here. - BBMRI.se
Transcription
here. - BBMRI.se
#19 IN THIS ISSUE Editorial: Providing sustainable and increasingly appreciated services 2 Interview with Anders Lönnberg, national coordinator of life science 3 New services at the BBMRI.se national biobanking facility 4 International R&D Collaborations of the National Cytology Biobank 5 National co-ordination of biobanking in Clinical Microbiology 6 SHARE-ERIC chose the BBMRI.se National Repository 7 HandsOn: Biobanks 2015 at BBMRI.it 8 The HandsOn: Biobanks concept 9 E-learning in Biobanks and Big Data: launching of the BOOC platform 10 New items in the BBMRI-ERIC Work Programme 11 National pilot of a fully automated freezing system dedicated to fresh frozen tissue 12 International co-operation among biobank facilities 13 Open Access to medical data and biospecimens receives political interest 14 International Evaluation of Open Source LIMS 15 A position paper by the Intelligence in Science group 16 #19 October 2015 2 biobank SWEDEN Public Opinion and Debate biobank SWEDEN 3 Life Sciences and Innovation in Health Care: Interview with Anders Lönnberg Editorial Providing sustainable and increasingly appreciated services Time flies fast. The current issue of Biobank Sweden is number 19 and it is now six years since BBMRI.se was started. The concept “National Research Infrastructure” was introduced in a landmark decision of the Infrastructure Committee of the Swedish Research Council on the 17th September 2009 and BBMRI.se was one of the first national research infrastructures to be launched. The definition of a national research infrastructure was that it should provide open access to advanced research services, regardless of the home university of the user. This was quite foresighted. Open Access and Open Science are key concepts for research and research infrastructures all over the world today. It is just a few decades ago when this was not so. There was once an era where every researcher had to re-invent the wheel on how to collect research materials by him/herself, intended only for his/her own use. In the past, there was also a time where provision of services and sharing of materials was mostly restricted to local researchers, usually employed by the same institute. But the strong arguments in favor of Open Access have prevailed. The restricting of services and/or materials have simply carried enormous costs, not only in duplication of work, expenses and fragmentation of research. It is said that persistence pays and we have experienced a gradual appreciation of the open access, national services that we provide. The current issue provides a number of examples of how BBMRI.se is expanding its services to an increasing basis of users all over the country. There are also examples of other cornerstones for sustainability. Stakeholder dialogue (as e.g. performed at conferences and workshops) is always a continuously important mode of action in the shaping of our future. Also, international networking and benchmarking is key to being able to provide internationally competitive services. Finally, one important aspect of sustainability is an increasing and diversified structure of our financial support. It is a long time since BBMRI.se was dependent on startup subsidies. Today, cost recovery in the form of user´s fees is an increasingly important part of our income. The costs for research and continuous development of the BBMRI.se infrastructure are increasingly covered by a variety of different international grants. With the cornerstones of sustainability in place, I think we have good prospects for being able to support medical research also over a long-term perspective. “Open Access and Open Science are key concepts for research and research infrastructures all over the world today.” Joakim Dillner Director In April this year, the Swedish government appointed a national coordinator for life science, Anders Lönnberg, that will propose action points to the Innovation Council of the Prime Minister of Sweden, Stefan Löfven. Lönnberg will be joining the views of industry, healthcare, academy, investors, patient organisations and industry associations at a high professional level. Anders Lönnberg has a long and successful career from various life science organisations, and the merger of hospitals at Huddinge and Solna to Karolinska University Hospital in his track record. The current engagements of Anders Lönnberg are member of the Stockholm County Council and acting member of the Swedish parliament. During 1987-1990 he was state secretary in the government office of Prime Anders Lönnberg Minister Ingvar Carlsson. He also has extensive experience from industry, as vice CEO of Novartis Sweden, a global pharmaceutical company, and CEO of an IT-business during many years, as well as chairman of confederations of academic professionals (SACO and SULF). -I have a lot of competent people in an advisory board and I see a remarkable spirit of cooperation, Anders Lönnberg says. Five main issues have been identified where Lönnberg and his advisors will provide input: 1) informatics and digitalization, 2) budget reward levels in healthcare, 3) qualification systems for scientists/healthcare professionals, 4) the Swedish innovation system, and 5) the orientation of the research proposition for 2016-2020. - Biobank issues are closely related to informat- ics and digitalization, and there we are aiming to provide input earlier than what´s expected for the research proposition of 2016. Another important issue is to revise budget reward levels in healthcare. At Swedish hospitals costs