Southampton researchers awarded over $3.3 million to advance precision medicine for inflammatory bowel disease

Researchers at the University of Southampton have secured more than $3.3 million from The Leona M. and Harry B. Helmsley Charitable Trust to develop new artificial intelligence approaches that could transform the diagnosis and treatment of inflammatory bowel disease (IBD).

Helmsley’s Crohn’s Disease Programme has committed more than $690 million to date to support impactful ideas and mobilise a global community dedicated to improving the lives of Crohn’s disease patients while pursuing a cure.

The three-year international project, ‘Catalyzing next-generation clinical and translational outcomes for IBD patients through optimization of real-world datasets,’ is led by Professor Sarah Ennis and the University’s Genetics of Inflammatory Bowel Disease Research Group. Paediatric Gastroenterologists Drs Mark Beattie and James Ashton and early career researchers Drs Alex Kadhim and Zach Green are instrumental to the Southampton team.

Working with collaborators at the Icahn School of Medicine at Mount Sinai in New York and the University of Berlin, the team will combine genomic data with information from electronic health records to support the identification of more precise, personalised diagnostics that better guide treatments for IBD patients.

IBD, which includes Crohn’s disease and ulcerative colitis, is a chronic inflammatory condition that primarily affects the digestive system. Its prevalence is rising, with projections suggesting that by 2030 around 1% of the UK population could be living with the condition.

Transforming clinical notes into data

Despite advances in understanding the genetics of IBD, many patients still face lengthy diagnostic journeys and uncertainty about which treatments are most likely to work for them.

One reason for this is that much of the information clinicians collect about patients is ‘locked’ in electronic health records.

Important details about symptoms, blood test results, disease progression and other health conditions are often recorded as free-text notes rather than in a standardised format. While healthcare records contain vast amounts of valuable data, information captured in these unstructured records cannot easily be used in research or linked with genomic datasets.

The Southampton-led project will therefore use artificial intelligence (AI) to convert these clinical notes into machine-readable data that can be integrated with genetic information.

Professor Sarah Ennis, Professor of Genomics at the University of Southampton, said:

“We now know an enormous amount about the genetics of inflammatory bowel disease, but translating those discoveries into direct benefits for individual patients remains a major challenge. By using artificial intelligence to transform medical records into structured, analysable data and combining it with genomic information, we can build a much clearer picture of why a patient is ill and what treatments are most likely to work.”

She added: “Ultimately, this is about moving beyond broad disease labels and towards a more precise understanding of each individual’s condition, helping clinicians make better-informed treatment decisions and improving outcomes for patients.”

International collaboration for patient benefit

The project combines some of the world’s most valuable IBD research resources, bringing together patient cohorts and expertise from Southampton, New York and Berlin.

Building on more than 15 years of patient recruitment through Southampton’s Genetics of Paediatric Inflammatory Bowel Disease Study, the team will draw on a longitudinal cohort of more than 2,000 patients, including over 800 children.

The project will also access two major IBD patient resources at the Icahn School of Medicine at Mount Sinai in New York: the Mount Sinai Crohn’s and Colitis Registry (MSCCR) and the Cho Laboratory Genetics Cohort (CLGC). Together, these cohorts provide large IBD patient populations ascertained from US healthcare systems, with linked electronic health records and genomic data. Together, these datasets create the opportunity to develop and validate new approaches across trans-Atlantic healthcare system.

The lead collaborator at Icahn is Dr Louis Cohen, Associate Professor of Gastroenterology. Professor Judy Cho was previously the Senior Associate Dean for Translational Genetics at Mount Sinai and the Principal Investigator of the NIDDK IBD Genetics Consortium. In August 2026, Dr. Cho was appointed to lead the US National Human Genomics Research Institute and will necessarily reduce her duties on the project but will contribute the wealth of her expertise in genetics of IBD in a Scientific Advisory role on the project.

Another key collaborating partner in the team is Professor Peter Robinson, who holds the Alexander von Humboldt Professor for Artificial Intelligence at the Berlin Institute of Health at Charité and creator of the internationally recognised Human Phenotype Ontology, which is used worldwide to standardise and describe clinical symptoms.

Together, the collaborating team will develop and test new AI-driven methods for transforming complex clinical records into structured datasets that can be used to help identify disease-causing genetic variants and support more personalised treatment strategies.

Delivering this ambitious programme requires expertise spanning medicine, genetics, artificial intelligence and digital infrastructure. The work will also be supported by the NIHR Biomedical Research Centre: Southampton and the Southampton Emerging Therapies and Technologies (SETT) Centre, as well as research software engineers and digital infrastructure specialists from the University’s iSolutions team.

Improving outcomes through precision medicine

The Southampton team has already demonstrated that combining advanced genomic analysis with detailed clinical information can reveal rare genetic disorders in patients initially diagnosed with Crohn’s disease. In some cases, these discoveries have led to revised diagnoses, changes in treatment and significant improvements in patient outcomes.

Building on previous successes in uncovering hidden genetic causes of disease and improving treatment decisions, the researchers hope this new international programme will help accelerate precision medicine for many more IBD patients in the UK, the United States and beyond.