Abstract P2-01-01: Next generation sequencing of circulating tumor DNA to predict recurrence in triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy
Authors: Chen Y-H , Hancock BA , Solzak JP , Miller KD , Radovich M 
Published: May 2016

Abstract
Background: Incorporation of next-generation sequencing to detect plasma-derived tumor DNA (ptDNA) is emerging as a popular method for tumor genotyping and for monitoring therapeutic response. The vast majority of studies so far have focused on detecting ptDNA from patients with metastatic disease. Herein, we tested whether ptDNA could be used as a biomarker to predict relapse in triple-negative breast cancer (TNBC) patients with residual disease after neoadjuvant chemotherapy and surgery.
Methods: BRE09-146 was a Phase II clinical trial that randomized TNBC patients with residual disease after neoadjuvant chemotherapy to Cisplatin or Cisplatin+Rucaparib. From the combination arm, 1ml of plasma was collected at four predefined time points post-surgery. In total, 39 patients with matched tumor, blood, and plasma were analyzed. Extracted DNA underwent library preparation and amplification using the Ion Ampliseq Oncomine Research Panel which consists of 134 cancer genes that are well-known to be mutated in cancer. Samples were then sequenced on an Ion Proton next-generation sequencer to at least 2500X coverage followed by bioinformatic analyses using the Torrent Variant Caller.
Results: We first detected high-quality somatic mutations in primary tumors. TP53 mutations were the most prevalent (70%) followed by AKT1 (8%). Somatic mutation frequencies in our trial were congruent with publically-available mutation data of TNBCs from The Cancer Genome Atlas. Using these somatic mutations, we then analyzed the plasma-sequencing data to detect the same mutations in the circulation. Out of 39 patients, 14 patients had a clinical relapse (median follow-up for disease free survival = 24 months). Of the 14 patients, we were able to detect somatic ptDNA in 4 patients (3 TP53 mutations, 1 AKT mutation). Notably, all 4 patients had a rapid recurrence (0.3, 4.0, 5.3, and 8.9 months). ptDNA-sequencing was unable to detect distant recurrence. The combination of a paucity of ptDNA molecules in the circulation of patients who have no evidence of disease along with a limited amount of plasma available per patient are potential factors for the inability to detect distant recurrence.
Conclusions: Next-generation ptDNA-sequencing of triple-negative breast cancer patients after neoadjuvant chemotherapy and surgery can detect rapid-recurrence but sensitivity to detect distant recurrence is limited. Studies to increase sensitivity by incorporating mutation calling from ptRNA along with ptDNA are currently underway.
Citation Format: Chen Y-H, Hancock BA, Solzak JP, Miller KD, Radovich M. Next generation sequencing of circulating tumor DNA to predict recurrence in triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-01-01.