are increasing, but productivity parameters stay low. There is also a slow introduction of new “Fast access to new treatment is part of the social contract for citizens...” medical treatments. It´s a problem of the system, and a solution at the national level is desirable. - In average, it takes 17 years to implement a new medical treatment, Lönnberg continues. Fast access to new treatment is part of the social contract for citizens, it promotes equality and underpins the will to pay taxes. The vision for Swedish life science is clear – to produce internationally leading research and healthcare using the cultural foundations of credibility and curiosity. The development of wellfunctioning triple helix collaboration systems (industry, academy, healthcare) is a key to success. - The citation index of Swedish medical research is rising again, Anders Lönnberg claims. Karolinska Institutet is for example one of the most cited universities outside of the USA. You have a reputation as a visionary, where do you think life science and healthcare is heading ten years from now? - We need to look at how medtech and medication can be delivered in the home environment with the patient as co-caregiver. Furthermore I think the proportion of the gross domestic product that goes to healthcare will increase. The progress of medicine is incredibly fast and the goal is to give people the opportunity to live long and well, not to press prices. Interview by Ulla Rudsander 4 biobank SWEDEN biobank SWEDEN 5 National Biobanking Services BBMRI.se Healthcare Biobanking Support Services New services at the BBMRI.se national biobanking facility The facility is now a well-established core facility for pre-analytical handling, storage and distribution of human biological samples and associated data. Today it hosts sample collections for over 200 research studies, and handles 8 million samples from almost a half million individuals. Robust IT-systems ensure full traceability as well as data security. We offer advice on study planning and support on legal requirements. The facility was developed as a strategic collaboration with KI Biobank, starting in 2010. As KI Biobank was launched already in 2004, the national facility is therefore very well experienced in providing advanced and reliable biobank services to medical researchers all over Sweden. Data services include storage and retrieval, configuration of data systems for researchers’ own labs (Lab Information Management System, LIMS), web survey systems and Customer Relations Management systems (CRM). Sample services include plasma and serum aliquoting, DNA-extraction, sample formatting and transport. We use magnetic bead-based separation for our automated DNA extractions that provide very high quality DNA at high throughput. Biobank Ethics This DNA is ideal for next-generation sequencing platforms and we have already extracted DNA from over 200 000 individuals. We use the Thermo Scientific QuantStudio Open Array platform to analyze 64, 128, 192 or 256 specific single nucleotide polymorphisms (SNPs) per sample. The Open Array platform is based on the proven TaqMan assay. So far, we have performed genotyping services on 30 000 samples. We separate mononuclear leukocytes from peripheral blood (PBMC) or from bone marrow suspension using gradient centrifugation. We separate granulocytes using Lymphoprep. Other methods are available on request. Photo: Gunilla Sonnebring, KI The BBMRI.se national biobanking facility at KI has developed some new services for simple genotyping and production of viable cells. These and all our other biobank services are described in our new service catalogue and associated price-list. Valentina Novak, responsible for services with handling of viable cells For further information download the biobanking service catalogue here: http://bbmri.se/Global/Publicerade%20dokument/ tj%C3%A4nstekatalog%20biobank.pdf by Camilla Lagerberg News In Brief The sixth Newsletter on Current Issues in Biobank Ethics and Law from the Centre for Research Ethics & Bioethics (CRB) and BBMRI.se is published (http://www.crb.uu.se/biobank-perspectives-3-2015/index. html). Highlights include: i) a statement paper in the American Journal of Bioethics on broad consent for biobank research ii) the launch of B3Africa that will bridge European and African biobanking and biomedical research and iii) the International Charter of principles for sharing bio-specimens and data that has received a recommendation from the International Rare Diseases Research Consortium (IRDiRC). International R&D Collaborations of the National Cytology Biobank The FORCEE (4C) project is a European research project with Prof Martin Widschwendter, MD at Institute for Women´s Health, University College London, as coordinator of the project. The project seeks to evaluate preliminary findings that testing cervical cells (as collected during cervical screening tests) can predict a woman’s cancer risk, not only for cervical cancer but also for breast, endometrial, and ovarian cancer. The Cytology Biobank at Karolinska University Hospital is a nationally and internationally positioned open access resource initiated by BBMRI.se, that is partner in 4C. We will follow the large cohort for development of these cancers and provide the 4C project with biopreserved cervical cells taken at baseline from women who did or did not develop any one of these four cancers. The Horizon 2020 call for applications in biomarker research attracted >130 applications, with 4C being top ranked. The 4C project involves People’s Republic of China Our initiative