Abstract 7622: ASPYRE-Lung: Validation of a simple, fast, robust and novel method for multi-variant genomic analysis of actionable NSCLC variants in tissue

Abstract

Abstract Genomic variant testing of tumors is critical for patients to access the full potential of personalized oncology therapeutics. Current methods such as NGS are costly and challenging to interpret, while PCR assays are limited in the number of variants they can cover. We developed ASPYRE® (Allele-Specific PYrophosphorolysis REaction) technology to address the urgent need for rapid, accessible and affordable diagnostics informing actionable genomic target variants of a given cancer. The targeted ASPYRE-Lung® panel for NSCLC covers 114 variants in 11 genes (ALK, BRAF, EGFR, ERBB2, KRAS, RET, ROS1, MET & NTRK1/2/3) to robustly inform clinical management, based on practice guidelines. The assay detects single nucleotide variants, insertions, deletions, and gene fusions from tissue-derived DNA and RNA simultaneously. We tested the limit of detection, specificity, analytical accuracy and analytical precision of ASPYRE-Lung using FFPE lung tissue samples from patients with NSCLC, variant-negative FFPE tissue from tonsil tissue, and FFPE-based contrived samples with controllable variant allele fractions. The sensitivity of ASPYRE-Lung was determined to be ≤ 3% variant allele fraction for single nucleotide variants and insertions or deletions, ≤ 100 copies for fusions, and ≤ 200 copies for MET exon 14 skipping. The specificity was 100% with no false positive results. The analytical accuracy test yielded no discordant variants between ASPYRE-Lung and orthogonal testing (targeted enrichment NGS) or contrived samples, and results were replicable across operators, reagent lots, runs, and real-time PCR instruments with a high degree of precision. The technology is simple and fast, requiring only four reagent transfer steps using standard laboratory equipment (PCR and qPCR instruments) with analysis via a cloud-based analysis algorithm. ASPYRE-Lung has the potential to be transformative in facilitating access to rapid, actionable molecular profiling of tissue for patients with NSCLC. Citation Format: Ryan T. Evans, Elizabeth Gillon-Zhang, Julia Brown, Katherine Knudsen, Candace King, Amanda S. Green, Ana-Luisa Silva, Justyna M. Mordaka, Rebecca N. Palmer, Alessandro Tomassini, Alejandra Collazos, Christina Xyrafaki, Iyelola Turner, Chau Ha Ho, Dilyara Nugent, Jinsy Jose, Simonetta Andreazza, Kristine von Bargen, Eleanor R. Gray, Magdalena Stolarek-Januszkiewicz, AIshling Cooke, Wendy J. Levin, Honey V. Reddi, Barnaby W. Balmforth, Robert J. Osborne. ASPYRE-Lung: Validation of a simple, fast, robust and novel method for multi-variant genomic analysis of actionable NSCLC variants in tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7622.