Abstract 447: Sensitive detection of ctDNA in low burden and ‘challenging’ cancers
Authors: Smith Christopher G. , Wan Jonathan C. , Heider Katrin , Mouliere Florent C. , Mair Richard , Eldridge Matthew , Brindle Kevin , Corrie Pippa G. , Stewart Grant D. , Rosenfeld Nitzan 
Published: August 2019

Abstract
Cell-free tumour derived DNA (ctDNA) analysis offers the potential for minimally-invasive early detection, diagnosis and monitoring of cancer in patients. However, the utility of ctDNA is proving challenging for some cancer types and in earlier stages of disease. We developed an approach for sensitive detection of ctDNA through combined application of Tailored Panel Sequencing (TAPAS) and aggregation of signal across mutant loci by INtegration of VAriant Reads (INVAR). We demonstrated its application to ‘challenging’ cancers that have been shown to release lower concentrations of ctDNA as compared to other cancers of similar size and stage: renal cancer (RCC) and glioblastoma (GB). We also utilised INVAR-TAPAS for early detection of cancers, as well as detection of residual disease after surgery. We applied INVAR-TAPAS to plasma and urine from 22 patients with RCC of varying subtype and disease stage, and demonstrated ~45% detection in both fluids (10/22 in plasma and 6/14 in urine). Of note, considering both fluids ctDNA was detected in a patient with a benign oncocytoma, and in 2/6 (33.3%) and 10/15 (66.7%) stage I-II and III-IV RCCs respectively. We also applied INVAR-TAPAS to plasma and cerebrospinal fluid (CSF) from 8 GB patients and observed ctDNA detection rates of 75% in both fluids, though levels were higher in CSF. For both diseases, comparison of INVAR-TAPAS and disease burden, as assessed by imaging, demonstrated that ctDNA levels in longitudinal plasma samples track disease course. Furthermore, by basing our analysis on mutations identified from multi-region sampled tissue data, we observed that mutations private to distinct tumour regions were represented in ctDNA (in all fluids tested), in-turn demonstrating that ctDNA overcomes heterogeneity. Finally, INVAR-TAPAS was applied to plasma samples collected from 33 patients with resected stage II-III melanoma. Samples were obtained within the first 6 months after surgery. We detected ctDNA in 50% of patient samples who later recurred, with detection associated with a significantly shorter disease-free interval (4.5 months vs. median not reached with 5 years’ follow-up; Hazard ratio (HR) = 3.69; 95% CI 1.44-9.46, P = 0.007) and overall survival (2.6 years vs. median not reached). In summary we demonstrated the ability of INVAR-TAPAS to sensitively detect and quantify ctDNA in various cancer settings. Of note, in these clinical samples we detected ctDNA to a mutant allele fraction of 1x10-5. Despite this sensitivity, detection of certain cancer types and earlier disease stages remains challenging. In these settings, improved isolation and detection methods (e.g. multi-analyte assays) may improve detection and ultimate utility of ctDNA in the future. Nonetheless, our data support liquid biopsy as both a predictive and prognostic biomarker with potential to guide clinical decision making in the future.
Citation Format: Christopher G. Smith, Jonathan C. Wan, Katrin Heider, Florent C. Mouliere, Richard Mair, Matthew Eldridge, Kevin Brindle, Pippa G. Corrie, Grant D. Stewart, Nitzan Rosenfeld. Sensitive detection of ctDNA in low burden and ‘challenging’ cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 447.