Biopsy-free circulating tumor DNA assay identifies actionable mutations in lung cancer

Abstract

Introduction: The potential of oncogene-driven targeted therapy is perhaps most fully realized in non-small cell lung cancer (NSCLC), given the number of genomic targets and approved matched therapies. However, invasive tissue biopsy at the time of each disease progression may not be possible and is associated with high morbidity and cost. Use of newly available "liquid biopsies" can circumvent these issues.

Results: 83% of subjects had at least one genomic alteration identified in plasma. Most commonly mutated genes were TP53, KRAS and EGFR. Subjects with no detectable ctDNA were more likely to have small volume disease, lepidic growth pattern, mucinous tumors or isolated leptomeningeal disease.

Methods: Subjects were individuals with NSCLC undergoing analysis of cell-free circulating tumor DNA using a validated, commercially-available next-generation sequencing assay at a single institution. Demographic, clinicopathologic information and results from tissue and plasma-based genomic testing were reviewed for each subject.

Conclusions: This is the first clinic-based series of NSCLC patients assessing outcomes of targeted therapies using a commercially available ctDNA assay. Over 80% of patients had detectable ctDNA, concordance between paired tissue and blood for truncal oncogenic drivers was high and patients with biomarkers identified in plasma had PFS in the expected range. These data suggest that biopsy-free ctDNA analysis is a viable first choice when the diagnostic tissue biopsy is insufficient for genotyping or at the time of progression when a repeated invasive tissue biopsy is not possible/preferred.

Keywords: cell-free DNA; circulating tumor DNA; next-generation sequencing; non-small cell lung cancer.

Figure 1. Frequency of non-synonymous alterations in 56 NSCLC patients

In the 56 cases with at least one detectable ctDNA alteration, there were 164 alterations in 39 different genes, including 133 single nucleotide variants (SNVs), 13 amplifications (Amp), and 5 insertion/deletions (Indels). SNVs that were characterized as variants of uncertain significance (VUSs) are shown in purple.

Figure 2. Percentage of patients with non-synonymous alterations by gene

The percentage of patients with alterations in each of the 39 genes found to have at least 1 ctDNA alteration. For genes with truncal driver mutations (as defined by NCCN NSCLC guidelines), the percentage of driver mutations is shown in blue. Frequency of all other non-synonymous mutations (i.e. non-driver mutations in NSCLC biomarkers or mutations in other genes) is shown in red.

Figure 3. Actionability in ctDNA positive cases

Frequency of patients whose ctDNA test identified a biomarker with an FDA approved targeted therapy in NSCLC, an FDA approved targeted therapy in a different indication, or a clinical trial.

Figure 4. Plasma tissue concordance in cases with actionable NSCLC biomarkers

(A) Rate of concordance between tissue and plasma for cases with an actionable NSCLC driver mutation and number of patients with actionable mutations for whom ctDNA was undetectable or tissue testing was either not done or was insufficient for analysis. (B) ctDNA tissue concordance in 7 paired tissue/plasma samples with actionable NSCLC driver mutations. T = Concurrent T790M mutation identified. (C) Identification of actionable driver mutations in cases with undetectable ctDNA or no tissue analysis/insufficient tissue.