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BBMRI.fi: an IT Infrastructure for shared biobanks

The BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) is an infrastructure established by 16 European states. Its aim is to promote the high quality, research-based use of the sample collections and associated data of European biobanks. Use of such collections assists in the development of diagnostics and treatment, as well as health promotion and disease prevention. Finland has several biobanks in operation. A common IT infrastructure is being created for these based on cooperation between the BBMRI and ELIXIR.

The BBMRI operates through national centres that coordinate the biobanks of member states. Service centres serving the customers of biobanks are also being established in member countries and under the
BBMRI. BBMRI.fi is a national cooperative body belonging to the BBMRI Network; its membership is made up of Finnish biobanks.

Finland’s biobanks

Five biobanks were operating in Finland in 2015. New ones will be set up in the near future. More than 100,000 Finnish sample collections were transferred to the National Institute for Health (THL) in June 2015. Sample collections can be used to identify the causes of diseases and the related impact of heredity,
the environment and lifestyle changes.

A total of 50 percent of samples from the Auria Biobank are cancer samples. The Auria Biobank focuses on cardiovascular, metabolic and cancer research, as well as research into neurological diseases. The biobank was established by the University of Turku and the University Hospital Districts of Southwest Finland, Satakunta and Vaasa.

The FHRB – the Finnish Hematology Registry and Biobank – operates throughout the country and collects blood and bone marrow samples from patients with haematological diseases. Such samples are required for research into methods of treating serious haematological diseases, particularly leukaemia. The FHRB biobank is owned by the Finnish Association of Haematology, the Institute for Molecular Medicine Finland (FIMM) and the Finnish Red Cross Blood Service. The Association of Finnish Cancer Patients is also involved in its activities.

The mission of the Academic Medical Center Helsinki (AMCH) is to support research aimed at health promotion and the understanding of disease mechanisms, as well as the development of products, diagnostic methods and treatment practices used in healthcare.

The HUB Biobank focuses on urological diseases and supports research in this field, based on biobank samples. The Biobank began sample collection at the beginning of 2015. Research based on samples
and data is aimed at improving the prevention, diagnostics and treatment of urological diseases. The HUB Biobank was founded by FIMM and the Hospital District of Helsinki and Uusimaa (HUS).

IT infrastructure of biobanks

Biobanks manage huge and important data sets. Tasks such as the alignment and management of genome data and imaging datasets are challenging. The aim is to create a national, web-based availability service
for biobank data, based on which users can search for materials suitable for research and product development.

Juha Knuuttila, Enterprise IT Architect at THL, coordinates IT cooperation between biobanks in Finland. Knuuttila views the biobanks’ IT infrastructure as central to national cooperation within the BBMRI.fi network.

”In Finland, IT infrastructure is highly developed in comparison to many other European countries. BBMRI.fi and the ELIXIR Centre in Finland are good examples of this. Both have a clear role to play. ELIXIR provides a good cloud service while the BBMRI offers specialised IT systems in support of biobank activities. The virtualised computing clusters of FIMM and CSC – IT Center for Science are available via a
cloud service. Cooperation as smooth as this is still rare at European level,” states Knuuttila.

Database pilots begun

The aim of the biobanks cooperation network is to agree on uniform practices relating to quality criteria, and to organise nationally consistent data transfer practices. Consistent ethical principles and maintaining
the confidence of the persons involved in research are another important area of national biobank activity.

In terms of IT, cooperation has been initiated through database pilots. For example, pathology archives form the key sample data of most Finnish hospital biobanks and biobank projects. A national digital pathology infrastructure has been created by digitalising pathology samples from university hospital archives, based on inter-biobank cooperation.

Digitalisation fosters the use of new applications such as DNA microchip technology and the development of tools for the analysis of large data sets, thereby promoting individualised health care. These services are part of the European BBMRI infrastructure.

”The goal is to create a unified Finnish interface connecting us to the European infrastructure.”

Harmonisation of data into a common database

However, much work remains to be done. With health care systems of several types in use, information is fragmented. Knuuttila believes that the greatest task lies in the harmonisation of data.

”To facilitate research cooperation, clinical data, demographic data and sample data should be combined in one place and an easily searchable format. Biobanks should therefore agree on which variables can be combined in the databases in a realistic and useful manner.”

Knuuttila believes that this would force the biobanks to work together, which would also benefit researchers and pharmaceutical companies. Knuuttila is leading the biobanks’ joint IT group.

”Obtaining patient data in a structured format would be useful to both the biobanks and hospitals.”

Towards a sample and data search service

THL, FIMM and CSC entered into Biomedinfra cooperation to meet the need for a joint organisation to exploit genetic data obtained from biobanks. This also required joint IT solutions. The project was sponsored by the Academy of Finland and Ministry of Education and Culture.

Four different services can currently be used through common interfaces. They comprise the sample and data register (National Institute for Health and Welfare, THL), the code, consent and event register (FIMM), the research access management service, i.e. REMS (CSC) and the availability database (FIMM).

”Each has a programming interface allowing them to exchange information.”

According to Knuuttila, no one else has created a programme like the one completed by the THL, CSC and FIMM.

”Open source solutions of this kind may also be attractive to biobanks.”

Knuuttila believes that the next key tasks are the creation of a common, webbased availability service through which users can explore the availability of samples and data belonging to different biobanks.

”This and next year, the focus will be on the creation of a joint availability service.”

Ari Turunen

 

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Further information

The National Institute for Health and Welfare (THL)

The THL is a national centre of expertise that provides reliable information in support of decision-making and action in the health and welfare sectors.
https://www.thl.fi
http://www.bbmri.fi

CSC – IT Centre for Science

CSC – The Finnish IT Center For Science is a non-profit, state-owned company administered by the Ministry of Education and Culture. CSC maintains and develops the state-owned, centralised IT infrastructure.
http://www.csc.fi
https://research.csc.fi/cloud-computing

ELIXIR

ELIXIR builds infrastructure in support of the biological sector. It brings together the leading organisations of 17 European countries and the EMBL European Molecular Biology Laboratory to form a common infrastructure for biological information. CSC – IT Center for Science is the Finnish
centre within this infrastructure.
http://www.elixir-finland.org
http://www.elixir-europe.org