Every month, one member of the TGMI team will tell us why they are so committed to the vision of the TGMI, and share a bit more about their work and interests. This week we hear from Fiona Cunningham, Variation Annotation Team Leader at EMBL-EBI.
What has been the main focus of your work to date?
I’m interested in problems where building large-scale systems for genomic data can lead to fundamental biological insights, particularly for understanding genomic variation. My team developed Ensembl’s Variant Effect Predictor (VEP), the software tool for annotating variation data. We focus on cataloguing and storing large-scale data, particular variants and phenotypes, coupled with the challenge of developing methods and tools to facilitate integration and broad access to these data. Without a catalogue and annotation of these data, understanding the genome sequence of an individual and assessing disease risk is impossible. I’m committed to the value of open data and standards, in particular to share data and facilitate the transfer of research knowledge into valuable resources.
What are you most excited about in genetic medicine?
It is an extremely poignant time to be working in genomics. Finally we can see the results of the Human Genome Project and subsequent research coming to a point where we can make real differences to medical treatment in an unprecedented manner. This can have a direct impact on individual lives, which is incredibly exciting and powerful.
What are you most concerned about in genetic medicine?
My concern is how little we currently understand. There is huge potential for positive change but there remains plenty of basic research required to comprehend how the genome works. In turn this will lead to improved foundational resources for genomic research and medicine, provided there is funding available.
Why did you get involved in TGMI?
With the cost of sequencing reducing, we can start to use sequencing technologies at greater capacity in in the clinic, which is really exciting. Most genomic research has produced tools and data that are best suited to the research environment, rather than a clinical one. The requirements are different. I’d like to understand these and be a part of facilitating the transition between the two.
What is the most important thing that you would like the TGMI to achieve?
I’d like TGMI to drive forward and consolidate existing resources to make them more used and effective, to develop and promote adoption of improved standards that result in genomic medicine being more accurate and efficient, especially in a healthcare setting.
If you had a magic wand (i.e. unlimited people/resources) what would you do to make genetic medicine work?
If we could do a ton of -omics on people, safely store and exchange the data in a standard and interoperable manner worldwide, know which transcripts are expressed when and in which tissues, understand how genes are regulated and interact, then I think this would be a good starting point. We’d have to know how to make sense of the data too.
Do you have a favourite gene? If so – what and why?
As my work has been with DNA variants for over a decade, I have favourite SNPs – there are also more to choose from! For example rs1426654 is associated with skin pigmentation. The A allele is associated with fair skin and the ancestral G with darker skin. The non-ancestral A is in the reference genome and the population frequency distributions are dramatically different across the world. It makes for pretty pie charts in Ensembl. The other is rs182549, which is located in the intron of the MCM6 but influences the lactase LCT gene. If you have the more evolutionary recent T allele, this allows you to continue to digest lactase so enjoy drinking milk.
What is a surprising fact that few people know about you?
A few years ago, I was convinced to go for a brief swim in the icy waters off the coast of Antarctica. It was in sea water by Paulet Island surrounded by icebergs, so the water was below 0 degrees and pretty chilly. After this it has become tricky to moan that any sea water is too cold for a trip to the beach!
If you had a chance to experience a completely different career for a week, what job would you try?
If I could also make a beautiful sound, I’d love to be able to sing a fabulous soprano aria in an opera house, or play Rachmaninov’s 2nd piano concerto, backed by an orchestra.