High detection rates of pancreatic cancer across stages by plasma assay of novel methylated DNA markers and CA 19-9.

Purpose: We have previously identified tissue methylated DNA markers (MDMs) associated with pancreatic ductal adenocarcinoma (PDAC). In this case-control study, we aimed to assess the diagnostic performance of plasma MDMs for PDAC. Experimental Design: Thirteen MDMs(GRIN2D, CD1D, ZNF781, FER1L4, RYR2, CLEC11A, AK055957, LRRC4, GH05J042948, HOXA1, PRKCB, SHISA9, and NTRK3) were identified and assays were optimized in plasma. Next, 340 plasma samples(170 PDAC cases, 170 controls) were assayed using target enrichment long-probe quantitative amplified signal method. Initially, 120 advanced stage PDAC cases and 120 healthy controls were used to train a prediction algorithm at 97.5% specificity using random forest modeling. Subsequently, the locked algorithm derived from the training set was applied to an independent blinded test set of 50 early-stage PDAC cases and 50 controls. Finally, data from all 340 patients were combined, and cross-validated. Results: AUC for the training was 0.93(0.89−0.96) for MDM panel, 0.91(0.87-0.96) for CA 19-9, 0.99(0.98−1) for the combined MDM-CA 19-9 panel and in test set 0.84(0.76-0.92) for MDM panel, 0.87(0.79-0.94) for CA 19-9, and 0.90(0.84-0.97) for MDM-CA 19-9 panel, significantly better compared to either MDMs or CA19-9 alone(p=0.0382 and 0.0490). Combining data sets, the cross-validated AUC was 0.9 (0.86−0.94) for MDM panel and 0.89 for CA 19-9(0.84-0.93) vs 0.97(0.94−0.99) for the combined MDM-CA 19-9 panel, p{less than or equal to}0.0001. Overall, cross-validated sensitivity of MDM-CA 19-9 panel was 92%(83-98%) with observed specificity of 92%, at the preset specificity of 97.5%. Conclusions: Plasma MDMs in combination with CA 19-9 detect PDAC with significantly higher accuracy compared to either biomarker individually.