In a prospective international cohort of 1,127 patients with advanced non-small cell lung cancer (NSCLC) and circulating tumour DNA (ctDNA)-guided treatment, ctDNA detection was associated with shorter survival, independently of clinicopathologic features and metabolic tumour volume. All patients enroled consented to tissue next-generation sequencing (NGS) with MSK-IMPACT and from June 2019, patients were eligible for additional plasma sequencing with MSK-ACCESS. Among the patients with detectable ctDNA, 23% matched to targeted therapy by ctDNA sequencing had longer survival than those not treated with targeted therapy.
Genomic alterations in ctDNA not detected by time-matched tissue sequencing were found in 25% of the patients. These ctDNA-only alterations disproportionately featured subclonal drivers of resistance and were associated with short survival. Findings from this largest prospective, international cohort of patients with advanced NSCLC who underwent ctDNA-guided treatment with longitudinal follow-up for survival are reported by Dr. Bob T. Li of the Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, Cornell University in New York, NY, USA and colleagues on 10 November 2022 in the Nature Medicine.
Community adoption of sequencing of ctDNA from plasma is rising, although the effectiveness of ctDNA for targeted therapy matching has been studied mostly in small cohorts with limited follow-up. Short-term studies have suggested that ctDNA-matched targeted therapy produces equivalent rates of radiologic response to tissue-matched therapy, but whether it translates to equal overall survival (OS) benefit is unknown. ctDNA detection is also thought to reflect aggressive tumour biology and disease burden, but whether its prognostic value is independent of tumour volume or clinical factors is not yet defined. Some ctDNA alterations may be observed in plasma, but not in tissue. Whether alterations corresponding to tumour heterogeneity have prognostic relevance or common genomic features is unclear.
Despite increasing commercial use of ctDNA detection, clinical interpretation is challenging without adequately powered studies to address such biological questions. Recent reviews have highlighted the need for large prospective studies confirming the clinical utility of liquid biopsies. To define the usefulness of ctDNA as a genomic biomarker to guide treatments and its association with and impact on survival, the investigators conducted a prospective international cohort study of patients with metastatic NSCLC undergoing plasma ctDNA sequencing.
Patients were enrolled at Memorial Sloan Kettering Cancer Center in New York, NY, USA, an academic cancer centre, and GenesisCare (Sydney, Australia), a community-based oncology practice including physicians affiliated with the University of Sydney. The study included adults with stage IV or recurrent NSCLC and either no known driver mutation before enrolment or progression of disease following targeted therapy. Of the 1,357 patients initially enroled in the study, 1,127 were included in the analysis.
All patients received ctDNA sequencing via the Resolution Bioscience ctDx Lung platform, a targeted NGS panel including known molecular drivers of NSCLC. Plasma was drawn on the day of study enrolment and could be redrawn subsequently at the provider’s discretion. Most patients (89%) provided a single sample. Only mutations passing a filter for germline variants were included in the analysis. All patients enroled consented to tissue NGS with MSK-IMPACT, a targeted capture sequencing assay cleared by the US Food and Drug Administration. From 10 June 2019, patients were eligible for additional plasma sequencing with MSK-ACCESS at the provider’s discretion. Both assays use matched white blood cell sequencing to remove clonal haematopoiesis and germline variants.
The study team confirmed lower failure rates and faster turnaround time with ctDNA compared to tissue; 164 of 1,219 (13%) tissue sequencing attempts failed after sample receipt due to insufficient material or sequencing failure. By contrast, 37 of 1,919 (2%) ctDx Lung or MSK-ACCESS samples failed. Only two patients did not have successful molecular profiling of either plasma or tissue. Time from blood draw (ctDNA sample collection or matched white blood cell collection for MSK-IMPACT) to sequencing report was shorter for plasma than for tissue sequencing: 33 days (interquartile range [IQR], 25–41) for MSK-IMPACT versus 11 days (IQR, 9–14) for MSK-ACCESS or ctDx Lung. Mutations detected in time-matched MSK-ACCESS and ctDx Lung assays were highly concordant.
