LEADERSHIP PERSPECTIVE: Dr Sean Ennis, Chief Scientific Officer, Genomics Medicine Ireland
Interview with Dr Sean Ennis, Chief Scientific Officer, Genomics Medicine Ireland – AI and Deep Learning in Genomics Research
Genomics Medicine Ireland (GMI) is an Irish life sciences company, leading large-scale, population-based genome research studies across the island of Ireland, examining the relationship between genetics, health and disease. The company was founded in 2015, principally by 4 founding partners with the vision of transforming the quality of life for people with debilitating diseases, including serious chronic and incurable conditions, such as immune-related diseases, neurological disorders and cancer.
GMI is building an extremely powerful disease-specific database of population genomics. This will create an unprecedented capability to examine the relationship between genetics and disease, allowing GMI to discover previously unknown genetic factors, that increase individual risk of a wide variety of major diseases. These discoveries will allow much earlier identification of disease propensity, leading to fundamentally new ways of disease avoidance and prevention.
Coulter:Pulse recently interviewed Dr Sean Ennis, Co-Founder of GMI to learn more about Artificial Intelligence, Genomics Research and the role that GMI is playing in this important area of Life Sciences. Sean has life-long experience in research in medical genetics. He has led and been involved in establishing collaborative approaches to investigating chronic conditions such as Motor Neuron Disease (ALS), Autism Spectrum Disorder and, more recently, Rare Diseases. He has extensive published research studies and is a frequent speaker in the area of genomics. Sean holds a PhD in genetics from University College Dublin. He is a lecturer at the School of Medicine & Medical Sciences at UCD, Investigator with the National Centre for Medical Genetics and National Children’s Research Centre. He is director of the UCD Academic Centre of Rare Diseases (ACoRD).
Pictured here are GMI’s co-founders, Sean Ennis, Maurice Treacy and Daniel Crowley.
Coulter:Pulse – What do you see as the most promising advances in Artificial Intelligence/Deep Learning for genomics research?
Sean – First of all, I should say that I am not a specialist in Artificial Intelligence but come to this from a background in genomics research. The main advances we have seen in our area of Life Science are in terms of genome sequencing. And the most significant developments in the current age for genomics have been from genotyping to exome sequencing and now to whole genome sequencing, which is beginning to be the go-to standard for genomics. A great deal of the early work has been relatively easy to manage but as the studies scale up there may at some point be a potential bottleneck in how we handle data and how we analyse it. Many people in the space believe that things will start to creak when we get over a certain threshold, at around 20 to 25 thousand samples per study. Then we will have to start thinking about different ways of looking at and analysing data and how we can optimise the research processes. This is where my interest in Artificial Intelligence stems from.
For the sorts of population-based studies that we are conducting, there are certain analyses and certain connections that we would expect to make and prepare for, but it’s often the unexpected connections that are important and may not necessarily be obvious from a linear type of analysis. How we train machines to be able to pick out these interesting cross-disease or cross-trace analyses will be most important. It is still very early days for artificial intelligence, nevertheless and there is a lot of hype around this topic. It’s really a case of trying to distinguish what is reality or potential reality from the hype. Genomics Medicine Ireland is doing standard analysis and setting up pipelines for the future and we are also investigating how, once we get to certain thresholds, we can tackle deep learning and train computers to look at data sets and make predictions from these.
Coulter:Pulse – Please can you give us some insights into the role that GMI is playing in genomics, outlining some of the key challenges and opportunities you are facing?
Sean – From a genetics standpoint, as a nation, we are more like each other in Ireland than in other parts of Europe. Such a homogeneous population, the infrastructure of medical facilities, hospitals and clinical research centres and the relative size of the country mean that we are in quite a unique position. Ireland’s medium size means we can have significant numbers of people with a common disease that is worth researching. All these factors combine to create a unique scenario for conducting genomic research. GMI is also a Venture Capital backed private company and one of our VC backers is a sovereign fund, i.e. backed by the Irish government. This gives us a great deal of flexibility. We can advance more quickly than a public company and perhaps take advantage of new technologies like Artificial Intelligence more quickly.
