Abstract P1-07-15: Detection of molecular alterations in breast cancer through next generation sequencing of both tumor tissue and circulating tumor DNA: The UC San Diego Moores Cancer Center experience
Authors: Shatsky RA , Parker BA , Schwab R , Helsten T , Boles SG , Subramanian R , Piccioni D , Kurzrock R 
Published: May 2019

Abstract
Background: Next generation sequencing (NGS) analysis of actionable molecular alterations has the potential to guide cancer treatment, especially for patients with advanced cancer who have progressed on standard treatment. In this study, we analyzed tumor biopsies and peripheral blood from 62 patients with advanced breast cancer by two different NGS clinical-grade assays for molecular alterations in tumor tissue or in circulating tumor DNA (ctDNA). We used these results to determine if these specimens have potentially “actionable” alterations that could guide cancer therapy.
Methods: From 2014 to 2016, 62 patients with advanced breast cancer had plasma sent for ctDNA analysis (Guardant360 assay; 54 to 70 genes) Thirty-eight of these patients (61%) also had tumor biopsies evaluated by NGS (FoundationOne®; 182 to 315 genes). Alterations were defined as mutations, insertions, deletions, truncations, or rearrangements or amplifications/copy number variations. Patients that harbored multiple alterations in the same gene were not counted as having separate alterations; however, if a gene amplification and an alteration were found in the same gene these were counted as separate events. Variants of unknown significance (VUS) and synonymous mutations were excluded from both assays. Data were collected and analyzed according to a UCSD Institutional Review Board approved protocol.
Results: The median age of our patients at the time of ctDNA analysis was 55 years (range, 44 to 84 years); the median age at the time of tissue biopsy for NGS was 52 years (range, 39 to 82 years). One patient was male. The most common receptor status was estrogen receptor (ER) and progesterone receptor (PR) positive, human epidermal growth factor receptor 2 (HER2) non-amplified or negative (neg)(N=44; 71%), followed by triple negative breast cancer (ERnegPRnegHer2neg) (N=10, 16%), triple positive (N=6, 1%) and finally ERnegPRnegHER2positive (N=2, 0.03%). One patient of 38 (2%) had no tumor alteration detected and 19 of 62 had no ctDNA alterations (31%). In 38 breast cancer patients with tumor NGS results, alterations were detected in 79 unique genes, with the most frequent being TP53 (37% of patients), PIK3CA (24%) and GATA3 (24%) genes. In the 62 patients with ctDNA analysis, 31 unique genes had at least one alteration, with the most frequent being TP53 (36% of patients) and PIK3CA (23%) and EGFR amplification (11%) (GATA3 was not analyzed in the ctDNA assay). Both assays had a high rate of detection for potentially actionable mutations: 41 out of 62 patients (66%) by ctDNA and 34 out of 38 (89%) by tumor NGS. No two patients harbored identical genomic profiles by either tumor NGS or plasma ctDNA analysis except for 1 patient who had no alterations detected by either assay.
Conclusions: Plasma and tissue NGS analysis appear to be complementary assays that yield a high percentage of potentially actionable alterations in patients with advanced breast cancer. Studies of the clinical impact of NGS-guided therapy in breast cancer are warranted.
Citation Format: Shatsky RA, Parker BA, Schwab R, Helsten T, Boles SG, Subramanian R, Piccioni D, Kurzrock R. Detection of molecular alterations in breast cancer through next generation sequencing of both tumor tissue and circulating tumor DNA: The UC San Diego Moores Cancer Center experience [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-07-15.