Abstract A060: Identification of tumour-specific variants from pleural effusion cell-free DNA as diagnostic markers of cancers affecting the lungs
Authors: MacKinnon Connie , Mustard Dr Colette , Brace Dr Nicole , Sage Dr Beth , Symonds Jenny , Nixon Colin , Bibby Dr Anna , Pritchard A/Prof Antonia 
Published: November 2024

Abstract
Background: Pleural mesothelioma (PM) can be difficult to diagnose due to a combination of the growth pattern of the tumour, the invasive nature of the biopsy procedure and the frailty of the patient. Some patients with PM develop a build-up of fluid around their lungs as their first clinical symptom. This fluid can make breathing difficult and is routinely drained as part of standard care. Currently, a cytological test can be performed to identify if PM cells are present in the fluid, however, while this is a specific test, it lacks sensitivity. We examined if (a) cell-free DNA (cfDNA) originating from tumours affecting the lung could be detected in this fluid and (b) if this cfDNA could be determined as coming from PM compared to non-small cell lung cancer (NSCLC), due to changes in genes that only occur in these types of tumours. Methods: Using the QIAamp MinElute ccfDNA Kit, we were able to isolate sufficient concentrations of cfDNA from pleural effusions (n=80) derived from patient samples procured by our colleagues at Southmead Hospital with either PM or NSCLC to perform gene panel sequencing. Using the QIAseq Targeted DNA Pro Human Lung Cancer Research Panel, with additional booster primers covering BAP1 and SETD2, we performed the library preparation in-house. Data analysis was carried out using the QIAGEN CLC Genomics Workbench, with the specific workflows for the gene panels and results were filtered by QC, proportion of variant reads and variant read count. Data were compared to expected variant frequencies published in TCGA. Results: Tumour-specific cfDNA was isolated from pleural effusions in the majority of samples tested. In a proportion of these, variants indicative of a specific type of tumour (PM or NSCLC) were readily detectable, at slightly lower than the expected frequencies than reported in TCGA. Conclusions and future work: This approach can act as a 'rule-in' clinically diagnostic test for the presence of PM or NSCLC in a higher proportion of people that can currently be identified through cytology testing. These individuals could be spared from receiving an invasive biopsy to diagnose their tumour. We are currently working on (i) increasing the sensitivity of this approach to identify more cases and (ii) if a bioinformatic method can identify tumour-specific copy number alterations from the gene panel sequencing data.
Citation Format: Connie MacKinnon, Dr Colette Mustard, Dr Nicole Brace, Dr Beth Sage, Jenny Symonds, Colin Nixon, Dr Anna Bibby, A/Prof Antonia Pritchard. Identification of tumour-specific variants from pleural effusion cell-free DNA as diagnostic markers of cancers affecting the lungs [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A060.