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 [email protected]
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 [email protected]
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
([email protected]; 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
[email protected]
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([email protected]).
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 [email protected]. Also visit
www.bbmri.se to find the
newsletter as a pdf.
Publisher: Joakim Dillner