Provision of WES Trio and Singleton Virtual Panel Analysis for Welsh Patients

Concepts

• wes trio
• cardiff
• laboratory services
• provision of wes trio
• welsh patients
• singleton virtual panel analysis
• wes
• patients
• trio
• singleton

Location

Cardiff and Vale of Glamorgan: All Wales Medical Genomics Service, Institute of Medical Genetics, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW

Description

In-line with All Wales Medical Genomic Service’s (AWMGS) commissioning model, AWMGS will procure from CeGaT whole exom sequencing (WES) for trio or singleton virtual panel analysis for patients where this testing cannot be accessed within the NHS E laboratory network. This genetic testing will ensure equity of access to genomic testing for Welsh patients and meet their need to seek a timely genetic diagnosis for their rare or inherited disease.

Total Quantity or Scope

NWSSP Procurement Services intends to award a contract on behalf of Cardiff and Vale University Health Board, AWMGS, for the supply of WES single and trio based testing from CeGAT. The contract is estimated to commence in July 2021, for a period of two years. The first year’s delivery will be capped at 175,000 GBP and reviewed to ensure that value for money is being achieved through the pick-up rate of pathogenic findings as a means of ensuring appropriate referrals and use of this bespoke service. The second year’s service will be capped at estimated 100,000 GBP assuming AWMGS are able to deliver in-house WES-based testing for Welsh patients within 2022/23 as currently planned.

Award Detail

CPV Codes

• 71900000 - Laboratory services

Legal Justification

All Wales Genomics Service (AWMGS) is commissioned by the Wealth Health Specialist Services Commission (WHSSC) to provide genetic testing for Welsh patients which is equitable to the provision NHS E makes available through the Rare and Inherited Disease Test Directory. NHS E patients can currently access a range of Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) tests for rare and inheritable diseases which the laboratory is unable to deliver in-house. In-house service developments are ongoing to enable the delivery of equivalent genetic tests but these will not go-live until 2022 – 24 (services will be introduced over a 18-24 month basis). Where feasible, AWMGS commission genetic tests from within the NHS network for Welsh patients. NHS E genetic laboratories currently provide Welsh patients with access to a small number of trio WES-based tests, e.g. Exeter genetic laboratory provides and a larger number of phenotype driven singleton virtual panel tests. Importantly, WGS based testing is not available at all to AWMGS patients from NHS E laboratories due to the centralised model developed by Genetics England. AWMGS will procure from CeGaT WES for trio or singleton virtual panel analysis for patients where this testing cannot be accessed within the NHS E laboratory network. For Single Exome Diagnostics, CeGaT will analyse a virtual panel of genes that are known to be associated with the patient’s phenotype. The virtual panel will be selected from a list of panels that have been curated by the NHS Genomic Medicine Service and are aligned to the NHSE Test Directory. These panels can be found at https://panelapp.genomicsengland.co.uk/ Targeted analysis of the ACMG genes is NOT requested for any samples received from AWMGS. Should incidental or secondary findings be identified through routine analysis and not as part of a targeted analysis, these may reported to the referring clinician depending on the preference of the patient that will be indicated on the customised referral form that has been designed to meet the needs of the AWMGS service. There is no alternative supplier within Europe providing an equivalent customised WES trio or singleton service to CeGAT which delivers against PanelApp green gene lists. Through procuring this specialist service from CeGAT AWMGS will ensure equity of access to genetic testing across NHS E and NHS W patient cohort in line with the commissioning model agreed with WHSSC.

Other Information

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