Abstract B027: Analytical validation of a 500+ gene comprehensive NGS assay to detect genomic alterations across 35 tumor types
Authors: Gerding Kelly M.R. , Valkenburg Kenneth C , Oliveras Christina , White James R. , Ettehadieh Leila , Cerquiera Gustavo , Gault Christopher , Hernandez James , Kong Eric , Angiuoli Samuel , Simmons John , Loftin Isabell , McElhinny Abigail 
Published: March 2020

Introduction: Advances in precision medicine for solid tumors have led to an increase in the number of molecular biomarkers and signatures associated with clinical decisions and clinical trial eligibility. In advanced disease settings, timely clinical decision making informed by robust and accurate molecular biomarker testing is increasingly important. As such, there is a need for a comprehensive, decentralized and rigorously validated diagnostic test. To address this need, we developed and analytically validated PGDx elioTM tissue complete (ETC) assay, which reports somatic single nucleotide variants (SNVs), insertions and deletions (indels), amplifications, and rearrangements, as well as microsatellite stability (MSI) and tumor mutational burden (TMB). Methods: &gt;500 FFPE tumor tissue specimens, across 35 tumor types and 9 organ systems, were analyzed using our 500+ gene targeted panel, ETC (assay in development). Accuracy of the results was compared to orthogonal methods, such as whole exome sequencing (WES), IHC, FISH, NGS, and other on-market IVD assays. Results for all variant types were analyzed for overall percent agreement (OPA). Additional analytical studies were performed to assess precision/repeatability for detection of somatic variants, evaluated across multiple operators, instruments and days. Results: 112 unique samples were evaluated for SNVs and indels by ETC and accuracy assessed via orthogonal validated NGS assays, demonstrating an OPA &gt;99.9%. Detection of amplification events was assessed in 176 samples and concordance with orthogonal FISH and IHC assays demonstrated &gt;93.0 % OPA. Rearrangement accuracy was evaluated across several clinically relevant translocations, with an &gt;94.0 % OPA when compared to FISH and an RNA-based sequencing method (n=270). 115 pan cancer samples were analyzed for microsatellite status and accuracy with PCR was determined, with an overall agreement of 100.0%. Lastly, TMB was determined in 118 samples and results compared to WES-derived TMB, displaying a high level of concordance (Pearson correlation, p=0.903) across a range of TMB scores (0.2-89.7 muts/Mbp). Conclusions: The PGDx elio tissue complete assay system, including proprietary, automated bioinformatics, provides accurate and reproducible results for the detection of clinically relevant genetic alterations across tumor types. 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 M.R. Gerding, Kenneth C Valkenburg, Christina Oliveras, James R. White, Leila Ettehadieh, Gustavo Cerquiera, Christopher Gault, James Hernandez, Eric Kong, Samuel Angiuoli, John Simmons, Isabell Loftin, Abigail McElhinny. Analytical validation of a 500+ gene comprehensive NGS assay to detect genomic alterations across 35 tumor types [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 B027. doi:10.1158/1535-7163.TARG-19-B027