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Estonian Genome Center to Genotype 35K Biobank Samples With Illumina Global Screening Array


TARTU, Estonia (GenomeWeb) – The Estonian Genome Center has selected Illumina's Global Screening Array to genotype 35,000 samples in the country's 52,000-sample biorepository. The center, which is seen as a bellwether for integrating genomic information with electronic medical health records, will use the data to inform efforts to prevent chronic, common diseases.

According to director Andres Metspalu, the center has previously genotyped roughly 15,000 samples using various Illumina arrays. It also recently carried out in partnership with the Broad Institute the sequencing of 2,500 whole genomes, plus an additional 2,500 whole exomes in collaboration with Nestle Health.
"By combining the deep sequences and genotype data, we will be able to impute rare variants for all individuals and investigate their effects in the rich health records of the participants," Metspalu told GenomeWeb during a recent site visit.
The center recently received €1 million ($1.1 million) through the Estonian Ministry of Education and Research to carry out the genotyping of the remaining 35,000 samples in its biobank. Researchers hope to combine that data with the country's e-health online database of medical records to develop tools for disease risk prediction, ultimately leading to better informed prevention and treatment decisions.
"For all biobank participants, we are extracting more and more disease diagnoses and drug prescriptions from the database of the Estonian Health Insurance fund," Metspalu said, noting that Estonia has a single-payer healthcare system. "This allows us to search for associations between genetic variants and their effects on drug response among individuals who have been prescribed specific drugs," he said.
Lili Milani, a senior research fellow and head of the center's sequencing and genotyping core facility, said that investigators will use the data generated and existing electronic medical records to design risk score predictions that will be validated using the biobank.  
"We have people who were healthy when they joined the biobank and then developed disease later in life," Milani told GenomeWeb. "That is something we get from extracting their health records," she said. "Then we can validate whether our genetic risk scores improve the prediction of who will get sick and who will not."
In tandem, the biobank is serving as a resource for the country's new Personalized Medicine Project, overseen by the Estonian Ministry of Social Affairs, which is set to commence next year. "We will start using these genetic risk scores and recontact those at high risk for disease," said Milani. "For example, if they are at high risk for cardiovascular disease, then they will receive statins, counseling on lifestyle, diet and so on for disease prevention," she said.
By the end of the project, the center hopes to have developed different tools for decision making in the clinic, including decision support software. Researchers will also compare the new genomic methods to standard care, to see if their prevention methods have a positive impact.
"The biobank is central to Estonian genome research," said Metspalu. "What we are doing is feeding into personalized medicine, which is mostly e-health, but using genomic data, which has never happened before," he said.
Illumina rolled out its Global Screening Array earlier this year. Using the product, nicknamed the GSA, customers can screen 24 samples per chip, he said. Each array contains 660,000 markers covering 26 populations, including about 50,000 markers specific to clinical research. Customers can also add up to 50,000 other markers relevant to their studies.
Peter Fromen, managing director of population sequencing initiatives at Illumina, said that the GSA has performed well, with the company seeing "very high volumes" in orders for association studies, population studies, and consumer genomics.
The deal with the Estonian Genome Center, though, is significant for the company, as it sees Estonia as a "model for how health systems can incorporate genomics into the clinic," Fromen told GenomeWeb.
"The richness of phenotypic information of participants in the biobank is definitely a bellwether example," said Fromen, who moved to the UK two years ago to better liaise with Genomics England, an Illumina partner, and other population genetics efforts in the region.  
"The breadth of information at the patient level on healthy individuals as well as patients across the population represents the prototype for best-in-class today certainly," Fromen said. "They have been exceptionally progressive in terms of thinking about how to manage the healthcare needs of a population by leveraging genomics and linking it to phenotyping data sets," he added.
Eric Lander, president of The Broad Institute of Harvard and MIT, similarly lauded the center's efforts during a visit two years ago, calling its activities "the cutting edge of what is possible." The Broad later carried out the whole-genome sequencing of 2,500 samples from the biobank.

Milani said that the center has already engaged some individuals whose genomes were sequenced and were found to carry high risk genetic variants as part of pilot projects. "We have a team of researchers, including a medical geneticist and a genetic counselor that are calling them back, taking a second sample, validating the finding, and then giving them genetic counseling based on confirmed findings with high impact," she said.  

"I think we are one of the first biobanks in the world where people really get some clinical advice," Metspalu said. The practice stands in contrast to the Icelandic experience, where debate continues about alerting biobank participants who may have potentially risky genetic profiles.

According to Metspalu, the current round of genotyping is only the first phase of what the center sees as a three-phase project lasting well into the next decade. In an envisioned second phase, the center will collect and genotype 100,000 samples per year between 2018 and 2020, while it will continue to genotype 12,000 samples each following year, working toward a goal of having much of the 1.3-million-person population of the country genotyped. All of this is subject to available funding.

He and Milani sought to distinguish the Estonian effort from other population genetics efforts in the UK, France, and Switzerland, which he said are focused on rare diseases and cancer, rather than chronic common diseases, like cardiovascular disease and diabetes, that can be prevented.

According to Fromen, other groups in the region are looking to Estonia as an example. "There are groups in the UK that are certainly interested in thinking of how they would introduce genotyping information linked to phenotypic information captured by electronic health records into a clinical setting to establish that baseline level of genomic information at the individual level," he said.

Moreover, he said that Europe has maintained a philosophy to deploy genomics to manage health care, which he called a "noble goal," though one driven by economics and utility. "I think Europe is a natural region to deploy programs like this," said Fromen. "But it's not just happening here," he noted. "We are seeing this in the US, Australia, Japan, Korea, and Singapore," he said. "It's all part of a global trend where nations are determining how to deploy genomic medicine within their healthcare systems."