Analytical performance of a comprehensive genomic profiling system to detect actionable genetic alterations in NSCLC

Background Comprehensive genomic profiling in NSCLC has become increasingly important for clinical management of advanced stage patients. Alteration status of EGFR, ALK, BRAF, and ROS1 are validated biomarkers linked to approved drugs, with many clinical trials enrolling on the basis of additional biomarkers, including Tumor Mutation Burden (TMB). It is therefore important to develop accurate and sensitive tools for tumor profiling, particularly in NSCLC where biopsy materials are limited. Here, we present results from ongoing analytical performance studies with the PGDx elio tissue complete - IUO assay, verifying our capabilities to accurately identify a range of genomic alteration types, comprising SNVs, indels, translocations, and TMB. Methods >300 specimens in NSCLC, comprising FFPE tissue and characterized cell lines were analyzed on our >500-gene targeted panel. Accuracy of the results were compared to orthogonal methods, such as whole exome sequencing (WES), IHC, FISH, and on-market IVD assays. Results were analyzed for the positive percent agreement (PPA) and negative percent agreement (NPA) for all variants assessed. Analytical studies were performed to assess the limit of blank, limit of detection, and repeatability for detection of these variants. Results Clinical FFPE and characterized cell line specimens (representing EGFR and BRAF SNVs, EGFR exon 19 deletions, and ALK and ROS1 translocations) were evaluated and demonstrated high concordance between PGDx elio tissue complete - IUO and orthogonal methods, with high PPA and NPA for SNV, indel, and translocation alterations analyzed. Repeatability studies demonstrated 100% PPA and 100% NPA for all variants assessed across operators, instruments, and days. The accuracy for panel-wide sequence mutations were assessed by comparing the results of >50 clinical samples (representing >500 SNVs and ~40 indels) run on PGDx elio tissue complete IUO and a validated NGS method, resulting in high PPA and NPA across all alterations analyzed. Reported alterations between PGDx elio tissue complete IUO and the independent NGS method displayed high sensitivity for analyzed SNVs (≥4% MAF) and indels (≥6% MAF). Finally, comparison of TMB results to WES data demonstrated TMB can be accurately and consistently reported from this panel, across a range of DNA inputs (50-200 ng) and tumor purities (10-30%). Conclusions The PGDx elio tissue complete - IUO >500-gene assay system, including our proprietary bioinformatics, provides accurate and reproducible results for the detection of clinically relevant genetic alterations in this NSCLC study. Further verification and validation studies of this gene panel are ongoing. The PGDx elio tissue complete assay will employ a decentralized, kitted model, increasing clinical accessibility to NGS and allow for delivery of highly accurate and timely results. Citation Format: Kelly Gerding, Laurel Keefer, Christine McCord, Amy Greer, Shantanu Shewale, Nicole Barkley, Eileen Sagini, Dorhyun Johng, Kenneth Valkenburg, Caitlin Gilley, Colby Ganey, Alvis Hu, Diandra Denier, Lorenzo Jones, Christina Oliveras, Gregory Joseph, Kartikeya Joshi, James Hernandez, Christopher Gault, Eniko Papp, Peibing Qin, Sonya Parpart-Li, James White, Mark Sausen, Siân Jones. Analytical performance of a comprehensive genomic profiling system to detect actionable genetic alterations in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3534.