Modulation of breast cancer cell-free DNA with surgical resection.

Abstract

11060 Background: Recently we demonstrated the ability to detect the presence of invasive breast cancer by next generation sequence (NGS) analysis of cell-free DNA (cfDNA) in serum without prior knowledge of the specific gene perturbations of the neoplasm (J. Clin. Oncology 2010; 28 (15S):10505). We hypothesized that cfDNA levels would hold promise as a marker to monitor therapeutic efficacy in breast cancer. In this study, we sought to determine whether cfDNA decreases after surgery in patients with operable invasive breast cancer. Methods: Serum was collected before and 1-4 weeks after surgery from 16 breast cancer patients and also from 24 age and gender matched controls. cfDNA was isolated from the serum, amplified by Chronix proprietary method and sequenced on an Illumina HiSeq platform. The breast cancer derived cfDNA sequences from each patient were compartmentalized in 250kbp bins, normalized, and compared to the mean (+/- 3SD) of the controls to identify regions of chromosomal number imbalance (CNI). Genomic DNA was isolated from the primary tumor and blood WBC buffy coat, pre-amplified, sequenced and subjected to comparative analysis with cfDNA. Results: Analysis of pre- and post surgery serum demonstrate that CNIs are present in the pre-surgery serum cfDNA that correlated with the associated tumor CNI and was not observed in WBC genomic DNA. The number of tumor associated CNI DNA biomarkers ranged from as low as 3 to as high as 865. In 13 of 16 patients (81%) analyzed, the post-surgery cfDNA was free of detectable tumor related-CNI DNA. In the remaining 3 patients, only a partial reduction in tumor specific CNI DNA serum biomarkers was observed, since some markers were still detectable after surgery. Conclusions: cfDNA from primary breast carcinomas accurately reflects tumor CNI. Removal of the primary tumor results in the elimination of tumor cfDNA in the majority of patients. Thus cfDNA may be of clinical value in evaluation of therapeutic efficacy on a real time basis. Further work is needed to determine if residual tumor CNI in cfDNA after surgery is a marker of minimal residual disease which can be pursued as a prognostic marker.