We have recently kicked off two collaborative studies with the Clinical Translational Research and Innovation Centre (C-TRIC), Western Health and Social Care Trust (Western Trust) and Ulster University to undertake comprehensive, population scale genomic research studies in Northern Ireland. We are inclusive of Northern Ireland, wherever they want to be involved and there is of course a great deal of crossover in terms of ancestral backgrounds. The first two studies focus on Multiple Sclerosis (MS) and Inflammatory Bowel Diseases (IBD), lifelong chronic diseases for which there is currently no known cause or cure. The studies have launched in the Western HSC Trust with roll out planned across Northern Ireland in early 2018.
Cross border collaboration initiatives in health and research projects are increasing as we trade on the homogeneity of the Irish population but this is not our exclusive focus. We are looking further afield in terms of more international studies as well and while Ireland studies can be seen as phase 1, we’re now moving into phase 2 as we look abroad for new collaborations.
Coulter:Pulse – It would be interesting for us to know how important the “human element” is to your success in driving your business towards its goals.
Sean – Top talent is difficult to find in the field of genomics and together with Coulter Partners we have had to look far and wide to find the right people but we have been very successful in attracting exceptional leadership to the team. This is a new and very exciting project, with plenty of promise and potential. Our recently appointed VP of Bioinformatics is an excellent example of the sort of talent we have been able to attract. He is a world leading researcher in his field and we have been delighted to see the snowball effect that has followed, as others are keen to join the outstanding team we are building.
VP Bioinformatics is a senior leadership role responsible for developing and applying cutting-edge approaches to processing, analysing, annotating, and interpreting population-scale human genome sequence data. The role includes leading bioinformatic analysis and computational infrastructure setup and development, including building analytical bioinformatics applications from the ground up and managing and prioritising multiple assignments in a dynamic environment. In addition to utilising traditional bioinformatics, we can in parallel look at how Deep Learning or Artificial Intelligence may be able to take us in new directions. In this context, we are also looking at how we develop data centres and other internal facilities to be able carry out this kind of work.
With Coulter Partners’ help, we have also appointed a VP for Clinical Partnerships to our senior management, who will lead the team accountable for the development and management of relationships with multiple research partner organisations and institutions that enable GMI to meet its sample collection goals. Research partners include Universities, hospitals, and individual medics and academics operating as Principal Investigators for research programmes.
Earlier this year we also worked with Coulter Partners to appoint our Head of Legal. Genomics research requires formal partnership arrangements with our research partners. There are also vitally important matters of patient data confidentiality, so having first rate legal expertise in our team is another example of how we are building our organisation.
Coulter:Pulse – Please could you tell us about some of the defining moments in your own career in Life Sciences to date?
Sean – I have had a long career in genetics, having started straight from school, aged 17, in the field of animal genetics. I am unusual in that I have many more years in this space than most people could ever hope to have, with over 40 years of experience in genomics and genetics! I spent my early days looking at cattle, horses and sheep, researching animal blood groups and biochemical genetics. Mad cow disease or BSE and scrapie were prevalent then and I was involved in developing the first bovine genome map.
In 2000, I decided to move into in human genetics, around the time that the first full sequence map of the human genome was launched. This was like going directly from the stone age to the space age. I was involved in the rare diseases area and we set up an academic centre at UCD around this research. We were early to the field of using what was known as SNP genotyping and exome sequencing. We used a combination of these and – what was called sequence capture – to do some early studies and speculated some funds on it, without knowing whether it would work. But it paid off very well and we achieved a couple of breakthroughs in rare diseases using these techniques.
This was an important turning point and we could see the power and potential that new technologies can enable. One can spend 30 years in a field and in a matter of weeks with new technology it’s very easy to be convinced of the power of that technology. Since then we’ve done a great deal more in this field. This then led me to the idea of larger scale genomic studies into common diseases as well as rare diseases. We are still doing some work in the rare diseases area and we also have projects in the area of cancer research; we have a large-scale project on brain tumours an area where little progress has been made for many years.
It is a truly exciting field that we are in and we are now very well positioned at GMI to make progress in the projects we are initiating. It is highly rewarding to work towards finding the cause of a disease and develop knowledge that will eventually affect people’s lives for the better. I look forward to achieving a breakthrough in common diseases and to making a significant impact in improving the quality of human life.
For further information please visit http://genomicsmed.ie/