for a National Cytology Biobank Infrastructure was presented as an invited lecture at the 5th Annual Biobank China on Precision Medicine Conference & Exhibition 2015, 4th International Conference on the Standard Construction of Beijing Biobank of Clinical Resources and the 1st China Cellular Resources Biostorage & Application Symposium (ABC2015) held on Sep. 14-15th 2015 in Shanghai. The conference attracted about 500 participants from over 10 countries, 20 provinces in China and 200 national and international universities, institutes, hospitals and companies. We exchanged experiences in precision medicine, biobanking, as well as standards and best practices in biobanking. Clinical applications and impact on health management was also a major subject during the conference. The BBMRI.se lecture was widely appreciated and we initiated a service with assistance on biobanking on cervical cells to the International Peace 14 European partners and was awarded a €7.9m grant to use “multi-omics” of cervical cells to predict women’s risk of breast, endometrial, ovarian, and cervical cancer. Supplementary funding of £1m is provided by the charity organization Eve Appeal. The partners at the FORECEE Kick-off Meeting, 10-11th September 2015, London Maternity & Child Health Hospital of China welfare institute (IPMCH), Dep. of Cervical Disease Center, Section of Cytology Biobank, Shanghai The first step in the service is to support implementation of the BBMRI.se Cytology Biobanking format at IPMCH. Prof. Hui-Juan Zhang MD. PhD (Dean of the Departments of Pathology-Cytology, and head of the Cervical Disease Center and the hospital´s biobank) and Dr. Yutong Song M.D. Ph.D. Director of Scientific Affairs and Associate Director of the Shanghai Clinical Research Center Biobank´s explained that the cytology biobank at the IPMCH was founded in 2012 with government support. There are about 2000 women per week attending the Cervical Disease Center. However, because of limited space only abnormal samples are saved. A homemade Excel database registers the patient´s name and sample labels and the position of the samples. There was a substantial interest in using the BBMRI.se concept for spaceefficient storage and efficient IT solutions. 6 biobank SWEDEN BBMRI.se Healthcare Biobanking Support Services National co-ordination of biobanking in Clinical Microbiology The BBMRI.se support to biobanking in clinical microbiology is considered a strategically important service of BBMRI.se. The service follows the same principles as the highly successful BBMRI.se support to biobanking in clinical cytology. Key concepts are that i) development work is a major part of the expenses, in time and money, of biobanks and that there can be major savings by performing coordinated development in a national network ii) because BBMRI.se performs high volume national purchasing, the costs of both equipment, IT solutions and consumables can be reduced, both in costs and in time required. Iii) the national purchasing also results in a national standardization in sample handling, making it possible to validly perform joint national studies of similarly enrolled and formatted samples. Similar to the cytology biobanking project, we have started with purchasing of 1-10 liquid handling robots that thus can fulfill the needs for clinical microbiology biobanking throughout Sweden. My background is as a biomedical scientist, having worked in clinical microbiology for >10 years. The opportunity to work with clinical samples both in clinical diagnostics and in science, and both for bacteria and viruses, is fantastic and is commonly based on the clinical microbiology biobanking infrastrcuture. I am chairperson of the National Microbiology Association (Riksföreningen för mikrobiologi), a clinical association aiming to have a contact member in every microbiology lab in Sweden and once per year meet for a two days conference. This year, I will be presenting about BBMRI.se and the services on support for clinical microbiology biobanking that we are offering. I have also started discussions with various healthcare regions (notably Region Skåne and Örebro) regarding which services to support clinical microbiology biobanking that BBMRI.se can help out with. Interested? Please contact Camilla.lagheden@ki.se Camilla Lagheden News In Brief Active enrollment in SWECRIT The BBMRI.se Board decided last year to support the launch of a national pilot for systematic biobanking from all patients admitted to critical care. Preparation for the project used a variety of BBMRI.se services, for example ELSI services to ensure a fully legally compliant project with the highest possible ethical standards. The project, SWECRIT, is now actively enrolling all patients in critical care in 3 major hospitals in Southern Sweden (Lund, Helsingborg and Kristianstad) and enrollment in Malmö will start on 1/11 2015. The annual enrollment target of the pilot is 3200 patients. For more information on SWECRIT, write to hans.friberg@skane.se BBMRI.se National Biobanking Services biobank SWEDEN 7 SHARE-ERIC chose the BBMRI.se National Repository In March 2011, The Survey of Health, Ageing and Retirement in Europe (SHARE) became the first European Research Infrastructure Consortium (ERIC). SHARE-ERIC is a multidisciplinary and cross-national panel database of micro data on health, socio-economic status and social and family networks of approximately 110,000 individuals (more than 220,000 interviews) from 20 European countries (+Israel) aged 50 or older. SHARE-ERIC enables analyzing the process of population ageing in