Abstract B075: Evolving molecular prescreening program to identify genomic alterations in the NOTCH pathway
Authors: Azaro Analia , Aguilar Susana , Dienstmann Rodrigo , Braña Irene , Hierro Cinta , Ochoa de Olza María , Martin-Liberal Juan , Vieito María , Matos Ignacio , Nuciforo Paolo , Tabernero Josep , Rodon Jordi , Vivancos Ana , Garralda Elena 
Published: August 2018

Abstract
Introduction: Over 2 years we have adapted our VHIO molecular prescreening program (PreScr) to identify genomic alterations in tumors of patients (pt) eligible for phase 1 clinical trials (Ph1) testing NOTCH inhibitors. This retrospective study aims to assess the prevalence of NOTCH pathway alterations in tumors and how this information was used to select therapies and to develop the PreScr. Methods: From Jan/2015 to Dec/2016, 1,832 pt had formalin-fixed, paraffin-embedded tumor samples (TS) analyzed for mutations (mut) using a customized developed Amplicon-Seq panel of 61 cancer-related genes (including FBXW7 [50% exon coverage], NOTCH1 [hotspots 5% exon coverage], NOTCH4 [hotspots 3% exon coverage]) run in Illumina MiSeq; 191 (TS) for Copy Number Alterations (CNAs) using a panel of 59 genes (including NOTCH1-4) run in NanoString NCounter; and 481 (TS) for gene expression using a panel of 26 genes (including NOTCH 1-4) run in Nanostring NCounter. NOTCH1-2 gene amplifications (ampl) were validated by FISH. Results: Tumor types samples were colorectal (CRC) n=468 (25%), lung (LC) n=273 (15%), breast (BC) n=176 (10%), gynecologic (GYNC) n= 111 (6%), head and neck (H&N) n=95 (5%), urinary (UC) n=91 (5%), brain primary tumors n= 34 (2%), and others n=513 (28%). Overall, FBXW7 mut were detected in 28 cases (GYNC 4.5%, CRC 3.7%, UC 2.2%, H&N 1%, others 0.6%). Most frequent co-occurring mut were TP53 (n=15) and APC (n=11). We found no mutations in NOTCH1 or NOTCH4. NOTCH2ampl (≥ 6 copies) were found in 3 cases (biliary tract 20%, BC 4.3%). We found no CNAs in NOTCH1/3/4. Outlier high expression (normalized z-score &gt; 4) of NOTCH family genes was detected in a variety of tumor types, including LC (NOTCH2/3), CRC (NOTCH1/2), BC (NOTCH3/4), UC (NOTCH3/4), and salivary gland (NOTCH1). Five pt were treated with Notch Gamma-secretase inhibitors in clinical trials (4 pt with FBXW7 mut and 1 pt with NOTCH2 ampl). Conclusion: We found a low prevalence of NOTCH pathway alterations in metastatic pt for Ph1 clinical trials. In order to increase the sensitivity for NOTCH mut detection, we will increase exon coverage of NOTCH genes. In parallel, outlier high expression data will be used to guide enrichment in future clinical trials. Our results reveal the challenges faced in an evolving PreScr to the NOTCH targeted therapy development.
Citation Format: Analia Azaro, Susana Aguilar, Rodrigo Dienstmann, Irene Braña, Cinta Hierro, María Ochoa de Olza, Juan Martin-Liberal, María Vieito, Ignacio Matos, Paolo Nuciforo, Josep Tabernero, Jordi Rodon, Ana Vivancos, Elena Garralda. Evolving molecular prescreening program to identify genomic alterations in the NOTCH pathway [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B075.