Panel of methylated DNA markers provides improved accuracy in detecting advanced neoplasia and other lesions that may require resection

Oct. 22, 2019

Pancreatic cystic lesions (PCLs) are relatively common and often detected incidentally. Although the majority of these cysts are benign, a subset is premalignant, and the risk of pancreatic cancer in these patients is significantly higher than in the general population.

Current guidelines for treatment of PCLs use a combination of clinical and imaging characteristics to identify high-risk and worrisome cysts that can be selected for close surveillance or surgical resection. However, current clinical and radiological imaging algorithms used to identify patients at risk of advanced neoplasia in pancreatic cysts often lack diagnostic accuracy, which can result in unnecessary surgery.

To address these issues, researchers at Mayo Clinic's campus in Rochester, Minnesota, in collaboration with several other leading academic medical centers, conducted an analysis of cyst fluid samples to identify and validate the performance of a panel of cyst fluid methylated DNA markers (MDMs) that can detect advanced neoplasia and discriminate PCLs with high-grade dysplasia (HGD) and pancreatic cancer (PC) from those with low-grade dysplasia (LGD) and no dysplasia (ND).

The MDMs tested in cyst fluid were derived from a panel of MDMs discovered and validated initially in pancreatic tissue. The results of this study were published in The American Journal of Gastroenterology (AJG) in 2019.


Using pancreatic tissue from patients with pancreatic cancer, precancer and normal pancreas, researchers performed unbiased whole-methylome discovery with predefined marker selection criteria to identify top candidate MDMs that differentiate HGD and cancer from LGD and ND.

To examine the accuracy of selected MDM candidates, they then performed multistep validation on an independent set of case group tissues (samples with HGD or PC) and control group tissues (samples with ND or LGD).

The researchers then assayed the top candidate MDMs via quantitative methylation-specific polymerase chain reaction using archival cyst fluid obtained from surgically resected PCLs to assess the diagnostic performance in a pilot study, followed by validation of their results in an independent cyst fluid sample set using prespecified marker cut-offs derived from the pilot study.


  • From a pool of 25 discriminant MDMs discovered in tissue, the researchers identified 13 that were chosen for a pilot study in 134 cyst fluid assays using samples obtained from 21 cases (8 HGD, 13 PC) and 113 controls (45 ND, 68 LGD).
  • A panel of two MDMs (TBX15, BMP3) demonstrated high sensitivity and specificity (> 90%) for differentiating cysts with no dysplasia or low-grade dysplasia from those with advanced neoplasia (HGD and cancer).
  • The discrimination demonstrated by the MDM panel was significantly better than that demonstrated by cyst fluid mutant KRAS or carcinoembryonic antigen (CEA), with areas under the receiver operating characteristic curve of 0.93 (95% confidence interval: 0.86-0.99), 0.71 (0.57-0.85), and 0.72 (0.60-0.84), respectively.
  • Cutoffs for the MDM panel applied to an independent cyst fluid validation set (31 cases and 56 controls) yielded similarly high discrimination, with areas under the receiver operating characteristic curve of 0.86 (95% confidence interval: 0.77-0.94, P = 0.2).


In this study, researchers identified and validated a panel of MDMs assayed in pancreatic cyst fluid that accurately differentiate high-grade precursor lesions and cancer from low-grade precursors and normal pancreas tissue. "These cyst fluid MDMs appear to detect advanced neoplasia in pancreatic cysts with high sensitivity and specificity, and performed this task better than currently available cyst fluid biomarkers," explains Shounak Majumder, M.D., a gastroenterologist at Mayo Clinic's campus in Rochester and lead author on the AJG article.

"The novel methylated DNA markers identified in this study demonstrated the potential to change the paradigm of clinical practice in patients with pancreatic cysts," says Dr. Majumder. "If we can accurately identify which cysts harbor early cancer or advanced precancer, we can determine which patients will benefit most from surgery versus ongoing surveillance."

According to Dr. Majumder, prospective studies that assess the diagnostic performance of these novel cyst fluid biomarkers in patients with PCL undergoing surgery as well as those undergoing clinical surveillance will help corroborate these findings and optimize marker combinations for clinical use.

For more information

Majumder S, et al. Novel methylated DNA markers discriminate advanced neoplasia in pancreatic cysts: Marker discovery, tissue validation, and cyst fluid testing. The American Journal of Gastroenterology. 2019;114:1539.