Abstract B049: Validation of the PGDx elio™ plasma complete for comprehensive genomic profiling of solid tumors through liquid biopsy with Epic Sciences
Authors: Cynthia Maddox, Kenneth C Valkenburg, Cesar Nalvarte, Amanda Harvey, Amy Greer, Ellen L Verner, Renee L Sears, Martin Blankford, Eric A Severson, Taylor J Jensen, Marcia Eisenberg, Shakti Ramkissoon
Journal: Clinical Cancer Research (2024)

Abstract Introduction: To help guide treatment decisions and enable clinical trial matching for cancer patients, tissue-based comprehensive genomic profiling (CGP) is an essential precision oncology tool. Liquid biopsy may be used as a complementary approach to assess tumor-specific DNA alterations circulating in the blood when tissue is limited or unavailable. PGDx’s elio™ plasma complete is a next-generation-sequencing (NGS), cell-free DNA (cfDNA) CGP assay that identifies clinically significant variants from the plasma of patients with advanced and metastatic solid cancers. Methods: The PGDx elio plasma complete is a hybrid-capture, DNA-based kitted solution, optimized for 25 ng of cfDNA input with a targeted panel covering coding exons for 521 genes, and is designed to detect single nucleotide variants (SNVs), small insertions and deletions (indels), copy number amplifications (CNAs), and translocations. It also evaluates blood MSI and tumor mutational burden (bTMB) to guide immunotherapy selection. This study presents the validation of the PGDx elio plasma complete assay to enable the processing of patient blood samples in Epic Sciences' CAP/CLIA-certified laboratory. In the validated configuration, patient plasma will be received and isolated at Epic Sciences and subsequently shipped to PGDx/Labcorp Oncology for cfDNA extraction, library preparation, sequencing, and bioinformatics analysis. Finally, clinical report generation will be carried out by Velsera’s CGW software. Analytical validation was assessed using 105 replicates of SeraCare® (n=21) and Horizon (n=3) reference materials to establish analytical sensitivity, accuracy, and reproducibility and repeatability. Specificity was assessed using 20 non-cancerous plasma samples that were also tested orthogonally. For clinical validation a cohort of &amp;gt;150 cancer patient plasma samples were evaluated, including lung, breast, colorectal, head and neck, pancreatic, and prostate cancers, and compared to Illumina’s TSO500 ctDNA or Labcorp Plasma Focus results. Results: Analytical sensitivity and specificity were evaluated for SNVs, indels, CNAs, fusions, MSI and bTMB. Across all variant types, sensitivity was ≥90%, and specificity was ≥95% at LoDs. The reproducibility and repeatability study resulted in ≥95% agreement for all variant types. Analytical sensitivity was calculated using vendor-verified variants in each control. SeraCare® controls and Horizon reference materials were used to assess variant concordance with an aggregate analytical performance across all control samples with ≥95% PPA and NPA for all variant types. Conclusions: The validation of the PGDx elio plasma complete liquid biopsy assay as part of the Epic Sciences' CAP/CLIA diagnostic workflow for cfDNA-based NGS demonstrates that the liquid biopsy approach is highly sensitive, specific, accurate, reproducible, and robust for comprehensive genomic profiling to complement tissue- based testing and inform clinical decision making. Citation Format: Cynthia Maddox, Kenneth C Valkenburg, Cesar Nalvarte, Amanda Harvey, Amy Greer, Ellen L Verner, Renee L Sears, Martin Blankford, Eric A Severson, Taylor J Jensen, Marcia Eisenberg, Shakti Ramkissoon. Validation of the PGDx elio™ plasma complete for comprehensive genomic profiling of solid tumors through liquid biopsy with Epic Sciences [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B049.