Abstract 364P
Background
In 2016 the World Health Organization updated the classification of central nervous system tumours to incorporate molecular analysis alongside histopathological evaluation. Under the revised system, diagnosis of oligodendroglioma requires presence of both an IDH mutation and codeletion of chromosomal regions 1p and 19q. In 2019, the All Wales Medical Genomics Service (AWMGS) introduced a bespoke multi-gene NGS panel for a range of tumour types, which included 10 genes/regions implicated in the diagnosis, prognosis and treatment of gliomas. The NGS panel was designed to detect 1p/19q codeletion to streamline glioma testing, also demonstrating the ability to successfully identify different driver mutations in tumours efficiently using a single test.
Methods
Validation involved evaluation of the panel for determining 1p/19q codeletion status in FFPE-extracted DNA from samples previously tested by FISH. The workflow consisted of SeqCap EZ HyperCap (Roche) protocol and sequencing on the Nextseq 550 (Illumina). Copy number variants (CNVs) were identified using the CNVkit software that calculates copy number ratio based on average read depths for on-target and off-target reads from NGS. Additionally, the NGS panel was designed with probes to target polymorphic SNPs along the full length of chromosome arms 1p and 19q used to assess loss of heterozygosity (LOH).
Results
The NGS panel showed a high degree of specificity (>99.9%), sensitivity (97.5%) and reproducibility, and could reliably detect 1p/19q codeletion in samples with >50% neoplastic cell content. Of the 46 glioma samples tested (amounting to 66 results), 98.5% of results were concordant with the expected result generated by FISH.
Conclusions
Validation demonstrated the utility of a custom-built, hybridisation-capture based NGS panel in identifying the 1p/19q codeletion. Using the NGS panel for concurrent detection of SNVs, indels and 1p/19q codeletion provides a more cost-effective, streamlined approach for glioma molecular characterisation, with the added benefit of reduced tissue requirement. Addition of 1p/19q analysis to the glioma service contributes to the comprehensive glioma service provided by AWMGS.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.