Abstract A056: Performance of multi-biomarker class reflex testing in a prospectively-collected cohort
Authors: Gainullin Vladimir , Bae Jin , Guthrie Violeta Beleva , Zhuang Fanglei , Ji Chen , Tyson Christopher , Evans Mark , Arvai Kevin , Gray Melissa , Kumar Madhav , Manesse Mael , Chen Xi , Uren Philip , Cerqueira Gustavo C. , Mazloom Amin , Garces Jorge , Beer Tomasz M. , Diehl Frank 
Published: November 2024

Abstract
Background: A multi-biomarker blood test has the potential to detect cancers in a broad range of organ types and stages. We previously trained and independently assessed the performance of two biomarker classes (methylation and protein; MP) for multi-cancer early detection (MCED) in a prospectively collected study (Cancer Res,2024;84(7Supp):LB100). Here, we assessed the addition of a somatic mutation reflex approach to samples with initially negative MP-results (MP-reflex; MP-r). Methods: This study included 3,160 samples (739 cancer and 2421 non- cancer) representing 20 organ types and all stages. Samples with negative MP results at a specificity threshold of ≥ 98.5% and detectable MP signals above pre-specified lower thresholds were analyzed for mutations using next generation sequencing. Classifier models and thresholds were developed using an independent training set. Sensitivity of the MP biomarker classifier was determined at a combined specificity of ≥98.5%. We also compared the performance of MP and MP-r configurations with prostate (n=52) and breast (n=88) organ types excluded. Results: At 98.5% specificity, the observed overall sensitivity for MP was 52.9%, with sensitivities of 15.3%, 39.8%, 71.2%, 87.2%, 26.7% and 37.5% for stages I, II, III, IV, I/II and unknown, respectively. At the same specificity of 98.5%, when an MP-r configuration was utilized, overall sensitivity was 55.8%, with sensitivities of 19.1%, 42.2%, 72.3%, 89.9%, 29.9% and 46.9% for stages I, II, III, IV, I/II and unknown, respectively. MP-r demonstrated absolute sensitivity increases of 3.8%, 2.5%, 1.1 %, 2.8%, 3.2%, 9.4%, and 2.8%, for stages I, II, III, IV, I/II, unknown, and overall, respectively. When breast and prostate cancers were excluded, test sensitivity for MP was 59.3%, with sensitivities of 17.2%, 51.9%, 76.4%, 88.3%, 31.9% and 41.4% for stages I, II, III, IV, I/II and unknown, respectively. When an MP-r configuration was utilized, overall sensitivity was 62.3% %, with sensitivities of 22.1%, 54.7%, 76.4%, 91.4%, 35.9% and 51.7% for stages I, II, III, IV, I/II and unknown, respectively. MP-r demonstrated absolute sensitivity increases of 4.8 %, 2.8%, 0.0%, 3.1%, 4.0%, 10.3%, and 3.0% for stages I, II, III, IV, I/II, unknown, and overall, respectively. Conclusions: Compared to MP alone (breast and prostate cancers excluded), an MP-r approach results in a relative sensitivity increase of 28% in Stage I cancers and 12.5% for Stage I/II cancers. MP-r is an efficient strategy to add a third biomarker class and enhance sensitivity of MP for the detection of early-stage cancer.
Citation Format: Vladimir Gainullin, Jin Bae, Violeta Beleva Guthrie, Fanglei Zhuang, Chen Ji, Christopher Tyson, Mark Evans, Kevin Arvai, Melissa Gray, Madhav Kumar, Mael Manesse, Xi Chen, Philip Uren, Gustavo C. Cerqueira, Amin Mazloom, Jorge Garces, Tomasz M. Beer, Frank Diehl. Performance of multi-biomarker class reflex testing in a prospectively-collected cohort [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 A056.