The Accelerating Medicines Partnership® in Common Metabolic Diseases brings together researchers from multiple institutions to work towards the goal of better understanding and treatment of common metabolic diseases. Get to know the members of the consortium in our CMDKP Spotlight articles.
Dr. Aoife McMahon (ORCID: 0000-0003-0978-0309), a member of the AMP® CMD Portal Team, is Project Lead for the Genetic Data Platform at the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus in Cambridge, UK.
Aoife's scientific background
After completing a Ph.D. in mouse neurobiology and a postdoc in Drosophila circadian/RNA biology, Aoife knew she didn't want to go the academic tenure track route, but still wanted to keep "doing science". She had a guiding interest in how genetic diversity manifests itself at multiple levels, from transcription all the way to the population level, and was looking to upgrade model organism again--this time, to human. She came across a job ad for a role she had never heard of before (Scientific Curator), but was interested in the project, which aimed to improve genome transcript annotation for the clinical reporting of genetic variants. She gave it a try and was immediately taken by the EMBL-EBI philosophy of open, interoperable data and working in a team to improve the foundational infrastructures that many scientists rely on.
Current research interests
Rather than doing research per se, Aoife describes her role as "science as a service". EBI's primary focus is on providing tools and resources to the global scientific community, with an emphasis on open data and data reuse. At the EBI, Aoife has contributed to a range of resources related to how human genetic variation contributes to health and disease. These resources allow genomic and clinical scientists to find, access, interrogate and share data. For example, the NHRGI-EBI GWAS Catalog and the PGS Catalog are, respectively, catalogs of human genome-wide association studies and polygenic scores. The Catalogs provide researchers with findable standardized representations of published works linked with the open datasets, which can then be reused and subjected to downstream analysis--for example, in the CMDKP.
EBI also contributes to the development of global bioinformatics standards, which are key to data sharing. An illustrative example is the Matched Annotation from NCBI and EMBL-EBI (MANE) initiative, a collaboration with RefSeq colleagues at NCBI has produced a default transcript for every protein-coding gene in the human reference genome, which is flagged for use as a universal standard. Having access to this standard annotation is of vital importance in a clinical setting where precise reporting of small genomic variations will help to streamline medical interpretation of genomic data.
As well as contributing to the CMDKP, Aoife is also part of the INTERVENE consortium, where her team is building a platform to allow users to apply polygenic scores on their own data.
Reflections on AMP-CMD and the CMDKP
The main role of Aoife's team is to enhance the data content of the portal. They identify and process datasets of interest that can be incorporated into the integrative analyses that the portal provides. From an institutional perspective, they bring expertise in the provision of infrastructure delivery at scale, including on data harmonization. In AMP-CMD, they also bring a non-US perspective to the table.
Asked what makes the AMP-CMD program special and how it feeds back to her own work, Aoife replied "It's really great to see the confluence of a diverse range of experts (disease domain specific, genomic, statistical, software, etc., etc.) working together to integrate and display multiple data types, and ultimately glean knowledge from data. Contributing to the portal really helps us examine the requirements of data integrators, and we can use these valuable insights to improve our processes to ultimately better serve the scientific community."