Abstract 2953: Adapting a molecular prescreening program to detect notch pathway alterations in the context of early drug development
Authors: Azaro Analía , Aguilar Susana , Ogbah Zighereda , Saavedra Omar , Vieito María , Matos Ignacio , Braña Irene , Felip Enriqueta , Carles Joan , Fariñas Lorena , Elez Elena , Macarulla Teresa , Saura Cristina , Dienstmann Rodrigo , Garralda Elena , Vivancos Ana 
Published: September 2020

Abstract
Introduction: Gene alterations in NOTCH signaling pathway have a prevalence ranging from &lt;1% to 13% across tumor types. Efforts in adapting molecular prescreening programs to emerging biomarkers are critical in the context of early clinical trials. The aim of this retrospective study is to assess the prevalence of NOTCH pathway alterations and compare the results of our two institutional panels with public databases (AACR Project GENIE) in order to guide drug development efforts and basket trials.
Methods: From Jan/2017 to Dec/2018, 1,697 patients (pts) had their FFPE tumor samples (either primary or metastasis) analyzed for mutations (mut) using a custom developed Amplicon-Seq panel of 59 cancer-related genes (including NOTCH1 [hotspots 5% exon coverage] and NOTCH4 [hotspots 3% exon coverage]) that was run in Illumina MiSeq (v1). Additionally, 502 samples were analyzed for Copy Number Alterations (CNA) using a panel of 44 genes (including NOTCH1-4) using NanoString nCounter (copy number between 4-6 copies were validated by FISH). From Jun/2018 to Jun/2019 an expanded NOTCH Amplicon-Seq panel v2 (including additional exons in NOTCH1 plus NOTCH2 and NOTCH3 hotspots regions) replaced the prior v1 panel and 618 samples were sequenced.
Results: Colorectal cancer (CRC) (n= 404 [24%]; n=241 [39 %]) and breast cancer (BC) (n=283 [17%]; n= 194 [31%]) were the most frequent tumor types for v1 and v2 panel cohorts, respectively. NOTCH1-4 mut were detected in 11 cases (0.64%). The highest rate of NOTCH pathway alterations (NOTCH1-4 mut plus CN gain or loss) was detected in BC (n=14 [7.7%]) with a clear enrichment in triple negative subtype. Higher prevalence of NOTCH1-4 mut was detected using expanded v2 panel, with 17 NOTCH1-4 mut cases (2.75%). Head & neck (H&N) (n=3 [5%]); BC (n=6 [3%]); and CRC (n=6 [2.5%]) were most common tumors. From all NOTCH1-4 gene mut detected, 8 were known actionable oncogenic driver mut and 9 were variants of unknown significance. When comparing our latest v2 results with GENIE database (mostly large NGS panels with exon capture), we found a similar prevalence in NOTCH1-4 mut in BC and CRC, but lower prevalence was seen in H&N, biliary and gastric tumors. We enrolled 4 pt in clinical trials with NOTCH inhibitors (3 NOTCH1 actionable mut pt (0.48%), 1 NOTCH3 actionable mut pt (0.16%).
Conclusion: Institutional efforts to increase coverage of NOTCH pathway genes improved the detection of actionable NOTCH1-4 mut. Differences in prevalence as compared to GENIE dataset may be attributed to the small number of samples tested with our v2 panel and larger panels covering all exons of NOTCH1-4 genes in GENIE cohort. Therefore, we keep evolving our NOTCH prescreening program for clinical trial enrichment.
Citation Format: Analía Azaro, Susana Aguilar, Zighereda Ogbah, Omar Saavedra, María Vieito, Ignacio Matos, Irene Braña, Enriqueta Felip, Joan Carles, Lorena Fariñas, Elena Elez, Teresa Macarulla, Cristina Saura, Rodrigo Dienstmann, Elena Garralda, Ana Vivancos. Adapting a molecular prescreening program to detect notch pathway alterations in the context of early drug development [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2953.