Ordering Whole Genome Sequencing
The North Thames GLH began live clinical testing for Whole Genome Sequencing at the beginning of 2021. This service is currently available for selected rare disease and cancer patients who will in parallel receive standard genomic tests where they are available.
Clinicians are now able to order WGS for eligible conditions as set out in the National Genomic Test Directory. A full list of indications eligible for WGS is also included at the end of this page.
While we remain in the Live Clinical Testing phase and await the delivery of informatics management systems from the NHSE and GEL, results may take longer than the expected 12 weeks. Whilst it may take a while to report results in these early stages, all samples received by the lab will be stored until they are able to be dispatched, and we are doing our best to improve turnaround times.
We expect WGS to enable faster and more accurate diagnoses for patients than current tests and, in some cases, help identify more personalised treatments based on a person’s DNA.
How to order Whole Genome Sequencing (WGS)
Before ordering
- Check patient is eligible for WGS, select clinical indication and check family structure using
- National Genomic Test Directory (contains full directory of genomic tests available)
- Test Selection Tool (WGS indications only)
- If using stored DNA please email gos-tr.wgsnorththamesglh@nhs.net to check that DNA is of appropriate quality and quantity. In email, please state the following:
1. Test type (ie. WGS)
2. Clinical Indication (see Test Directory or Test Selection Tool)
3. Where parental samples are coming from (ie. fresh or stored). Not applicable for cancer.
- Previously we were unable to use DNA extracted before October 2018. However, this restriction has been lifted, and it is now acceptable to use DNA extracted prior to this date as long as the quantity and the quality of the DNA is sufficient.
Patients that have had WGS through the 100,000 Genomes Project are not eligible for WGS through the Genomic Medicine Service.
To order
Samples cannot be processed until the lab has all of the following forms correctly and fully completed:
| Rare Disease | Cancer |
| Record of discussion form | Record of discussion form |
| Test order form (Rare Diseases) | Test order form (cancer) |
| Germline sample | Germline sample |
| Tumour sample |
- Please note that you will need to complete one Record of Discussion form for each family member
- There is a family member test order form in the Rare Disease clinican pack provided in ‘Further Resources’
- There is more information about Patient Choice (related to the Record of Discussion form) at the bottom of this page
- If you have a nominated consultee consenting on behalf of a patient over 16 who lacks sufficient capacity, you will need to complete the ‘Consultee Declaration ’ form in addition to the ‘Record of Discussion’
- For Rare Disease Whole Genome Sequencing (WGS) the North Thames Rare Disease Laboratory at GOSH will no longer routinely issue separate reports for the parents in trio/duo referrals where there is no primary finding in the proband. A report will be issued for the proband as usual. The laboratory will generate separate reports for parents where there is a finding in the proband that presents a significant recurrence risk to offspring or other family members.
Please note, many WGS cases will need to be discussed at an MDT. You must be prepared to attend an MDT if you wish to order WGS for your patient. If this is not possible then the patient should be referred to a clinician familiar with WGS and MDTs.
Further Resources
The Clinician Packs (Rare Disease and Cancer) contain all the forms you will need in order to submit a WGS request as well as patient information and clinician guidance.
Patient information leaflets and record of discussion forms are now available in 11 languages;
There are also visually accessible patient information sheets (Rare Disease and Cancer).
Additional information to support you in delivering WGS can be found here. National guidance and Standard Operating Procedures (SOPs) can be found here. If you have any WGS related questions please contact the GLH through the designated WGS email address
gos-tr.wgsnorththamesglh@nhs.net
If you have any questions or queries related to WGS or Mainstreaming, feel free to attend one of our monthly WGS & Mainstreaming Genomic Medicine sessions. More information can be found here.
Patient Choice
For Whole Genome Sequencing, you must ensure you have your patient’s consent for their genomic testing before you send the sample to the Laboratory for testing. No test will be reported without the applicable signed consent, which is recorded on the Record of Discussion form. Given the situation during COVID where many appointments are being conducted remotely, the record of discussion form can be completed virtually by following the Remote Patient Choice Policy.
