Biobank resources for future patient care: developments, principles and concepts

The aim of the overview is to give a perspective of global biobank development is given in a view of positioning biobanking as a key resource for healthcare to identify new potential markers that can be used in patient diagnosis and complement the targeted personalized drug treatment. The fast progression of biobanks around the world is becoming an important resource for society where the patient benefit is in the focus, with a high degree of personal integrity and ethical standard. Biobanks are providing patient benefits by large scale screening studies, generating large database repositories. It is envisioned by all participating stakeholders that the biobank initiatives will become the future gateway to discover new frontiers within life science and patient care. There is a great importance of biobank establishment globally, as biobanks has been identified as a key area for development in order to speed up the discovery and development of new drugs and protein biomarker diagnostics. One of the major objectives in Europe is to establish concerted actions, where biobank networks are being developed in order to combine and have the opportunity to share and build new science and understanding from complex disease biology. These networks are currently building bridges to facilitate the establishments of best practice and standardizations.     

Model requirements for Biobank Software Systems

Biobanks are essential tools in diagnostics and therapeutics research and development related to personalized medicine. Several international recommendations, standards and guidelines exist that discuss the legal, ethical, technological, and management requirements of biobanks. Today's biobanks are much more than just collections of biospecimens. They also store a huge amount of data related to biological samples which can be either clinical data or data coming from biochemical experiments. A well-designed biobank software system also provides the possibility of finding associations between stored elements. Modern research biobanks are able to manage multicenter sample collections while fulfilling all requirements of data protection and security. While developing several biobanks and analyzing the data stored in them, our research group recognized the need for a well-organized, easy-to-check requirements guideline that can be used to develop biobank software systems. International best practices along with relevant ICT standards were integrated into a comprehensive guideline: The Model Requirements for the Management of Biological Repositories (BioReq), which covers the full range of activities related to biobank development. The guideline is freely available on the Internet for the research community. AVAILABILITY: The database is available for free at http://bioreq.astridbio.com/bioreq_v2.0.pdf.     

生物样本库及其伦理问题简介

随着分子和基因组信息对流行病学影响的增加,无数遗传流行病学研究和后人类基因组计划的研究都越来越依赖人类生物样本库的使用。生物样本库的范围也已横跨学术或者医院环境下的小数量收集到大规模的全国性储藏。尽管生物样本库的概念并不新,但是在基因组研究和后人类基因组计划的背景下,伴随它们十几年极大发展的是无数待解决的伦理挑战。从生物样本库的概念着手,介绍了其与一般遗传数据库的区别以及建立生物样本库的意义;然后介绍并比较国际上已有的生物样本库,以及其伦理问题和伦理法律框架的发展趋势。     

Biobank governance: a lesson in trust

Biobanks are controversial due to their ethical, legal, and social implications. Recent discussion has highlighted a central role for governance in helping to address these controversies. We argue that sustainable governance of biobanks needs to be informed by public discourse. We present an analysis of a deliberative public engagement to explore the public values, concerns, and interests underlying recommendations pertaining to biobank governance. In particular, we identify five themes underlying expressed goals and concerns of participants regarding the development, operation and application of biobank research. Ultimately, we argue that, for the deliberants, governance represented a way to achieve trust in biobanks through accountability, transparency and control. As discussion of biobank governance moves the conceptual to the specific, policy makers and researchers should acknowledge the importance of the public viewpoint in maintaining trust; this acknowledgement is of importance to the ultimate success and longevity of biobanks.     

Beyond and within public engagement: a broadened approach to engagement in biobanking

Social studies on biobanking have traditionally focused on public engagement, that is, engagement with donors, patients and the general public as an important factor of sustainability. In this article, we claim that, in order to fully understand the way biobanks work, it is necessary to pay attention to a number of other actors, which have an equal, if not greater, impact on their practices and strategies. This means taking a broadened approach to biobank engagement. By using data collected from interviews with different biobank experts based in five different countries (UK, Canada, Finland, Spain and Iceland), we identify seven communities, including the public, that emerge as relevant. Such relationships condition the way biobanks develop, act and plan. The discussion illustrates how the relationships with those seven communities are articulated. We conclude that there is a need for a broadened approach to biobank engagement in order to understand biobank sustainability.     

