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Genome of Europe, a European scientific initiative, commenced in recent weeks with the goal of making the genomes of at least 100,000 Europeans shareable as a reference cohort to scientists across the region. The participants sequenced to create the Genome of Europe will be selected to represent the population groups that live in Europe, and the data will be used to tailor personalized medicine, such as polygenic risk scores, for people of different ancestries.
Genome of Europe – building a Pan-European Genomic Database
Estonia will play a role in the Genome of Europe initiative by contributing genomic data that is representative of its own population, but also by spearheading related communication efforts, to gauge and improve knowledge of genomics and personalized medicine among Europeans.
The 100,000 genomes that will be sequenced as part of the Genome of Europe project will contribute some of the genomes needed to achieve the aims of the 1+ Million Genomes Initiative, a pan-European effort that began in 2018 with the goal to sequence 500 000 new genomes to make more data accessible to researchers. By pooling genomic data, European researchers hope to be able to gain more insight into the ways that genetics influences common and rare diseases, as well as to identify ways in which individuals might reduce their risk for developing conditions later in life.
“We have too many patients and not enough doctors,” said Andres Metspalu, a geneticist and professor of genomics and biobanking at the Institute of Genomics at the University of Tartu. “This is why we need prevention.”
Metspalu played an integral role in promoting the idea for and organizing Genome of Europe. The project is related to achieving the objectives of the 1+ Million Genomes initiative, the declaration for which has been signed by 27 countries since 2018, but also associated projects, Beyond 1 Million Genomes (B1MG) and the European Genomic Data Infrastructure (GDI).
B1MG ran from 2020 through 2023 with €4 million in funding from the EU’s Horizon Europe program. The project developed guidelines on how to best implement the 1+ Million Genomes initiative, including recommendations for building a federated network of genomic data in Europe. GDI is a larger project with a budget of €40 million that commenced in 2022.
The goal of the GDI is to support the deployment of the technical capacity for accessing genomic data. This will allow countries that do not have the resources established for genomic data sharing to invest in and build their own nodes to do so. Estonia, with its long-established biobank, has been investing in developing such architectures since the launch of its genome project in 2000.
According to Metspalu, Genome of Europe represents the “third leg of this stool,” along with B1MG and the GDI. Backed with €45 million in funding, it will establish a pan-European reference database consisting of newly generated whole-genome sequences representative of the entire European population.
Ensuring diversity and ethical standards in genomic research
At least 40 subpopulations of different ancestral backgrounds will be included, Metspalu noted, which should provide for the inclusion of historically underrepresented populations in future clinical genetic studies. The University of Tartu for its part will sequence 368 individuals, 268 of whom are ethnic Estonians and 100 ethnic Russians. Ministry of Social Affairs is covering the half of the cost and EU is paying the other half.
“The goal is maximum heterogeneity,” said Metspalu. “By involving as many minorities living in Europe as possible, we can ensure the best possible access to medicine for all European citizens in the future, irrespective of their origin.”
In total, 49 partners from 27 European countries are involved in the Genome of Europe project. The European Commission is covering half €20 million of the €45 million budget through its Digital Europe Programme, while national governments will contribute the remaining funds.
André Uitterlinden, a professor of complex genetics from the Erasmus University Medical Centre in Rotterdam, the Netherlands, is Genome of Europe’s coordinator. The project is expected to conclude by early 2028.
Genome of Europe has numerous goals. These include creating a community to support the reference genome project, assessing different sequencing platforms for future use in personalized medicine, and addressing questions around ethics, data security, and compliance.
“This project will be guided by ethical, legal, and societal considerations while upholding stringent data security standards,” Metspalu noted. “It will build international guidelines for the responsible use of whole-genome sequencing that leads to better healthcare for EU citizens.”
Resulting data will be embedded within the infrastructure established by the GDI, so that it is interoperable and accessible to participating researchers. There will also be impact studies. Through such case studies, the researchers will examine the project’s contribution to understanding diversity, enabling multi-ancestry imputation, and enhancing genetic risk profiling.
Advancing imputation and public understanding in genomics
According to Metspalu, being able to impute an individual’s data from a smaller dataset is key. Whole-genome sequencing will provide a thorough look at the genomic diversity of individuals from certain populations. It’s too costly to sequence the genome of every indvidual and less expensive genotyping arrays are used to provide genome-wide data instead. However, based on data generated by arrays, scientists can estimate or impute what other variations they carry by referencing the whole-genome sequencing data of people of the same ancestral background.
While genetic variation between, say, Northern Europeans is not always so divergent to skew the results of a polygenic risk score designed on Northern European cohorts, such scores might not work as well in individuals with Middle Eastern, Asian, or African backgrounds, for example. Here, having access to a population reference database will allow researchers to design more specific tests, and to adjust the tests that exist, to improve their performance across the board. Such data also can factor in drug metabolism, for example, and better understanding a patient’s genetic diversity could help to better select therapies for diseases using pharmacogenomics.
“Through imputation we can get data that will help prevent and treat disease,” Metspalu stated.
In fact, Metspalu said that this need for better polygenic risk scores and pharmacogenomics panels spurred him to push for the new Genome of Europe project. “I saw that more data was needed, and that we would need a pan-European database for imputing results,” he remarked.
For its part, the University of Tartu will also be tasked with communicating the project to Europeans, so that they understand and see the value in the undertaking. “Sequencing is easy,” said Metspalu, “but we need to communicate it.”
He said that, on average, knowledge of genetics has risen in Europe, but some countries tend to be more skeptical than others and some have better knowledge than others. “This is what we will be working with,” said Metspalu.
Advancing sequencing and breast cancer prevention
Of the approximately €560,000 allocated to the University of Tartu for the Genome of Europe project, about half will be used for sequencing individuals and the other half to support outreach activities, Metspalu said. This will include an international survey to gain more insight into the level of genetic knowledge and attitudes of European citizens towards personalized medicine and the project itself.
Metspalu added that genotyping data is already available for 20 percent of the Estonian population, and that the country is moving forward with plans to use polygenic risk scores to improve breast cancer prevention. Next year, Estonia will launch a prevention program based on genetic information to encourage women with a high polygenic risk score for breast cancer to seek mammography screening 10 years earlier than the current suggested age for first screening.
“Similar programs have the potential to become accessible to all European citizens in the future thanks to the reference genome database established through the Genome of Europe project,” he said.
This article is written by Justin Petrone. This article was funded by the European Regional Development Fund through Estonian Research Council.
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