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DNA testing predicts bowel cancer risk in people with IBD

Tim Gunn
by Tim Gunn | News

30 January 2025

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Lab-grown bowel cancer cells seen through a microscope. They are colour-enhanced and appear blue.
Human bowel cancer cells. Annie Cavanagh. Source: Wellcome Collection.

A new DNA testing method can identify which people with inflammatory bowel disease (IBD) have the highest risk of bowel cancer, according to a study by our scientists at the Institute of Cancer Research (ICR) in London. 

The team are now looking to develop their technology into a test doctors can use to improve how they intercept and prevent bowel cancers linked to Crohn’s disease, ulcerative colitis and other types of IBD. 

The approach should also ensure fewer people with IBD need surgery or regular colonoscopies to lower or monitor their cancer risk.

Understanding the links between inflammatory bowel disease and bowel cancer

Approximately 500,000 people in the UK have IBD. The most common types are Crohn’s disease and ulcerative colitis. 

Because they irritate the lining of the bowel, these conditions can sometimes cause abnormal, pre-cancerous cells to form there. 

Around 3 in 10 people with these abnormal cells will develop bowel cancer within 10 years. Before this study, there was no good way of telling who those 3 in 10 people might be. 

So, working with doctors at St Mark’s Hospital, the UK’s specialist bowel hospital, the research team went looking for clues that could help us make more accurate predictions. By comparing the DNA changes in different samples, they found that pre-cancerous cells that gain or lose lots of copies of genes (short sections of DNA which carry out specific jobs) are far more likely to develop into bowel cancer. 

Using that information, the team then created an algorithm that calculates the risk of bowel cancer based on the exact pattern of DNA changes in pre-cancerous bowel cells. 

The new study (published today in the journal Gut) shows that the algorithm is more than 90% accurate at predicting which pre-cancerous cells will develop into bowel cancer within 5 years.  

The next step is to develop the technology into a test that can be used in hospitals. 

A more targeted way to prevent IBD-linked bowel cancer

Currently, all people with pre-cancerous growths (known as low grade dysplasia (LGD)) caused by IBD are classed as high-risk for bowel cancer. 

There are two options to lower that risk: bowel removal surgery, which has life-changing side effects, or regular monitoring with colonoscopies, which are invasive and time-consuming, and can cause worry and anxiety. 

“Most people with ulcerative colitis or Crohn’s disease won’t develop bowel cancer,” explained ICR Professor Trevor Graham, the senior author on the new paper. “But for those that have these conditions and are showing signs of pre-cancer in their colon, there are some tough decisions to make. 

“Either they have it monitored regularly, in the hope that it doesn’t become cancer, or they have their bowel removed to guarantee they don’t get cancer in the future. Neither of these options are particularly pleasant.” 

When it becomes available, the new test should mean fewer people with IBD have to face that difficult choice. Those that still need to weigh up surgery and surveillance will also have much more guidance to help them do so. 

“Our test and algorithm give people with IBD, and the doctors who care for them, the best possible information so that they can make the right decision about how to manage their cancer risk,” Graham said. “We can accurately identify those people at high risk whilst putting the minds of many others at rest.” 

Craig and Farina’s story

Craig and Farina

Craig Foster, from Waterlooville, lost his wife Fariba to bowel cancer in February 2024. Fariba, who worked as a dental receptionist, had lived with ulcerative colitis since she was 18, when she had three-quarters of her bowel removed to help her manage the condition.  

“Cancer takes no prisoners and it doesn’t matter who you are or from what walk of life, everyone is affected in some way,” said Craig.  

“Fariba had managed her condition well for around 17 years with minimal hospital visits, but for the last 18 months, she’d been having a few issues. Eventually, it was decided doctors would remove the bowel completely to improve her quality of life and she had surgery last summer.  

“She went for what she thought was a routine follow-up appointment after her operation, but she was told the devastating news that she had stage 3 bowel cancer. They explained they that when they removed the remaining part of her bowel they had discovered the disease and tests confirmed their worst fears. 

“Fariba died just six months after she was diagnosed. Even though it was a short time, it was the worst time. 

“Research like this will save lives. It gives me comfort to know that there are scientists working right now so that no-one has to experience the same situation Fariba was in.” 

The power of genome sequencing

To carry out the study, Graham’s team collected samples of LGD cells from 122 people with IBD and tested them for DNA changes.

Around a third of the participants went on to develop bowel cancer over the next five years. Genomic sequencing showed that the cells in their samples had far more variations in the number of gene copies in their DNA.

The version of the test the team is now developing for hospitals will use the same genome sequencing approach to look for copy number changes in tissue samples taken during colonoscopy, the method currently used to identify and monitor LGD.

Information from the sequencing can then be fed into the team’s algorithm, which calculates risk based on specific DNA changes, alongside other information such as the size of the growth, how easy it was to remove during biopsy and how inflamed the gut is overall.

In future studies, the scientists are also hoping to develop a less invasive testing method involving a blood or a poo sample.

The Cancer Research UK view

“Treatment for bowel cancer is far more likely to be effective if you catch the disease earlier,” said Dr Iain Foulkes, our executive director of research and innovation. “Having Crohn’s or colitis is a known risk for bowel cancer, but the risk varies widely between different people, and until now we have had to take a one-size-fits-all approach to preventing it.

“Genome sequencing is now far cheaper and more widespread than ever before, and it’s changing how we look at cancer. Getting a full readout of tumour DNA means we can see a much bigger picture of how someone’s cancer started and how it is likely to change over time.

“With this research, we can focus resources on treating people with IBD who are at really high risk, saving health services valuable time and money. We can also give those at lower risk peace of mind and remove the fear of bowel cancer in the future.”

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