Population biobanks: Organizational models and prospects of application in gene geography and personalized medicine

Population biobanks are collections of thoroughly annotated biological material stored for many years. Population biobanks are a valuable resource for both basic science and applied research and are essential for extensive analysis of gene pools. Population biobanks make it possible to carry out fundamental studies of the genetic structure of populations, explore their genetic processes, and reconstruct their genetic history. The importance of biobanks for applied research is no less significant: they are essential for development of personalized medicine and genetic ecological monitoring of populations and are in high demand in forensic science. Establishment of an efficient and representative biobank requires strict observance of the principles of sample selection in populations, protocols of DNA extraction, quality control, and storage and documentation of biological materials. We reviewed regional biobanks and presented the organizational model of population biobank establishment based on the Biobank of Indigenous Population of Northern Eurasia created under supervision of E.V. Balanovska and O.P. Balanovsky. The results obtained using the biobanks in transdisciplinary research and prospective applications for the purposes of genogeography, genomic medicine, and forensic science are presented.     

Power to the people: a wiki-governance model for biobanks

Biobanks are adopting various modes of public engagement to close the agency gap between participants and biobank builders. We propose a wiki-governance model for biobanks that harnesses Web 2.0, and which gives citizens the ability to collaborate in biobank governance and policymaking.     

The consent problem within DNA biobanks

Large prospective biobanks are being established containing DNA, lifestyle and health information in order to study the relationship between diseases, genes and environment. Informed consent is a central component of research ethics protection. Disclosure of information about the research is an essential element of seeking informed consent. Within biobanks, it is not possible at recruitment to describe in detail the information that will subsequently be collected because people will not know which disease they will develop. It will also be difficult to describe the specific research that will be performed using the biobank, other than to stipulate categories of research or diseases that are not included. Potential subjects can only be given information about the sorts of research that will be performed and by whom. Organisations responsible for biobanks usually argue that this disclosure of information is adequate when seeking informed consent, especially if coupled with a right to withdraw, as it would not be feasible or it would be too expensive to seek consent renewal on a regular basis. However, there are concerns about this 'blanket consent' approach'. Consent waivers have also been proposed in which research subjects entrust their consent with an independent third party to decide whether subsequent research using the biobank is consistent with the original consent provided by the subject.     

Population biobanking in selected European countries and proposed model for a Polish national DNA bank

Population biobanks offer new opportunities for public health, are rudimentary for the development of its new branch called Public Health Genomics, and are important for translational research. This article presents organizational models of population biobanks in selected European countries. Review of bibliography and websites of European population biobanks (UK, Spain, Estonia). Some countries establish national genomic biobanks (DNA banks) in order to conduct research on new methods of prevention, diagnosis and treatment of the genetic and lifestyle diseases and on pharmacogenetic research. Individual countries have developed different organizational models of these institutions and specific legal regulations regarding various ways of obtaining genetic data from the inhabitants, donors’ rights, organizational and legal aspects. Population biobanks in European countries were funded in different manners. In light of these solutions, the authors discuss prospects of establishing a Polish national genomic biobank for research purpose. They propose the creation of such an institution based on the existing network of blood-donation centres and clinical biobanks in Poland.     

Biobanking and international interoperability: samples

In terms of sample exchange, international collaborations between biobanks, or between biobanks and their research partners, have two important aspects. First, the donors’ consent usually implies that the scope and purpose of any sample transfer to third parties is subject to major constraints. Since the legal, ethical and political framework of biobanking may differ substantially, even between countries of comparable jurisdictional systems, general rules for the international sharing of biomaterial are difficult, if not impossible, to define. Issues of uncertainty include the right to transfer the material, the scope of research allowed, and intellectual property rights. Since suitable means of international law enforcement may not be available in the context of biobanking, collaborators are advised to clarify any residual uncertainty by means of bilateral contracts, for example, in the form of material transfer agreements. Second, biobank partners may rightly expect that the biomaterial they receive for further analysis attains a certain level of quality. This implies that a biobank has to implement stringent quality control measures covering, in addition to the material transfer itself, the whole process of material acquisition, transport, pre-analytical handling and storage. Again, it may be advisable for biobank partners to claim contractual warranties for the type and quality of the biomaterial they wish to acquire.     

