Abstract 1052: Background variability in plasma ctDNA levels in patients with advanced lung cancer in the absence of treatment
Authors: Vega Diana M. , Markovets Aleksandra , Abbosh Christopher , Quinn Katie , Chang Kyle , Wienke Sara , Hartmaier Ryan , Hellmann Matthew , Barrett J Carl , Hodgson Darren 
Published: June 2023

Abstract
Introduction: Molecular response (MR) is defined as a reduction in circulating tumor DNA (ctDNA) levels between baseline and early on-treatment timepoint(s). MR is predictive of long-term outcomes in several advanced cancers treated with different therapeutic modalities. Common MR thresholds include reductions in ≥50%, or 100% (clearance) in ctDNA levels. A better understanding of the background variability in measured plasma ctDNA levels in the absence of therapy is required to enable improved interpretation of MR, especially as its use increases in drug development and clinical management.
Methods: In the largest study of double baseline pre-treatment ctDNA samples reported to date, paired screening and pre-treatment cycle 1 day 1 (C1D1) samples (IQR: 8-24, median 17 days apart) from 360 patients with advanced EGFRm non-small cell lung cancer (NSCLC) from the FLAURA (1L, N=132) and AURA3 (2L, N=228) trials were compared to characterize background variability in ctDNA. ctDNA was quantified using NGS (Guardant Health G360 and OMNI) and ddPCR (Biodesix) assays. Various potential drivers of background variability, such as ctDNA quantification platforms, coverage, and number of variants at baseline were evaluated to better understand any underlying confounding effects.
Results: Pre-treatment background variability was consistently observed in both AURA3 and FLAURA cohorts. Most of the variability reflected any increase in pre-treatment ctDNA in 28% (64/228) of cases in AURA3, and 13% (17/132) of cases in FLAURA. Variability reflecting a ≥50% decrease in pre-treatment ctDNA was observed in 8% (18/228) of cases in AURA3 and 9% (12/132) of cases in FLAURA, with only 2% of cases showing ctDNA clearance in AURA3 and 0% in FLAURA. Testing technical replicates sequenced a year apart and comparing ctDNA levels quantified with NGS v. ddPCR for potential sources of technical variability did not show large variability. Moreover, sources like cell-free DNA input, allele frequency levels, and days in between screening and C1D1 were tested but could not fully account for the variability observed.
Conclusion: Although pre-treatment increases in ctDNA levels were expected in patients with advanced cancer, background variability also included reductions in ctDNA that may be confounded as MR. Understanding the impact of factors on the transient nature of ctDNA is key, but as momentum mounts to use ctDNA as a biomarker of therapeutic response, it is crucial to test and account for background variability rates to improve MR interpretability. Additional work is warranted to elucidate the background variability rate in other cancer types and settings.
Citation Format: Diana M. Vega, Aleksandra Markovets, Christopher Abbosh, Katie Quinn, Kyle Chang, Sara Wienke, Ryan Hartmaier, Matthew Hellmann, J Carl Barrett, Darren Hodgson. Background variability in plasma ctDNA levels in patients with advanced lung cancer in the absence of treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1052.