ctDNA detection was associated with shorter survival (hazard ratio [HR] 2.05, 95% confidence interval (CI) 1.74–2.42; p < 0.001) independently of clinicopathologic features and metabolic tumour volume. All multivariate analyses confirmed the independent prognostic value of ctDNA detection. ctDNA detection is influenced by histology, disease extent and clinical factors, findings that were confirmed in this cohort. Of 335 patients with extrapulmonary disease on time-matched positron emission tomography imaging, 248 (74%) had detectable ctDNA; by contrast, 49 of 122 (40%) patients with intrapulmonary disease had detectable ctDNA (chi-squared test, p < 0.001). In a multivariate model including extrapulmonary disease and clinical features as variables, ctDNA detection independently predicted worse survival. In addition, advanced age was associated with worse survival, whereas receipt of targeted therapy was associated with better survival.
A total of 418 (37%) patients were treated with targeted therapy after study entry; 255 (23%) patients had molecular targets identified on ctDNA, and 163 (14%) patients were matched based on tissue analysis only. The odds of matching to targeted therapy by ctDNA were lower in smokers, patients with non-adenocarcinoma histology and patients with intrapulmonary disease only. Among patients treated with targeted therapy, those with detectable ctDNA had worse survival. Among patients with detectable ctDNA, those matched to targeted therapy by liquid biopsy had longer OS than those not receiving targeted therapy (HR 0.63, 95% CI 0.52–0.76; p < 0.001). Among patients without detectable ctDNA, those treated with targeted therapy did not have longer survival than those not treated with targeted therapy to a statistically significant extent (HR 0.92, 95% CI 0.7–1.2; p > 0.1), suggesting greater relative benefit to targeted therapy among those patients with detectable ctDNA.
Of 429 patients with tissue sequencing (MSK-IMPACT) within 30 days of ctDx Lung sequencing, 109 (25%) patients had mutations or copy number alterations detected in ctDNA that were absent on tumour sequencing (ctDNA-only alterations). Three of these patients had EGFR T790M mutations, leading to changes in treatment. Additional potentially actionable ctDNA-only mutations included one KRAS G12C mutation, one BRAF V600E mutation and one RET fusion; none of these led to changes in treatment due to their absence in tissue. The subgroup of patients with ctDNA-only alterations had worse survival than those with tissue-matched ctDNA alterations. ctDNA-only alterations are common and have significant prognostic value. A subgroup of 26 patients had no common alterations observed between ctDNA and tissue. These patients also had worse survival than those with tissue-matched ctDNA alterations.
The relative proportions of ctDNA-only alterations to tissue alterations, however, showed over-representation of commonly subclonal alterations in secondary resistance genes, in particular, RICTOR, NTRK1, MET and ERBB2 amplifications and PIK3CA mutations.
To test whether the worse survival seen in patients with ctDNA-only alterations is a result of underlying tumour genetics, the study team performed multivariate survival analysis including the presence of any ctDNA alteration, the presence of a ctDNA-only alteration and the presence of specific pathogenic gene alterations in either ctDNA or tissue. As expected, based on previous tissue-based analyses, patients with ALK, RET and EGFR alterations had better survival, as expected given frequent treatment with targeted therapy among this group, while the presence of STK11 alterations was associated with worse survival. The presence of RICTOR, NTRK, MET, ERBB2 and PIK3CA alterations was not associated with worse survival. Conversely, the presence of ctDNA alterations and the presence of ctDNA-only alterations were both independently associated with worse survival. These findings suggest that ctDNA–tissue divergence, and not the genomic changes themselves, is prognostic and highlight the utility of liquid biopsies for detecting meaningful spatial genomic heterogeneity when paired with tissue sequencing.
This study has a number of limitations; for example, the non-random, real-world nature of this study makes it challenging to assess the survival benefit of any single targeted therapy with ctDNA matching.
This work was supported by a grant from the Antidote Health Foundation for Cure of Cancer, the US National Institutes of Health, the Molecular Diagnostics Service in the Department of Pathology, and the Marie-Josee and Henry R. Kravis Center for Molecular Oncology.
Jee J, Lebow ES, Yeh R, et al. Overall survival with circulating tumor DNA-guided therapy in advanced non-small-cell lung cancer. Nature Medicine; Published online 10 November 2022. DOI: https://doi.org/10.1038/s41591-022-02047-z