Filling the skills gap to advance genomic medicine: an interview with Emily Perry
By upskilling researchers on bioinformatics skills and tools, EMBL alumna Emily Perry is helping to make genomic medicine more accessible
Genomic medicine is a rapidly evolving field that harnesses the power of biological data to transform healthcare and improve patient outcomes. By analysing an individual’s genomic information, healthcare providers can develop personalised treatment and administer therapeutics for more specific targets. To find out more about this field and how data sharing can support genomic medicine, we spoke to EMBL alumna Emily Perry.
After working at EMBL’s European Bioinformatics Institute (EMBL-EBI) as an Ensembl outreach team leader, Perry started a new position at Genomics England. Here, Perry discusses new technology to enable genomic medicine and the skills she gained during her time at EMBL-EBI that apply to her new role as Research Engagement Manager at Genomics England.
Can you tell us about your current role and how it relates to genomic medicine?
Genomics England is a government-owned limited company that provides genomic services for the NHS. We started with the 100,000 Genomes Project, which aimed to sequence the genomes of cancer or rare disease patients and their families.
The goal of this was to explore the causes of these diseases and improve treatment options. As a result, the Genomics England Research Environment was created: a controlled platform where registered researchers can access whole genomes, phenotypes, and full patient hospital records. My role involves teaching and training people on how to use the Research Environment, access various data types, and perform analyses using available tools and software.
Can you tell us about what you were doing during your time at EMBL?
At EMBL-EBI, I was working as part of the Ensembl project, focusing on teaching and training researchers on how to use the Ensembl platform which provides genome data and gene annotation for numerous organisms.
My time at EMBL-EBI enabled me to develop my bioinformatics skills to better support researchers using Ensembl. My role slowly evolved into becoming an interface between the Ensembl developers and researchers, helping to bridge gaps in their understanding and communication.
At Genomics England, my role is similar in terms of teaching and training, but the data and tools are different. The main distinction is that Genomics England deals with controlled data sharing due to the sensitive nature of patient information.
How did your time at EMBL influence your career path?
When I joined EMBL, I wasn’t a bioinformatician but was hired for my ability to interface between people with different knowledge levels. Over time, I gained a broad knowledge about everything in Ensembl and even learned how to code in three languages. I also gained experience in science outreach, communication, and teaching. I learned how to break down and explain difficult concepts, making them accessible to people. These skills are invaluable in my current role at Genomics England.
How can data sharing support genomic medicine?
Open data enables researchers from diverse backgrounds to access, analyse, and build upon existing genomic knowledge. This collaborative approach accelerates the development of new diagnostic tools and treatments. By sharing genomic data, researchers can identify new genetic variants and potential drug targets. This knowledge can lead to more accurate diagnoses and the development of personalised treatments for rare and common diseases alike.
Open data also fosters collaboration between researchers, healthcare providers, and pharmaceutical companies, leading to the development of more effective treatments and therapies. Having open access to the huge range of genomic data out there encourages the development of new tools and resources, which can help address the skills gap in bioinformatics and genomics research. This can empower researchers to make meaningful contributions to the field, ultimately benefiting patients.
How are new technologies enabling work in genomic medicine?
AI is being used to help interpret genomes in the clinic, and at Genomics England, we’re also working towards AI-aided clinical image analysis. This will provide a faster and better understanding of clinical data and potentially will lead to improved diagnostic and treatment options.
Do you use EMBL-EBI data resources in your current role?
We frequently use Ensembl gene data for annotation and leverage the Ensembl open-access tools and resources for our projects. Ensembl provides quick access to genomic information and the Variant Effect Predictor (VEP) is great for determining what effect a variant – such as an SNP, insertion or deletion – will have on a gene, transcript, or protein sequence.
What needs to change to allow genomic medicine to progress?
The complexity and diversity of data sources used in genomic medicine can make these data difficult to integrate and analyse. Efforts made to improve the compatibility and standardisation of global genomic data will help with this enormously. Also, many researchers and clinicians currently lack the necessary bioinformatics skills required to analyse these genomic sequencing data. Filling this skills gap is crucial for the advancement of genomic medicine.
It’s also important to think about the ethical considerations involved in obtaining sensitive genomic data and how consent should be given. Ensuring that people are comfortable consenting to their data being used is important and for us, this involves addressing challenges related to consent from different ethnic groups and levels of education. Genomic databases are predominantly composed of data from white populations but efforts must be made to include and analyse data from people of different ethnicities to ensure that the benefits of genomic medicine are available to all.
Establishing similar projects in other countries, particularly those with underrepresented populations, will require significant financial investment and collaboration between countries and organisations. By addressing these challenges, genomic medicine can progress and become a more effective and inclusive field.
What are you most excited about in your field?
Seeing genomic medicine transition from just a concept to a real-life application that impacts people’s lives. The advancements in this field have the potential to revolutionise healthcare and make a significant difference to patient care.