LAS: a software platform to support oncological data management

The rapid technological evolution in the biomedical and molecular oncology fields is providing research laboratories with huge amounts of complex and heterogeneous data. Automated systems are needed to manage and analyze this knowledge, allowing the discovery of new information related to tumors and the improvement of medical treatments. This paper presents the Laboratory Assistant Suite (LAS), a software platform with a modular architecture designed to assist researchers throughout diverse laboratory activities. The LAS supports the management and the integration of heterogeneous biomedical data, and provides graphical tools to build complex analyses on integrated data. Furthermore, the LAS interfaces are designed to ease data collection and management even in hostile environments (e.g., in sterile conditions), so as to improve data qualit

Controlled access under review : improving the governance of genomic data access

In parallel with massive genomic data production, data sharing practices have rapidly expanded over the last decade. To ensure authorized access to data, access review by data access committees (DACs) has been utilized as one potential solution. Here we discuss core elements to be integrated into the fabric of access review by both established and emerging DACs in order to foster fair, efficient, and responsible access to datasets. We particularly highlight the fact that the access review process could be adversely influenced by the potential conflicts of interest of data producers, particularly when they are directly involved in DACs management. Therefore, in structuring DACs and access procedures, possible data withholding by data producers should receive thorough attention

Introduction : biofutures/biopresents

Two very different reports produced for the UK government in the last three years have connected the state of our physical health with that of our material wealth. The first of these was produced in 2003 by the Bioscience Innovation and Growth Team (BIGT) titled Improving National Health, Improving National Wealth, whilst the second, called Health Inequalities-Status Report on the Programme for Action, was produced in 2005 by the Department of Health (DH).1 The former produced a series of recommendations designed to 'secure' the economic position of the UK bioscience industry and through this the health of the UK population, whilst the latter repeated the finding that socio-economic status and physical health are strongly related, revealing significant spatial and social health inequalities across the UK (see Batty, 2005; Shaw et al., 2005). These different understandings of the health-wealth link provide a useful foil to explore the central focus of this special issue, namely the construction and definition of particular problems and their solutions encompassing the technoscience of new genetics. Here the popular term technoscience is used to denote a technological context that promotes and maintains forms of scientific enquiry and understanding particular to that set of artefacts: in its simplest formulation, it posits that technology is both shaped by and shapes society. In this special issue we seek to explore the specific technoscientific context in which the biosciences-molecular biology, genetics, genomics, proteomics-are situated and subsequently promulgated: their biopresents and their biofutures. Using the government reports above to illustrate the context of the biosciences reveals two very different approaches to understanding national healthcare. The BIGT report implies that our health is dependent upon ensuring future industrial performance through building 'a mutually advantageous collaboration between the NHS and industry for patient benefit' (2003, p. 5). In contrast, the DH report implies that our health is dependent upon existing resource distribution with the government response, according to Shaw et al. (2005), consisting of an 'individualistic rhetoric of behavioural prevention [of illness]' as opposed to building 'mutually advantageous' alliances between different institutions. This is exemplified in the DH proposal for 'health trainers' for deprived areas which Caroline Flint MP, Minister for Public Health, says would assist people in adopting 'a healthier way of life' (quoted in Batty, 2005). Other wide-ranging changes to the UK health service have also been oriented towards promoting such an agenda based on personal choice, healthier lifestyles and medical innovations derived from modern biotechnology (i.e. targeted at individuals). Furthermore, this agenda has been supported by the extension of privatized provision of services across the NHS [see Pollock (2004) for a critical review]

Stakeholder engagement to ensure the sustainability of biobanks: a survey of potential users of biobank services

