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Data Resources

ELIXIR data sources

 

ELIXIR Finland offers data storage services, access to supercomputers and software tools as well as training. Through ELIXIR, life scientists have access to substantial biological and medical data sets.

Over the past ten years, the amount of data produced by bio and medical research has increased dramatically. This has resulted in data collections that require significant resources to maintain. Small, specialised data resources have also increased. ELIXIR uses biomedical data to create quality criteria to identify the most important data resources in Europe. In future, such data will be easy to find as it will be accessible in accordance with the FAIR principles (findable, accessible, interoperable, reusable) of open data.

ELIXIR data sources include, for example, sequence data, nucleotide transcript data, data on protein expression and information on the structure and function of drug-like small molecules. Data generated through metabolomics is also obtained. Metabolomics is a method used for the comprehensive study of small-molecule metabolites and their structure, function and synergistic effects in the cells, tissues, blood and secretions of the body.

Many resources of the ELIXIR nodes, such as files, tools, real-time search interfaces and application programming interfaces (API) are always available.

ELIXIR nodes share and store data and provide computing resources, software and tools for member organisations. ELIXIR Hub creates the data registers and defines standards for the data. It also establishes a decentralised computing infrastructure for biomedical data in Europe.

ELIXIR data resources have been divided into two categories, “core” and “deposition”.

https://www.elixir-europe.org/platforms/data/core-data-resources

https://www.elixir-europe.org/platforms/data/elixir-deposition-databases

ELIXIR’s key data sources have been duplicated for CSC and merged with CSC’s computing resources. On the other hand, the national data resources maintained by CSC do not meet the “core” and “deposition” criteria of ELIXIR. The situation will change in future. The objective of recording the genomes of the Finnish population for health care purposes is a good example of this. The collected data is valuable for research. The national genome research strategy includes a plan to make this data anonymous in order to support both public and private research. The other Nordic countries also share this vision.

Biobanks and other Finnish data sources

 

Finland has a long tradition of collecting and analysing biobank samples and the associated clinical data. The National Institute for Health and Welfare (THL), the Institute for Molecular Medicine Finland (FIMM) and CSC – IT Center for Science will collaborate within the framework of three biomedical infrastructure projects in Europe: Biobanking and Biomolecular Resources Research Infrastructure (BBMRI), European Advanced Translational Research Infrastructure in Medicine (EATRIS) and European Life Science Infrastructure for Biological Information (ELIXIR).

BBMRI is responsible for biobanks utilised in both clinical research and research conducted on the health effects of lifestyle and the environment. EATRIS, in turn, applies the results of basic research to medical science.

DNA Sample Management

 

The DNA sample management laboratory of the Public Health Genomics Unit operates at Biomedicum in Meilahti. The laboratory carries out the isolation and further processing of DNA as research services and manages large sample materials. More than 700,000 DNA samples from a number of national and international research projects are stored. The Public Health Genomics Unit works in cooperation with the biobank of the Institute for Molecular Medicine Finland (FIMM) and is part of the national BBMRI.fi network of biobanks.

The services include freezers, automation, robotics, sample management and quality assurance.
http://www.fimm.fi/en/biobanking/collections/

 

FINRISK

 

Finland’s national FINRISK study is conducted by the Chronic Disease Prevention Unit of the National Institute for Health and Welfare. FINRISK is a large population survey on the risk factors of chronic, non-communicable diseases. The series of studies, conducted for the first time in 1972 in Eastern Finland and every five years since then, has provided valuable information on the origin and prevention of major chronic diseases. The study has been utilised in various ways in the design and follow-up of health policy. Comparable studies that include extensive and long series of time are extremely rare in the world. A total of 71,921 Finns have participated in the research project in 1972–2007.

The survey is carried out every five years using independent and representative random samples from the populations of the selected research areas. The latest survey was conducted in the spring of 2012 with 5,834 Finns taking part. Information on the health, lifestyle and chronic diseases of Finnish people was collected in this survey. The study was conducted in five different areas in Finland. A total of 10,000 randomly selected people between 25 and 74 years of age were invited by post to take part.

