Toward a common language for biobanking.
Ontology highlight
ABSTRACT:
SUBMITTER: Fransson MN
PROVIDER: S-EPMC4266732 | biostudies-other | 2015 Jan
REPOSITORIES: biostudies-other
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Project description:Biobanks can have a pivotal role in elucidating disease etiology, translation, and advancing public health. However, meeting these challenges hinges on a critical shift in the way science is conducted and requires biobank harmonization. There is growing recognition that a common strategy is imperative to develop biobanking globally and effectively. To help guide this strategy, we articulate key principles, goals, and priorities underpinning a roadmap for global biobanking to accelerate health science, patient care, and public health. The need to manage and share very large amounts of data has driven innovations on many fronts. Although technological solutions are allowing biobanks to reach new levels of integration, increasingly powerful data-collection tools, analytical techniques, and the results they generate raise new ethical and legal issues and challenges, necessitating a reconsideration of previous policies, practices, and ethical norms. These manifold advances and the investments that support them are also fueling opportunities for biobanks to ultimately become integral parts of health-care systems in many countries. International harmonization to increase interoperability and sustainability are two strategic priorities for biobanking. Tackling these issues requires an environment favorably inclined toward scientific funding and equipped to address socio-ethical challenges. Cooperation and collaboration must extend beyond systems to enable the exchange of data and samples to strategic alliances between many organizations, including governmental bodies, funding agencies, public and private science enterprises, and other stakeholders, including patients. A common vision is required and we articulate the essential basis of such a vision herein.
| S-EPMC3477856 | biostudies-other
Project description:BACKGROUND:Efforts to improve informed consent have led to calls for providing information a reasonable person would want to have, in a way that facilitates understanding of the reasons why one might or might not want to participate. At the same time, advances in large-scale genomic research have expanded both the opportunities and the risks for participants, families, and communities. To advance the use of effective consent materials that reflect this landscape, we used empirical data to develop model consent language, as well as brief questions to assist people in thinking about their own values relative to participation. METHODS:We conducted in-person interviews to gather preliminary input on these materials from a diverse sample (n?=?32) of the general population in Nashville, Tennessee. We asked them to highlight information they found especially reassuring or concerning, their hypothetical willingness to participate, and their opinions about the values questions. RESULTS:Consent information most often highlighted as reassuring included the purpose of the biobank, the existence and composition of a multidisciplinary oversight committee, the importance of participants' privacy and efforts to protect it, and controlled access to a scientific database. Information most often highlighted as concerning included the deposition of data in a publicly accessible database, the risk of unintended access to data, the potential for non-research use of data, and use of medical record information in general. Seventy-five percent of participants indicated initial willingness to participate in the hypothetical biobank; this decreased to 66% as participants more closely considered the information over the course of the interview. A large majority rated the values questions as helpful. CONCLUSIONS:These results are consistent with other research on public perspectives on biobanking and genomic cohort studies, suggesting that our model language effectively captures commonly expressed reasons for and against participation. Our study enriches this literature by connecting specific consent form disclosures with qualitative data regarding what participants found especially reassuring or concerning and why. Interventions that facilitate individuals' closer engagement with consent information may result in participation decisions more closely aligned with their values.
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Project description:Previously, we investigated the effect of fungal VOCs on the behavior of phylogenetically different soil bacteria (Schmidt et al 2015). In these experiments we showed that VOCs emitted by several fungi can lead to phenotypical responses in bacteria, for example, by inducing a change in motility (Schmidt et al 2015). We observed that the plant pathogenic fungus Fusarium culmorum produced a unique cluster of VOCs consisting primarily of terpenes. When exposed to the VOCs emitted by this fungus, the rhizobacterium Serratia plymuthica PRI-2C responded with an induction of motility. It is plausible that in soil, microorganisms sense changes in their environments via shifts in VOCs blend and adapt their behavior accordingly (Garbeva et al 2014). Although several studies indicated that VOCs can be used as signaling molecules in microbial inter-species interactions, the following questions remain unanswered as how are VOCs perceived as signals by the microorganisms and which regulatory pathways and genes are involved in the response? To answer these questions, the rhizosphere isolate S. plymuthica PRI-2C was grown alone or exposed to VOCs emitted by F. culmorum. The bacterial transcriptome and proteome were analyzed under each situation to identify the molecular basis of the bacterial response to fungal VOCs.