depth. The Swedish team in SHARE-ERIC (lead by Professor Gunnar Malmberg of Umeå University) chose to use the BBMRI.se National Repository for long term storage of blood samples. The sixth wave of data collection in SHARE-ERIC introduces collection of dried blood spot samples for measurements of pre-defined biomarkers as objective health measures. Also, from each individual a set of blood spots dried on filter paper will be stored to allow future analysis of additional biomarkers. The BBMRI.se National Repository is proud the Swedish team of SHARE-ERIC decided to use our services for long term storage of its valuable samples. International initiatives typically store samples in an international, central facility but Swedish law prohibits long-term storage of biobank samples abroad. By being a national node in the international BBMRI-ERIC biobanking platform, BBMRI.se has good possibilities to offer services that are standardized to the services offered by other national nodes in BBMRI-ERIC. The BBMRI.se National Repository offers flexible and internationally harmonized, high-quality storage services for customers from both universities and healthcare. We take a national responsibility for saving valuable legacy collections that otherwise would have been lost. Also, we offer a broad range of contract services in biobanking, including long-term storage (at both minus 20 C and minus 80 C) and handling of samples in various formats, registry linkage services, retrieval services and services to display specimen collections for potential users. For inquiries about our services please contact Project Leader Lars I. Andersson (Lars.i.andersson@ki.se; 076-209 96 87). Facts BBMRI.se National Repository: • The BBMRI.se National Repository offers flexible and high-quality storage services for customers from both universities and healthcare. • Contract services include long-term storage and handling of samples of various formats, registry linkage services, retrieval services and services to display specimen collections for potential users. • Long-term storage at -20°C, -30°C and -80°C are available. • Registration in a LIMS assures traceability of samples and all daughter aliquots. • The services are flexible with respect to formats of samples and labels, making the BBMRI.se National Repository well suited for storage of legacy collections. • A freezer hostel service offers space for freezer with connection to temperature supervision to let. • The BBMRI.se national repository takes a national responsibility for saving valuable legacy collections that otherwise would have been lost. 8 biobank SWEDEN biobank SWEDEN 9 Stakeholder Dialogue and Education Stakeholder Dialogue and Education HandsOn: Biobanks 2015 at BBMRI.it The HandsOn: Biobanks concept On 29-31st of July 2015, the 4th HandsOn: Biobanks (HOBB) Conference was hosted by the Italian node of BBMRI (BBMRI.it) in Milan. There was a wide range of participants, ranging from academia, industry, medical doctors, patient groups, policy makers, public representatives and legislators. The first HOBB conference was arranged 2012 by a BBMRI.se team led by Mats G. Hansson in Uppsala and the same scientific structure has been preserved also when HOBB has later been organized in the Netherlands, Finland and now in Italy. There are plenary and parallel sessions, keynote lectures, posters, ethics café discussions and interactive idea labs. The plenary sessions and keynote lectures focused on the usefulness of clinical biobanks, infrastructures for sharing genomic and healthrelated data, development of personalized medicine, as well as international collaboration and partnership between academia and industry. Interactive idea labs gave perspectives on the latest developments in the biobank area and utilization of biobank-derived genomic data. As usual, the interactive exhibition “The Route” presented practical aspects of collection, storage and use of different biospecimens. The ethics café discussions dealt in particular with the Data Protection Act and had participants of experts from academy, industry and authorities that regulate ethical and legal aspects of biobank related research. The day before HOBB2015, the EU paroject BioSHaRE arranged a one-day conference “LATEST TOOLS and SERVICES for DATA SHARING”, where IT tools for data harmonization and pooling from multiple biobanks and databases were presented and discussed. Sharing data between different biobanks and databases can maximize utility of biobank research towards precision medicine and personalized prevention, especially for rare diseases. Storing and analyzing big data has technical challenges, as huge amounts of data are arriving as a result of the rapid advancement of next generation sequencing technologies. In a HOBB2015 keynote lecture Jim Dowling presented BiobankCloud – the EU project that is developing “cloud-computing platform as a service for the storage, analysis and interconnection of biobank data” (http://www.biobankcloud.com). The goal of BiobankCloud is to provide biobanks with the tools to securely store, analyze and share large amounts of data. The next Hands on Biobanks, HOBB2016, will focus on technical, ethical and legal perspectives of health research data management and will be arranged by the Austrian node of BBMRI (BBMRI.at). SAVE THE DATE: September 27-29, 2016. Report by Davit Bzhalava The interactive biobanking conference concept HandsOn: Biobanks (HOBB) actually arose from a request from the Swedish Research Council that BBMRI.se should organize open User´s Meetings. Some creative thinking ensued