Early detection of pancreatic cancer using 5-hydroxymethylation profiles in plasmaderived cell-free DNA.

672 Background: Pancreatic cancer is one of the deadliest cancers, with approximately 15-20% of patients who present at diagnosis with a resectable disease. The major barrier to better outcomes is the lack of early-detection molecular tools to enable timely intervention. We have developed a test that enables the detection of pancreatic cancer from a simple blood draw. The test incorporates a novel, genome-wide sequencing-based epigenomics detection method that enriches for DNA loci that undergo active de-methylation. The measurement of 5-hydroxymethylcytosine (5hmC) provides a unique and stable biomarker for the early detection of cancer including pancreatic cancer. Methods: Whole-blood was obtained from a training cohort of 660 individuals (consisting of 132 pancreatic cancers (PaCa) and 528 non-cancers) and a validation cohort of 2,150 individuals (consisting of 102 PaCa and 2,048 non-cancers). Cell-free DNA (cfDNA) was isolated from plasma from which 5hmC and whole-genome libraries were generated and sequenced. Logistic regression algorithms were employed using 5hmC feature sets combined with physical characteristics of DNA fragments to optimally partition cancer from non-cancer samples. Results: Cross validation of the training model yielded an overall sensitivity of 65.9%,(95% CI, 57.2%–73.9%), early-stage (stage I-II) sensitivity of 57.1% (95% CI, 44%–69.5%) and a specificity of 98%. The model was further validated in a separate, non-overlapping set of blinded and independently processed samples and yielded an early-stage sensitivity of 68.3% (95% CI, 51.9%–81.9%) and a specificity of 96.9% (95% CI, 96.0%–97.6%). Conclusions: Our results demonstrate that plasma-derived cfDNA 5hmC profiles enable the accurate detection of early-stage PaCa, providing a valuable non-invasive tool especially for those individuals at high risk for the disease, including individuals with genetic predisposition and newly diagnosed type 2 diabetes. A larger clinical study (NODMED - NCT05188586) is ongoing and will provide clinical validation for the detection in individuals at high risk for this deadly disease.