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

Daniel Xia; Klaudia Nowak; Alberto Jose Leon; Neil Winegarden; Ada Wong; Natalie Boruvka; Phedias Diamandis; Runjan Chetty; Trevor Pugh; Tong Zhang; Kenneth Aldape; Tracy Stockley; Stefano Serra

doi:10.1016/j.labinv.2023.100145

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

Lab Invest. 2023 Jul;103(7):100145. doi: 10.1016/j.labinv.2023.100145. Epub 2023 Mar 31.

Authors

Affiliations

¹ Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Hematopathology and Transfusion Medicine, University Health Network, Toronto, Ontario, Canada. Electronic address: daniel.xia@uhn.ca.
² Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Anatomical Pathology, University Health Network, Toronto, Ontario, Canada.
³ Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
⁴ Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; 10X Genomics, Burlington, Ontario, Canada.
⁵ Advanced Molecular Diagnostics Laboratory, University Health Network, Toronto, Ontario, Canada.
⁶ Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Anatomical Pathology, University Health Network, Toronto, Ontario, Canada; Deciphex/Diagnexia, Dublin, Ireland.
⁷ Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
⁸ Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland.
⁹ Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Advanced Molecular Diagnostics Laboratory, University Health Network, Toronto, Ontario, Canada; Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada.

PMID: 37004911
DOI: 10.1016/j.labinv.2023.100145

Abstract

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 laboratories. We suggest that similarly accessible PCRs could be developed for other differentials in pathology that do not have sensitive and specific immunohistochemical stains.

Keywords: DNA methylation; ddPCR; gastric adenocarcinoma; molecular diagnostics; pancreatic adenocarcinoma.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenocarcinoma* / diagnosis
Adenocarcinoma* / genetics
DNA Methylation
Esophagus
Humans
Pancreatic Neoplasms* / diagnosis
Pancreatic Neoplasms* / genetics
Polymerase Chain Reaction
Stomach Neoplasms* / diagnosis
Stomach Neoplasms* / genetics

Supplementary concepts

Adenocarcinoma Of Esophagus