding DNA as well as mitochondrial DNA.  The exome makes up only 1.5% of the whole human genome, however, all protein-coding genes are found in the exome.
Whole-exome sequencing and targeted panels, only see part of the story as they focus on reduced areas of the genome. As a result, for some genomic conditions whole-genome sequencing may be most appropriate.
The National Test Directories for rare diseases and cancer have set out the clinical conditions or indications where there is clear evidence for the value of genomic testing for patients. Each clinical indication listed has a set of criteria that sets out which patients are eligible.
The directory is updated regularly and is available here.
Training and support is available to all health professionals to ensure you feel comfortable and confident to obtain consent from a patient. Clinical genetics are available to support you with complex cases and we would encourage you to build a relationship with your local clinical genetics departments.
The NHS National Test Directory lists all the genomic tests that are currently available. The Directory states the eligibility criteria for each test.
No. All genomic tests are commissioned and funded centrally by NHS England.
Single-gene testing is not available for most genes, but clinicians can request a panel test that includes the gene in question.
Please make it clear which gene you are interested in on the referral form.
Genomic tests will be performed to nationally agreed standards in one of our dedicated genomic laboratories at either Guy’s Hospital, Kings College Hospital or the Royal Brompton. Each laboratory specialises in different tests.
Each test has a different national turnaround time. This is the time it takes for the laboratory to complete the test and return it to the health professional.
Depending on which test you need, it could take days, weeks or sometimes months.
We publish our turnaround times every month. For the latest times click here.
You will receive a comprehensive test report from the laboratory which follows national guidelines.
You will be contacted to talk through the findings and subsequent report. Â This may involve a multidisciplinary team meeting if the laboratory needs more information from you, or the findings are complex.
The report will include the types of tests used, the key findings, and a diagnosis if confirmed and it is recommended that you talk through the report with your patient, and that a copy of the report is kept in their medical records and shared with them as appropriate.
A patient’s genomic test results will become part of their patient record. A copy will be held within a national system which is only available to healthcare professionals.
It is normal practice for an NHS laboratory to store extracted DNA from a sample after the current testing is complete, as it may be used for future analysis and act as a control to ensure consistency and quality of testing, for example when testing family members.
For Whole Genome Sequencing, the data from genomic tests are entered into a secure national database for the NHS Genomic Medicine Service. This system will store data about the test and results. Only people with approved access will be able to access this data.
As part of the NHS Genomic Medicine Service, all patients will be given the option to contribute their genomic data to a secure library so that approved researchers may access that data in a form that does not identify them. If patients choose to do this, then the data will be helping scientists, researchers, and other patients, by developing the treatments of tomorrow.
To find out more about how genomic data can support research please see the Genomics England website.
Please check the turnaround times for the test you have ordered. If you have requested a test and have not received the results by the turnaround times, please contact the laboratory for current turnaround times:Â gst-tr.southeastglh@nhs.net
There may be different reasons for an inappropriate referral. Usually it is due to either an inappropriate sample (where the wrong sample has been received) or due to an issue with eligibility (either insufficient clinical details or a request from a specialist other than those permitted by the Test Directory). See our referral forms for sample types for different tests, and see the Test Directory Eligibility Criteria for further information about eligibility.
We provide genomic testing for all 28 NHS Trusts within South London, Sussex, Kent and parts of Surrey. These include:
Surrey
- Frimley Health NHS Foundation Trust
- Royal Surrey County Hospital NHS Foundation Trust
- Ashford & St. Peter’s Hospitals NHS Foundation Trust
- Surrey & Borders NHS Foundation Trust
London
- Royal Brompton & Harefield NHS Foundation Trust
- Guys and St Thomas’ NHS Foundation Trust
- Lewisham & Greenwich NHS Trust
- King’s College Hospital NHS Foundation Trust
- Oxleas NHS Foundation Trust
- South London & Maudsley NHS Foundation Trust
- Kingston Hospital NHS Foundation Trust
- Croydon Health Services NHS Trust
- St George’s University Hospitals NHS Foundation Trust
- Epsom & St Helier University Hospitals NHS Trust
- South West London & St George’s Mental Health NHS Trust
- Hounslow & Richmond Community Healthcare NHS Trust
Kent & Medway
- Dartford & Gravesham NHS Trust
- Medway NHS Foundation Trust
- East Kent Hospitals University NHS Foundation Trust
- Maidstone & Tunbridge Wells NHS Trust
- Kent & Medway Social Care Partnership Trust
- Kent Community Health NHS Foundation Trust
Sussex
- Queen Victoria Hospital NHS Foundation Trust
- Surrey & Sussex Healthcare NHS Trust
- East Sussex Healthcare NHS Trust
- University Hospitals Sussex NHS Foundation Trust
- Sussex Community NHS Trust
- Sussex Partnership NHS Foundation Trust
National Genomic Test Directory
Please visit our National Genomic Test Directory (NGTD) page.
The Test Directory can be filtered to make it easier to find tests relating to your specialty. You may find that some tests that you previously ordered now have a different name in the Test Directory.
If you are having difficulty finding the relevant test please contact the laboratory: gst-tr.southeastglh@nhs.net
The National Genomic Test Directory (NGTD) outlines all genetic tests funded by NHS England, and is developed by expert groups including clinicians, scientists, health economists, policy experts, public representatives and patient organisations.
Any genomic tests not included are out of scope of the GLH. The NGTD will be updated annually as evidence arises to suggest the inclusion of new genes. Information about the process for updating the NGTD can be found on the NHS England website.
NHS England have also published a National Genomic Test Directory Frequently Asked Questions (FAQ) document.
The NGTD is updated annually as evidence arises to suggest the inclusion of new genes.  Information about the process for updating the NGTD can be found on the NHS England website.
