Clinical Implications of Circulating Tumor DNA Tumor Mutational Burden (ctDNA TMB) in Non-Small Cell Lung Cancer

Abstract

Background: Tissue tumor mutational burden (TMB) has emerged as a potential biomarker predicting response to anti-programmed cell death-1 protein receptor (PD-1)/programmed cell death-1 protein ligand (PD-L1) therapy, but few studies have explored using circulating tumor DNA (ctDNA) TMB in non-small cell lung cancer (NSCLC).

Materials and methods: A total of 136 patients with NSCLC with ctDNA testing were retrospectively evaluated from a single institution, along with a validation cohort from a second institution. ctDNA TMB was derived using the number of detected mutations over the DNA sequencing length.

Results: Higher ctDNA TMB was significantly correlated with smoking history (p < .05, chi-squared test). Among patients treated with immune checkpoint inhibitors (n = 20), higher ctDNA TMB was significantly correlated with shorter progressive free survival (PFS) and overall survival (OS; 45 vs. 355 days; hazard ratio [HR], 5.6; 95% confidence interval [CI], 1.3-24.6; p < .01, and OS 106 days vs. not reached; HR, 6.0; 95% CI, 1.3-27.1; p < .01, respectively). In a small independent validation cohort (n = 12), there was a nonsignificant numerical difference for higher ctDNA TMB predicting shorter OS but not PFS. ctDNA TMB was not correlated with RECIST tumor burden estimation in the subset of patients treated with immune checkpoint blockade.

Conclusion: The findings indicate that higher ctDNA TMB, at the current commercial sequencing length, reflects worse clinical outcomes.

Implications for practice: Biomarkers to identify patients who will respond to immune checkpoint blockade are critical. Tissue tumor mutational burden (TMB) has emerged as a viable biomarker to predict response to anti-PD-1/PD-L1 therapy, but few studies have explored the meaning and potential clinical significance of noninvasive, blood-based TMB. Here, we investigated circulating tumor DNA (ctDNA) TMB and present data demonstrating that current ctDNA TMB may reflect tumor burden and that ctDNA panels with a greater number of mutations may be necessary to more accurately reflect tissue TMB.

Keywords: Circulating tumor DNA (ctDNA); NSCLC; PD‐1; PD‐L1; Tumor mutational burden (TMB).

Figure 1.

Circulating tumor DNA TMB landscape. (A): Schematic demonstrating the three methods of calculating TMB: excluding nonsynonymous potentially functional variants (method 1), excluding synonymous variants (method 2), and including using all detected mutations (method 3). (B): Demonstrates the landscape of TMB scores in the population based on including all detected mutations (method 1). Abbreviations: MBp, megabase pairs; TMB, tumor mutational burden; VUS, variants of unknown significance.

Figure 2.

Survival curves including progression‐free survival (PFS) and overall survival (OS) based on circulating tumor DNA (ctDNA) tumor mutational burden (TMB) for patients treated with immune checkpoint blockade. ctDNA TMB was associated with significantly shorter PFS (45 vs. 355 days; HR, 5.6; 95% CI, 1.3–24.6; p < .01) and OS (106 days vs. not reached; HR, 6.0; 95% CI, 1.3–27.1; p < .01) based on TMB high (red curves) vs. low (blue curves) (A, B). In the validation cohort, ctDNA TMB was not associated with PFS (65 vs. 64 days; HR, 1.1; 95% CI, 0.31–4.2; p > .05) with a numerically shorter, but nonsignificant, OS difference (236 vs. 511 days; HR, 2.8; 95% CI, 0.56–14.4; p = .17) (C, D). Proportional hazards regression model and stratified log ranks tests were performed. Kaplan‐Meier estimation compared survival distributions based on TMB low versus TMB high. Abbreviations: CI, confidence interval; HR, hazard ratio.

Figure 3.

Survival curves including progression‐free survival (PFS) and overall survival (OS) based on mutant allele frequency (MAF) for patients treated with immune checkpoint blockade. MAF was significantly correlated with shorter PFS (51 vs. 355 days; HR, 6.2; 95% CI, 1.6–24.1; p < .01) and OS (135 days vs. not reached; HR, 6.1; 95% CI, 1.6–23.7; p < .01) (A, B) based on MAF high (red curves) vs. low (blue curves). In the validation cohort, MAF was not associated with PFS (44 vs 114 days; HR, 2.3; 95% CI, 0.58–8.8; p = .21), but did predict shorter OS (236 vs. 595 days; HR, 7.7; 95% CI, 1.2–49.1 p < .05) (C, D). Proportional hazards regression model and stratified log ranks tests were performed. Kaplan‐Meier estimation compared survival distributions based on TMB low versus TMB high. Abbreviations: CI, confidence interval; HR, hazard ratio.