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» WP4: Infrastructures »  Databases And Biobanks

DATABASES AND BIOBANKS


Databases dedicated to radiation research
There are a number of databases and biobanks covering both human and animal radiation exposure/contamination studies including GENEPI, STORE, ERA, and the Janus Tissue Archives described below.

RBSTORE Logo
Of particular interest is the STORE database which has been created by the STORE consortium.  This FP7 funded project has recently been completed and the database is in the process of being transferred to DoReMi.  The database has been developed to store and share data from past, present, and future experiments in radiobiology.  It also acts as a pointer to biological material associated with the experimental data.  Finally, STORE has developed a set of SOPs for performing various molecular analyses from archived tissue samples which has been independently validated. 
A current priority of STORE is to add data from already completed and ongoing experiments.  If you have data that you would like to upload to this valuable resource, please visit the website or contact the DoReMi helpdesk for further information.  Uploading the data is simple and the database is compatible with virtually all data formats.
The following additional information is provided by the STORE website and has been slightly modified
The sharing of data and biomaterials from publicly funded experimental radiation science will yield substantial scientific rewards through re-analysis and new investigations. To that end, the STORE Consortium has created a platform for the storage and dissemination of both data and biological materials from past, present and future radiobiological research. The platform consists of a combined “Data Warehouse” and physical repository that enables the sharing of experimental data sets and materials. STORE provides a single portal to radiobiological information that is presently distributed over scientific centres worldwide, and it provides the necessary Standard Operating Procedures (SOPs) for the evaluation of archived tissue useability.

Under DoReMi STORE will continue:

1)
To provide a “one-stop-shop” portal integrating international databases, such as e.ERA, Chernobyl Tissue Archive,
     JANUS, and other repositories currently active, such that the user can find material and data held remotely.

2) To archive primary (raw) data or pointers to that data in public databases, from radiobiological experiments and      
     studies. This resource is open to individual investigators and to funding agencies as a potential central repository
     for data sharing.

3) To physically archive threatened material resources which the Consortium and Advisory Board believe are a valuable      resource to the Community, and whose state of preservation is consistent with STORE benchmarks.

4) To provide a single point of access to the integrated biomaterial resources through standardised request procedures.
     
The provision of a central portal is intended to help in the dissemination of awareness of the existence of these resources, many of which are, anecdotally, underused because their availability and existence is unknown. The      generation of benchmarks for sample preservation and usability by preparation of SOPs will also help to disseminate      formal standards by which the usefulness of archive material of this type can be assessed.
Future goals are to establish additional SOPs for new technologies for preparation of material from tissue samples; to actively pursue materials arising from ongoing research; and to collect materials that have arisen from multi-centre studies on humans and animals exposed to radiation.

ERA

The following information is provided by the ERA website.
The European Radiobiological Archives are a BfS service function for radiobiological research. Information and data from past animal experiments are made available to the scientific community.

A large number of long-term studies on experimental animals exposed to ionising radiation have been performed world-wide in the past. Large-scale experiments involving tens of thousands of animals are unlikely ever to be conducted again for financial and ethical reasons. The possibility of returning to mine the existing data in new ways adds enormous added value to the original funding of these studies. The retrospective analysis of earlier animal studies is an important resource for modelling and evaluating new risk parameters. With great foresight the European Union (EU) and European Late Effects Project (EULEP) have created a database collecting and collating data from almost all of the available animal radiation biology studies carried out in Europe. This database is called the European Radiobiology Archives (ERA). Comparable archiving activities were initiated in the USA (establishing the National Radiobiology Archives (NRA)) and in Japan (establishing the Japanese Radiobiology Archives (JRA)). The three archives include data from almost all radiobiological animal experiments carried out between 1960 and 1998 in Europe, USA and Japan. This information is jointly available in the ERA database. ERA alone includes 151 studies from 21 labs.