Biobanks are important infrastructures facilitating biomedical research. After a decade of rolling out such infrastructures, a shift in attention to the sustainability of biobanks could be observed in recent years. In this regard, an increase in the as yet relatively low utilisation rates of biobanks has been formulated as a goal. Higher utilisation rates can only be achieved if the perspectives of potential users of biobanks-particularly researchers not yet collaborating with biobanks-are adequately considered. To better understand their perspectives, a survey was conducted at ten different research institutions in Germany hosting a centralised biobank. The survey targeted potential users of biobank services, i.e. researchers working with biosamples. It addressed the general demand for biosamples, strategies for biosample acquisition/storage and reasons for/against collaborating with biobanks. In total, 354 researchers filled out the survey. Most interestingly, only a minority of researchers (12%) acquired their biosamples via biobanks. Of the respondents not collaborating with biobanks on sample acquisition, around half were not aware of the (services of the) respective local biobank. Those who actively decided against acquiring biosamples via a biobank provided different reasons. Most commonly, respondents stated that the biosamples required were not available, the costs were too high and information about the available biosamples was not readily accessible. Biobanks can draw many lessons from the results of the survey. Particularly, external communication and outreach should be improved. Additionally, biobanks might have to reassess whether their particular collection strategies are adequately aligned with local researchers' needs

Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

Despite the tremendous success, pitfalls have been observed in every step of a clinical metabolomics workflow, which impedes the internal validity of the study. Furthermore, the demand for logistics, instrumentations, and computational resources for metabolic phenotyping studies has far exceeded our expectations. In this conceptual review, we will cover inclusive barriers of a metabolomics-based clinical study and suggest potential solutions in the hope of enhancing study robustness, usability, and transferability. The importance of quality assurance and quality control procedures is discussed, followed by a practical rule containing five phases, including two additional "pre-pre-" and "post-post-" analytical steps. Besides, we will elucidate the potential involvement of machine learning and demonstrate that the need for automated data mining algorithms to improve the quality of future research is undeniable. Consequently, we propose a comprehensive metabolomics framework, along with an appropriate checklist refined from current guidelines and our previously published assessment, in the attempt to accurately translate achievements in metabolomics into clinical and epidemiological research. Furthermore, the integration of multifaceted multi-omics approaches with metabolomics as the pillar member is in urgent need. When combining with other social or nutritional factors, we can gather complete omics profiles for a particular disease. Our discussion reflects the current obstacles and potential solutions toward the progressing trend of utilizing metabolomics in clinical research to create the next-generation healthcare system.11Ysciescopu

Recommendations for a Dutch Sustainable Biobanking Environment

Biobanks and their collections are considered essential for contemporary biomedical research and a critical resource toward personalized medicine. However, they need to operate in a sustainable manner to prevent research waste and maximize impact. Sustainability is the capacity of a biobank to remain operative, effective, and competitive over its expected lifetime. This remains a challenge given a biobank's position at the interplay of ethical, societal, scientific, and commercial values and the difficulties in finding continuous funding. In the end, biobanks are responsible for their own sustainability. Still, biobanks also depend on their surrounding environment, which contains overarching legislative, policy, financial, and other factors that can either impede or promote sustainability. The Biobanking and Biomolecular Research Infrastructure for The Netherlands (BBMRI.nl) has worked on improving the national environment for sustainable biobanking. In this article, we present the final outcomes of this BBMRI.nl project. First, we summarize the current overarching challenges of the Dutch biobanking landscape. These challenges were gathered during workshops and focus groups with Dutch biobanks and their users, for which the full results are described in separate reports. The main overarching challenges relate to sample and data quality, funding, use and reuse, findability and accessibility, and the general image of biobanks. Second, we propose a package of recommendations—across nine themes—toward creating overarching conditions that stimulate and enable sustainable biobanking. These recommendations serve as a guideline for the Dutch biobanking community and their stakeholders to jointly work toward practical implementation and a better biobanking environment. There are undoubtedly parallels between the Dutch situation and the challenges found in other countries. We hope that sharing our project's approach, outcomes, and recommendations will support other countries in their efforts toward sustainable biobanking