Paired comparison of routine molecular screening of patient samples with advanced non-small cell lung cancer in circulating cell-free DNA using OncoBEAM^TM EGFR V2, targeted next-generation sequencing Plasma-SeqSensei^TM Solid Cancer IVD Kit and custom-validated NGS assay

Abstract Background: Noninvasive genotyping using plasma cell-free DNA (cfDNA) has the potential to obviate the need for some invasive biopsies in cancer patients. We sought to validate an ultra-deep plasma Next-Generation Sequencing (NGS) assay for patients with Non-Small-Cell Lung Cancers (NSCLC) for detecting Minimal Residual Disease (MRD) following curative-intent NSCLC treatment or EGFR detection at an early stage. Patients and Methods: We carried out targeted NGS using the Plasma-SeqSensei™ Solid Cancer IVD Kit on cfDNA extracted from plasma. Somatic alterations were filtered, removing somatic mutations attributable to clonal hematopoiesis. Sensitivity and specificity for plasma detection of known oncogenic drivers were calculated. In a subset of cases, validation was carried out using an orthogonal OncoBEAMTM EGFR V2 assay, as well as with a custom-validated NGS assay. Results: In comparison with the OncoBEAMTM EGFR V2 kit, we observed a 75% concordance with the Plasma-SeqSensei™ Solid Cancer IVD Kit. The 25% genomic discordances were respectively observed in 5%, 7% and 13% linked to the limit of coverage of the OncoBEAMTM EGFR V2 kit, the limit of EGFR sensitivity of the Plasma-SeqSensei™ Solid Cancer IVD Kit and the larger KRAS, PIK3CA, BRAF coverage of the Plasma-SeqSensei™ Solid Cancer IVD Kit. In comparison with the custom-validated NGS assay, we observed a 68% concordance with the Plasma-SeqSensei™ Solid Cancer IVD Kit. The 32% genomic discordances were respectively observed in 5%, 11% and 16% linked to the limit of coverage of the Plasma-SeqSensei™ Solid Cancer IVD Kit, the limit of covered sensitivity of the custom-validated NGS assay and the additional oncodrivers analysis only covered by the custom-validated NGS assay. Benefitting from the higher coverage from targetable BRAF, KRAS, PIK3CA targetable alterations, the plasma targeted NGS Plasma-SeqSensei™ Solid Cancer IVD Kit showed 13% additional discordances with the Plasma OncoBEAMTM EGFR V2 kit. Most of these additional somatic alterations were cross-validated in our orthogonal custom-validated NGS assay, used in the routine management of patients. The custom-validated NGS assay sensitivity is determined for MAF at 1%, explaining the limit of sensitivity with the Plasma-SeqSensei™ Solid Cancer IVD Kit. Conclusions: Plasma-SeqSensei™ Solid Cancer IVD Kit resulted in de novo detection of targetable oncogenic drivers and resistance mechanisms in patients with NSCLC, including when tissue biopsies were inadequate for genotyping with high sensitivity and accuracy for low and high cfDNA inputs. Citation Format: David Barthelemy, Emmanuel Grolleau, Gaelle Lescuyer, Florence Geiguer, Arnaud Gauthier, Julie Balandier, Margaux Raffin, Claire Bardel, Bruno Bouyssounouse, Claire Rodriguez-Lafrasse, Sébastien Couraud, Anne-Sophie Wozny, Lea Payen-Gay. Paired comparison of routine molecular screening of patient samples with advanced non-small cell lung cancer in circulating cell-free DNA using OncoBEAMTM EGFR V2, targeted next-generation sequencing Plasma-SeqSensei™ Solid Cancer IVD Kit and custom-validated NGS assay. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6691.