Abstract 1211P
Background
PDAC is a cancer with high mortality and low survival. Its early detection is critical because symptoms often occur only at advanced stages. However there is no reliable screening tool to identify high-risk patients. ctDNA methylation in blood has recently emerged as a promising new target to differentiate PDAC plasma from normal plasma for early PDAC detection.
Methods
Reduced representation bisulfite sequencing libraries were made in 46 PDAC tissues, 30 para-tumor tissues and 20 PDAC plasmas to screen PDAC-specific markers, which was conducted by quantifying and comparing methylation levels of genomic regions and individual CpG sites between those groups of samples. Markers were validated in plasma samples from PDAC patients (N = 84) and normal controls (N = 64) to propose a classifier in blood. The best-performing markers were then selected to develop a targeted sequencing panel, which has been tested on a larger collection of plasma samples from patients covering a variety of pancreatic diseases to build a prediction model for PDAC and validate its sensitivity and specificity.
Results
We profiled genome-wide methylation patterns of PDAC tissues to identify 171 discriminatory markers. We reiterated training and cross-validating PDAC classification models using SVM method, and achieved an average sensitivity of 86% and specificity of 88%. To prove the feasibility of a non-invasive detection in plasma, a targeted methylation assay using those markers was tested on PDAC- and normal plasmas, which yielded an average sensitivity of 68.4% and a specificity of 85.8%. We refined the panel by selecting the most discriminatory markers and formulated a smaller panel for a more efficient target capture, which is validated in an independent cohort of 200 plasma DNA samples that included PDAC patients, chronic pancreatitis patient and normal controls from multiple centers.
Conclusions
We have developed an NGS based target assay covering PDAC-specific DNA methylation targets by screening and validation on PDAC tissue and plasmas. It has shown encouraging results to classify PDAC plasma from non-malignant diseases, demonstrating its potential to be further optimized into non-invasive diagnostics for blood-based early PDAC screening.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
Peking Union Medical College Hospital.
Funding
Singlera Genomics Ltd.
Disclosure
Q. He: Leadership role, Shareholder/Stockholder/Stock options, Full/Part-time employment: Singlera Genomics. Z. Su: Leadership role, Shareholder/Stockholder/Stock options, Full/Part-time employment: Singlera Genomics. All other authors have declared no conflicts of interest.