Changing the lives of people with inflammatory bowel disease

Posted on: October 30, 2019 by Natalia Jiménez Lozano

Among the most exciting things we do at Atos is to help accelerate cutting-edge research. A prime example of this has been work kicked off by a research team at the 2018 BioData Hackathon. This looks set to create a new way for people suffering from digestive-related health problems to monitor their own microbiome in order to access effective treatment and advice.

Grand challenge

In July 2018, the biodata hackathon was held at the Wellcome Genome campus in Hinxton, near Cambridge in the UK. This two-day event was a special opportunity for 111 of the brightest and best hackers to work creatively and collaboratively to find ways to offer real-world benefits to people in the sphere of genomes and biodata.

As sponsors of the hackathon, Arm, Marvell and Atos were invited to set one of five Grand Challenges for the hackers to address. The challenge we set was: ‘How can we use mobile technology to transform biological data processing?’. In particular, we wanted participants to explore the convergence between high performance computing (HPC) and artificial intelligence (AI) to process and extract insight from genomic information.

17 judges from academic and research institutions, business angels and CEOs of leading health tech companies decided the winners for each challenge. I’m delighted to say that the winners of ours were Team GoGut, with a pioneering mobile device for people suffering from digestive-related health problems to monitor their own microbiome.

Challenges of living with inflammatory bowel disease (IBD)

Millions of people suffer from ongoing digestive-related health problems; IBDs , for example, can be difficult to live with and are often misdiagnosed. Yet the correct early intervention can significantly improve patients’ quality of life and reduce healthcare costs, hospitalization and surgery rates.

This is where new clinical research combined with advances in computing transform what is possible. With studies suggesting that changes to gut microbiota may be a cause of IBDs, monitoring and measuring a person’s gut microbiome could offer a powerful non-invasive way of better understanding IBDs and the efficacy of different treatments. Thanks to recent developments in genome sequencing technology and edge computing, there are new opportunities to study, diagnose and treat IBDs out of the lab.

Team GoGut: genome sequencing on a mobile device

Team GoGut came up with a device that enables the constant monitoring, diagnosis and management of IBDs in the comfort of patients’ own homes. A next-generation portable sequencer is attached to a mobile device, with integrated HPC ‘at the edge’. As this is augmented with AI analytics, it can quickly respond to downward trends or identify positive stimuli; this enables patients and their clinicians to assess the disease, then monitor its progression and how different treatments are working.

Analysis of all this data could be used to make recommendations on lifestyle, diet or medication changes based on reactions observed in patients with similar microbiome profiles. As more and more patients use the device, more and more data could be collected and analyzed, making diagnoses and recommendations even more powerful.

What next?

The next stage of development is to further test the solution using the most advanced HPC platform in Europe. This is in collaboration with Arm, Atos and Marvell on Mont-Blanc, a series of projects to investigate and develop new processors for HPC based on European technologies.

As part of Mont-Blanc, Atos has built a new Arm-based prototype called Dibona, which will be used to move Team GoGut’s idea to the next level. Dibona is the first commercial Arm-based HPC system in the world and is available to Mont-Blanc partners and end-users to test Atos’ software and scientific applications on a state-of-the-art Arm architecture.

I look forward very much to seeing the next stages in development for Team GoGut and their work, which is helping to create a healthier future and a better quality of life for people all over the world. And if you want to read more about this story, please read our paper.

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About Natalia Jiménez Lozano
Director, Atos HPC, AI & Quantum Life Sciences CoE, Distinguished Expert and member of the Scientific Community
Natalia has a MSc in Biochemistry and PhD in Molecular Biology. Working in life sciences and technology since 2012, following 14 years in bioinformatics research, Natalia’s contributions have already been profound and significant. Having pioneered the development and application of the Precision Medicine model and since seen her vision realised in frontline care, in 2020 she achieved her dream of opening the HPC, AI and Quantum Life Sciences Centre of Excellence in Cambridge. She has been instrumental in starting a new chapter for Atos, partners, and customers to accelerate innovation to improve health outcomes and wellbeing of people worldwide.  

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