Research collaboration aims to accelerate rare disease diagnostics by combining clinical information, machine learning algorithms, and genetic testing

September 9, 2021

The Rare3k research initiative aims to bring efficiency to rare disease diagnostics. By connecting large amounts of data from biobanks, healthcare, and genetic diagnostics, the study aims to develop algorithms that could accelerate the identification of patients who could benefit from genetic testing to confirm their diagnosis.

Rare3k is a research initiative formed by Helsinki Biobank, Helsinki University Hospital (HUS), and Blueprint Genetics. In the study, biobank samples of patients with a rare genetic disease who previously lacked a confirmed diagnosis are sequenced and analyzed.

In the first phase of this research initiative, a cohort of approximately 100,000 sample donors is being used to identify patients with a diagnosis or clinical suspicion of Wilson’s disease, achondroplasia and hypochondroplasia, transthyretin amyloidosis (aTTR) and inherited retinal dystrophies. These rare diseases were chosen based on ongoing development of targeted therapies for their treatment. Within the Rare3K initiative, the aim is to identify a total of 3,000 individuals for clinical-grade exome sequencing and comprehensive clinical interpretation. Expert clinicians at Helsinki University Hospital have a seminal role in the initiative, paving the road to translate research findings to clinical care.

A central part of the study is to test whether algorithms for analyzing electronic medical records (EMR) can be developed to identify individuals who would be likely to receive a molecular diagnosis with genetic testing. Finnish hospital biobanks, housing hundreds of thousands of DNA specimens linked with disease history, and comprehensive clinical information from the Helsinki University Hospital data lake, offer a unique opportunity for this development.

“Our focus is to find new ways to identify individuals with clinical features suggesting a rare disease, helping to remove barriers in the identification of patients who would benefit from genetic diagnostics. This collaboration is pioneering new ways to combine clinical practice and genetics research to create opportunities for providing individualized care to patients. The initiative also demonstrates the value of biobanks as a resource for future medical research with great potential benefits for patients through improved access to diagnosis and novel treatments,” says Professor and Scientific Director Olli Carpén, University of Helsinki and Helsinki Biobank.

”Our goal is to answer an unmet need in the field and find a practical solution for identifying individuals in biobanks who could benefit from receiving an accurate genetic diagnosis. As technology develops, machine learning-based algorithms could be a game-changer in the way genetic testing is targeted to individuals in hospital databases. We look forward to expanding this concept to other rare inherited diseases in the next phases of the study,” says Samuel Myllykangas, PhD, Blueprint Genetics Executive Director of Strategy.

”Pfizer is proud to sponsor the Rare3K initiative. Nearly 80% of all rare diseases are genetic in origin yet many patients wait several years to receive an accurate diagnosis. Finland has a unique ecosystem for Public-Private Partnership and advanced genome research offers a unique opportunity to allow for earlier diagnosis and research of rare diseases. We hope that what we learn from this collaboration will prove beneficial for Finnish patients and the broader rare disease community,” says Dirk Vander Mijnsbrugge, Vice President Medical Affairs Pfizer Rare Disease.


Rare3k in short:

  • The project aims to accelerate rare disease diagnostics by creating algorithms to identify patients who have the highest probability to benefit from genetic testing
  • The Helsinki Biobank cohort is approximately 100,000 individuals, and the study aims to identify and sequence 3,000 individuals representing the rare disease groups of interest
  • The genetic testing results will be given to the biobank and, from there, to the Helsinki University Hospital (HUS) physicians involved in the patients’ treatment for follow up
  • The initiative is funded by Blueprint Genetics, Business Finland, and chosen pharma partners such as Pfizer Finland
  • The findings of this initiative will be published in scientific journals and clinical conferences


Further information:

Helsinki University Hospital / Helsinki Biobank:
Chief Science Officer at Helsinki Biobank, Senior Physician at HUS Helsinki University Hospital & Professor of Pathology at Helsinki University Olli Carpén,

Blueprint Genetics:
Chief Strategy Officer Samuel Myllykangas,
Communication Specialist Saara Salonoja,

Pfizer Finland:
Country Medical Director Jaakko Parkkinen, tel +358 9 430 040
Rare Disease Nordic Medical Lead, Merja Väkeväinen, tel +358 9 430 040


About Helsinki Biobank:
Helsinki Biobank is a hospital based biobank founded by the Hospital District of Helsinki and Uusimaa (HUS), the University of Helsinki, Kymenlaakso Social and Health Services (Carea) and the South Karelia Social and Health Care District (Eksote). It collects and provides biological samples and associated clinical information as well relevant expertise and services for medical research and R&D purposes. Helsinki Biobank sample repository currently contains both prospectively collected samples from over 100 000 individuals as well as retrospective sample collections such the HUS pathology archive containing diagnostic FFPE samples from 1,4 million individuals.

About Blueprint Genetics:
Blueprint Genetics, a Quest Diagnostics company, is a leading specialty genetics and bioinformatics company focused on providing genetic testing for inherited diseases. The company is based in Helsinki and Seattle, with a customer base spanning over 70 countries.

About Pfizer Finland:
Good health is vital to all of us; as are sustainable solutions to the most pressing healthcare challenges we are facing globally. We at Pfizer are committed to applying science and our global resources to develop breakthroughs that change patients’ lives, to improve health and well-being at every stage of life. Our goal is to ensure that people have the opportunity to lead healthier lives with access to effective and innovative treatments when they need them. Breakthroughs that change patients’ lives.

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