Safeguarding donors’ personal rights and biobank autonomy in biobank networks: the CRIP privacy regime

Governance, underlying general ICT (Information and Communication Technology) architecture, and workflow of the Central Research Infrastructure for molecular Pathology (CRIP) are discussed as a model enabling biobank networks to form operational “meta biobanks” whilst respecting the donors’ privacy, biobank autonomy and confidentiality, and the researchers’ needs for appropriate biospecimens and information, as well as confidentiality. Tailored to these needs, CRIP efficiently accelerates and facilitates research with human biospecimens and data.     

‘It is an entrustment’: Broad consent for genomic research and biobanks in sub‐Saharan Africa

In recent years, there has been an increase in the establishment of biobanks for genetic and genomic studies around the globe. One example of this is the Human Heredity and Health in Africa Initiative (H3Africa), which has established biobanks in the sub‐region to facilitate future indigenous genomic studies. The concept of ‘broad consent’ has been proposed as a mechanism to enable potential research participants in biobanks to give permission for their samples to be used in future research studies. However, questions remain about the acceptability of this model of consent. Drawing on findings from empirical research about the role of trust in decision‐making, we argue that an account of entrustment may be an appropriate way of addressing current challenges of seeking consent for biobank research in Africa. We propose a set of key points to consider that can support the proposed entrustment framework.     

Biobanken

Biobanks have become an indispensable component of biomedical research. However, the long-term and unrestricted use of data and biomaterials included in most biobanks pose several legal, ethical and organizational challenges. Therefore, the German Telematics Platform for Medical Research Networks (TMF) has instigated a number of projects addressing the problems arising from the establishment and maintenance of biobanks, each time aiming at the provision of generic solutions to the research community in the form of texts and concepts. After a representative review of existing biobanks in Germany and Europe we provide an overview of the TMF work on biobanking. In addition, two infrastructural projects will be reviewed which should render biobanking in Germany and Europe more efficient and transparent in the future, namely the “Biobanking and Biomolecular Resources Research Infrastructure”(BBMRI) of the European Commission and the National Biobank Register that is currently being set up by the TMF.     

