Noninvasive, Multitarget Stool DNA Methylation Assay Under Study in Early Detection of Multiple Gastrointestinal Cancers

Get Permission

A prospective study in China found that a noninvasive, multitarget stool DNA methylation assay was accurate in the early detection and identification of the tissue of origin of gastrointestinal cancers.1 The study, conducted by Li-Yue Sun, MD, of Guangdong Second Provincial General Hospital, Guangzhou, China, was presented at the 2023 ASCO Breakthrough in Yokohama, Japan, and virtually.

“The multitarget stool DNA methylation assay allowed [the] early and accurate detection and identification of tissue-of-origin gastrointestinal cancers.”
— Li-Yue Sun, MD

Tweet this quote

With an estimated 4.8 million new cases and 3.4 million deaths worldwide, in 2018, cancers of the gastrointestinal tract accounted for more than one-quarter (26%) of the global cancer incidence and more than one-third (35%) of all cancer-related deaths.2

Although the U.S. Food and Drug Administration (FDA) has approved several types of stool-based tests and the SEPT9 gene methylation blood-based assay in the detection of colorectal cancer, there are no FDA-approved early detection tests for multiple gastrointestinal cancers.

Study Methodology

The researchers prospectively enrolled 124 patients diagnosed with gastrointestinal cancers who had not undergone treatment and 92 healthy controls who underwent gastrointestinal cancer–related examinations every 3 years. The types of gastrointestinal cancers included colorectal, gastric, esophageal, pancreatic, and ampullary.

Stool DNA was extracted from the supernatant of a mixture containing 5 g of fresh stool and 25 mL of preservative solution using the stool DNA extraction kit. The researchers then subjected the samples to bisulfite conversion using the EZ DNA Methylation Kit; then the samples were treated with a stool DNA multitarget methylation assay kit to detect the methylation levels of three target regions of stool DNA, including the genes PDX1, COL4A2-1, and FGF5, with quantitative polymerase chain reaction.

Based on the guidelines of the study protocol, a positive result was defined as a ∆Ct value (∆Ct = Ct [target gene] – Ct [GAPDH]) of less than 10 for any of the three genes (where Ct = cycle threshold in gene expression measurement and GAPDH = glyceraldehyde-3-phosphate dehydrogenase). Multiple logistic regression models for single gastrointestinal cancers were constructed, including the ∆Ct value of each gene to adjust for the tissue of origin of the gastrointestinal cancers.

Key Results

The study results showed that, overall, 98 of 124 patients (79%) tested positive for cancer, and 88 of 92 healthy controls (96%) tested negative for cancer. For each gastrointestinal cancer type, the positivity rates were 71%, 83%, 75%, 81%, and 91% for colorectal (24 of 34), gastric (19 of 23), esophageal (18of 24), pancreatic (17of 21), and ampullary cancers (20 of 22), respectively.

The researchers also found that among four positive healthy controls, three were diagnosed as advanced adenomas, and one was a pregnant woman. For the multiple logistic regression model, the sensitivity was 88% (30 of 34) for colorectal cancer, 91% (21 of 23) for gastric cancer, 88% (21 of 24) for esophageal cancer, 90% (19 of 21) for pancreatic cancer, and 95% (21 of 22) for ampullary cancer.

“The multitarget stool DNA methylation assay allowed [the] early and accurate detection and identification of tissue-of-origin gastrointestinal cancers,” concluded the study authors. 

DISCLOSURE: Funding for this study was provided by Guangdong Second Provincial General Hospital. The study authors reported no conflicts of interest.


1. Sun LY, Shen J, Zhong YY, et al: A novel, noninvasive multitarget stool DNA methylation assay for early detection of gastrointestinal cancers. 2023 ASCO Breakthrough. Abstract 41. Presented August 3, 2023.

2. Arnold M, Abnet CC, Neale RE, et al: Global burden of 5 major types of gastrointestinal cancer. Gastroenterology 159:335-349.e15, 2020.