2018-07-19 | PXD004819 | Pride
Project description:Language has been argued to arise, both ontogenetically and phylogenetically, from specific patterns of brain wiring. We argue that it can further be shown that core features of language processing emerge from particular phasal and cross-frequency coupling properties of neural oscillations; what has been referred to as the language 'oscillome.' It is expected that basic aspects of the language oscillome result from genetic guidance, what we will here call the language 'oscillogenome,' for which we will put forward a list of candidate genes. We have considered genes for altered brain rhythmicity in conditions involving language deficits: autism spectrum disorders, schizophrenia, specific language impairment and dyslexia. These selected genes map on to aspects of brain function, particularly on to neurotransmitter function. We stress that caution should be adopted in the construction of any oscillogenome, given the range of potential roles particular localized frequency bands have in cognition. Our aim is to propose a set of genome-to-language linking hypotheses that, given testing, would grant explanatory power to brain rhythms with respect to language processing and evolution.
| S-EPMC6206218 | biostudies-literature
Project description:Recent decades have seen a move toward evidence-based medicine to inform the clinical decision-making process with reproducible findings from high-quality research studies. There is a need for objective, quantitative measurement tools to increase the reliability and reproducibility of studies evaluating the efficacy of healthcare interventions, particularly in the field of physical and rehabilitative medicine. Surface electromyography (sEMG) is a non-invasive measure of muscle activity that is widely used in research but is under-utilized as a clinical tool in rehabilitative medicine. Other types of electrophysiological signals (e.g., electrocardiography, electroencephalography, intramuscular EMG) are commonly recorded by healthcare practitioners, however, sEMG has yet to successfully transition to clinical practice. Surface EMG has clear clinical potential as an indicator of muscle activation, however reliable extraction of information requires knowledge of the appropriate methods for recording and analyzing sEMG and an understanding of the underlying biophysics. These concepts are generally not covered in sufficient depth in the standard curriculum for physiotherapists and kinesiologists to encourage a confident use of sEMG in clinical practice. In addition, the common perception of sEMG as a specialized topic means that the clinical potential of sEMG and the pathways to application in practice are often not apparent. The aim of this paper is to address barriers to the translation of sEMG by emphasizing its benefits as an objective clinical tool and by overcoming its perceived complexity. The many useful clinical applications of sEMG are highlighted and examples provided to illustrate how it can be implemented in practice. The paper outlines how fundamental biophysics and EMG signal processing concepts could be presented to a non-technical audience. An accompanying tutorial with sample data and code is provided which could be used as a tool for teaching or self-guided learning. The importance of observing sEMG in routine use in clinic is identified as an essential part of the effective communication of sEMG recording and signal analysis methods. Highlighting the advantages of sEMG as a clinical tool and reducing its perceived complexity could bridge the gap between theoretical knowledge and practical application and provide the impetus for the widespread use of sEMG in clinic.
