Abstract P6-07-02: Targeted next generation sequencing of advanced breast cancers identifies potentially actionable alterations and variants of standard biomarkers in the majority of patients
Authors: Estrada MV , Warner J , Rioth M , Balko JM , Rexer B , Sanders ME 
Published: May 2016

Abstract
Background: Molecular tumor profiling is increasingly important in the management of oncologic patients. Targeted next-generation sequencing (T-NGS), using formalin fixed paraffin embedded (FFPE) clinical samples, allows for molecular characterization of genes with known or potential therapeutic and prognostic importance in cancer. Actionable alterations include those with on- or off-label therapeutic implications, those that might be biomarkers of response to clinical trial agents, or those which are non-indicators for response.
Design: We correlated information on patients with metastatic or refractory locoregional recurrence of breast cancer (BC) with potentially actionable genetic alterations detected by a commercially available T-NGS assay, which sequences the coding regions of 315 genes and introns of 28 genes involved in rearrangements selected for their demonstrated role in solid malignancy. We developed an informatics pipeline to capture test results in real-time and store them for subsequent research analysis. Results were analyzed by clinical subtype (estrogen receptor positive [ER+]; HER-2 amplified [HER2+]; triple-negative [TN]) for actionable alterations, most frequently altered genes/pathways and variants of standard biomarkers not detected by routine studies.
Results: Between 11/2013 and 4/2015, 141 FFPE samples from 139 patients were tested by T-NGS. At least one potentially actionable genetic alteration was identified in 98% of patients (median 5.5 alterations/tumor [range 0-18]). 64% had alterations predicting sensitivity to approved BC therapies and 10% to approved therapies in other tumor types. An additional 1231 variants of uncertain significance (VUS) (median 9 per tumor [range 0-28]) were identified. The most frequently altered genes were TP53 (64%), PIK3CA (37%) and MYC (24%). Genes involved in cell cycle, DNA damage and PIK3CA/mTOR pathways were highly altered among all receptor subtypes. The RAS/MAPK pathway was more commonly altered in ER+ (28%) vs. HER2+ (13%) and TN (17%). CCND1 amplifications were found in 16% (57% ER+, 30% HER2+, 13% TN) and FGFR1 amplifications in 13% (61% ER+, 22% HER2, 17% TN). Co-amplification of 8p and 11q (including FGFR1/ZNF703 and CCND1/FGF3/FGF4/FGF19) was found in 28% of patients (ER+ 21%, HER2+ 25%, TN 7.5%). The combination of PIK3CA mutation and MAP3K1/MAP2K4 alteration occurred in 12% of patients (82% ER+, 18% TN). 4 ESR1 mutations and 2 amplifications (all in ER+) as well as 4 HER2 mutations (1 ER+ and 3 TN) were also identified. The number of patients receiving genotype-directed treatments informed by T-NGS results and patient outcome after genotype-directed treatment will be subsequently presented.
Conclusion: Mutation profiling using T-NGS identified potentially actionable alterations in a majority of advanced BC patients, providing novel yet rational therapeutic options and facilitating clinical trial enrollment. T-NGS results will be used to guide therapy in increasing numbers of BC patients.
Citation Format: Estrada MV, Warner J, Rioth M, Balko JM, Rexer B, Sanders ME. Targeted next generation sequencing of advanced breast cancers identifies potentially actionable alterations and variants of standard biomarkers in the majority of patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-07-02.