Samples and data accessibility in research biobanks. An explorative survey

Biobanks, which contain human biological samples and/or data, provide a crucial contribution to the progress of biomedical research. However, the effective and efficient use of biobank resources depends on their accessibility. In fact, making bio-resources promptly accessible to everybody may increase the benefits for society. Furthermore, optimizing their use and ensuring their quality will promote scientific creativity and, in general, contribute to the progress of bio-medical research. Although this has become a rather common belief, several laboratories are still secretive and continue to withhold samples and data. In this study, we conducted a questionnairebased survey in order to investigate sample and data accessibility in research biobanks operating all over the world. The survey involved a total of 46 biobanks. Most of them gave permission to access their samples (95.7%) and data (85.4%), but free and unconditioned accessibility seemed not to be common practice. The analysis of the guidelines regarding the accessibility to resources of the biobanks that responded to the survey highlights three issues: (i) the request for applicants to explain what they would like to do with the resources requested; (ii) the role of funding, public or private, in the establishment of fruitful collaborations between biobanks and research labs; (iii) the request of co-authorship in order to give access to their data. These results suggest that economic and academic aspects are involved in determining the extent of sample and data sharing stored in biobanks. As a second step of this study, we investigated the reasons behind the high diversity of requirements to access biobank resources. The analysis of informative answers suggested that the different modalities of resource accessibility seem to be largely influenced by both social context and legislation of the countries where the biobanks operate

an explorative survey

Biobanks, which contain human biological samples and/or data, provide a crucial contribution to the progress of biomedical research. However, the effective and efficient use of biobank resources depends on their accessibility. In fact, making bio-resources promptly accessible to everybody may increase the benefits for society. Furthermore, optimizing their use and ensuring their quality will promote scientific creativity and, in general, contribute to the progress of bio-medical research. Although this has become a rather common belief, several laboratories are still secretive and continue to withhold samples and data. In this study, we conducted a questionnaire-based survey in order to investigate sample and data accessibility in research biobanks operating all over the world. The survey involved a total of 46 biobanks. Most of them gave permission to access their samples (95.7%) and data (85.4%), but free and unconditioned accessibility seemed not to be common practice. The analysis of the guidelines regarding the accessibility to resources of the biobanks that responded to the survey highlights three issues: (i) the request for applicants to explain what they would like to do with the resources requested; (ii) the role of funding, public or private, in the establishment of fruitful collaborations between biobanks and research labs; (iii) the request of co-authorship in order to give access to their data. These results suggest that economic and academic aspects are involved in determining the extent of sample and data sharing stored in biobanks. As a second step of this study, we investigated the reasons behind the high diversity of requirements to access biobank resources. The analysis of informative answers suggested that the different modalities of resource accessibility seem to be largely influenced by both social context and legislation of the countries where the biobanks operate

When data sharing gets close to 100%. What human paleogenetics can teach the open science movement

This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% ± 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals’ editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers’ awareness of the importance of openness and transparency for scientific progress may complement stakeholders’ policies in achieving very high sharing rates. Second, widespread data sharing does not necessarily coincide with a prevalent use of practices which maximize data findability, accessibility, useability and preservation. A detailed look at the different ways in which data are released can be very useful to detect failures to adopt the best sharing modalities and understand how to correct them. Third and finally, the case of human paleogenetics tells us that a widespread awareness of the importance of Open Science may be important to build reliable scientific practices even in the presence of complex experimental challenges

Mitochondrial DNA variation of southern Tunisian populations

Due to its complex history of migrations and colonization of African, European and Asian people, the Tunisian territory is an ideal area to study the effects of cultural change on the genetic structure of human populations. We investigated the mtDNA genetic variation of Tunisian populations in order to detect the possible impact of recent historical events on their gene pool. Two Arab and three Berber communities were analysed using a comparison dataset of 45 other populations including African, Arabian, Asian, European and Near Eastern groups. The results obtained were compared with those produced using a large panel of autosomal SNPs. We observed a slight but important difference between the populations that inhabit the southern and central-northern areas of the country. Furthermore, robust signatures of genetic isolation were detected in two Berber populations (Nouvelle Zraoua and Tamezret) and in the seminomadic Arab group of the R’Baya. Our investigation suggests that the genetic structure of investigated southern Tunisian populations retains signatures of historical events which occurred between 7th-17th century, particularly the trans-Saharan slave trade and the emigration of Berbers in remote areas of the south during the Arab conquest

Open data, Science and Society: launching Oasis, the flagship initiative of the Istituto Italiano di Antropologia

The Open Data philosophy has gained considerable momentum in recent years, both in society and the scientific community. The accessibility via web of open data from the public sector has remarkably increased in the last decade, although there are substantial differences among nations (http://datacatalogs.org/). The expectation of many citizens, organizations and pressure groups (the so called “open government” movement) is that the free release of data from public administrations may help increase government transparency and accountability