| S-EPMC7594523 | biostudies-literature
Project description:BackgroundThe availability of well-annotated prostate tissue samples through biobanks is key for research. Whereas fresh-frozen tissue is well suited for a broad spectrum of molecular analyses, its storage and handling is complex and cost-intensive. Formalin-fixed paraffin-embedded specimens (FFPE) are easy to handle and economic to store, but their applicability for molecular methods is restricted. The recently introduced Hepes-glutamic acid-buffer mediated Organic solvent Protection Effect (HOPE) is a promising alternative, which might have the potential to unite the benefits of FFPE and fresh-frozen specimen. Aim of the study was to compare HOPE-fixed, FFPE and fresh-frozen bio-specimens for their accessibility for diagnostic and research purposes.Methods10 prostate cancer samples were each preserved with HOPE, formalin, and liquid nitrogen and studied with in-situ and molecular methods. Samples were H&E stained, and assessed by immunohistochemistry (i.e. PSA, GOLPH2, p63) and FISH (i.e. ERG rearrangement). We assessed DNA integrity by PCR, using control genes ranging from 100 to 600 bp amplicon size. RNA integrity was assessed through qRT-PCR on three housekeeping genes (TBP, GAPDH, ?-actin). Protein expression was analysed by performing western blot analysis using GOLPH2 and PSA antibodies.ResultsOf the HOPE samples, morphologic quality of H&E sections, immunohistochemical staining, and the FISH assay was at least equal to FFPE tissue, and significantly better than the fresh-frozen specimens. DNA, RNA, and protein analysis of HOPE samples provided similar results as compared to fresh-frozen specimens. As expected, FFPE-samples were inferior for most of the molecular analyses.ConclusionsThis is the first study, comparatively assessing the suitability of these fixation methods for diagnostic and research utilization. Overall, HOPE-fixed bio-specimens combine the benefits of FFPE- and fresh-frozen samples. Results of this study have the potential to expand on contemporary prostate tissue biobanking approaches and can serve as a model for other organs and tumors.
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Project description:Next-generation DNA and RNA sequencing requires intact nucleic acids from high-quality human tissue samples to better elucidate the molecular basis of cancer. We have developed a prostate biobanking protocol to acquire suitable samples for sequencing without compromising the accuracy of clinical diagnosis. To assess the clinical implications of implementing this protocol, we evaluated 105 consecutive radical prostatectomy specimens from November 2008 to February 2009. Alternating levels of prostate samples were submitted to Surgical Pathology as formalin-fixed, paraffin-embedded blocks and to the institutional biobank as frozen blocks. Differences in reported pathologic characteristics between clinical and procured specimens were compared. Clinical staging and grading were not affected by the biobank protocol. Tumor foci on frozen hematoxylin and eosin slides were identified and high-density tumor foci were scored and processed for DNA and RNA extractions for sequencing. Both DNA and RNA were extracted from 22 cases of 44 with high-density tumor foci. Eighty-two percent (18/22) of the samples passed rigorous quality control steps for DNA and RNA sequencing. To date, DNA extracted from 7 cases has undergone whole-genome sequencing, and RNA from 18 cases has been RNA sequenced. This protocol provides prostate tissue for high-throughput biomedical research and confirms the feasibility of actively integrating prostate cancer into The Cancer Genome Atlas Program, a member of the International Cancer Genome Consortium.
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2016-05-22 | GSE71338 | GEO
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Project description:A systematic nomenclature for allergens originated in the early 1980s, when few protein allergens had been described. A group of scientists led by Dr. David G. Marsh developed a nomenclature based on the Linnaean taxonomy, and further established the World Health Organization/International Union of Immunological Societies (WHO/IUIS) Allergen Nomenclature Sub-Committee in 1986. Its stated aim was to standardize the names given to the antigens (allergens) that caused IgE-mediated allergies in humans. The Sub-Committee first published a revised list of allergen names in 1986, which continued to grow with rare publications until 1994. Between 1994 and 2007 the database was a text table online, then converted to a more readily updated website. The allergen list became the Allergen Nomenclature database (www.allergen.org), which currently includes approximately 880 proteins from a wide variety of sources. The Sub-Committee includes experts on clinical and molecular allergology. They review submissions of allergen candidates, using evidence-based criteria developed by the Sub-Committee. The review process assesses the biochemical analysis and the proof of allergenicity submitted, and aims to assign allergen names prior to publication. The Sub-Committee maintains and revises the database, and addresses continuous challenges as new "omics" technologies provide increasing data about potential new allergens. Most journals publishing information on new allergens require an official allergen name, which involves submission of confidential data to the WHO/IUIS Allergen Nomenclature Sub-Committee, sufficient to demonstrate binding of IgE from allergic subjects to the purified protein.
| S-EPMC6019191 | biostudies-literature