Whole Genome Sequencing - Rare Disease C&S GLH

The implementation of Whole Genome Sequencing (WGS) for Rare Disease as a routine diagnostic service is being carried out through distinct phases, with clinical indications from the National Genomic Test Directory eligible for WGS as part of these phases. We are currently in phase 1.

The clinical indications listed below are eligible for WGS testing, and from the 1st July 2021 all routine testing for these will be carried out by WGS testing.

Code

Clinical indication

Reporting laboratory

R27.3

Congenital malformation and dysmorphism syndromes - microarray and sequencing

Referring centre’s local laboratory

R29.4

Intellectual disability – microarray, fragile X and sequencing

Referring centre’s local laboratory

R69.5

Hypotonic infant

Referring centre’s local laboratory

R143.4

Neonatal diabetes

Exeter Genetics Laboratory

R98.2

Likely inborn error of metabolism - targeted testing not possible

West Midlands Genetics Laboratory

R104.3

Skeletal dysplasia

Oxford  Genetics Laboratory

R100.3

Rare syndromic craniosynostosis or isolated multisuture synostosis

Oxford  Genetics Laboratory

R54.3

Hereditary ataxia with onset in adulthood

Oxford  Genetics Laboratory

R55.4

Hereditary ataxia with onset in childhood

Oxford  Genetics Laboratory

R59.3

Early onset or syndromic epilepsy

Oxford  Genetics Laboratory

R61.4

Childhood onset hereditary spastic paraplegia

West Midlands Genetics Laboratory

R83.3

Arthrogryposis

West Midlands Genetics Laboratory

R381.2

Other rare neuromuscular disorders

West Midlands Genetics Laboratory

R84.4

Cerebellar anomalies

Oxford  Genetics Laboratory

R85.2

Holoprosencephaly - NOT chromosomal

West Midlands Genetics Laboratory

R86.3

Hydrocephalus

West Midlands Genetics Laboratory

R87.3

Cerebral malformation

Oxford  Genetics Laboratory

R88.3

Severe microcephaly

West Midlands Genetics Laboratory

R109.3

Childhood onset leukodystrophy

West Midlands Genetics Laboratory

R193.4

Cystic renal disease

North Bristol Genetics Laboratory

R89.3

Ultra-rare and atypical monogenic disorders

Referring centre’s local laboratory

A guide and frequently asked questions document for the Genomic Medicine Service and Whole Genome Sequencing can be found here.

This document contains helpful information on the Genomic Medicine Service, how to use PanelApp, and how to request testing and complete forms for Whole Genome Sequencing. If you have a query regarding Whole Genome Sequencing, please check whether your question is present within the frequently asked questions section before contacting the laboratory.

In brief, in order to request a WGS test for your patient you will need to complete the following steps:

Step 1 Check patient eligibility

Eligibility criteria for rare diseases can be found in the rare and inherited disease eligibility criteria document for the Genomic Medicine Service here.

If you need to query whether you can request WGS for your patient then please contact bwc.centralsouthglh@nhs.net.

Step 2 Collect patient samples

Blood samples in EDTA are required in order to extract DNA for Whole Genome Sequencing. This should be at least 1-3 mL for neonates and 3-5 mL for other patient referred. Blood samples should be sent to your local genetics laboratory and will be forwarded on to the West Midlands Regional Genetics Laboratory for DNA extraction and sending for Whole Genome Sequencing. Samples can either be sent with the Whole Genome Sequencing test order form (see below), or with a standard genomics referral form with WGS noted on the form (and the Whole Genome Sequencing test order form and Record of Discussion form sent by e-mail).

For the clinical indications currently being tested, it is highly recommended that a trio is referred for testing (proband and biological parents), however it is acceptable to refer a duo (proband and one biological parent) or singleton where one or more parents are not available.

It is possible for a stored DNA sample to be used for Whole Genome Sequencing, but the sample must have been extracted in a UKAS-accredited laboratory and will be required to pass all quality control checks. Please contact your local laboratory if you think that there is stored DNA available for testing. However, a fresh blood sample is always preferred if possible.

If the DNA extracted from a blood sample you have sent from patient, or from stored DNA, does not pass the quality control checks required then you will be notified of this and requirement for a new blood sample to be sent.

Step 3 Complete Test Order form and Record of Discussion form

Whole Genome Sequencing requires:

All forms should be e-mailed to bwc.centralsouthGLH@nhs.net. Please see the FAQ/Guide document for further information on how to complete the Test Order and Record of Discussion forms. All forms should be completed in full with all pages of the forms completed. These forms should not be used for non-Whole Genome Sequencing testing.

Where a patient is not able to complete a Record of Discussion form (deceased/lacks capacity) then a Consultee Declaration form can be completed by a consultee of the patient –  Whole Genome Sequencing Consultee Declaration form.pdf [pdf] 184KB

Turnaround times

There is currently a 6-week turnaround time for Whole Genome Sequencing data to be received back from Illumina/Genomics England once samples have been sent. There is then a 6-week turnaround time for the reporting laboratory to analyse and report the results to the referring clinician. Results should therefore be received within 12 weeks. However, please note that this turnaround time starts when all of the forms and samples have been received. You will receive a report to state your patient’s samples have been sent for Whole Genome Sequencing when samples have been sent.

Reports

Whole Genome Sequencing data will be analysed and reported by the specific laboratory as in table above.