Domesticated Animal Biobanking: Land of Opportunity

In the past decade, biobanking has fuelled great scientific advances in the human medical sector. Well-established domesticated animal biobanks and integrated networks likewise harbour immense potential for great scientific advances with broad societal impacts, which are currently not being fully realised. Political and scientific leaders as well as journals and ethics committees should help to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals.In the last decade, human biobanking has emerged as an important driver of scientific activities, and biobanks are indisputably an invaluable resource for all types of research aimed at improving public health. The combination of accessible and well-characterized biological samples of various types linked with a multitude of associated data is driving scientific discoveries at unprecedented speed and making previously unthinkable lines of research a reality [1,2].Unfortunately, biobanking of animal samples is by far less well-established. In March 2015, Nature published an article, titled “Inside the first pig biobank,” describing a newly established biobank of porcine samples to be used in studying human diabetes and hailing it as a pioneering effort in animal biobanking [3]. A PubMed search confirmed that in comparison to human biobanking there appears to be negligible activity in the animal biobanking sector. Searching titles, abstracts, and keywords with the search keys “biobank,” “biobanking,” “genebank,” and “gene bank” and limiting the results to publication dates in 2015, only 9 of 498 search results referred to animal biobanks (see S1 Data). This apparent lack of activity in the animal biobanking sector is also reflected in a 2015 editorial of Biopreservation and Biobanking, the official journal of the International Society for Biological and Environmental Repositories (ISBER), which caters to biobanks of any species. The authors conclude that even though there has been increasing participation from the non-human biobanking sector in the annual ISBER meetings, there is still a pronounced lack of submissions to the journal pertaining to non-human biobanking, and human biobanking issues continue to dominate ISBER activities [4]. The roadmap of the European Council’s European Strategy Forum on Research Infrastructures (ESFRI) reveals that there are projects under way involving human (Biobanking and BioMolecular Resources Research Infrastructure [BBMRI]), marine (European Marine Biological Resource Centre [EMBRC]), microbial (Microbial Resource Research Infrastructure [MIRRI]), and mouse model (Infrafrontier) biobanks, with general animal biobanks starkly missing on that list [5].Naturally, some non-human biobanks storing animal samples, amongst others, do exist. The most active are likely the natural history collections, because they have the intrinsic task to collect, catalogue, and store specimens. The Global Genome Biodiversity Network (GGBN), established in 2011, acts as an umbrella organisation for biodiversity repositories and aims to establish standards and best practices as well as increase sample accessibility through its data portal [6]. A search of the most common domesticated animal species (cattle, sheep, goat, pig, horse, chicken, and dog) yielded only 13 records in the GGBN member repositories.However, some domesticated animal biobanks and less formalized sample collections can be found. Their hosting institutions range from veterinary hospitals, zoos, breeding and diagnostics companies, national farm animal genetic resource gene banks, to research institutes and universities. Depending on their purpose, the stored types of samples vary greatly and range from healthy tissue samples, diseased pathogenic tissue samples, DNA, and RNA to reproductive materials. An example of a well-established physical non-human biobanking infrastructure serving a university is the Swedish University of Agricultural Sciences’ (SLU) Biobank (http://www.slu.se/slubiobank). This biobank also offers a data portal for increasing the visibility and accessibility of non-human sample collections no matter where they are stored. This data portal would be redundant if all samples, together with their associated data, were stored in established biobanks that ensured the visibility of their samples through a network such as GGBN. In contrast, the European Genebank Network for Animal Genetic Resources (EUGENA), coordinated by the European Regional Focal Point on Animal Genetic Resources (http://www.rfp-europe.org), is an emerging networking activity specifically targeting only national farm animal genetic resource collections [7]. These disparate examples demonstrate that there is a lack of a unified and generalized approach to sample collections in the domesticated animal sector.Nonetheless, there are numerous examples of how different disciplines and stakeholders, and ultimately the general public, have already benefitted from the availability of biobanked domesticated animal samples.Even though the pig biobank was commended as a pioneering effort [3], there are in fact a number of biobanks that accommodate animal models for the study of human disease. The domestic dog, for example, with its unique population history, breed structure, and hundreds of spontaneous genetic conditions has proven to be an excellent model for gene mapping in simple and complex disorders [8]. Targeted and effective breeding programs over the past 150 years have created hundreds of distinct breeds that form genetic isolates with reduced genetic heterogeneity. This simplifies genetic studies because fewer susceptibility loci with higher impact contribute to complex disease and allow genetic breakthroughs with smaller study cohorts as compared to the corresponding human conditions [9].The annotation of the canine genome facilitated a rapid evolution of genomic tools and development of several canine biobanks across the continents [10]. Collectively, these biobanks house hundreds of thousands of DNA samples and tissue specimens for hundreds of conditions with medical relevance to humans. Importantly, many canine biobanks maintain active collaborative networks with the breeder community and dog fanciers as well as veterinary clinics and hospitals for patient recruitment and health updates.Besides playing an instrumental role for human health, biobanked animal samples heavily impact developments in food production and the sustainable management of the world’s finite resources. Biobanks in animal breeding, often referred to as gene banks, were initially established with the advent of new reproductive techniques, such as artificial insemination, and typically stored semen and embryos. These biobanks recently played a critical role in the swift implementation of genomic selection, which uses genome-wide SNP markers to predict the genetic merit of breeding individuals [11,12]. The efficient use of genomic selection requires large reference panels of individuals whose genetic values are known with high confidence. In cattle breeding, these are bulls with large numbers of offspring with recorded performance data, such as milk yield. Genomic selection could only be implemented so swiftly and successfully because DNA or semen samples from a large number of bulls were available from cattle breeding company biobanks, and these samples could be linked to performance records of the respective bulls’ offspring. This technology was first adopted by the dairy industry and can potentially result in a 60%–120% increase in the rate of genetic gain. Together with advanced