Abstract P4-01-08: Characterization of circulating tumor free DNA (ctDNA) obtained from patients with metastatic breast carcinoma (MBC) undergoing systemic therapies using comprehensive genomic profiling
Authors: Zhang Q , Gerratana L , Zhang Y , Flaum L , Gradishar W , Platanias L , Cristofanilli M 
Published: May 2019

Abstract
Introduction:Therapeutic benefit from individual treatments in patients with MBC is limited to small subsets of patients and of short duration due to tumor heterogeneity. Novel molecular diagnostics including ctDNA has been shown to predict response or resistance and survival. However, the frequency of detection of actionable mutations using ctDNA is variable based upon tumor related factors and diagnostic platform sensitivity (e.g. ddPCR or NGS). We evaluated a novel NGS technology in the ability of detecting driver and clonal genomic abnormalities in samples from MBC patients. Moreover, we wanted to compare the new technology to another state-of-the-art, commercially available diagnostic ctDNA testing with similar sensitivity to demonstrate both are able to detect genomic abnormalities in MBC.
Methods: This study included 30 samples from 15 patients with stage III/IV BCa treated at NMH (2016-2017) and who received standard systemic treatments based on disease subtypes longitudinally characterized for ctDNA before or 3 months after systemic therapies respectively. ctDNA from clinical plasma samples was first analyzed using PredicinePLUS, a NGS-based assay (Predicine Inc) with a 180-gene panel for genomic alterations mutations. The results were then independently analyzed with Guardant360TM (Guardant Health), a 73-gene panel. Matched pairs variations between Guardant360TM and Predicine was compared by Wilcoxon signed-ranks test. The prognostic impact of ctDNA was tested through Cox regression.
Results: Genomic Alterations (SNVs, Indels and copy number variations) were detected on 43 genes by PredicinePLUS assay. All samples (100%) demonstrated at least 1 somatic alterations. There were 75 mutations detected within 29 genes, and the variant frequency of mutated genes ranges from 0.11% to 68.56%. Median variant frequency was around 3.42%. Key cancer related genes including TP53, ESR1, PIK3CA, PTEN and BRCA1, are frequently mutated. Copy number variation were detected on 18 genes, among which 15 genes showed copy number gain, including MYC, PIK3CA, CCND1, and 3 genes (ATM, BRCA1 and CDKN2A) with copy number loss. There were no significant difference of % ctDNA (P=0.3967) and number of variations (P=0.5) between results of Predicine and Guardant360TM, neither to the comparison of main detected alterations (BRCA1, ESR1, MYC, PIK3CA and TP53) with Guardant360TM and Predicine (P=1). Furthermore, results from Predicine indicated that there is correlation with treatment response and benefit. A significant decrease on variations in %ctDNA levels (P=0.028) and variations in the number of genomic variants (P=0.028) after systemic therapies, was associated with longer overall survival.
Conclusions: Our study describes a novel diagnostic platform with the ability to identify ctDNA mutation and copy number variations in patients with MBC receiving systemic therapy. We also confirm that when comparing ctDNA using NGS platforms with similar sensitivity, the results are robust and reproducible which indicates that these technologies can be reliably and routinely used as non-invasive method for monitoring response to systemic therapies and predict the prognosis in MBC.
Citation Format: Zhang Q, Gerratana L, Zhang Y, Flaum L, Gradishar W, Platanias L, Cristofanilli M. Characterization of circulating tumor free DNA (ctDNA) obtained from patients with metastatic breast carcinoma (MBC) undergoing systemic therapies using comprehensive genomic profiling [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-01-08.