Pre-diagnosis plasma cell-free DNA methylation profiling reveals signatures of cancers up to7 years prior to clinical detection

Abstract Cancer survival rates are significantly improved when detected at early stages, particularly when the tumour is still localised to the tissue of origin. However, effective screening tools for early cancer detection is currently limited to a subset of cancer types. Profiling cell-free DNA (cfDNA) patterns has emerged as a prominent non-invasive biomarker for detection and subtyping of cancers. However, owing to difficulties in observing the early development of human malignancies as cancers are often detected once they become symptomatic, most cancer biomarker and evolution studies to date have primarily examined the genomics from solid tumour or liquid biopsies following a diagnosis. Utilizing cfDNA as a screening tool for early cancer detection requires profiling of blood plasma samples collected from asymptomatic individuals prior to the diagnosis of cancers to enable assessment of the earliest detectability and predictive performance of potential biomarkers. Here, we leverage the Canadian Partnership for Tomorrow’s Health Project (CanPaTH), to profile blood plasma collected prior to the clinical detection of underlying cancers. Specifically, we use cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq), a highly sensitive assay for profiling cfDNA methylomes, to profile over 300 blood plasma samples collected up to seven years prior to the detection of a breast, prostate or pancreatic cancer, in addition to matched controls with no history of cancer free through follow-up. We identified differentially methylated signatures in pre-diagnosis cfDNA that discriminated cancer-free controls from pre-diagnosis cancer cases up to seven years before diagnosis, and demonstrated that these markers were reflective of differentially methylated in cancer tissue relative to normal tissue and peripheral blood leukocytes. Further, predictive modelling reveals that cfDNA methylation markers in blood are predictive of pre-diagnosis breast cancer cases, achieving an average test AUROC of 0.75 (95% CI: 0.70 - 0.80). Predictive models trained solely with pre-diagnosis cfDNA methylation samples were also predictive of prostate and pancreatic cancer samples collected following diagnosis, achieving an average test AUROCs of 0.95 (95% CI: 0.93-0.96) and 0.96 (95% CI: 0.94-0.97) respectively. In our current studies, we focus specifically on breast, prostate and pancreatic cancer cases, and are extending this to further pan-cancer applications in subsequent investigations. Citation Format: Nicholas Cheng, David Soave, Kimberly Skead, Tom Ouellette, Scott Bratman, Daniel De Carvalho, Philip Awadalla. Pre-diagnosis plasma cell-free DNA methylation profiling reveals signatures of cancers up to7 years prior to clinical detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3385.