Distinguishing Gastric/Esophageal Adenocarcinoma from Pancreatic Adenocarcinoma Using Methylation-Based Droplet Digital PCR

The goal of this study was to develop a methylation-based droplet digital PCR to separate 2 cancer classes that do not have sensitive and specific immunohistochemical stains: gastric/esophageal and pancreatic adenocarcinomas. The assay used methylation-independent primers and methylation-dependent probes to assess a single differentially methylated CpG site; analyses of array data from The Cancer Genome Atlas network showed that high methylation at the cg06118999 probe supports the presence of cells originating from the stomach or esophagus (eg, as in gastric metastasis), whereas low methylation suggests that these cells are rare to absent (eg, pancreatic metastasis). On validation using formalin-fixed paraffin-embedded primary and metastatic samples from our institution, methylation-based droplet digital PCR targeting the corresponding CpG dinucleotide generated evaluable data for 60 of the 62 samples (97%) and correctly classified 50 of the 60 evaluable cases (83.3%), mostly adenocarcinomas from the stomach or pancreas. This ddPCR was created to be easy-to-interpret, rapid, inexpensive, and compatible with existing platforms at many clinical lab-oratories. We suggest that similarly accessible PCRs could be developed for other differentials in pathology that do not have sensitive and specific immunohistochemical stains.(c) 2023 United States & Canadian Academy of Pathology. Published by Elsevier Inc. All rights reserved.

Automated summary

The goal of this study was to develop a methylation-based droplet digital PCR for separating two cancer classes without sensitive and specific immunohistochemical stains. The assay used independent primers and dependent probes to assess a differentially methylated CpG site and achieved high accuracy in classifying gastric/esophageal and pancreatic adenocarcinomas. This easy-to-interpret, rapid, and inexpensive method can be implemented in clinical laboratories for differential diagnosis.