The following table gives an overview on the information that is available in the archives:

 

Labs

Studies

Groups

Animals total

Animals with data

ERA

21

149

4,623

232,587

93,445

NRA

11

143

1,861

190,471

115,801

JRA

14

39

367

29,537

3,396

Sum

46

331

6,851

452,595

212,642

http://janus.northwestern.edu/janus2/images/top_bar.jpg
http://janus.northwestern.edu/janus2/images/nasa_logo.gifhttp://janus.northwestern.edu/janus2/images/nu_logo_small.jpghttp://janus.northwestern.edu/janus2/images/doe_logo.gif

The following information is provided by the Janus website.
The Janus Experiments, carried out at Argonne National Laboratory from 1972 to 1989 and supported by grants from the US Department of Energy, investigated the effects of neutron and gamma radiation on mouse tissues primarily from B6CF1 mice.

Highlights

  • 49,000 mice were irradiated: Death records were recorded for 42,000 mice; gross pathologies were recorded for 39,000 mice; and paraffin embedded tissues were preserved for most mice
  • Mouse record details type and source of radiation [gamma, neutrons]; dose and dose rate [including life span irradiation]; type and presence/absence of radioprotector treatment; tissue/animal morphology and pathology
  • Total doses of 90-5111 cGy gamma rays, or 1-320 cGy neutrons
  • Protracted low dose rate treatments, short term higher dose rate treatments, variable dose rates with a same total dose, etc. in some cases in conjunction with radioprotectors
  • Normal tissues, tumors, metastases were preserved
  • Standard tissues saved: lung, liver, spleen, kidney, heart, any with gross lesions (including mammary glands, Harderian gland with eye, adrenal gland, gut, ovaries or testes, brain and pituitary, bone)


The following information is provided by the GENEPI website.
GENEPI is currently the largest tissue bank and database worldwide dedicated exclusively to research on the effects of radiation. It was created by a multidisciplinary radiotherapy team with the aim of investigating the genetic basis of the variation in individual radiation sensitivity. If successful this research may usher in an era of individualised radiotherapy treatment and predictive assay for radiation response.
As well as normal tissues (lymphocytes, blood, stroma, skin, and mucosa) tumour samples are also collected from radiotherapy patients with malignancies in the most common tumour sites: breast, head & neck, lung, prostate and rectum. The tissues are stored in dispersed biobanks linked to a central database documenting the patient's disease and treatment specific data (including dose-volume histograms and treatment plans) as well as a rigorously graded outcome assessment.
A separate database for extreme overreactors and a tool for selecting areas of interest in the stored dose distributions are currently under development. The GENEPI software features a public query facility allowing prospective users to assess, after self-registration, whether the tissues needed for their research projects are available within the required parameters and quantity.

Other Databases of interest
Other databases could also be of interest to radiobiologists as even though they are not focused on radiation research there are elements of low dose radiation exposure (primarily medical) within the studies.  The best example to date is the BBMRI.
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The following information is provided by the BBRMI website.
BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) was one of the first projects entering the European Research Infrastructure preparatory phase of the ESFRI roadmap funded by the European Commission (EC). The preparatory phase of BBMRI came to its end in January 2011. Over the past 3 years BBMRI has grown into a 54-member consortium with more than 225 associated organisations (largely biobanks) from over 30 countries, making it one of the largest research infrastructure projects in Europe.
BBMRI will form an interface between biological specimens and data (from patients and European populations) and top-level biological and medical research. This can only be achieved through a distributed research infrastructure with operational units in most if not all participating Member States. BBMRI will be implemented under the ERIC (European Research Infrastructure Consortium) legal entity with headquarters (central coordination) in Graz, Austria, responsible for coordination of the activities of National Nodes established in participating countries. By December 2011, 13 countries (Austria, Bulgaria, Czech Republic, Estonia, Finland, Greece, Italy, Latvia, Malta, the Netherlands, Norway, Spain, and Sweden) have signed the Memorandum of Understanding (MoU) where they express their aim to establish BBMRI as an ERIC and become Members of BBMRI-ERIC. The application to the European Commission has been submitted. The expected start date of BBMRI-ERIC operations is the second half of 2013.

If you know of other relevant databases or biobanks that ought to be included, please let us know by contacting the DoReMi helpdesk.