DNA methylation test identifies origins of gastric cancer, other GI malignancies
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Key takeaways:
- Testing correctly identified 79% of patients with GI cancer as positive.
- Nearly all (96%) of healthy controls tested negative.
A multitarget stool DNA methylation assay accurately detected and identified the tissue of origin for multiple gastrointestinal cancers, according to study results presented at ASCO Breakthrough.
“Stool is a promising sample for GI cancer detection because it contains the host’s exfoliated cells and circulating-free DNA derived from GI cancer cells,” researcher Li-Yue Sun, MD, of the department of oncology at Guangdong Second Provincial General Hospital in China, said in a press release. “Our study aims to develop a noninvasive, multitarget stool DNA methylation test for the early detection and localization of GI cancers.”
Background and methods
GI cancers account for nearly one-third of the world’s cancer burden; however, outside of colorectal cancer, reliable noninvasive tests to aid with early detection do not exist, according to investigators.
Sun and colleagues developed a noninvasive multitarget stool DNA methylation test designed to allow for early detection and localization of GI cancers.
Researchers enrolled 124 patients (54.8% male; median age, 60 years) who had been histologically diagnosed with GI cancer but not yet undergone treatment. The analysis also included 92 healthy controls (median age, 57 years) who underwent GI cancer-related examinations every 3 years.
Researchers extracted stool DNA from the supernatant of a mixture of 5 g fresh stool and 25 mL preservative solution. Investigators analyzed methylation levels of three target regions of stool DNA — PDX1, COL4A2-1 and FGF5.
Results, next steps
More than three-quarters (79%; n = 98) of the 124 patients diagnosed with GI cancer tested positive, whereas 88 of 92 (96%) healthy controls tested negative.
An analysis broken down by GI cancer type showed the assay demonstrated positivity rates of 71% (n = 24 of 34) for colorectal cancer, 83% (n = 19 of 23) for gastric cancer, 75% (n = 18 of 24) for esophageal cancer, 81% (n = 17 of 21) for pancreatic cancer, and 91% (n = 20 of 22) for ampullary cancer.
An analysis of the four healthy controls who tested positive revealed three had advanced adenomas.
Sun and colleagues used machine learning to create multiple logistic regression models. When they combined machine learning with DNA methylation analysis, they calculated positivity rates of 88% for colorectal cancer and esophageal cancer, 90% for pancreatic cancer, 91% for gastric cancer and 95% for ampullary cancer.
“The results of this study demonstrate the promising utility of machine learning applied to genomics for detection of cancer in the future,” Peter Paul Yu, MD, FACP, FASCO, director of cancer research at Palo Alto Medical Foundation and an ASCO expert, said in the release. “These findings will need to be confirmed in a larger, prospective, multicenter study.”
References:
- Novel, non-invasive DNA methylation assay shows promise for detection of multiple GI cancers, according to new study in China (press release). Available at: https://old-prod.asco.org/about-asco/press-center/news-releases/novel-non-invasive-dna-methylation-assay-shows-promise. Published July 31, 2023. Accessed July 31, 2023.
- Sun L, et al. Abstract 41. Presented at: ASCO Breakthrough; Aug. 3-5, 2023; Yokohama, Japan.
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Sun L, et al. Abstract 41. Presented at: ASCO Breakthrough; Aug. 3-5, 2023; Yokohama, Japan.
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