Abstract LB-228: Noninvasive profiling of molecular dynamics in patients receiving HER2 targeted therapies by cell-free DNA analysis
Authors: Gedvilaite Erika , Stewart Caitlin , Yang Julie , Reichel Jonathan , Stephens Dennis , Offin Michael D. , Jing Xiaohong , Meng Fanli , You Daoqi , Berger Michael F. , Li Bob , Tsui Dana WY 
Published: August 2018

Abstract
Background: The ERBB2/HER2 gene has long been known as an important oncogene in human cancer. Overexpression of HER2 influences the development of various cancers, and amplification of the gene is often found in aggressive forms of breast cancer, leading it to be an important biomarker in many targeted therapies. The goal of our study is to (i) detect the presence of HER2 amplification in plasma cell-free DNA (cfDNA) using two approaches: shallow Whole Genome Sequencing (sWGS) and digital droplet PCR (ddPCR).
Methods: Tumor biopsy DNA from 3 patients was collected from surgeries performed either at diagnosis, disease progression, or relapse prior to enrollment on the trial. Plasma and matched control (buffy coat) were collected from patients before treatment (baseline) and at disease progression. The time of collection between tumor and baseline plasma was 71-913 days. Tumor specimens were analyzed using MSK-IMPACT, a comprehensive 468 gene platform, while plasma cfDNA and matched buffy coat DNA was analyzed using sWGS, ddPCR (using an assay previously reported that detection HER2 amplification by targeting regions on HER2 and a reference region 17q21.31), and a deep targeted sequencing assay that interrogate 60 frequent cancer drivers.
Results: MSK-IMPACT revealed HER2 amplifications (1.5-15.4 fold) in all tumor samples. DdPCR analysis revealed HER2 amplification in all matched plasma samples (1.25-29.82). SWGS analysis of cfDNA detected HER2 amplifications in 5 of the 6 samples (2 baseline and all progression), and missed in one sample, which later confirmed to have the lowest low mutant allele fraction (MAF) among all samples analyzed: deep targeted sequencing analysis of that particular sample reveals a APC X215 mutation at 3% at baseline which later increased to 25% at disease progression, accompanied by the detection of HER2 amplification. In that particular patient, deep sequencing data reveal distinct dynamics of TP53, APC and PIK3CA, indicating the underlying tumor molecular evolution is highly heterogeneous.
Conclusions: These results confirm that the detection of gene amplification in cfDNA is dependent on both the magnitude of amplification and the amount of tumor-derived MAF in the particular plasma sample. Noninvasive analysis of cfDNA allows the tracking of gene amplification and the dynamics of multiple cancer drivers during targeted therapies.
Citation Format: Erika Gedvilaite, Caitlin Stewart, Julie Yang, Jonathan Reichel, Dennis Stephens, Michael D. Offin, Xiaohong Jing, Fanli Meng, Daoqi You, Michael F. Berger, Bob Li, Dana WY Tsui. Noninvasive profiling of molecular dynamics in patients receiving HER2 targeted therapies by cell-free DNA analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-228.