R14: Acutely unwell children with a likely monogenic disorder (rapid genome testing)

The R14 test, sometimes called a rapid trio whole genome sequencing (WGS) test, is for acutely unwell children with a likely monogenic condition, in whom rapid testing is required to guide immediate clinical management.

Typically, children eligible for this test will be in neonatal or paediatric intensive care. Testing is indicated when there is a likely monogenic condition underlying the child’s clinical presentation which is thought highly likely to have immediate clinical management or therapeutic implications.

R14 can be requested in other exceptional circumstances if clinically indicated, and if results may immediately affect patient and/or family management. Examples include:

• children with other acute clinical presentations thought likely to be caused by a monogenic condition, in whom a genetic diagnosis would have immediate clinical management or therapeutic implications (examples include acute developmental regression, acute neurodegeneration and severe epilepsy); and
• in the early stages of a subsequent pregnancy where there is an affected sibling with an undiagnosed, rare, likely monogenic condition for which the couple would consider prenatal testing, or if the immediate postnatal management of the baby would be changed by a molecular diagnosis.

On occasion, an R14 test may be appropriate for an adult in intensive care or with an acute presentation highly suggestive of a monogenic condition, in whom a genetic diagnosis would guide immediate clinical management.

It is not appropriate to use R14 testing to exclude a genetic diagnosis when a non-genetic cause is highly likely to explain the clinical presentation (for example, infection, prematurity, non-accidental injury or hypoxic ischaemic encephalopathy).

Sometimes, the specialist Exeter Clinical Laboratory will advise that there is a more appropriate test that should be used instead of R14 – for example, if highly specialist interpretation of the results may be required, such as in a diagnosis of newborn respiratory distress syndrome.

Since October 2022, the R14 test has used WGS technology (prior to this date, exome sequencing technology was used).

Typically, samples are requested from the affected child and both parents, in order to undertake what is called a trio test. The R14 trio test employs an inheritance-based, gene-agnostic bioinformatics approach, which enables analysis of nearly all 22,000 genes in one test in order to identify the gene changes that may be related to the child’s condition. A gene-agnostic approach would not be suitable if either parent was thought to be affected by the same condition as their child, or if the condition under investigation was thought to be variably penetrant – not everyone who carries a gene change has associated features. In these circumstances, an R14 test can still be undertaken using WGS technology and a gene panel analysis approach.

If one or both parents are unavailable, duo (with one parent) or singleton (child only) R14 testing can be undertaken. In these circumstances, WGS technology and a gene panel analysis approach would typically be used. The requesting clinician and the R14 team at the Exeter Clinical Laboratory will need to discuss which gene panels would be most clinically appropriate based on the child’s phenotype. The Exeter Clinical Laboratory uses panels listed in the NHS Genomic Medicine Service (GMS) Signed Off Panels Resource for R14 tests that require a gene panel approach – for example, R59 Early onset or syndromic epilepsy.

The R14 test is performed by the Exeter Clinical Laboratory, part of the South West Genomic Laboratory Hub. There is a two- to three-week turnaround time from receipt of the samples to the report being issued. More information about the R14 test and the specific test request and record of discussion forms for R14 are available from the R14 rapid genome sequencing service webpage.

• Finding a genetic diagnosis that explains the child’s condition. This diagnosis might affect treatment or management of their condition. It may provide information about risk to other family members or to future children. The diagnostic yield for the R14 test is 41% (as of April 2023).
• The test finds a gene change of uncertain clinical significance (known as a variant of uncertain significance) – this means that it is not certain whether the change could cause a genetic condition. We all have a lot of variation in our genes, and it can be difficult to decide whether a gene change is just part of normal variation or whether it could be the cause of the child’s condition. In this situation, extra discussion and sometimes extra tests are required to help clinicians decide.
• No genetic cause for the child’s health problems is found. This does not rule out a genetic condition. We have not yet discovered the cause of all genetic conditions, and not all gene changes are detectable, even with this detailed testing.
• Very occasionally (less than 1 in 100 tests), an unrelated unexpected or incidental gene change might be discovered. If knowing this could make a difference to the future health of the child, parents or other family members, it will be discussed with the referring clinician before the result is reported.

The test will show if a parent is not the child’s biological parent (non-paternity or non-maternity) and would also reveal an incestuous relationship between the parents. If this is a concern, please raise it with the Exeter Clinical Laboratory in advance of requesting the test. Should it be identified during the test, the result would be discussed with the referring clinician before any report is issued.

• Contact your local clinical genetics team. Local pathways may vary, but all R14 requests must be discussed with, and agreed by, a local clinical genetics consultant and by the Exeter Clinical Laboratory before any samples are sent.
• There are specific test request and record of discussion forms that you can use to request and obtain consent for the R14 test.
• A separate record of discussion form should be used for all individuals being tested, usually the child and both parents. The form should be kept in the patient records and should not be sent to the laboratory.
• General GeNotes guidance is available on how to complete record of discussion forms.
• Only a single test request form is required for the whole family. You will need to provide details of the requesting clinician, patient identifiers, ethnicity, consanguinity and detailed clinical information that includes the results of any imaging and non-genomic testing. The use of human phenotype ontology terms is optional. Should any new clinical information become available during testing (such as MRI results or evolution of the phenotype), it should be communicated to the laboratory via email as soon as possible because it may aid interpretation of the results.
• EDTA samples are required from the child and both parents, where possible.

• As part of the record of discussion, all families are asked if they agree to being contacted to discuss relevant research opportunities in the future. This is a personal decision for families, and they do not need to agree in order to access the test.

For clinicians

• Exeter Clinical Laboratory: R14 rapid genome sequencing service
• Genomics England: NHS Genomic Medicine Service (GMS) Signed Off Panels
• Gov.uk guidance: Code on genetic testing and insurance
• NHS England: National Genomic Test Directory

References:

• French CE, Delon I, Dolling H and others. ‘Whole genome sequencing reveals that genetic conditions are frequent in intensively ill children’. Intensive Care Medicine 2019: issue 45, pages 627–636. DOI: 10.1007/s00134-019-05552-x

For patients

• R14 rapid genome sequencing service: Information for patients and families (PDF, one page)