Abstract P5-01-22: Genomic landscape of circulating tumor DNA in early-stage breast cancer
Authors: Takahashi Yoko , Ming Yoon , Shibayama Tomoko , Maeda Tetsuyo , Miyagi Yumi , Ogiya Akiko , Kitagawa Dai , Soeda Ikumi , Morizono Hidetomo , Fujishima Makoto , Ueno Takayuki , Ohno Shinji , Nakamura Yusuke , Low Siew-Kee 
Published: March 2020

Abstract
Introduction Breast cancer is the frequently diagnosed cancer worldwide and, the common cause of cancer deaths in women. In some women, breast cancer has already metastasized in distant organs at diagnosis, which is generally hard to cure. Thus, early cancer detection is a key to improve survival. Circulating tumor DNA (ctDNA) can be detected in the plasma and serum of patients with advanced cancer, acting as a potential noninvasive source to characterize the somatic genetic features of the tumors. Limited data are available on whether ctDNA analyses would be applicable to early cancer, but blood monitoring of circulating markers such as circulating tumor cell (CTC) and cell-free DNA (cfDNA) may improve earlier detection. A previous study showed that detection rate of ctDNA is as low as 33% in breast cancer (Cohen et al., 2018). We assessed the potential to detect mutations in cfDNA in patients with different stages of primary breast cancer by using a bigger panel with better coverage to see whether it can improve detection rate. Methods Patients with previously untreated breast cancer were enrolled in our hospital between April 2018 and April 2019. Pre-treatment plasma samples were collected for cfDNA analysis to measure ctDNA by using Oncomine Pan-Cancer Panel (targeted next generation sequencing integrated with molecular barcode and targets mutations, copy number variations and fusions). We also sequenced paired buffy coat to evaluate clonal hematopoiesis (CH)-related mutation that might lead to false positive detection.Result A total of 86 Stage 0-IV breast cancer patients were enrolled in this study. Median total coverage was 27,148-71,702 reads with an average of 54,604 reads. Median mol coverage were 1,739-6,133 reads with an average of 3,962 reads. Plasma cell free total nucleic acid (cfTNA) concentration increased with advancing stage of disease. Overall detection rate of ctDNA for breast cancer patients was 50% (N=43/86). The detection rate of each Stage was as follows: Stage 0 29% (n=2/7); Stage I 55% (n=17/31), Stage II 41% (n=12/29), Stage III 100% (n=3/3) and Stage IV 100% (n=4/4). Top genes with mutation detection was TP53 in 21%, FBXW7in 6% and PIK3CAin 6%. Mutations in AKT1, GNASand EGFRwere found in 3% of patients. Mutation distribution of top mutated genes was 35% in TP53, 10% in PIK3CA, 8% in FBXW7, 6% in EGFR. The 4 genes made up 59% of all mutations detected. Paired buffy-coat sequencing identified CH-related mutations in TP53, GNASand IDH2, which were commonly reported genes with CH-related mutations.Discussion Our detection rate was better than the previous study (Cohen et al.) probably due to a bigger panel with better coverage. The possible clinical applications of ctDNA mutations include monitoring treatment response not only for advanced cancer but also for early breast cancer including neoadjuvant therapy and minimal residual disease after surgery of breast cancer.CH-related mutations should be excluded to avoid misinterpretation of CH-related mutations as tumor-derived mutations.Conclusion This study provides additional evidence that liquid biopsy is able to detect ctDNA in patients with breast cancer. The mutations identified will aid clinical management of disease. We also demonstrate that cfDNA sequencing provides genomic landscape of circulating tumor DNA in early-stage breast cancer.
Citation Format: Yoko Takahashi, Yoon Ming, Tomoko Shibayama, Tetsuyo Maeda, Yumi Miyagi, Akiko Ogiya, Dai Kitagawa, Ikumi Soeda, Hidetomo Morizono, Makoto Fujishima, Takayuki Ueno, Shinji Ohno, Yusuke Nakamura, Siew-Kee Low. Genomic landscape of circulating tumor DNA in early-stage breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-01-22.