Abstract 4130: Detection of FGFR1 and FGFR2 amplification in triple-negative breast cancer using digital droplet PCR and DNA-based microarrays.
Authors: Vinayak Shaveta , Nadauld Lincoln D. , Miotke Laura , Rumma Rowza T. , Telli Melinda L. , Ji Hanlee P. , Ford James M. 
Published: August 2014

Abstract
Background: Triple-negative breast cancers (TNBC) lack targeted therapeutic strategies and identification of potential oncogenic targets is imperative. Fibroblast growth factor (FGF) pathway has been implicated in mammary tumorigenesis and is a potential target in TNBC. Amplification of FGFR2 (fibroblast growth factor receptor 2), identified using genomic studies, has been reported in 4% of TNBCs. Selective FGFR inhibitors are in clinical development and patient selection for these trials is important. Preclinical data suggests that cell lines with FGFR amplification are sensitive to FGFR inhibitors. The aim of this study was to identify FGFR1 and FGFR2 amplification in TNBCs using a quantitative and sensitive methodology of digital droplet polymerase chain reaction (ddPCR) and compare to our results from a DNA-based microarray analysis.
Methods: Fresh-frozen breast tumor core biopsies were collected from patients enrolled onto a TNBC neoadjuvant clinical trial. DNA from each tumor and matched germline-derived sample (n=56 pairs) was hybridized to Affymetrix Molecular Inversion Probe (MIP) array to determine copy number variation (CNV). ddPCR was used to assess amplification in FGFR1 and FGFR2 in 11 and 53 tumor/ germline DNA sample pairs respectively. The ddPCR technology utilizes TaqMan chemistry PCR primers and probes specific for FGFR1 and FGFR2. It quantitates copy number by streaming emulsion droplets single-file into a capillary that leads past a two-color detector, where the positive droplets for the target and reference genes are quantified. Copy numbers for target genes are calculated by comparing to an internal control (ultra-conserved region of chromosome 1).
Results: CNV in FGFR1 and FGFR2 was assessed in 56 TNBCs. No FGFR1 amplifications were identified in any of the samples. FGFR2 amplifications were identified in 2/56 (4%) tumor samples. ddPCR was used to assess quantitative copy number in 53 paired tumor/ germline DNA samples for FGFR2 and 11 paired samples for FGFR1. High amplifications with 6-8 copies of FGFR2 were identified in 2/53 (4%) of the TNBCs. These two samples were the same as the ones identified to have a high copy gain by CNV analysis. No FGFR1 amplifications were identified by ddPCR and this was consistent with our CNV analysis result.
Conclusions: Our FGFR amplification results were in congruence using two different methodologies. No FGFR1 amplification was identified in the TNBC samples assessed and FGFR2 amplification was identified in 4%. ddPCR was done on fresh-frozen TNBCs in this study but this technology can be applied to formalin fixed paraffin embedded tumors as well. ddPCR can detect multiple cancer genome amplifications and has a potential for large scale application. There are several FGFR inhibitors in clinical trials and ddPCR methodology is a clinically applicable strategy for identifying patients with FGFR amplification.
Citation Format: Shaveta Vinayak, Lincoln D. Nadauld, Laura Miotke, Rowza T. Rumma, Melinda L. Telli, Hanlee P. Ji, James M. Ford. Detection of FGFR1 and FGFR2 amplification in triple-negative breast cancer using digital droplet PCR and DNA-based microarrays. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4130. doi:10.1158/1538-7445.AM2013-4130