genotyping and reproductive technologies, genomic selection has the potential to increase genetic improvement both in often neglected traits, such as feed efficiency and fertility, and in traits that only recently have become of interest, such as methane output in ruminants or adaptation to climate change [12]. Improvements in these traits are of great interest for ensuring global food security and sustainable management of our limited resources. Without the availability of the gene bank samples, as well as associated performance data records, this transformation would have taken decades, if it had happened at all.Biobanks also play an integral part in worldwide conservation efforts to counteract the well-documented loss of genetic diversity in production animals [13,14]. Slowly, the general perception that these repositories are only to be used in emergencies and as a last resort is changing. In 2012, the USDA National Animal Germplasm Program, for example, harboured more than 700,000 gamete and tissue samples from over 18,000 animals representing more than 130 breeds. From this repository, samples from more than 3,300 animals had been requested and distributed for use in research and industry by 2012. The applications included quantitative trait locus (QTL) studies, assessment of genetic distances, cryobiology research, generation of an experimental research line, reduction of inbreeding, and re-introduction of genotypic combinations lost in current production populations [14]. Samples from rare and endangered breeds are also finding use in research and development of the leading breeding companies. For example, in the Netherlands, a consortium of university and dairy industry partners genotyped samples from rare local cattle breeds to gain insight into the genetic background of milk fatty acid composition. Genomic-assisted introgression could ultimately be used to introduce favourable alleles found in the rare breeds into more widely used breeds.Biobanked samples also played an important role in fighting a viral infection, infectious pancreatic necrosis (IPN), which is common in farmed fish. This virus can lead to rates of >90% mortality in farmed Atlantic salmon, which, therefore, poses a threat to animal welfare and aquaculture industries. In 2008, a major QTL for IPN-resistance was detected in Atlantic salmon. Already, a year later, AquaGen, which supplies about 55% of Atlantic salmon eggs used commercially in Norway, was employing marker-assisted selection to produce IPN-resistant fish. This swift implementation of the QTL in marker-assisted selection was only possible due to the availability of biobanked samples collected in a challenge test in 2005 [15].In addition to combatting disease in animals, biobanked domestic animal samples also play a crucial role in fighting emerging infectious diseases that are often zoonotic, meaning that they can be transmitted between vertebrate animals and humans. Having access to samples of species that act as reservoirs of a disease greatly facilitates the work of public health responders during infectious disease outbreaks [16]. In this context, the collection and traceable link of associated samples, such as parasites, pathogens, and other microbiota, to their parent sample becomes especially important.We are convinced that these examples leave no doubt that biobanked animal samples hold great potential both for advancing human and animal health and welfare as well as securing future food production. Furthermore, the recent advent of cost-efficient gene modification technologies [17] envisages many production, performance, and health applications in livestock and companion animals and further adds interest in animal biobanks.When examining the causes for the low levels of activity in large-scale domesticated animal biobanking, both in regard to the establishment or use of existing physical biobanking infrastructures as well as overarching data portals, a number of hypotheses come to mind. The industries connected to domesticated animal biobanking, such as livestock and companion animal production and veterinary care, are dwarfed by the healthcare industry, so monetary incentives would presumably play a much smaller role. Legislation may have acted as a driver in the formalization and shaping of biobanks and differential legislation regarding the handling, storage, and sharing of human versus animal biosamples, and associated data may thus have led to disparate developments. It is moreover conceivable that the community around domesticated animal biobanking is more fragmented and consists of more diverse stakeholders (academic, non-profit, industrial) than the human biobanking community, which could explain the absence of large-scale cooperative umbrella projects. Moreover, there may be greater difficulties in drafting material transfer agreements for reproductive materials than for other types of samples.We will only be able to exploit the full potential if we, in parallel with human and biodiversity biobanking, tackle the challenges of standardized sampling, processing, and storage, sample visibility and accessibility, standardized codes for diagnoses, collection and storage of associated data with the possibility for updates, as well as ethical and regulatory issues. Here, it is advisable that the domesticated animal sector ensures full compatibility with and relies on existing initiatives wherever feasible. Especially important in this context is to ensure a link between samples and associated phenomic and genomic data, such as derived sequence data. To achieve agreement on standards, both in terms of sample processing and storage and sample visibility and accessibility, actors from veterinary hospitals, zoos, breeding and diagnostics companies, national farm animal genetic resource gene banks, research institutes, universities, and policymakers need to join forces. This is where we momentarily see a lack of coordinated efforts.To respond to these challenges and to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals, we propose that scientific and political leaders need to (i) acknowledge the inadequacy of the current situation, (ii) create opportunity and support for the establishment of an international research infrastructure for animal biobanking, and (iii) motivate academic and industrial stakeholders to develop and coordinate biobanks based on lessons learned from human and biodiversity biobanking.In Europe, the European Council’s ESFRI could play a leading role in the establishment of a domesticated animal biobanking network, including best practices, direly needed standards, and a common ontology. In a landscape analysis of European research infrastructures, the 2016 ESFRI roadmap acknowledges a gap in the agricultural and bio-economy sector and explicitly lists livestock facilities including gene banks [5]. While an increase in activities regarding biobanking of farm animal genetic resources is certainly relevant, we consider this not to be far-reaching enough. A step in the right direction would be to begin with compiling information on all existing animal biobanks, analogous to BBMRI’s catalogue for European human biobanks [18], which currently contains information on 340 biobanks (http://www.bbmriportal.eu/).Moreover, ethics committees should require the storage of samples and associated data in formalized biobanks for the approval of scientific experiments. Similarly, journals should apply the same standard to samples and associated data, as they currently apply to molecular data, in terms of storage in formalized repositories prior to publication.     

