Supporting the future of genomics research Genome sequencing generates vast quantities of data, that must be processed, analysed and interpreted to draw meaningful conclusions, which requires a range of skills. The INTEGRATE programme provides interdisciplinary training to doctoral students, helping build a fuller picture of the relationship between genomics data and human disease, as Professor Eva Szegezdi and Dr Sandra Healy explain. The analysis of genomics data allows us to gain deep insights into the root causes of different diseases, which could in the future lead to earlier diagnosis and more targeted, effective treatments. As coordinator of the INTEGRATE programme, Professor Eva Szegezdi is working to help the next generation of researchers develop their skills and contribute to the ongoing development of the integrative genomics field. “The INTEGRATE programme specialises in human genomics, related to human diseases and physiology,” she outlines. INTEGRATE is a doctorate training programme, led by the University of Galway in Ireland, under which 20 PhD students are conducting research across a range of topics. “Some PhD students are conducting microbiome research for example, looking at what kinds of microbes live with us and how they shape our health,” says Professor Szegezdi. “We also have students looking into cancer genomics and neurodegenerative diseases.”
INTEGRATE programme This research is very much interdisciplinary in nature, bringing together elements of several different fields, including biomedicine and computational science. Genomic sequencing generates large amounts of data and analysing and interpreting it in a disease context requires both advanced computational skills and a good understanding of biology, says Professor Szegezdi. “Integrative genomics is largely a computational science, generating outputs which can then be linked to biological validation studies,” she explains. The students came from different academic backgrounds, so it was important to provide a foundation training first and address any knowledge gaps. “Some of the students had a background in biology for example, but lacked computational skills. Thus, the
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the opportunity to meet the supervisors during the first semester and chat to researchers in the lab, which helped them identify topics of interest. “The students had access to all the projects, so they were able to suss out the topics and research groups that interested them, and select their PhD project from there,” continues Dr Healy. Studying for a PhD is highly demanding, and the cohort structure of the programme has encouraged the formation of peer support networks, which Dr Healy says are invaluable in research. “It’s important not to feel isolated,” she stresses. “During the initial training period each cohort of students lived and worked together and formed really strong connections with each other, which have served them well during their PhD and beyond. Students have access to a Slack channel for technical questions for example, so they can ask for help and advice from students not only in their own cohort, but also in the cohorts that are ahead of them.”
This ultimately is about preparing students for their future careers, whether in industry or academia, and helping them find their own path. INTEGRATE itself is set to conclude in the Summer of 2026, but Professor Szegezdi and her colleagues are keen to build on the success of the programme, and are working to secure funding. “We would like to establish a new programme in the future,” she says. Further research will support the ongoing development of the field; one prominent area is genomics testing, and Professor Szegezdi believes that it will become a mainstream diagnostic tool in the near future. “Genomics testing holds huge importance in disease prevention, as it enables us to identify several risk factors,” she explains. “For example, a rare cancer might affect 10 people out of 100,000 – if we could do a genomics screen for it, we could identify people with a specific mutation. Genomics screening can identify people at the highest risk of developing a disease.”
“Integrative genomics holds huge importance in disease prevention, as it enables us to identify disease risk factors and detect people at the highest risk of developing a disease.” Career development
Changes to marks on our DNA can be shaped by both our genetic makeup and by the environment and these can contribute to our disease risk. Integrate PhD student Anna Großbach is investigating how genetic risk for disease evolves across our lifetime from childhood to late adulthood.
students all undertook a four-month training programme at the University of Galway when they started their PhD, gaining a robust foundation knowledge complementing their background knowledge,” says Dr Sandra Healy, Programme Manager for the Research Ireland Centre for Research Training in Genomics Data Science at the University, a member of the project team. The next step was then to look at how integrative genomics techniques are applied in different areas. Training was provided on the application of ‘omics techniques in cancer genomics, common and rare diseases, agriculture and pathogen surveillance, while advanced genomics data science training modules were also included. “These modules cover advanced techniques,
such as machine learning and AI. There are essentially three layers to the training – basic, applied, and advanced,” outlines Dr Healy. Once the initial four-month training programme was over, students were able to choose a research project, based at one of the five partner universities across Ireland. “We are working with 150 supervisor PIs based across the five universities, and every year they submit proposals for research projects,” says Dr Healy. “The proposals were reviewed for quality and suitability for the INTEGRATE programme, then offered to the students, who had the freedom to choose the project which interested them.” This student-led approach to project selection is a distinctive aspect of the INTEGRATE programme. The students had
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The students also spent some time outside their university on a placement, either in industry or at an international academic institution, broadening their experience in terms of sectors and countries which helps them clarify their future career paths. This is an important consideration in the programme, and as students come close to submitting, there is an increasing focus on soft skills and career planning. “There’s now more of an emphasis on areas like communication skills, network building and career development planning” says Dr Healy. Many of the students have taken the lead in this respect and taken further, personalised training, based on their own career development plans and the experiences of their peers. “A lot of our students are very driven and investigate methods outside the particular discipline they studied,” outlines Professor Szegezdi. “The students communicate with each other, make recommendations, and if there is interest, we can make courses or modules more broadly available.”
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A good example is the BRCA1 and BRCA2 mutations, which are associated with a heightened risk of developing breast cancer, and screening programmes have been established in the UK for women between the ages of 50-70. Screening programmes for other types of cancer would enable earlier diagnosis in many cases, increasing the likelihood of a successful outcome. “Cancer treatment is far more likely to be successful if it is diagnosed in the early stages,” stresses Professor Szegezdi. The INTEGRATE programme contributes to this wider goal, equipping students with the skills and knowledge they will need to identify biomarkers and develop new therapies, working across the academic and commercial sectors. “The idea is that these students will contribute to an innovative, dynamic economy,” says Dr Healy. “We have been able to build a comprehensive research infrastructure, which is part of the genomics CRT programme in Ireland.”
INTEGRATE
INTEGRATE programme
Project Objectives
The aim of the INTEGRATE Doctorate School is to advance research and training in integrative genomics, combining genomic, computational, and clinical data to drive precision medicine. Supported by MSCA COFUND and Research Ireland, it is training 20 PhD researchers in biomedical and data science through collaborations across academia, industry, healthcare, and policy sectors.
Project Funding
This research was funded by Research Ireland through the Research Ireland Centre for Research Training in Genomics Data Science under Grant number 18/CRT/6214 and by the EU’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant H2020-MSCA-COFUND-2019-945385.
Project Partners
• Royal College of Surgeons in Ireland (RCSI) • University College Dublin (UCD) • University College Cork (UCC) • Trinity College Dublin (TCD)
Contact Details
Project Coordinator, Prof Eva Szegezdi, Biomedical Sciences Building, University of Galway, Ireland. T: +091-495037 E: eva.szegezdi@universityofgalway.ie W: https://integrategenomics.eu/ W: https://genomicsdatascience.ie/
Dr Eva Szegezdi, Dr Sandra Healy, and Anna Großbach (left to right)
Prof Eva Szegezdi is Senior Lecturer in Biochemistry at the University of Galway, Director of Blood Cancer Network Ireland and coordinator of the INTEGRATE programme. Her research explores bone marrow interactions driving leukemia cell resistance to chemotherapy. Dr Sandra Healy is the manager of the Research Ireland Centre for Research Training in Genomics Data Science where she manages 100 PhD students across 5 Irish universities. She spent most of her career in Industry and academia as a research scientist before moving into research management roles. Anna Großbach is a final year PhD student at the University of Galway and an INTEGRATE MSCA fellow. Her research is investigating how genetic risk for disease changes across the life course.
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