Bolstering Pandemic-Afflicted Research with Big Data
The pandemic may have hampered research and collaboration, but it offered opportunities for exciting new projects on readily available datasets like the UK Biobank.
Thomas Dinneen joins us from Trinity College Dublin, where he has just completed his PhD studies. His research focused on uncovering the genetic reasons for the variable cognitive and neurodevelopmental outcomes of carriers of copy number variants associated with neurodevelopmental conditions. At Maynooth University, he is a research assistant working on the SFI-SIRG project “Discovery to clinical utility of rare mutations by whole genome sequencing in neurodevelopmental conditions”.
As part of his PhD studies, Thomas worked on the UK Biobank, one of the world’s largest, biomedical research biobanks. Here is a blog post he wrote about his experience of running a UK Biobank workshop for researchers based on the island of Ireland.
Running my first academic workshop during a pandemic might have seemed a bit far-fetched, but it was more successful and rewarding than I had hoped. Here is my experience in developing and delivering an online workshop during the COVID-19 pandemic.
The COVID-19 pandemic completely changed how we interact, work, and participate in research. In 2020, most non-essential health research was completely shut down, with no access to labs, no means to collect new data from participants, and no in-person meetings. While the research questions and challenges remained unchanged, how they could be investigated had.
However, researchers were quick to adapt to this new research landscape. Meetings and conferences were moved online, research protocols were altered to fit with lockdown measures, and there was a refocus on readily available datasets as alternative avenues of research, e.g., using biobank data. But these changes did not mitigate all of the pandemic disruptions, and some research stalled entirely.
While working with large-scale biobank data is an excellent alternative to stalled lab-based experiments, for many, this is impractical due to a lack of expertise and confidence to work with big data.
A Big Data Workshop?
Recognising this problem, I ran an online workshop with my colleagues at Trinity College Dublin and Maynooth University on using the UK Biobank for health research based in Ireland. It aimed to help those seeking alternative datasets, establish new collaborative projects, and encourage the use of the UK Biobank in Ireland.
The UK Biobank (UKB) needs little introduction. It is one of the largest biomedical research cohorts in the world, with deep genetic and rich phenotypic data on over 500,000 participants. Over 20,000 researchers use the UKB worldwide, and over 1,800 peer-reviewed papers have been published using the dataset. For a country like Ireland, which does not have a population biobank, the UKB is a reasonable alternative. Ireland is demographically similar to the UK in many ways, and around 10% of the cohort is of Irish descent. Despite this, there was sparse use of the resource here in Ireland. Given this underutilisation of the UKB and the pandemic, it was an opportune time to run a workshop.
Our agenda for the day was first to provide talks from experts on using the UKB, a thesis-in-three session for PhD candidates working with UKB data and a collaboration session for all workshop participants. I pitched the workshop to the UKB, who was immediately interested and generously funded it. They also agreed to send a representative to introduce the UKB and its plans.
On the day
The workshop took place online on the 21st of May 2021. One hundred twenty-four researchers, from PhD candidates to Principal Investigators, registered, and there were 92 attendees on the day. It was open to researchers based on the island of Ireland from a mixture of biomedical research, computational biology, biostatistics, and data science backgrounds. They came from ten higher education institutions, some from the biomedical private sector. (Figure 1.)
Figure 1. Research locations and fields of workshop attendees. DCU = Dublin City University; MU = Maynooth University; NUIG = National University of Ireland Galway; QUB = Queen’s University Belfast; RCSI = The Royal College of Surgeons in Ireland; TCD = Trinity College Dublin; TUD = Technological University Dublin; UCC = University College Cork; UCD = University College Dublin.
I invited speakers from various biomedical research fields who gave thorough overviews of the UKB and expert advice on conducting analyses. Six PhD candidates gave thesis-in-three presentations displaying the diversity of projects ongoing in Ireland. The collaboration session was the day's highlight, with eight teams of 4-5 researchers from mixed research backgrounds participating. The teams had 20 minutes to develop a UKB project idea that incorporated the skills of each team member, and a UKB expert judged the projects. A fantastic outcome was that the winning team of the collaboration session were inspired to follow up with their project idea.
The workshop established a new research collaboration and led to the submission of several project ideas for approval. Attendees provided very positive feedback of the day, with one PI saying that he was “delighted and impressed with the workshop”, and he is now encouraging his students to apply for the UKB. 13 attendees added they would apply for UKB data after attending the workshop.
On a personal note, organising and leading this event as a PhD candidate was very daunting, but the experience was invaluable. Co-ordinating all this was certainly no mean feat and tested my organisation, communication, and time-management skills. Not to mention the additional challenges in hosting a large workshop online. However, the encouragement and direction from my supervisors, help from colleagues, support from the UKB, the fantastic talks of the speakers, and the enthusiastic participation of attendees culminated in producing an informative, productive, and enjoyable workshop.
The UKB and other biobanks provided a lifeline for health research during the pandemic. Whether that was to provide a final chapter for a PhD thesis, establish new collaborations or generate pilot data for a research grant. This workshop showed that big data biomedical cohorts could bolster health research, even during a pandemic.