and on 20-21 September 2012, the first HandsOn:Biobanks conference was arranged in Uppsala, Sweden by BBMRI.se together with BBMRI.fi and Biobank Norway. hibition ‘THE ROUTE’ from sample to research result (where a number of hot issues were debated in the Ethics & Trust science café), in keynote lectures, educational sessions, idea labs and a ‘knowledge sharing’ programme. We also helped organize, together with P3G, ISBER, BioSHaRE.eu, ENGAGE and ESBB, a preconference called International Biobanking Summit: Future directions. A major theme was that the conference should be useful, not only to the biobankers, but primarily to the Users. We specifically invited researchers, policymakers and industry to come and join a dialogue on how biobanking services can improve the research process and the value of research. Mats G. Hansson in discussions at Ethics & Trust XXscience café, Uppsala 2012 We used interactive workshops, an interactive exhibition, lectures, debates, posters, seminars, lunches and coffee breaks to discuss and develop ideas for how the different user groups could get the best out of biobanking and medical registries. There were eight major themes, divided into two parts: THE RESEARCH PROCESS: ethics & regulation, biobanking practice, sample analysis, and data analysis THE VALUE OF BIOBANKING: ethics & trust, health economy, clinical practice and drug development. These themes were echoed in our interactive ex- of HOBB2012. Our goal was to attract around 300 participants in total. Both meetings had over 400 participants from 27 countries. The positive feedback was more than we ever had expected. So the ‘HandsOn: Biobanks’ became a yearly event, maintaining the interactive format and user focus In 2013 HOBB was arranged by BBMRI.nl in The Hague, Netherlands, with the theme “Connecting communities”. In 2014 the focus was on clinical biobanks and personalized medicine with the theme: “From Biobanks to Medical Innovations”, arranged by BBMRI.fi in Helsinki, Finland. This year, 2015, the conference was organized by BBMRI.it in Milan, Italy, with the theme “The EXPOnential relevance of biobanking. Clinical biobanks for personalized medicine”. Read more about the conference on page 5. Next year, 2016, HOBB will be arranged in Vienna, Austria, 27-29 September, with the theme “Biobanks for Health Innovation”. See you there! by Sofie Petersson 10 biobank SWEDEN Education & International Networking E-learning in Biobanks and Big Data: launching of the BOOC platform Massive Open Online Courses (MOOCs) is an increasingly popular way to deliver education at most Swedish universities. A MOOC is open for anyone to attend and is given entirely on the internet (no need to attend physically). The concept has in particular been promoted by top-ranked American universities. BBMRI.se is now launching a Biobanking Open Online Course, BOOC, inspired by the MOOC concept. BOOC uses the open source Learning Management System Moodle and is targeting both graduate level students and biobank professionals. Moodle was released as an open source software already in 2002 and there are today tens of millions of Moodle users. Completely virtual Moodle conferences, iMoots, have been organised since 2010. As Open Science and innovative use of eScience are central concepts for BBMRI.se, establishment of an inexpensive and flexible educational infrastructure based on eLearning was a high priority for us. The first BOOC pilot will be an online course given in parallel with the physical course entitled “Biobanks and Big Data: Possibilities and Challenges” organized by the BBMRI.se Southern Sweden Service Center at Lund University and Copenhagen University on the 2-6th November at Medicon Village in Lund. We had the opportunity to interview one of the course organizers (Eva Ortega-Paino). How does the content of this course compare to the course you organized last year? Last year, the topic was focused on the use in research and clinics of the samples stored in the biobanks (“Biobanking science in the era of personalized medicine”). This year we have a different per- spective. “Biobanks and Big Data: Possibilities and Challenges” will focus on the main core of the data produced. What is the set-up of the course? We will have field/onsite visits to the Danish National Biobank and Beijing Genomics Institute which has its European headquarters in Copenhagen. We have registered students from many places, e.g. from Africa and also from seven European countries). More than 70 participants are already registered for the 2-day symposium which is intertwined in the course. Right now we are working to get the BOOC e-learning platform in place, work done by myself and Ulla Rudsander in the weeks approaching the beginning of the course. How will the online format mix with the physical format? As it is a pilot, it will be a stepwise learning process about which parts of the course (e.g. basic principles of biobanking, state-of- the-art symposium lectures or examination presentations), that benefit most from open access eLearning. The lessons learned will lay the ground for the next BBMRI.se course, planned for the spring of 2016 in Stockholm. International Networking biobank SWEDEN 11 New items in the BBMRI-ERIC Work Programme As BBMRI.se is the national node of the European biobanking infrastructure BBMRI-ERIC, both providing input to and supporting the development of the BBMRI-ERIC are core activities of BBMRI.se. The BBMRI-ERIC work programme for 2015 is now public and contains several important new items. There is a major focus on access to samples and