Pinpointing The Roots Of Gastric Cancer With AI

Scientists have used artificial intelligence to identify mutations in the non-coding regions of the human genome that are responsible for causing gastric cancer.

AsianScientist (May 1, 2018) – In a study published in Nature Communications, scientists in Singapore have used artificial intelligence (AI) to accurately pinpoint cancer mutations.

Cancer is one of the leading causes of death worldwide, and gastric cancer is the fourth most lethal cancer in the world. Although much has been learnt about cancer through the study of the two percent of DNA that comprise our genes, the other 98 percent, termed non-coding DNA, is still mostly unchartered territory.

In this study, a team of scientists led by Dr. Anders Skanderup, principal investigator at the Genome Institute of Singapore, used two AI methods to analyze the entire genomes of 212 gastric tumors over the span of a few months. The analysis would have otherwise taken 30 years to complete on a standard modern computer.

Using computer clusters at GIS and the National Supercomputing Centre Singapore, the analysis uncovered several new cancer-associated mutation hotspots located throughout the genome. It also provided new evidence that mutations in the non-coding DNA may cause cancer by altering the three-dimensional genome structure.

“We focused on computational and data-driven approaches to study the root of cancer so as to develop better strategies to combat it. Our findings suggest that mutations at 11 non-coding sites regulating the three-dimensional structure of the genome are staggeringly frequent. Approximately one in every four gastric cancer patients have mutations at these specific sites,” said Skanderup.

The researchers also noted that these non-coding mutations are frequent in other types of gastrointestinal cancers such as colorectal, pancreatic and liver cancer. These mutations may be used as biomarkers of the development and progression of gastrointestinal cancers.

“Sophisticated machine learning techniques such as the one developed in this study are absolutely essential towards decoding the information encoded in our genomes. If experimentally validated, these findings point towards a mechanism of cancer development missed by previous studies,” said Professor Patrick Tan, director of the Singhealth Duke-National University of Singapore Institute of Precision Medicine, who is a co-lead author of the study.



The article can be found at: Guo et al. (2018) Mutation Hotspots at CTCF Binding Sites Coupled to Chromosomal Instability in Gastrointestinal Cancers.

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Source: A*STAR; Photo: Shutterstock.
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