Mine, Yours, Ours? Sharing Data on Human Genetic Variation

The achievement of a robust, effective and responsible form of data sharing is currently regarded as a priority for biological and bio-medical research. Empirical evaluations of data sharing may be regarded as an indispensable first step in the identification of critical aspects and the development of strategies aimed at increasing availability of research data for the scientific community as a whole. Research concerning human genetic variation represents a potential forerunner in the establishment of widespread sharing of primary datasets. However, no specific analysis has been conducted to date in order to ascertain whether the sharing of primary datasets is common-practice in this research field. To this aim, we analyzed a total of 543 mitochondrial and Y chromosomal datasets reported in 508 papers indexed in the Pubmed database from 2008 to 2011. A substantial portion of datasets (21.9%) was found to have been withheld, while neither strong editorial policies nor high impact factor proved to be effective in increasing the sharing rate beyond the current figure of 80.5%. Disaggregating datasets for research fields, we could observe a substantially lower sharing in medical than evolutionary and forensic genetics, more evident for whole mtDNA sequences (15.0% vs 99.6%). The low rate of positive responses to e-mail requests sent to corresponding authors of withheld datasets (28.6%) suggests that sharing should be regarded as a prerequisite for final paper acceptance, while making authors deposit their results in open online databases which provide data quality control seems to provide the best-practice standard. Finally, we estimated that 29.8% to 32.9% of total resources are used to generate withheld datasets, implying that an important portion of research funding does not produce shared knowledge. By making the scientific community and the public aware of this important aspect, we may help popularize a more effective culture of data sharing

Perspectives on Open Science and scientific data sharing::an interdisciplinary workshop

Looking at Open Science and Open Data from a broad perspective. This is the idea behind "Scientific data sharing: an interdisciplinary workshop", an initiative designed to foster dialogue between scholars from different scientific domains which was organized by the Istituto Italiano di Antropologia in Anagni, Italy, 2-4 September 2013.We here report summaries of the presentations and discussions at the meeting. They deal with four sets of issues: (i) setting a common framework, a general discussion of open data principles, values and opportunities; (ii) insights into scientific practices, a view of the way in which the open data movement is developing in a variety of scientific domains (biology, psychology, epidemiology and archaeology); (iii) a case study of human genomics, which was a trail-blazer in data sharing, and which encapsulates the tension that can occur between large-scale data sharing and one of the boundaries of openness, the protection of individual data; (iv) open science and the public, based on a round table discussion about the public communication of science and the societal implications of open science. There were three proposals for the planning of further interdisciplinary initiatives on open science. Firstly, there is a need to integrate top-down initiatives by governments, institutions and journals with bottom-up approaches from the scientific community. Secondly, more should be done to popularize the societal benefits of open science, not only in providing the evidence needed by citizens to draw their own conclusions on scientific issues that are of concern to them, but also explaining the direct benefits of data sharing in areas such as the control of infectious disease. Finally, introducing arguments from social sciences and humanities in the educational dissemination of open data may help students become more profoundly engaged with Open Science and look at science from a broader perspective

Search for Eccentric Black Hole Coalescences during the Third Observing Run of LIGO and Virgo

Despite the growing number of confident binary black hole coalescences observed through gravitational waves so far, the astrophysical origin of these binaries remains uncertain. Orbital eccentricity is one of the clearest tracers of binary formation channels. Identifying binary eccentricity, however, remains challenging due to the limited availability of gravitational waveforms that include effects of eccentricity. Here, we present observational results for a waveform-independent search sensitive to eccentric black hole coalescences, covering the third observing run (O3) of the LIGO and Virgo detectors. We identified no new high-significance candidates beyond those that were already identified with searches focusing on quasi-circular binaries. We determine the sensitivity of our search to high-mass (total mass $M>70$ $M_\odot$) binaries covering eccentricities up to 0.3 at 15 Hz orbital frequency, and use this to compare model predictions to search results. Assuming all detections are indeed quasi-circular, for our fiducial population model, we place an upper limit for the merger rate density of high-mass binaries with eccentricities $0 < e \leq 0.3$ at $0.33$ Gpc$^{-3}$ yr$^{-1}$ at 90\% confidence level.Comment: 24 pages, 5 figure

Model-independent search for the presence of new physics in events including H → γγ with s \sqrt{s} = 13 TeV pp data recorded by the ATLAS detector at the LHC

Abstract A model-independent search for new physics leading to final states containing a Higgs boson, with a mass of 125.09 GeV, decaying to a pair of photons is performed with 139 fb−1 of s $$\sqrt{s}$$ = 13 TeV pp collision data recorded by the ATLAS detector at the Large Hadron Collider at CERN. This search examines 22 final states categorized by the objects that are produced in association with the Higgs boson. These objects include isolated electrons or muons, hadronically decaying τ-leptons, additional photons, missing transverse momentum, and hadronic jets, as well as jets that are tagged as containing a b-hadron. No significant excesses above Standard Model expectations are observed and limits on the production cross section at 95% confidence level are set. Detector efficiencies are reported for all 22 signal regions, which can be used to convert detector-level cross-section limits reported in this paper to particle-level cross-section constraints