Serial Next-Generation Sequencing of Circulating Cell-Free DNA Evaluating Tumor Clone Response To Molecularly Targeted Drug Administration

Abstract

Purpose: We evaluated whether next-generation sequencing (NGS) of circulating cell-free DNA (cfDNA) could be used for patient selection and as a tumor clone response biomarker in patients with advanced cancers participating in early-phase clinical trials of targeted drugs.

Experimental design: Plasma samples from patients with known tumor mutations who completed at least two courses of investigational targeted therapy were collected monthly, until disease progression. NGS was performed sequentially on the Ion Torrent PGM platform.

Results: cfDNA was extracted from 39 patients with various tumor types. Treatments administered targeted mainly the PI3K-AKT-mTOR pathway (n = 28) or MEK (n = 7). Overall, 159 plasma samples were sequenced with a mean sequencing coverage achieved of 1,685X across experiments. At trial initiation (C1D1), 23 of 39 (59%) patients had at least one mutation identified in cfDNA (mean 2, range 1-5). Out of the 44 mutations identified at C1D1, TP53, PIK3CA and KRAS were the top 3 mutated genes identified, with 18 (41%), 9 (20%), 8 (18%) different mutations, respectively. Out of these 23 patients, 13 received a targeted drug matching their tumor profile. For the 23 patients with cfDNA mutation at C1D1, the monitoring of mutation allele frequency (AF) in consecutive plasma samples during treatment with targeted drugs demonstrated potential treatment associated clonal responses. Longitudinal monitoring of cfDNA samples with multiple mutations indicated the presence of separate clones behaving discordantly. Molecular changes at cfDNA mutation level were associated with time to disease progression by RECIST criteria.

Conclusions: Targeted NGS of cfDNA has potential clinical utility to monitor the delivery of targeted therapies.

©2015 American Association for Cancer Research.

Figures

Figure 1

Monitoring of somatic genomic alterations in plasma during targeted therapy. Allele frequency (AF) of the identified mutations is represented on the left Y-axis while the sum of the target lesions on CT scan is represented on the right Y-axis. SD: stable disease according to RECIST criteria; PD: progressive disease. The colored box depicts the time on treatment. The second graph depicts the evolution of cfDNA concentration during this time frame in ng/ml of plasma. A. Patients with decreasing AF during therapy. B. Patients with increasing AF during therapy. C. Patients with mixed or discordant AF changes during therapy.

Figure 1

Monitoring of somatic genomic alterations in plasma during targeted therapy. Allele frequency (AF) of the identified mutations is represented on the left Y-axis while the sum of the target lesions on CT scan is represented on the right Y-axis. SD: stable disease according to RECIST criteria; PD: progressive disease. The colored box depicts the time on treatment. The second graph depicts the evolution of cfDNA concentration during this time frame in ng/ml of plasma. A. Patients with decreasing AF during therapy. B. Patients with increasing AF during therapy. C. Patients with mixed or discordant AF changes during therapy.

Figure 2

Serial monitoring of cfDNA samples with multiple mutations. A. Samples with different mutations, and different AF, with similar trends during the course of disease. B. Patients with dominant mutations with AF with differing trends during treatment. These findings suggest the presence of heterogeneous clonal responses to drug administration.