Information was collected through questionnaires, measurements taken in connection with physical examinations, laboratory analyses of blood samples and from national registers. The results are used in epidemiological research, health promotion work and health policy decision-making.

All participants took part in a basic study which included a physical examination (e.g. height, weight, fat percentage measurement and blood pressure) and completing a questionnaire. Some of the participants were given the opportunity to take part in various sub-studies, such as a nutrition study which involved an interview about 48 hours of food consumption. One third of the participants were randomly selected for a physical activity study in which physical activity was studied using waist-worn activity monitors. Those attending basic studies in Helsinki, Turku, Joensuu, Kuopio and Oulu were invited to a fitness test.

http://www.thl.fi/fi_FI/web/fi/tutkimus/hankkeet/finriski

 

Canine DNA Bank

 

The University of Helsinki and Folkhälsan are conducting extensive genetic research on dogs. The sequencing of the canine genome has opened up many opportunities for uncovering the genetic background of the hereditary diseases, build, coat colour, size and various behavioural characteristics of different breeds. The unique population history and breed structure of dogs make them great candidates for genetic research. Compared to similar human studies, genetic studies on dogs make it possible to identify genes, even those causing multifactorial diseases, from a much smaller collection of samples.

After humans, dogs have the second largest number of different hereditary diseases. The aim is to identify genetic defects causing these diseases. The University of Helsinki and Folkhälsan have launched numerous projects involving dozens of different breeds. The subjects of research include, for example, neurological disorders, visceral diseases, connective tissue diseases, cancers, autoimmune diseases as well as personality and various behavioural disorders.

A canine DNA bank has been established at Biomedicum Helsinki for the purpose of genetic research. The samples submitted for research are stored in the DNA bank. Information on the dog and its owner is stored in a secure database. A large collection of samples together with up-to-date health and other information about the dog (e.g. behaviour) provides countless possibilities for genetic research.

The aim of genetic research is to identify genetic defects leading to different hereditary diseases and other breed-specific traits in order to develop genetic tests for diseases for the purposes of breeding and to apply the gained knowledge in the study of human diseases. A new genetic discovery also opens up possibilities for a better understanding of disease mechanisms and provides the basis for developing diagnostic methods, treatments and potential medications.

http://www.koirangeenit.fi/projektit/koirien-dna-pankki/

 

Feline DNA Bank

 

The completion of the sequencing of the feline genome in early 2008 has enabled diverse genetic research on cats. It has become possible to identify genes that predispose cats to diseases, clarify our knowledge of the domestic cat’s origin and the history of various cat breeds and better understand the genetic background of different feline characteristics. The research is conducted under the faculties of veterinary medicine and medicine of the University of Helsinki and the Folkhälsan Research Center at the university campuses in Viikki and Meilahti.

The aim is to build a comprehensive DNA bank of Finnish pedigree cats that can be used to map the hereditary diseases and characteristics of cats. The research is possible only with the samples submitted by cat owners and breeders. A feline DNA bank has been established at Biomedicum for the purpose of genetic research. The samples submitted for research are stored in the DNA bank. Information on the cat and its owner is stored in a secure database.

http://www.kissangeenit.fi/tutkimuksesta/dna-pankki/

 

Genoscoper

 

Genoscoper is a Finnish company that provides DNA diagnostics services for animal care and breeding. Researchers are able to manage their research data with the cloud services of the Finnish node.

Genoscoper conducts, for example, parentage determinations and various genetic tests on dogs, cats, horses and alpacas. DNA tests can be used to map the diversity of dog breeds and the hereditary diseases typical of different breeds as well as verify the parentage of puppies. Genoscoper is the only operator in Finland providing the SynchroGait test for gait performance and the risk of breaking to gallop in horses. Both serological and DNA blood group determinations and feline leukaemia virus and immunodeficiency virus tests (FeVL and FIV) are performed on cats.

Genoscoper cannot perform genetic diagnoses without, for example, the canine reference genome (ENSEMBL database), which is obtained via ELIXIR.

http://www.genoscoper.com/

 

Auria Biobank

 

Auria Biobank is the first clinical biobank established in Finland. It obtained a licence to operate from the National Supervisory Authority for Welfare and Health, Valvira on March 10, 2014. Auria Biobank has been established by the University of Turku and the hospital districts of Southwest Finland, Satakunta and Vaasa. Approximately 80% of the samples in Auria Biobank are cancer samples. In accordance with the specialities of the hospital districts of Southwest Finland and Satakunta, the biobank supports research in cancer, diabetes and cardiovascular diseases in particular.