data (how to retrieve samples and data), but also on international access to tools and facilities for generation of high quality research infrastructures (how to collect internationally useful samples and data). The work programme is structured in seven work plans: einfrastructure, quality, population-based cohorts, clinical biobanks, biobank outreach, biological expert centres and European common services. See table below for further information on the 14 work streams emanating from the work plans, and priorities of these work streams. The quality work plan includes important new activities such as quality management system, self-evaluation tools for biobanks, and implementation of BRIF (Biological Resource Impact Factor – the internationally agreed scoring system used to measure quality of biobanks). There is a new clinical biobanks work plan that aims to lay out the basis for international collaboration in establishing biobank networks in clinical research. Initially, this work plan will focus on biobanks with breast cancer tissue. There is a work plan for population-based biobanks that has as an aim to create a European Cohort Consortium, with harmonized data and a joint computing and storage strategy. The work stream for rare diseases (RD) within the work plan on common services has established cross-talk with RDoriented initiatives to provide support services/ helpdesk facilities and return-on-investment models. The emerging work stream for biobanking of infectious materials, also that one within the work plan on common services, aims to build capacities for the study and surveillance of highly pathogenic micro-organisms. Apart from the membership fees, BBMRI-ERIC is now supported by a large number of grants from the EU. There are six projects funded by the Horizon 2020 programmes INFRADEV, INFFASUPP, WIDESPREAD, or EINFRA, and two projects funded by EU Framework Programme 7. If you want to join the pilot online course or symposium, please email ulla.rudsander@ ki.se to obtain further details. The BBMRI.se Board decided in its June meeting to launch strategic pilot projects during the autumn of 2015, particularly focusing on national projects with clear plans on the services to be provided and the long-term sustainability. Following nationwide consultation with BBMRI.se node coordinators and BBMRI.se service centers, the BBMRI.se Board decided to launch 4 strategic projects during autumn 2015. The pilot launch of BOOC is one of these projects. WORK PROGRAMME 2015 CORE WORK PROGRAMME 2015 AMENDMENT 2015/1 12 biobank SWEDEN 13 biobank SWEDEN Healthcare Biobanking Support Services International Networking National pilot of a fully automated freezing system dedicated to fresh frozen tissue International co-operation among biobank facilities - for better services and higher impact Biobanked fresh frozen tissue is a highly valuable source of tissue for both routine diagnostics and research. Many of the pathology departments in Sweden have biobanked fresh frozen tissue (often malignant cancer tissue), routinely for several years, sometimes decades, leading up to thousands of fresh frozen tissue samples stored at several different sites. These samples “An important outcome is to provide an infrastructure with clearly annotated samples published in an open access catalogue...” are usually stored in hundreds of boxes, usually fitting 100 samples/box, taking up large spaces in minus 80°C freezers. Every time a sample is requested, the whole box of samples has to be removed from the freezer in order to find the tube containing the wanted tissue. This is very much unwanted and, when it comes to large requests, is not very “user-friendly” to the personnel that have to work in these conditions at very low temperature. A fully automated freezing system, that allows “cherry picking” of samples, could eliminate these problems (i.e. one sample at a time can be selected for retrieval without affecting other samples). At the moment, there is to our knowledge no automated biobank in Sweden dedicated to handling fresh frozen tissue. The automated system will provide both a better environment for the fresh frozen samples, since these freezers usually work at minus 150°C, which is much better for the samples. It will also provide a safer and more uniform handling, make the inventory of the samples easier as well as maintaining a high traceability. Our national pilot project will start by reformatting the fresh frozen tissues that have been collected at the Dept. of Pathology, Örebro University Hospital since the mid 1980’s. An important outcome is to provide an infrastructure with clearly annotated samples published in an open access catalogue, where researchers can then search for suitable fresh-frozen tissue for research projects. If successful, the project could result in an expansion of this strategy also to other sites in Sweden, ultimately providing a much needed open-access infrastructure of the fresh frozen tissue that is available in Sweden. No more manual handling of frozen tissues. Interested? Please contact maria.svensson@regionorebrolan.se The BBMRI.se Board decided in its June meeting to launch strategic pilot projects during the autumn of 2015, particularly focusing on national projects with clear plans on the services to be provided and the long-term sustainability. Following nationwide consultation with BBMRI.se node coordinators and BBMRI.se service centers, the BBMRI.se Board decided to launch 4 strategic projects during autumn 2015. The National Pilot of an Automated System for Fresh-Frozen Tissue is one these