Abstract B029: Comparison of a comprehensive NGS profiling assay and conventional molecular testing approaches for detection of clinically relevant alterations in NSCLC
Authors: Weingartner Elizabeth , Gerding Kelly M.R. , Cerquiera Gustavo , Gault Christopher , Hernandez James , Valkenburg Kenneth , Keefer Laurel , Sagini Eileen , Johng Dorhyun , Gilley Caitlin , Ganey Colby , Ettehadieh Leila , Denier Diandra , Oliveras Christina , Joshi Kartikeya , Kong Eric , Papp Eniko , Greer Amy , White James R. , Nichol Donna , Simmons John 
Published: March 2020

Abstract
Introduction: Genomic analysis using next-generation sequencing (NGS) enables simultaneous detection of targetable alterations and biomarkers with emerging clinical utility in non-small cell lung cancer (NSCLC) patients. Importantly, many of these alterations are mutually exclusive and tumor tissue for molecular testing is often limited. As such, we developed PGDx elioTM tissue complete (ETC) as a comprehensive NGS assay capable of detecting somatic single nucleotide variants (SNVs), insertions and deletions (indels), amplifications, and rearrangements, as well as microsatellite stability (MSI) and tumor mutational burden (TMB). Here, we present the performance of this assay in detecting key clinical variants in NSCLC. Methods: Studies comprising &gt;300 NSCLC specimens (FFPE tissue and characterized cell lines) were analyzed using ETC, a 500+ gene assay (under development), across key clinically relevant variants in NSCLC, including tumor mutation burden (TMB). Accuracy of the results were compared to orthogonal methods (e.g. whole-exome sequencing (WES), IHC, FISH) and analyzed for the overall percent agreement (OPA). Additionally, archival FFPE samples from 46 NSCLC patients previously found to harbor ALK translocations, MET amplifications, MET exon 14 skipping mutations, EGFR mutations, and/or ROS1 translocations were also analyzed. The results were compared to orthogonal methods and the overall genomic landscape evaluated. Results: Clinical FFPE and characterized cell line specimens were evaluated for the following alterations: EGFR mutations (L858R, T790M, and Exon 19 deletions), BRAF V600E mutations, and ALK and ROS1 translocations. Compared to orthogonal methods, the NGS assay demonstrated &gt;93% OPA across all variants. Comparison of TMB results to WES data demonstrated high accuracy and precision, across a range of DNA inputs (50-200 ng) and tumor purities (10-30%). In the 46 retrospective NSCLC cases, the NGS assay identified 15 ALK translocations, 6 MET amplifications, 1 MET exon 14 skipping mutation, and 5 EGFR mutations, with most being mutually exclusive. The majority of cases were confirmed by orthogonal assays, with the few apparent discordances likely due to tumor heterogeneity, assay distinctions, or analyte input. Higher TMB was found in cases without targetable alterations. Conclusions: ETC provides accurate and reproducible results for the detection of clinically relevant alterations in NSCLC. Further verification and validation studies of this gene panel are ongoing. Overall NGS showed excellent concordance with orthogonal variant detection methods. Importantly, ETC demonstrated added value in assessing all genomic alteration types in a single assay, as well as reporting composite genomic scores, suggesting that NGS may offer a comprehensive solution to molecular testing.
Citation Format: Elizabeth Weingartner, Kelly M.R. Gerding, Gustavo Cerquiera, Christopher Gault, James Hernandez, Kenneth Valkenburg, Laurel Keefer, Eileen Sagini, Dorhyun Johng, Caitlin Gilley, Colby Ganey, Leila Ettehadieh, Diandra Denier, Christina Oliveras, Kartikeya Joshi, Eric Kong, Eniko Papp, Amy Greer, James R. White, Donna Nichol, John Simmons. Comparison of a comprehensive NGS profiling assay and conventional molecular testing approaches for detection of clinically relevant alterations in NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B029. doi:10.1158/1535-7163.TARG-19-B029