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Finnish Researchers, Pharma Partners to Genotype 500K Samples as Part of New €59M Study


NEW YORK (GenomeWeb) – Perched at the Northeastern edge of Europe, Finland has long been known for its first-rate Nordic healthcare system as well as its genetically isolated population.

Now, researchers from the country have decided to take advantage of both by partnering with multiple pharmaceutical companies to genotype 500,000 samples collected through the nation's biobanks.

The project, dubbed FinnGen, was announced this week and is slated to run through mid-2023. It has a budget of €59 million ($70 million) and is being coordinated by the Institute for Molecular Medicine Finland (FIMM) at the University of Helsinki.

Aarno Palotie, research director at FIMM, said that FinnGen was inspired by similar national efforts, such as the Estonian Genome Project in neighboring Estonia, as well as the UK Biobank, which, with its repository of 500,000 genotyped samples, he deemed the "poster child" for all biobank initiatives.

"The trend has been for years that we need larger amounts of samples to understand the genetic background of complex diseases," said Palotie. "Finland has a special opportunity due to the Nordic Healthcare Registries Data and also the genetic isolate structure," he said.

That concept, of tapping into centralized electronic health records with the country's unique genetic heritage, had been in discussion for years. Ultimately, according to Palotie, FinnGen's instigators opted to pursue a public-private partnership, bringing in support from seven pharmaceutical companies: Abbvie, AstraZeneca, Biogen, Celgene, Genentech, Merck, and Pfizer.

Tekes, the Finnish funding agency for innovation, is investing €20 million in FinnGen, while the project's pharma participants will cover the rest of the €59 million budget in roughly equal amounts, Palotie said.

"This is a precompetitive research cooperation," said Palotie of pharma's interest. "They need to have these types of resources," he said. "It provides them with a larger data background where they can do genetic analysis or [from which they can] retrieve genetic data. That is their interest."

Andrew Peterson, a principal scientist of molecular biology at Genentech, part of the Roche Group, said that as part of the project Genentech scientists will be involved in determining strategies for genotyping, creating structures for data handling and analysis, and helping to design clinical endpoints from the available raw data sources that describe disease state and treatment.

"We are eager to fully participate in all of these aspects so as to understand the disease associations that will be found," Peterson said. "Only by fully understanding the process and the findings will we be able to make use of this information in drug development."

The value for Genentech will come from gaining more insight into genetic associations with disease, Peterson said. He said that combining Genentech's internal data with that from FinnGen will be "critical for the success of drug development" and was a "significant reason" that the company selected to participate.

According to Peterson, two levels of analysis will be undertaken in FinnGen, "standard analyses" that will be carried out in a centralized fashion with the results available to all of the partners and internal analyses that will be done by partners using their own tools and perhaps additional proprietary data together with the FinnGen data. "The results of the bespoke analyses are private," he said.  "We will be participating by helping to design the standard analyses and by carrying out our own bespoke analyses."

Peterson noted that the project is being initiated in a transformative period for pharma, one where companies are moving from an "era when cell culture and animal models provided the most important information for decision making, to an era where information about human biology and the effects of genetic variants provide the critical insights.

"This is an enormous shift and profoundly valuable," he added.

Peterson noted that Genentech will continue to invest in projects like FinnGen with "an eye to maximizing our ability to use human biology and genetics in decision making."

While participating pharma companies' internal drug development programs, such as for neurodegenerative diseases like Parkinson and Alzheimer's disease, will no doubt drive their interest, Palotie said that FIMM and its academic collaborators in Finland have a "more holistic" approach to harnessing the power of the future database. "It will provide us with a number of opportunities to look at shared genetic backgrounds, comorbidities, and at some classes of diseases based on genetic background," Palotie said. "These types of research questions are the ones that we are specifically interested in."

FinnGen is being coordinated by researchers from the University of Helsinki and at Helsinki University Central Hospital, and nine different biobanks across the country will be collecting samples as part of the initiative. According to Palotie, the participating Finnish biobanks already have about 200,000 existing samples that will be used in the project, while organizers will look to collect 300,000 more, mostly through university hospitals. The key phenotypic data will be culled from national EHRs, which include hospital outcharge data, prescription medication purchase data, cause of death data, and cancer treatment data.

"We will not interview for this collection or collect specific cohort data," Palotie added, "but it's possible to recontact individuals if we want more in-depth data."

All of the samples will be genotyped on a custom microarray. FinnGen's organizers are currently in negotiations with vendors to provide the chip, Palotie said, but are not ready to announce their partner for the project. He added that roughly 70,000 samples have already been genotyped on other arrays as part of other research projects, meaning that about 430,000 samples will ultimately be genotyped as part of FinnGen. Moreover, organizers have sequencing data on Finnish individuals from other research projects that will serve as a reference panel for imputation.

Palotie noted that all of the samples will be coded prior to analysis, and that the study will be carried out following the "highest standards of data security."

Kimmo Pitkänen, Director of Helsinki Biobank, said that biobanks participating in FinnGen will provide the DNA samples to the project. Patients will be recruited through standard hospital biobank procedures, and samples will be most likely be collected concurrently with blood sampling for diagnostic purposes.

"Particularly here at Helsinki University Hospital, the patient biobank consenting and sampling has been built as part of hospital routine," he noted. Pitkänen reiterated that roughly 200,000 samples had already been collected, mostly by the National Institute for Health and Welfare's THL Biobank.

"It will be a mixture of patient samples, population cohort samples and even, presumably, very healthy voluntary blood donors from the Finnish Red Cross Blood Service Biobank," he said of the data collection.

Helsinki Biobank will be responsible for coordinating and harmonizing the sample collection at a national level. And since genetic data will be returned to the biobanks, FinnGen will enable the biobanks to enrich their biological data repositories, Pitkänen said.

"The combination of clinical data and genomic data, hopefully even other omics data from the same patients, can be taken even further in the hospital biobank setting," Pitkänen said. He also noted that the samples and the FinnGen genotyping data, after a grace period, will be made available for new research and R&D projects, originating both within and outside the FinnGen consortium.

"In the end, it is all about big data, the combination of large patient numbers, deep clinical data, and genetic data," said Pitkänen. "This is all made possible through the strengths of the Finnish innovation and healthcare environment."