Scallop - A Tryggve use case on analysing genetic and medical data
The study of the human genome is undeniably an essential part of understanding health and diseases. Imagine that you had access to genetic and medical data from thousands of patients with various medical backgrounds, but you lacked an adequate way to work with the data across borders – what would be the solution?
This was the case for Scallop, now a use case in NeIC’s Tryggve project. The Scallop Consortium was established to create a cooperative framework between research groups, with the aim of exploring what the human genome can tell us about the links between protein levels and illnesses. In June 2016, the consortium joined the Tryggve project, which enabled them to surmount the barriers to sharing of medical data across borders.
“Scallop is about mapping the human genome for parts that affect the proteins that float around in our body,” explains Lasse Folkersen, “because all these proteins may potentially be what is making people sick or healthy. Although we know a lot about the proteins and the mechanisms of the body, we don’t know everything.” Lasse Folkersen is a leading scientist at St. Hans Hospital in Copenhagen and he works as the lead analyst for the Scallop Consortium. He explains that the point of the project is to use genomics data to create beneficial health solutions that can be applied in practice.
“In this specific project we have many different researchers around Northern Europe and particularly in Scandinavia who have seen this question coming and have been taking relevant blood samples. Before the consortium was created, there were 10-15 separate groups around Northern Europe who had these kinds of data.” The groups created the consortium to be able to work together and merge their existing data, which gave them a stronger evidence base for finding out what parts of the genome match different proteins. Folkersen adds that this can eventually reveal which proteins may be the drug targets of the future.
Secure sensitive data collaboration
As DNA samples can reveal unknown health conditions about patients, the data is highly sensitive, Folkersen explains. “When it comes to clinical data, the stakes are raised. Then you can say that DNA sets the bar even higher here, because it is one of the most personal things you can think of. It is completely unique to you and that’s why we try to do everything we can to make it secure.” Without the opportunity to provide access to the sensitive data across borders in a highly secure manner, the research would lose its credibility. The research will be neither possible nor ethical unless patients are guaranteed that their information is protected.
So how does Tryggve help ensure that the data is secure? Tryggve facilitates and develops access to secure e-Infrastructure for data, which allows Scallop to host its large-scale biomedical research in a secure environment. One of the key elements to this is creating a system where data can be processed, but never downloaded. Folkersen points out how this allows everybody to contribute without relinquishing control of their own data.
According to Folkersen, even though the consortium had already been established, with all the data they needed at hand, without Tryggve’s support the barriers to processing health data would have made the project infeasible. “I think Tryggve has been the complete enabler, without it I don’t think we would have set up this at all,” he states. Tryggve has provided access to the Danish National supercomputer – Computerome, that offers a secure private cloud environment for sharing the 25,000 samples between countries. This support has been invaluable. The variety in national legal restrictions on health data makes it challenging to navigate, and taking risks is not an option, Folkersen says. What helps to make the use case a success is that Tryggve sets the bar higher. “That is a core motivation for Tryggve because we understand and want to handle these security concerns. Now we have this secure space that exists by all the security standards and that is updated to cutting-edge standard.”
Being a use case in Tryggve has given Scallop new opportunities to be a fully international and Nordic research project. When asked what the consortium would look like without Tryggve, Folkersen says that the most likely scenario would be a more dispersed and less connected project. He also emphasises that the technical skills provided by Computerome personnel at Tryggve are not easy to find elsewhere. “I think that’s the key, right? I don’t know how to create that kind of server, so the support we are getting from Tryggve is essential,” he points out.
Although the project is still in the early phases, Folkersen is clear that they already have great expectations for the future. “I feel Scallop is getting pretty successful now, we have gathered samples from over 20 000 people and that is the biggest study of this kind that exists.” The sheer size of the project is unique in this field of research, and the key element of the success so far is that patients, funders and researchers trust the system in place. “I like to think that the reason many different research groups have chosen to trust in the system, is because they feel confident that data are handled in a good manner and they can look their patients and volunteers in the eye and assure them that the data are secure.” The data are already giving hints about how protein regulation functions and Folkersen sees the next stage as bringing new answers to whether the proteins we are sharing are actually causing diseases.
Scallop is only one of several use cases receiving support from Tryggve that benefits the users and gives Tryggve an opportunity to test the systems developed. Collaborating with the national providers in the Nordic countries makes the storage, analysis and sharing of sensitive medical data legal, ethical and secure. Tryggve continuously facilitates cooperation across the Nordics, which is particularly advantageous for research consortiums such as Scallop. “The Nordics are traditionally good at bio-bank research because we have things in order here, with good infrastructure and a high level of regulation. This makes it easier to create a Nordic collaboration here,” says Folkersen
Tryggve is the name for the Nordic collaboration for sensitive data funded by NeIC and ELIXIR nodes of participating countries. Tryggve develops state-of-the-art scalable infrastructure for safe, efficient, ethical, and legal storage, analysis and sharing of sensitive personal data for biomedical research between countries. The outcomes of the Tryggve project will enable researchers to conduct their research utilising sensitive data in secure settings and facilitate Nordic collaboration in biomedical research.
NeIC continues more than 10 years of Nordic collaboration on e-Infrastructures. It works to accelerate the development and provisioning of cost-effective, best-in-class eInfrastructure services beyond national capabilities. It is a distributed organisation consisting of technical experts from academic high-performance computing centres across the Nordic countries.
The National Life-Sciences Supercomputing facility in Denmark “Computerome”
Computerome is the Danish national infrastructure for health care and life sciences as well as representing as the Danish infrastructure in Elixir and NordForsk since 2014.
More information: http://computerome.dk/