Abstract 6601: Analytical validation of a robust integrated genomic and epigenomic liquid biopsy for biomarker discovery, therapy selection, and response monitoring
Authors: Jiang Tingting , Wu Indira , Kim Yvonne , Alla Nageswara , Tran Giao , Ma Dustin , Shah Forum , Zhao Jun , Chen Sai , Gnerre Sante , Hazar Melis , Wang Hao , Barbacioru Catalin , Ryall Karen , Jambusaria Ankit , Chakravarthy Anupam , Zunino Anthony , Pham Theresa , Ghadiri Farsheed , Diehl Evan , Morck Benjamin , Sanchez Arancha , Dayan Rochelle , Liu XianXian , Werbin Jeffrey , Lai Jill , Kennedy Brett , Eppler Ross , Odegaard Justin , Chuang Han-Yu , Eltoukhy Helmy 
Published: April 2023

Background: Despite its revolutionary impact, cancer genomics alone provides little information on tumor phenotype or functional state, which are governed by epigenetic mechanisms, notably methylation of regulatory regions. Tumor and host epigenetic methylation signatures reflect not only tumor phenotype, such as histology, prognosis, protein expression, and functional sub-type, but also that of the tumor microenvironment and the patient, including immune status, therapy-related adverse events, comorbidities, and disease location. Epigenetic markers also provide more sensitive and precise measures of tumor burden, opening up applications for longitudinal therapy response and monitoring. Here we report the initial validation of GuardantINFINITY, a liquid biopsy assay combining genomic information from &gt;800 genes with characterization of the blood-quiet regulatory methylome, both at single-molecule sensitivity from a single tube of peripheral blood.

Methods: Analytical performance was assessed using 594 cancer patient cfDNA, cell line, and cancer-free donor samples at 5-30ng cfDNA input.

Results: Reportable ranges established for SNVs were ≥0.04% variant allele fraction (VAF), ≥0.04% for indels, ≥0.06% for fusions, ≥2.12 copies for amplifications (CNAs), &lt;1.7 copies for copy loss. Observed 95% limits of detection (LoD) were 0.282% for SNVs across all genes (0.2% for oncogenic hotspots), 0.397% for non-homopolymeric indels, 0.05% for fusions, 2.5 copies for CNAs, 16.3% VAF or 1.84 copies for gene deletions, 7.3 copies for viral (HPV, EBV) detection, and 0.06% for MSI-H. For promoter and sample-level methylation, LoDs were 0.06% and 0.05% tumor fraction, respectively. cfDNA cancer samples demonstrated 100% accuracy for SNVs and Indels above 0.5% VAF and 100% for CNAs and fusions across the reportable range. The analytical false positive rate per base was 6.84e-6 for SNVs, 3.42e-6 for indels, and 0 for CNAs and fusions, with positive predictive values of 97.5% for SNVs, 98% for indels, and 100% for CNAs above 2.5 copies and all tested fusions.

Conclusions: GuardantINFINITY is a patient-care-ready liquid biopsy capable of integrated genomic and epigenomic analysis of all solid tumors at single-molecule sensitivity. In addition to traditional genotyping compatible with Guardant360 for more content, the technology’s demonstrated LoD showed the potential for ultra-sensitive ctDNA detection for MRD and recurrence surveillance, tumor fraction quantitation for therapy monitoring, oncogenic virus detection, immunogenotyping, epigenotyping, and tumor phenotype characterization, representing a new standard in biomarker discovery.

Citation Format: Tingting Jiang, Indira Wu, Yvonne Kim, Nageswara Alla, Giao Tran, Dustin Ma, Forum Shah, Jun Zhao, Sai Chen, Sante Gnerre, Melis Hazar, Hao Wang, Catalin Barbacioru, Karen Ryall, Ankit Jambusaria, Anupam Chakravarthy, Anthony Zunino, Theresa Pham, Farsheed Ghadiri, Evan Diehl, Benjamin Morck, Arancha Sanchez, Rochelle Dayan, XianXian Liu, Jeffrey Werbin, Jill Lai, Brett Kennedy, Ross Eppler, Justin Odegaard, Han-Yu Chuang, Helmy Eltoukhy. Analytical validation of a robust integrated genomic and epigenomic liquid biopsy for biomarker discovery, therapy selection, and response monitoring [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 6601.