Abstract 1512: Detection of somatic alterations in plasma from lung cancer patients

Abstract

Abstract Tumor-specific (somatic) mutations in plasma can serve as biomarkers for tumor detection, monitor tumor response to specific therapies, detect residual disease after surgery, and long-term follow-up. The intrinsic low abundance of circulating cell-free tumor DNA (cfDNA) makes the detection and quantification of such mutations in plasma a challenging task. This small scale study aims to establish a comprehensive strategy to be used in the detection of clinical relevant somatic alterations in plasma of lung cancer patients. Plasma samples obtained at different stages of disease progression and/or treatment were collected from a group of 11 lung cancer patients and used to isolate cfDNA. Genetic alterations in the EGFR gene (p.E746_A750del and p.L858R) identified at diagnosis in tumor biopsies were used as surrogate markers to optimize and validate the next generation sequencing strategy and data analysis workflow. The Ion AmpliSeq Colon and Lung cancer panel was used to analyze hotspot and targeted regions of 22 genes implicated in colon and lung cancers, including the EGFR gene mutations mentioned. The amplified products were used to prepare libraries and were sequenced using the Ion PGM system. Quantitative real time PCR and digital PCR assays were used to confirm selected results. Tumor derived genetic alterations could be identified in as little as 10ng of cfDNA. EGFR alterations identified in cfDNA mirrored the alterations identified in all tumor biopsies. EGFR alterations with allelic frequencies as low as 3% could be detected in cfDNA. Additionally, in case of samples collected after therapy, a clear decrease in the cfDNA allelic frequency of the EGFR mutation, that made the patient eligible for therapy, was observed. Furthermore, the screening of a larger panel of genes allowed the identification in two cases of additional gene mutations (e.g. MET and KRAS) that may have impact in the clinical management of patients. In this study, we demonstrate the capacity to identify clinically relevant somatic EGFR mutations in plasma. The possibility to assess information from a larger panel of genes makes this strategy attractive for further optimization of treatment options. The strategy is now being extended to a larger cohort of patients to push forward the concept of liquid biopsy in the clinical management of cancer patients. Citation Format: Jose L. Costa, Ana Justino, Ana Barroso, Barbara Parente, Jose C. Machado. Detection of somatic alterations in plasma from lung cancer patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1512. doi:10.1158/1538-7445.AM2014-1512