Abstract 4090: Analytical validation of PanTracer LBx performance, a comprehensive pan-solid tumor liquid biopsy assay
Authors: Christodoulos Pipinikas, Faqiang Wu, Daniel Whang, Rebecca Hong, Samuel Koo, Qinqin Zha, Jieying Chu, Rachel Schell, Jiannan Guo, Giovanni Marsico, Tim Forshew, Amber Chevalier, Andrew Lukowiak, Heng Xie, Gregory Jones
Journal: Cancer Research (2025)

Abstract Introduction: Pan-solid tumor comprehensive genomic profiling (CGP) assays have gradually replaced single gene and smaller, tumor-specific panels to identify actionable somatic mutations in patients with advanced cancer. While tissue-based CGP remains important for clinical decisions, invasive biopsies can be challenging in terms of material quantity/quality and/or risk to patients. Plasma-based CGP assays provide the potential for rescuing cases where tissue fails, providing faster results to enable treatment decisions, monitoring treatment through repeated sampling, or capturing tumor heterogeneity. As such, CGP via liquid biopsy (LBx) represents an asset to patients and the options for such testing spans several to hundreds of genes. Here we describe initial results of the analytical validation (AV) process of a large deep sequencing panel aiming to establish the initial performance characteristics of the PanTracer LBx CGP assay. We also provide initial preliminary comparison data to an established highly sensitive targeted panel. Methods: PanTracer LBx, a next-generation sequencing (NGS) assay based on TSO500 chemistry, is designed to detect key classes of somatic alterations across solid tumors, such as SNVs and small InDels (517 genes), CNVs (59 genes), fusions (23 genes) and key immune signatures. AV was performed in a CAP/CLIA certified laboratory across the above mutation classes to determine key assay performance characteristics: limit of detection (LoD), limit of blank (LoB), precision and analytical sensitivity/specificity using clinical samples with orthogonal data. Results: LoD90, was assessed by measuring the detection of somatic variants present in SeraSeq complete ctDNA reference material at different %VAF levels (0.1%-2%) and DNA concentrations. Using a Probit regression model, LoD90 for SNVs and InDels was determined as 0.17% and 0.31%, respectively, and 1.23x for CNVs. LoB for SNVs/InDels and CNVs, assessed by calculating the cumulative per gene specificity across 21 healthy donors subjected to sequencing, was 0%. Analytical sensitivity and specificity were determined by sequencing late-stage cancer samples and comparing results to those obtained with an amplicon-based assay (InVisionFirstTM-Lung). Positive and negative percent agreement with the orthogonal method was 96.9% and 99.3%, respectively. Precision (inter-assay, -lot and -operator) was &amp;gt;95%. Conclusions: Performance evaluation of PanTracer LBx assay met all pre-specified AV acceptance criteria. Fusion LoD90 analysis is ongoing and will be presented during the meeting with additional results including input metrics and preliminary clinical validation. Based on a large panel targeting different classes of somatic variants across multiple genes, it offers results consistent with a smaller, established targeted panel with the addition of more biomarkers that may be informative or actionable. Citation Format: Christodoulos Pipinikas, Faqiang Wu, Daniel Whang, Rebecca Hong, Samuel Koo, Qinqin Zha, Jieying Chu, Rachel Schell, Jiannan Guo, Giovanni Marsico, Tim Forshew, Amber Chevalier, Andrew Lukowiak, Heng Xie, Gregory Jones. Analytical validation of PanTracer LBx performance, a comprehensive pan-solid tumor liquid biopsy assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4090.