projects. The BBMRI.se biobank facility at Karolinska Institutet (KI) has had the good fortune to establish collaboration with the biobank facility at Mayo Clinic (MC) in Rochester, Minnesota, US. The two biobank facilities have been benchmarking their activities to support interactions in medical research at the two organizations. Initial areas for co-operation include sharing insights on for instance technology exchange, biobank sample handling and cohort access. Over the last 20 years a growing number of researchers at KI and MC have been collaborating on medical research projects in many disease areas. This has led to sharing of data and samples, the key interest of biobank facilities. Formerly, each new interaction needed a new agreement and separate planning process for material and data transfer. Time was being lost reinventing wheels, before we realized we could make it simpler and more effective without cutting corners. Picture legend: The KI-Mayo biobank team, from left to right: Back: James Cerhan, Janet Olson, Mine Cicek (MC) Middle: Jolene Farmer Bolster (MC), Kicki Kjaergaard, Camilla Lagerberg (KI) Front: Cecilia Björkdahl, Cecilia Agardh, Mark Divers (KI), Steve Thibodeau (MC) Benchmarking to help research across the borders During 2015 we visited each other’s biobank facilities. In April, KI went to Mayo in Minnesota, and in September MC visited the BBMRI.se facilities at KI in Stockholm. The collaboration has created a practical tool kit for researchers to share research samples and data according to common formats (see table 1). One highlight is a new standard legal agreement for the transfer of material and data in either direction, designed as a common template approved by the legal staff of both KI and MC. This way, we will avoid losing time when drafting and negotiating a completely new agreement for each project. We have also learnt a lot about our respective technical platforms as well as how our customers use our facilities. We see real opportunities for continued collaboration, for instance with: • data management (co-partnering on platform development) • dynamic access to securely stored samples • the interface with genomics as it starts transforming clinical practice (the individualized medicine vision becoming a reality) • how we interact with society at large in being open and informative about the purpose of biobanks in public health • interaction with industry MC has a clear strength in the close and very productive hospital integration of the biobank. MC is making strong progress in implementing individualized medicine concepts with genomic initiatives, and has been very active in fostering links with the local community to win support and trust. The BBMRI.se facility has been particularly effective in applying biobanking broadly across disease areas, providing service to many, diverse research projects and demonstrating impact of biobanking on clinical practice. >>>> 14 biobank SWEDEN Connecting cohorts We found that we have similar views on Open Access concepts, and the linking of biobank cohorts. The Mayo cohort (also called the Mayo Clinic Biobank) has assembled a rich collection of samples, data and survey information from a large group of the general population, in a similar manner as some of the BBMRI.se cohorts. All are intended to be available as open assets for medical research. Despite being independently planned and executed, the similarities in cohort design were very apparent. Even though each of these cohorts is relatively large in its own right, connecting them offers a considerable synergy. The human factor Our benchmarking meetings were marked by a great spirit of partnership. The human element in this must not to be underestimated - and we believe this is particularly apparent in the photo, which is a fine reflection of the atmosphere throughout both meetings! Mark Divers Figure 1: A joint tool kit for researchers Tool Information to researchers Check-lists • Starting new collections • Using existing samples • Sample withdrawal • Ethical approval Material & Data Transfer Key contacts Communication material • Slide-sets • Web-page • Flyers and posters Comment Overview on the biobanks services and collaboration Simple “how-to” guidelines for different processes Although the PMI initiative will yield its greatest Status 4Q2015 Under construction benefits many years down the road there could be some near-time successes, derived from the cancer studies or from insights into pharmacogenomics (the provision of the right drug for the right patient at the right dose, based on genomic profiles). References https://www.whitehouse.gov/the-press-office/2015/01/30/fact-sheet-president-obama-sprecision-medicine-initiative N Engl J Med 372;9 February 26, 2015, p 793-795 http://www.fda.gov/newsevents/testimony/ ucm446525.htm Open Source Information Technology Under construction International Evaluation of Open Source Laboratory Information Management Systems Common agreement template Complete Names & contact details for Complete each biobank Presentation materials to present Under construction the cross biobank opportunities Public Opinion & Debate Open Access to medical data and biospecimens receives widespread political interest The President Obama administration has launched the Precision Medicine Initiative (PMI), prevention and treatment of disease that takes into account individual variability. The President’s budget of 2016 will provide a $215 million investment for the National Institutes of Health (NIH), the Food and Drug Administration (FDA), and the Office of the National