Abstract 1125: Characterizing the cfDNA fragmentome in patients with hepatocellular carcinoma

Abstract Hepatocellular carcinoma (HCC) is the third leading cause of cancer death globally and is one of the most rapidly increasing causes of cancer mortality in North America and Europe due to metabolic and emerging risk factors. Here, we show that cell-free DNA (cfDNA) fragmentation profiles reflected underlying disease biology and that a machine learning classifier detected HCC across diverse populations and was enhanced by incorporating patient clinical risk and protein concentrations. Characteristics of the cfDNA fragmentome, including genome-wide chromatin, repeat elements, methylome, and mutational profiles, were altered in patients with HCC, including those with metabolic risk factors and aflatoxin exposure. Novel whole-genome tissue-of-origin deconvolution analyses identified increased representation of cfDNA originating from hepatocytes (p=2.4x10-10) and CD8+ T cells (p=5.8x10-7) and decreased contribution of NK cells (p=3.0x10-6) in patients with cancer. Using a previously locked fragmentome classifier for liver cancer detection, we analyzed 377 individuals with and without HCC from two distinct geographic cohorts. We found that the cfDNA fragmentome classifier detected HCC across all stages and diverse etiologies with a sensitivity of 70% (95% CI=65%-75%) and specificity of 94% (95% CI=90%-97%), outperforming the commonly used alpha-fetoprotein (AFP) biomarker which had a sensitivity of 62% (95% CI=57%-67%) and specificity of 93% (95% CI=88%-96%). A combined approach using cfDNA fragmentomes, AFP, and clinical risk achieved a sensitivity of 74% (95% CI=66%-80%) at a specificity of 85% (95% CI=78%-89%) in transplant curable disease (Milan criteria) in both cohorts and was more sensitive than standard-of-care AFP and ultrasound performance for early-stage disease (reported 63% sensitivity at 84% specificity). This study provides insights into the origins of altered cfDNA and circulating proteins for populations at risk of liver cancer and supports the use of a genome-wide fragmentome approach for non-invasive detection of HCC. Citation Format: Hope Orjuela, Carter Norton, Shashikant Koul, Daniel C. Bruhm, Akshaya V. Annapragada, Sarah Short, Keerti Boyapati, Adrianna Bartolomucci, Vilmos Adleff, Nicholas A. Vulpescu, Kauí Lebarbenchon, Jacob Carey, Carter Portwood, Andrei Sorop, Razvan Iacob, Speranta Iacob, Liana Gheorghe, Simoni Dima, Katherine A. McGlynn, Manuel Ramirez-Zea, Jillian Phallen, Robert B. Scharpf, John Groopman, Victor E. Velculescu, Zachariah Foda. Characterizing the cfDNA fragmentome in patients with hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1125.