Abstract 3664: Evaluation of on-treatment tumor molecular dynamics using plasma whole genome sequencing (pWGS) and whole exome sequencing (pWES) of circulating tumor DNA (ctDNA) in patients (pts) with metastatic non-small cell lung cancer (NSCLC): An exploratory analysis of KEYNOTE-598
Authors: Shah Minita , Dettman EJ , Albright Andrew , Chen Cai , Kobie Julie , Varadan Vinay , Samkari Ayman , Peña Carol , Cristescu Razvan , Cao Z Alexander 
Published: March 2024

Abstract
Background: ctDNA-based pWES is a promising tool to examine tumor genomics using a non-invasive liquid biopsy to serially monitor changes during tumor evolution and treatment. Here, we evaluate on-treatment tumor molecular dynamics using ctDNA-based pWGS and pWES in pts with metastatic NSCLC that responded to pembrolizumab (pembro) monotherapy and later experienced PD in KEYNOTE-598 (NCT03302234).
Methods: In KEYNOTE-598, pts had metastatic NSCLC (PD-L1 tumor proportion score ≥50%) and received first-line pembro ± ipilimumab for ≤35 cycles. Cell-free DNA (cfDNA) was isolated and sequenced from plasma samples at baseline (BL), during on-treatment response (cycle 5 [C5]), and at PD (discontinuation [D]) from pts with objective response to pembro monotherapy and subsequent PD. ctDNA burden (tumor fraction [TF]) was estimated using low-pass pWGS by quantifying tumor content in cfDNA as a function of aneuploidy. All samples with TF &gt;1.5% underwent high-depth pWES. ctDNA burden was estimated from pWES data using maximum somatic allele frequency (MSAF). Correlation between TF and MSAF was evaluated using the Spearman coefficient (r). Variant allele frequency (VAF) and normalized VAF (nVAF) were used to determine variant clonality.
Results: In total, 23 pts with initial response to pembro and subsequent PD had plasma samples available from BL, C5, and D. Samples from 22 pts had TF &gt;1.5% by pWGS and underwent pWES. MSAF by pWES was correlated with TF by pWGS at BL (r = 0.68), C5 (0.80), and D (0.59). ctDNA TFs at BL and D (mean = 8.1% and 4.9%, respectively) were higher than C5 (2.0%). In a pooled variant-level analysis (nVAF &gt;0.25) of samples from pts with high TF (≥2.5%) at both BL and D (n = 10), 786 (46%) of variants were present at BL and D, 391 (23%) were present at BL only, and 540 (32%) were present at D only. Variants shared between BL and D had higher clonality (mean nVAF = 0.46) than BL-only (0.38) or D-only variants (0.4). In general, shared variants had similar nVAFs at BL and D but in some pts nVAFs increased at D, suggesting evolution of tumor subclones during treatment. TP53 was mutated in 9 of 10 pts with high TF and was shared at BL and D in 6 pts (mean nVAF = 0.49), present at BL only in 1 pt (0.11) and at D only in 2 pts (0.43). KRAS G12V and Q61H hotspot mutations were observed in 2 pts at D-only and may be related to immune editing.
Conclusions: Comprehensive pWES is feasible with sufficient ctDNA burden (TF ≥2.5%). ctDNA dynamics demonstrated molecular profiles characteristic of recurrence with high TF at BL and D and were consistent with radiographic determination of response/progression. Tumor variants at BL and D generally had a common clonal trunk with clones disappearing or appearing de novo.
Citation Format: Minita Shah, EJ Dettman, Andrew Albright, Cai Chen, Julie Kobie, Vinay Varadan, Ayman Samkari, Carol Peña, Razvan Cristescu, Z Alexander Cao. Evaluation of on-treatment tumor molecular dynamics using plasma whole genome sequencing (pWGS) and whole exome sequencing (pWES) of circulating tumor DNA (ctDNA) in patients (pts) with metastatic non-small cell lung cancer (NSCLC): An exploratory analysis of KEYNOTE-598 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3664.