Data sharing across biobanks: epistemic values,data mutability and data incommensurability

Despite the centrality of epistemic issues in biobank knowledge generation, there is currently a lacuna in research addressing the epistemic assumptions of biobank science and data sharing. The article addresses this lacuna. Using the insights of philosophical and sociological analysis, we examine standardization and harmonization and central challenges biobank data-sharing faces. We defend two central epistemic values, namely “spatial and temporal translatability” and “epistemic adequacy” which foster effective biobank knowledge generation. The first refers to the way in which biobank data need to be re-usable and re-purposable by bioscience researchers who did not create them. Given the perennial issues of data mutability and incommensurability, we also propose “epistemic adequacy.” In uncovering the social and epistemic foundations of biobank science, we emphasize issues essential for achieving effective and transparent biobank practice and productive communication and engagement with the public about the nature, potential and limits of biobanks.     

Biobanks and the phantom public

This paper surveys the current state of knowledge about the relationship between different national publics and biobanks, how different publics perceive biobanks, and which issues are identified as important by various stakeholders. We discuss existing studies and emerging governance strategies dealing with the biobank–publics interface and argue that the search for phantom (biobank) public(s) is on, but still much needs to be done. We argue that the existing data originate in a relatively few regions, among them Northern Europe, the United Kingdom, and in certain U.S. states and are often based on survey research with small samples and short questionnaires. Combined usage of qualitative and quantitative methodology in studies is still rare though of great importance in order to investigate distributions of public opinion and also to be able to explain these patterns. Many important questions in the relationship between publics and biobanks are unexplored, or the existing data are inconsistent.     

Establishing a neurological-psychiatric biobank: banking, informatics, ethics

The recent development of genetic databases and biobanks in a number of countries reflects scientist's beliefs in the future health benefits to be derived from genetic research. The NEPSYBANK is a national program of the Hungarian Clinical Neurogenetic Society with comprehensive participation of the Neurology and Psychiatry Departments of Medical Universities and the National Institute of Psychiatry and Neurology. The NEPSYBANK forms a part of the national biobank project (www.biobank.hu). The goal is to establish nationwide collaboration and common biobanking standards on quality, access, and protection of integrity in the field of neurology and psychiatry. Biological materials and databases are already collected in stroke, epilepsy, multiple sclerosis, motoneuron diseases, dementia, movement disorders, schizophrenia, and alcohol addiction. In peripheral neuropathies, neuropathic pain syndromes, muscle diseases, migraine, myasthenia gravis, depression, panic disease, anxiety, autism, and software development is in progress. The resources have been expanded by continued prospective collection of samples and data and important bottlenecks in sample purification, sample retrieval, in protection of the integrity of the research participants, as well as in guaranteeing the security and confidentiality of the participant's information have been harmonized. The development of uniform consent management, comprehensive sample overview and quality standards for health care-related biobanking may provide a unique opportunity for Hungary in molecular clinically oriented research. The program is a diseased-based research biobank with comprehensive collection of phenotypic and environmental information as well as biobanking of DNA, RNA or buffy coat, plasma, and erythrocytes stored at -80 degrees C. The biobank has a neuropathological part as well: storing conventional pathology and biopsy specimens. The analytical and informational demands being created by biobanking requires a "connectivity of community" that has not traditionally been present in the life sciences. As you put more resources into something, your silos tend to become taller, and we need to avoid this. The life science and healthcare community should be ignored working in individual "silos."     

SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images

The demand for accurate and reproducible phenotyping of a disease trait increases with the rising number of biobanks and genome wide association studies. Detailed analysis of histology is a powerful way of phenotyping human tissues. Nonetheless, purely visual assessment of histological slides is time-consuming and liable to sampling variation and optical illusions and thereby observer variation, and external validation may be cumbersome. Therefore, within our own biobank, computerized quantification of digitized histological slides is often preferred as a more precise and reproducible, and sometimes more sensitive approach. Relatively few free toolkits are, however, available for fully digitized microscopic slides, usually known as whole slides images. In order to comply with this need, we developed the slideToolkit as a fast method to handle large quantities of low contrast whole slides images using advanced cell detecting algorithms. The slideToolkit has been developed for modern personal computers and high-performance clusters (HPCs) and is available as an open-source project on github.com. We here illustrate the power of slideToolkit by a repeated measurement of 303 digital slides containing CD3 stained (DAB) abdominal aortic aneurysm tissue from a tissue biobank. Our workflow consists of four consecutive steps. In the first step (acquisition), whole slide images are collected and converted to TIFF files. In the second step (preparation), files are organized. The third step (tiles), creates multiple manageable tiles to count. In the fourth step (analysis), tissue is analyzed and results are stored in a data set. Using this method, two consecutive measurements of 303 slides showed an intraclass correlation of 0.99. In conclusion, slideToolkit provides a free, powerful and versatile collection of tools for automated feature analysis of whole slide images to create reproducible and meaningful phenotypic data sets.     

Combining efficiency and concerns about integrity when using human biobanks

In the debate about human bio-sampling the interests of patients and other sample donors are believed to stand against the interests of scientists and of their freedom of research. Scientists want efficient access to and use of human biological samples. Patients and other donors of blood or tissue materials want protection of their integrity. This dichotomy is reflected in the Swedish law on biobanks, which came into effect 1 January 2003. In this article I argue that if the basic interest of scientists using human biological samples is in increasing knowledge and developing better treatments, and if the concept 'integrity' is properly understood, then sample donors should also be interested in promotion of efficiency as well as in the protection of their integrity. The basic premise of this argument is that donors of samples have interests related to the donation and use of samples as well as to the use of the results of the research, that is, new medical products and treatments. They have a role both as donors or participants in research and as end users of the research. I conclude that if (i) access to information acquired through biobank research is strictly limited to researchers, (ii) the information is protected by secrecy safeguards through coding and (iii) the procedures governing the research are open to public and democratic control, then most research using human biobanks may be carried out on the basis of making general information available when collecting biological samples, without further contact with participants.     

Getting a Fair Share: Attitudes and Perceptions of Biobank Stakeholders Concerning the Fairness of Sample Sharing

Biobanks are essential tools for furthering a broad range of medical research areas. However, despite the plethora of national and international laws and guidelines which apply to them, the access and sharing policies of biobanks are only sparsely addressed by regulatory bodies. The ‘give and take’ process of biosample sharing is largely left up to biobank stakeholders themselves to oversee; it is therefore both in stakeholders' power, and in their interest, to ensure that sample accessibility is fair. This is an important step in motivating researchers to collaborate and pool samples, and is crucial to fostering trust in the absence of universally accepted standard practices. To date, little attention has been paid to how fairness considerations affect scientific material sharing, and no empirical research has been carried out to determine the role that fairness plays in collaborative studies. In order to begin to gain understanding in this area, we interviewed 36 biobank stakeholders currently working in Switzerland, focusing on their perceptions of current and optimal fair sharing practices. Our findings reveal that fairness is an important feature of exchange situations for these stakeholders, and that they have well‐formed notions about the practical elements of fair sample access, although ideas about the concept of fairness itself are vague. In order to support efforts to network biobanks, attention should be paid to this issue to reassure all involved that they are getting a fair share in their cooperative efforts.