The National Genomic Research Library
The patient choice form for Whole Genome Sequencing also documents whether or not patients consent to their data included in the National Genomic Research Library (NGRL), for use in research, and to be re-contacted regarding relevant research projects in the future.
Please do try discuss consent for research with your patients. Experience has shown that many people feel very positive about helping further research and using this kind of anonymised data can prove invaluable for researchers and often results in significant patient benefit.
Patients’ choices regarding the NGRL can be recorded on page 3 of the record of discussion form, and, for those who lack capacity, on the consultee declaration form.
To help make the WGS/NGRL pathway more manageable and potentially reduce the workload of clinicians, a hotline service targeting patients who need more time to consider whether they would like to share their data with the NGRL is being piloted.
The hotline is open Monday to Friday 9am-5pm and is overseen by members of the Genomic Research Team at Great Ormond Street Hospital. This team are available to consent WGS patients for the NGRL and answer questions they may have in relation to their participation. Please note, this team cannot complete clinical consent for WGS. All paperwork for WGS must be completed by the clinician so that testing is not delayed.
If you would like to refer your patient to this service, please indicate the patient’s decision on page 3 of the record of discussion form, and leave a contact number for the patient as shown below.
Please send the completed form to gos-tr.NTGenomicsAssociate@nhs.net
Alternatively, please ask your patient to call us on 0207 762 6870, or email us using the above email address.
For non-WGS tests you should continue to follow processes that are currently in place for test consent and initiation.
Indications eligible for WGS
Cancer
Paediatric (<25 years old)
- All solid tumours at initial diagnosis and/or relapse
- All haematological malignancies at initial diagnosis and/or relapse
Adult
- All sarcomas at initial diagnosis and/or relapse (Excluding GIST)
- Acute leukaemia
- Central nervous system malignancies
- Triple negative breast cancer
- High grade serous ovarian cancer
Rare Diseases
Please check the Rare & Inherited Disease Eligibility Criteria to see if you can order this test for your patients.
| Code | Clinical Indication Name |
| R83 | Arthrogryposis |
| R84 | Cerebellar anomalies |
| R87 | Cerebral malformation |
| R61 | Childhood onset hereditary spastic paraplegia |
| R109 | Childhood onset leukodystrophy |
| R27 | Congenital malformation and dysmorphism syndromes – microarray and sequencing |
| R193 | Cystic renal disease |
| R59 | Early onset or syndromic epilepsy |
| R54 | Hereditary ataxia with onset in adulthood |
| R55 | Hereditary ataxia with onset in childhood |
| R85 | Holoprosencephaly – NOT chromosomal |
| R86 | Hydrocephalus |
| R69 | Hypotonic infant with a likely central cause |
| R29 | Intellectual disability – microarray, fragile X and sequencing |
| R98 | Likely inborn error of metabolism – targeted testing not possible |
| R143 | Neonatal diabetes |
| R381 | Other rare neuromuscular disorders |
| R100 | Rare syndromic craniosynostosis or isolated multisuture synostosis |
| R88 | Severe microcephaly |
| R104 | Skeletal dysplasia |
| R89 | Ultra-rare and atypical monogenic disorders |
| R135 | Paediatric or syndromic cardiomyopathy |
| R31 | Bilateral congenital or childhood onset cataracts |
| R32 | Retinal disorders |
| R33 | Possible X-linked retinitis pigmentosa |
| R34 | Sorsby retinal dystrophy |
| R35 | Doyne retinal dystrophy |
| R36 | Structural eye disease |
| R15 | Primary immunodeficiency |
| R56 | Adult onset dystonia, chorea or related movement disorder |
| R57 | Childhood onset dystonia, chorea or related movement disorder |
| R58 | Adult onset neurodegenerative disorder |
| R60 | Adult onset hereditary spastic paraplegia |
| R62 | Adult onset leukodystrophy |
| R78 | Hereditary neuropathy or pain disorder – NOT PMP22 copy number |
| R257 | Unexplained paediatric onset end-stage renal disease |