New research collaboration helps shorten the path to diagnosis for rare disease patients through analysis of biobank samples

June 7, 2022

Helsinki Biobank, Helsinki University Hospital (HUS) and its Rare Disease Center, and Blueprint Genetics announce promising results from the first phase of the Rare3K research initiative. The unique collaboration has pioneered new ways to find individuals in biobanks who may benefit from genetic testing to obtain an accurate diagnosis.

Treatment of rare diseases requires accurate diagnosis which is often challenging to achieve. Rare3K, in its first phase, has focused on patients with a diagnosis or clinical suspicion of Wilson’s disease, growth disorders, transthyretin amyloid (aTTR) polyneuropathy, or inherited retinal dystrophy. These rare diseases were chosen based on ongoing development of targeted therapies for their treatment.

To date, over 1,000 samples from the Helsinki Biobank have been sequenced and analyzed. Novel diagnoses were obtained for 10% of the cohort of patients with growth disorders, and 8% for inherited retinal dystrophies, including patients with formerly inconclusive or lacking genetic test results. In all four cohorts, previously known genetic diagnoses were also confirmed. As part of the initiative, expert clinicians from the Helsinki University Hospital will follow up with the diagnosed patients to discuss future clinical care.

In addition, the study has helped obtain novel information about diagnostic yields as well as the correlation between clinical symptoms and genetic alterations. Finnish biobanks store hundreds of thousands of DNA samples linked with comprehensive clinical information from hospital registries. This has proven to be an invaluable resource for medical research. The data will be further utilized for the development of algorithms that can accelerate finding those individuals for whom genetic testing would likely yield an accurate diagnosis.

“We at Helsinki Biobank and HUS are extremely pleased about Rare3k initiative and its potential clinical impact. Biobanks are often regarded as research infrastructures or just repositories of human specimens. This initiative shows that biobanks can serve as a bridge between research and clinical care. With help of expert clinicians the initiative paves path to individualized medicine and provides benefit to biobank sample donors,” says professor Olli Carpén, Scientific Director of Helsinki Biobank and Principal Investigator of Rare3K.

“The first results from the Rare3K research initiative demonstrate the great benefits of this new type of collaboration between biobanks, hospitals, and diagnostic laboratories. We are, however, just getting started and look forward to continuing our plans to develop algorithms that could transform the way patients are directed to genetic testing. This is a unique opportunity to help improve access to diagnosis and novel treatments for patients,” says Samuel Myllykangas, PhD, Blueprint Genetics General Manager and Executive Director of Strategy.

“For most rare diseases, the time to a correct diagnosis can often take multiple years. The early identification of a rare disease is challenging yet important as it allows adequate follow-up by specialized centers which mostly yields a better outcome for patients,” commented Dirk Vander Mijnsbrugge, Vice President Medical Affairs, Pfizer Rare Disease. “The first results of this unique collaboration are therefore extremely promising as they hold the potential for an earlier diagnosis and consequently the possibility of better longterm outcome. We look forward to future results of this initiative and to see how we can apply the learnings to the benefit of other rare diseases with a genetic origin.”


Rare3K in short:

  • The objective of the Rare3K project, launched in July 2021, is 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 for analyzing electronic medical records (EMR) to find individuals who would be likely to receive a molecular diagnosis with genetic testing
  • The Helsinki Biobank cohort is approximately 100,000 individuals, and the study aims to select and sequence 3,000 donors representing the various rare disease groups
  • The data and samples in the research project are deidentified for genetic analysis and the information necessary to re-identify patients is only known by Helsinki Biobank
  • The genetic testing results are 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 presented at clinical conferences


Further information:

Helsinki University Hospital / Helsinki Biobank:

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

Blueprint Genetics:

Samuel Myllykangas, General Manager,

Pfizer Finland:

Piia Aarnisalo, Country Medical Director, tel +358 9 430 040
Merja Väkeväinen, Rare Disease Nordic Medical Lead, 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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