Helsinki Biobank

 

Helsinki University Central Hospital (HUCS) -area of special responsibility and the University of Helsinki have established a clinical biobank that supports the translational research done in the region, and network with national and international biobanks. The research field of Helsinki Biobank is the research done in health and medical science in HUCS area. Helsinki Biobank operates to support research which aims at promoting population health, understanding the factors in disease mechanisms or the development of health care products.

Hematological Biobank (FHRB Biobank)

 

Hematological Biobank is owned by the Finnish Association of Hematology, Institute for Molecular Medicine Finland and Finnish Red Cross Blood Service. The Association of Finnish Cancer Patients is also involved in Hematological Biobank. Biobanks’s research area covers the prevention, diagnosis, treatment and follow-up of hematological disorders. Hematological Biobank is a national biobank and collects samples and data from patients with hematological disorder in all Finnish hematological units that have made an agreement on sample collection. The aim of the Hematological Biobank is to collect a comprehensive and high quality sample and data repository for hematology research.

Biobank of Eastern Finland

 

The Biobank of Eastern Finland was established by the hospital district of North Savo, The South Savo Social and Health Care Authority, the hospital district of Eastern Savo, Siun sote – Joint municipal authority for North Karelia social and health services and the University of Eastern Finland. The Biobank of Eastern Finland aims to mediate high quality human samples to medical research to promote development of new products and services that promote public health.

Central Finland Biobank

 

The Central Finland Hospital District and the University of Jyväskylä established a biobank in Jyväskylä that aims to promote research and to support the development of diagnostics and treatment.

Northern Finland Biobank Borealis

 

The population of Northern Finland is uniquely homogeneous, which makes the sample collections of the Northern Finland Biobank especially valuable for research. Northern Ostrobothnia Hospital District (PPSHP), the University of Oulu (UO), Nordlab and the hospital/healthcare districts of Lapland, Länsi-Pohja, Central Ostrobothnia and Kainuu have agreed to establish a biobank in Northern Finland.

Finnish Clinical Biobank Tampere

 

Finnish Clinical Biobank Tampere (FCBT) was established by Pirkanmaa Hospital District, University of Tampere, Etelä-Pohjanmaa Hospital District and Kanta-Häme Hospital District. FCBT’s license to operate was granted by the National Supervisory Authority for Welfare and Health, Valvira, on September 8th, 2015.

FCBT’s role is to support disease prevention, studies on the effectiveness or side effects of treatment of patients, and studies exploiting pathological findings. The main focus of the biobank, in accordance with the research strategy defined by the University of Tampere and Pirkanmaa Hospital District, is research in cardiovascular disease, cancer, immunology and type 1 diabetes.

THL Biobank

 

THL Biobank belongs to the National Institute for Health and Welfare. THL Biobank’s registered areas of research include population’s health promotion, identification of factors involved in disease mechanisms, and disease prevention. THL Biobank is a country-wide biobank and hosts a remarkable collection of population and disease-specific samples for research purposes.

Blood Service Biobank

 

The research area of Blood Service biobank is health promotion and prevention of diseases and is specialized in transfusion medicine. The biobank collects samples from blood donors during their blood donation.

 

Further information on Finnish biopanks:

https://www.biopankki.fi/en/

Other data sources

 

EMBL data resources and tools

http://www.ebi.ac.uk

The European Genome-phenome Archive (EGA)

The European Genome-phenome Archive (EGA) is one of the largest public cloud data repositories in the world that contains human data compiled from various bioscience research projects. CSC collaborates with EMBL-EBI to create services that cover data description, data access and interoperability.

https://www.ebi.ac.uk/ega/

Vertebrate and eukaryotic genome library:

http://www.ensembl.org/

Protein libraries:

Universal Protein Resource: www.uniprot.org/

Protein Data Bank: www.rcsb.org/pdb/