How genomic data is powering healthcare in Estonia

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Genomic medicine has the power to transform and personalize the healthcare experience. However, despite this tremendous promise, genomic data is typically only used outside of routine healthcare workflows to treat rare diseases or prioritize cancer diagnosis. Healthcare organizations face challenges in ensuring the confidentiality of genomic data in various workflows. Additionally, most physicians have not been trained to interpret the meaning of genomic results about treatment options and communicate them to patients.

The Estonian Genome Center hopes to change that. The research group is leading an ambitious pilot program to sequence the DNA of 200,000 Estonian citizens, securely manage large-scale data, and weave information about regular medical examinations and treatments. It is an effort to respect patient safety at every step. The lessons learned from this pilot project could potentially help healthcare organizations around the world.

A focus on common ailments

At a recent press conference, Lili Milani, director of the Estonian Genome Center, explained how he hopes to transform everyday healthcare for all Estonians. She said countries like the UK, France and Sweden have all developed advanced personalized medicine programs, but these are mainly focused on cancer and rare diseases.

In contrast, Estonia is exploring how to apply personalized medicine to frontline doctors.

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“We use genomics to prevent common chronic diseases,” Milani said.

The death rate from heart disease in Estonia is much higher than in other Western countries like Finland, but adherence to medical treatment is about half.

"We think we could motivate people to improve their health behavior with the right approach," she said.

Protect privacy at scale

The first step is to turn raw blood samples into useful genomic data. Milani said it used to cost around $1,000 to scan an entire human genome a few years ago. Since then, the cost has dropped to around $100 thanks to a recent breakthrough from Ultima Genomics.

However, most research has focused on analyzing a much smaller subset of DNA for single nucleotide polymorphisms (SNPs), which looks for around 700,000 significant variants in people. This type of analysis is much cheaper to do on a large scale. When they started in 2001 the cost was around $300 per sample and is now under $50.

Data is only permitted for medical research or treatment with the consent of the patient. Data cannot be used to raise insurance rates and cannot be analyzed without patient consent. Use for criminal investigations is also prohibited. While it can help solve serious crimes, Milani said allowing it to be used for this purpose could discourage participation.

The Genome Center has developed a new data encryption and key management infrastructure to protect the confidentiality and privacy of each participant at scale. Actual genomic data is stored separately from any personally identifiable information (PII). When teams need to conduct a study, they extract genomic data from each individual using a unique key to connect genomic results to data from other patients. This is done in a special room without internet access or telephone.

The center also stores actual blood samples for future analysis, such as the discovery of new clinically relevant SNPs. Each sample is labeled with a unique barcode...