Base-Position Error Rate Analysis of Next-Generation Sequencing Applied to Circulating Tumor DNA in Non-Small Cell Lung Cancer: A Prospective Study

Abstract

BackgroundCirculating tumor DNA (ctDNA) is an approved noninvasive biomarker to test for the presence of EGFR mutations at diagnosis or recurrence of lung cancer. However, studies evaluating ctDNA as a noninvasive “real-time” biomarker to provide prognostic and predictive information in treatment monitoring have given inconsistent results, mainly due to methodological differences. We have recently validated a next-generation sequencing (NGS) approach to detect ctDNA. Using this new approach, we evaluated the clinical usefulness of ctDNA monitoring in a prospective observational series of patients with non-small cell lung cancer (NSCLC).Methods and FindingsWe recruited 124 patients with newly diagnosed advanced NSCLC for ctDNA monitoring. The primary objective was to analyze the prognostic value of baseline ctDNA on overall survival. ctDNA was assessed by ultra-deep targeted NGS using our dedicated variant caller algorithm. Common mutations were validated by digital PCR. Out of the 109 patients with at least one follow-up marker mutation, plasma samples were contributive at baseline (n = 105), at first evaluation (n = 85), and at tumor progression (n = 66). We found that the presence of ctDNA at baseline was an independent marker of poor prognosis, with a median overall survival of 13.6 versus 21.5 mo (adjusted hazard ratio [HR] 1.82, 95% CI 1.01–3.55, p = 0.045) and a median progression-free survival of 4.9 versus 10.4 mo (adjusted HR 2.14, 95% CI 1.30–3.67, p = 0.002). It was also related to the presence of bone and liver metastasis. At first evaluation (E1) after treatment initiation, residual ctDNA was an early predictor of treatment benefit as judged by best radiological response and progression-free survival. Finally, negative ctDNA at E1 was associated with overall survival independently of Response Evaluation Criteria in Solid Tumors (RECIST) (HR 3.27, 95% CI 1.66–6.40, p < 0.001). Study population heterogeneity, over-representation of EGFR-mutated patients, and heterogeneous treatment types might limit the conclusions of this study, which require future validation in independent populations.ConclusionsIn this study of patients with newly diagnosed NSCLC, we found that ctDNA detection using targeted NGS was associated with poor prognosis. The heterogeneity of lung cancer molecular alterations, particularly at time of progression, impairs the ability of individual gene testing to accurately detect ctDNA in unselected patients. Further investigations are needed to evaluate the clinical impact of earlier evaluation times at 1 or 2 wk. Supporting clinical decisions, such as early treatment switching based on ctDNA positivity at first evaluation, will require dedicated interventional studies.

Dynamics of multiple resistance mechanisms in plasma DNA during EGFR‐targeted therapies in non‐small cell lung cancer

“…Recent data from tumour sequencing suggested EGFR may be subclonal in a small subset of EGFR‐mutant NSCLC tumour (McGranahan et al , ), which agrees with our hypothesis. A recent plasma‐based study also reported 4 out of 24 NSCLC patients had EGFR‐sensitizing mutations detected in plasma at T0 but absent when the patients progressed, which agreed with our findings (Pecuchet et al , ). The fact that EGFR T790M was not detected in the third group suggested that the cancers have developed resistance mechanisms that are alterative to the EGFR pathway, which agreed with the observations of alternative drivers in plasma in some patients.…”

The interplay of circulating tumor DNA and chromatin modification, therapeutic resistance, and metastasis

“…In stage II-IV NSCLC patients, ctDNA can be detected in 100% of the blood sample, and only 50% of patients in stage I can be detected [96]. They also found that the level of ctDNA in newly diagnosed patients with advanced lung cancer is associated with bone metastases and liver metastases [132]. The level of ctDNA in patients with early and late tumors may be related to a variety of factors.…”

HPV circulating tumor DNA to monitor the efficacy of anti‐PD‐1 therapy in metastatic squamous cell carcinoma of the anal canal: A case report

“…In addition to "liquid biopsy" applications, changes in ctDNA levels during treatment have been investigated as a possible biomarker to monitor the efficacy of chemotherapy in several types of cancer, such as lung, breast or colorectal cancer patients. [17][18][19] However, the proof-of-concept has not yet been established for new immunotherapeutic agents such as PD-1 inhibitors. Somatic alterations associated with SCCA have been extensively evaluated.…”