Cardiff and Vale University Health Board
Whole genome sequencing (WGS) is a DNA based next generation sequencing method that enables analysis of an entire genome and has the potential to detect a variety of genomic abnormalities in one test.
There is evidence that WGS for paediatric oncology patients provides clinical utility beyond standard of care testing through more accurate diagnosis, prognosis and wider treatment options (Trotman et al., 2022).
This project involves setting up a whole genome sequencing (WGS) service for paediatric oncology patients, at diagnosis, whose disease has relapsed or progressed or whose treatment has exhausted all standard of care options (<25years).
This will be achieved by collecting samples from patients undergoing standard of care testing, with a prospective consent form, so that relevant sample pathways can be established and validated within the All Wales Medical Genomics Laboratory (AWGL). Existing standard of care samples will be used plus additional sample types. We estimate that this service will be utilised by approximately 80 patients per year.
In order to implement WGS for paediatric cancer samples, a technical pathway needs to be established within AWGL for the use of fresh/frozen solid tumour samples for a solid tumour paediatric WGS cancer pathway and bone marrow or blood samples for a haemato-oncology paediatric WGS cancer pathway. Suitable germline samples are also needed for these pathways in order that germline variants (excluding cancer predisposition genes) can be subtracted from the somatic genome for analysis.
A technical WGS pathway (PCR free WGS) already exists at AWGL for rare disease (blood) samples and samples from acutely unwell children as part of a whole genome sequencing service for these patients. This technique can be adapted for paediatric oncology samples.
A bioinformatics and analysis and reporting pathway then needs to be put in place for these samples from paediatric oncology patients in Wales.