Applications to request new tests are usually open between June-August each year, and the GLH is happy to support clinicians with their submissions.
Rare and Inherited Conditions
There is a Test selection Tool NHS England | Public Genetic Test Directory (genomics.nhs.uk) if you enter the disorder in the search box, a list of suggested panels is generated.
By clicking on a suggested panel – under further info a list of genes that are included is generated.
For DNA-based tests you can request additional tests where we have DNA stored already. Please complete a new request form and forward it to gst-tr.southeastglh@nhs.net
Yes you can, as long as your primary clinical indication falls within the Phase 1 and Phase 2 indications listed in the table. Then, if your patient has other symptoms, too, you can add one of the panels which are listed as ‘GMS Rare Disease Virtual’ on panelapp e.g. Hearing loss panel.
Whole Genome Sequencing
In general, it is recommended to send a trio (affected patient plus parents) for WGS. This makes it easier to analyse the variant data and more likely to reach a diagnosis than with a singleton referral.
However, there are many circumstances where parents may not be available and the case can be referred as a singleton or a duo.
Yes. Patients and family members can make a Subject Access Request (SAR) to have their raw genomic data. Clinicians should inform patients that this data would need to be interpreted by a genomics expert and is not presented as a clinical report outlining all genomic changes. The clinician should contact the WGS service desk at gst-tr.southeastglh@nhs.net if their patient wishes to make a SAR.
For Rare and inherited conditions, a Germline Sample is required: peripheral blood (2-5ml EDTA), stored DNA, cultured fibroblasts.
For cancer a Germline Sample is required: peripheral blood (2-5ml EDTA), stored DNA, cultured fibroblasts, for haematological malignancies a skin biopsy is required. A tumour sample is also required:
- For Solid tumours: Fresh frozen tissue (at least 1 core biopsy), tumour cells must account for at least 30% of the nucleated cells present
- For haematological malignancies: Bone marrow aspirate, peripheral blood
Proband and both parents is the preferred family structure as adding affected siblings can complicate the analysis. If a pertinent result is found through WGS, targeted testing may be offered to affected siblings, if appropriate.
Clinicians will receive a report once analysis is complete. You may be asked to provide further information or attend an MDT / GTAB before the report is issued.
If the policy was taken out before the patient received their test result, they are not obliged to update their provider on the test and its findings for as long as the cover is in place and remains unaltered. Further information on the patients current and future responsibility towards insurance providers is provided by Genetic Alliance UK and the Association of British Insurers. Code on Genetic Testing and Insurance ABI.
To find out more about which insurance companies are registered with the ABI and subject to the above terms please visit:Â ABI members.
Analysis for WGS is panel based so please ensure that the correct clinical indication is entered in the Test Order Form so that the right panels are applied. For Rare Diseases, clinicians are able to add additional panels, if appropriate.
Reanalysis is available where there is clinical need and where reanalysis is likely to increase the chance of a diagnosis due to new gene associations, additional clinical information, improved bioinformatics.
Requests for WGS data reanalysis may be accepted as appropriate if the following criteria are met:
There must be a high expectation that reanalysis will yield a diagnosis. For example:
- The change to gene panel content or bioinformatic improvements introduced since the last analysis was performed, is significant so that the probability of achieving a diagnosis is sufficient enough to justify reanalysis. It is not expected that reanalysis will be significantly productive within at least 2 years of the last analysis.
AND
There must be a clinical trigger for the reanalysis. For example:
- There is a new significant change in the clinical presentation of the patient or family member (e.g. evolving phenotype) meaning application of additional GMS approved gene panel(s) would be relevant and updating the HPO terms provided will support more effective analysis in Exomiser;
- New treatment becomes available so reanalysis could influence the patient’s clinical management;
- The proband is deceased and the family initiate further investigation through the appropriate clinician, due to potential management implications for themselves and/or the wider family.
If you consider that re-analysis should be performed please contact the laboratory: gst-tr.southeastglh@nhs.net
Patient’s DNA samples should not be sent for resequencing via the current GMS WGS pathway apart from in specific circumstances.
Outlined below are possible exceptions for which it is acceptable to submit patients and their family members for WGS through the GMS pathway:
- Patient submitted to 100,000 Genomes Project as a singleton but it is now possible to test as a Trio (for clinical indications whereby trio analysis is the optimal family structure) and the primary analysis detected lots of potential candidate variants which trio analysis will help to classify.
- There is immediate clinical urgency AND an expectation that a new test would yield a new diagnosis, e.g. The original analysis was done several years ago, the phenotype has substantially altered and a molecular diagnosis is likely to contribute to urgent clinical decisions. The patient can be tested through the relevant test from the GMS National Test Directory (including WGS if clinically eligible).
Yes.
National Genomic research library (NGRL)
The National Genomic Research Library (NGRL) is a national research database owned by Genomics England which holds the genomic, health and sample data of patients who have undergone whole genome sequencing (WGS). All rare disease and cancer patients who are consented for WGS have the opportunity to share their anonymised data with this library.
This anonymised data is vital for advancing research, helping us to improve our understanding of human disease and develop treatments that can benefit patients with many conditions. More information about the NGRL can be found on the Genomics England website (https://www.genomicseducation.hee.nhs.uk/supporting-the-nhs-genomic-medicine-service/national-genomic-research-library-information-for-clinicians/)
The NGRL allows approved access to the pseudonymised health data, genomic data and samples of patients and family members who have had WGS and consented to their data being accessed to the library.
While patients can be identified if necessary (e.g. If a diagnosis is found or there is potentially relevant research), NGRL governance specifies that researchers will not be able to identify individuals.
You can apply to become a member of the academic research community (GECIP) by following this link https://www.genomicsengland.co.uk/research/academic/join-gecip