Coordinator for Health Information Technology (ONC). The objectives of the Precision Medicine Initiative are more and better treatments of cancer, creation of a voluntary national research cohort, commitment to protecting privacy, regulatory modernization and supporting public-private partnerships. The cohort of more than 1 million American volunteers will share genetic data, biological samples, and diet/lifestyle information, all linked to their electronic health records, if they so choose. The cohorts will be assembled in part from existing cohorts studies (many funded by NIH) that already have collected or are well positioned to collect data from participants in the new initiative. The White House is reviewing privacy and trust principles to maximize the benefits of a national research cohort while minimizing the risks inherent in large-scale data collection, analysis and sharing. 15 biobank SWEDEN The regulatory oversight will be provided by the FDA, investigating the analytical and clinical capabilities of NGS, Next Generation Sequencing. NGS pose unique challenges to applying FDA´s traditional regulatory approach because NGS can identify an essentially unlimited number of variants, and it would be difficult, if not impossible, to demonstrate performance on every possible detectable variant, as it would for other tests. The outcome of the regulatory oversight could result in novel metrics and computational methods, making use of shared databases for assessing performance. >>>> Open Source softwares are an increasingly popular branch of the Open Science tree. In large parts of the world, it would be economically impossible to purchase commercial IT systems, making the IT infrastructure a significant bottleneck for international collaboration. Open Source softwares are a potential solution to this problem, as many international collaborative networks jointly have a very large number of programmers and other IT experts employed. Use of Open Source softwares is therefore a possible approach to promote international collaboration as well as facilitating collaboration between many partners who use the same software solutions. The BCNet (Biobank and Cohort Building Network) is a network of biobanks and cohorts initiated by the WHO/IARC (International Agency for Research on Cancer) with focus on capacitybuilding in Low and Middle Income Countries. BCNet has perfomed an international evaluation of all open source LIMS systems available. The systems reviewed were OpenELIS, OpenSpecimen, LabKeyServer, BikaLIMS and Open-LIMS, and they were reviewed according to functionality, ease of installation and cost. The five differ- ent Open Source LIMS have different functional origins, such as public health laboratories for OpenELIS, data analysis requests for LabKey Server and BikaLIMS, laboratory experiment management for Open-LIMS, and biobanking for OpenSpecimen. The different systems have been in use for >10 years, except for Open-LIMS which was published in 2010. The evaluation concluded gave 2 of the systems the highest score (Open Specimen and BikaLIMS) and as they have different functional origins both systems will be recommended. BBMRI.se is already using both these systems. OpenSpecimen is used in a pilot at the BBMRI.se SouthernSweden Service Center and BikaLIMS is used in our ongoing collaboration between European and African biobanks in the B3Africa project. The entire evaluation can be downloaded from bbmri.se here: http://bbmri.se/Global/Nyhetsarkiv/2015/ LIMS_Evaluations_Final.pdf If you are interested to use either OpenSpecimen or BikaLIMS, please inquire at the BBMRI.se IT Services(info@bbmri.se). 16 biobank SWEDEN Public Opinion & Debate The Day of Action Recommendations: A position paper by the Intelligence in Science group A Day of Action led by BBMRI-ERIC was organized on 16 June 2015 with the aim of alerting EU policy makers to the harmful effects the General Data Protection Regulation could have on statistical, scientific and historical research and on healthcare if strict restrictions, including a requirement for specific consent, with only a narrow exception, in science and health research, are introduced. Participating organisations urged EU policy-makers to recognize the technical and ethical safeguards which already exist in research and to ensure that research and healthcare are not hindered by the General Data Protection Regulation. The Day of Action Recommendations on the general Data Protection Regulation are: i) The regulation should safeguard the interests of patients in medical research ii) The regulation should maintain the distinction between use of personal data for historical, statistical or scientific purposes, and data processing which is potentially harmful to data subjects iii) Harmonised rules for research at EU level would be preferable to promote transnational research collaboration. iv) The exemption from consent and other exemptions provided for historical, scientific, and statistical research in the Commission´s proposed General Data Protection Regulation and in the council´s general approach should be maintained to avoid negative effects on research. biobank SWEDEN is the newsletter of the BioBanking and Molecular Resource Infrastructure of Sweden (BBMRI.se). BBMRI.se is part of the European biobanking infrastructure BBMRI ERIC and is funded by the Swedish Research Council and by partner universities. To stay informed subscribe to info@bbmri.se. Also visit www.bbmri.se to find the newsletter as a pdf. Publisher: Joakim Dillner
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