Open Data in the Era of the GDPR: Lessons from the Human Cell Atlas

The Human Cell Atlas (HCA) is striving to build an open community that is inclusive of all researchers adhering to its principles and as open as possible with respect to data access and use. However, open data sharing can pose certain challenges. For instance, being a global initiative, the HCA must contend with a patchwork of local and regional privacy rules. A notable example is the implementation of the European Union General Data Protection Regulation (GDPR), which caused some concern in the biomedical and genomic data-sharing community. We examine how the HCA's large, international group of researchers is investing tremendous efforts into ensuring appropriate sharing of data. We describe the HCA's objectives and governance, how it defines open data sharing, and ethico-legal challenges encountered early in its development; in particular, we describe the challenges prompted by the GDPR. Finally, we broaden the discussion to address tools and strategies that can be used to address ethical data governance.

Genomics4RD: An integrated platform to share Canadian deep-phenotype and multiomic data for international rare disease gene discovery

Despite recent progress in the understanding of the genetic etiologies of rare diseases (RDs), a significant number remain intractable to diagnostic and discovery efforts. Broad data collection and sharing of information among RD researchers is therefore critical. In 2018, the Care4Rare Canada Consortium launched the project C4R‐SOLVE, a subaim of which was to collect, harmonize, and share both retrospective and prospective Canadian clinical and multiomic data. Here, we introduce Genomics4RD, an integrated web‐accessible platform to share Canadian phenotypic and multiomic data between researchers, both within Canada and internationally, for the purpose of discovering the mechanisms that cause RDs. Genomics4RD has been designed to standardize data collection and processing, and to help users systematically collect, prioritize, and visualize participant information. Data storage, authorization, and access procedures have been developed in collaboration with policy experts and stakeholders to ensure the trusted and secure access of data by external researchers. The breadth and standardization of data offered by Genomics4RD allows researchers to compare candidate disease genes and variants between participants (i.e., matchmaking) for discovery purposes, while facilitating the development of computational approaches for multiomic data analyses and enabling clinical translation efforts for new genetic technologies in the future.

184 Effects of The Coronavirus Pandemic on Medical and Surgical Education: Results of An International Survey by The International Association of Student Surgical Societies (IASSS)

Aim

Coronavirus disease 2019 (COVID-19) presents a variety of unforeseen challenges to medical students and surgical trainees. Adaptations to the content and delivery of medical education are inevitable as institutions respond to the virus. Departments face significant restructuring, with important implications for training. Our aim was to assess the global impact of the first wave of COVID-19 on medical and surgical education.

Method

Between 12 May and 26 May 2020, an online survey was conducted and circulated to contacts of the International Association of Student Surgical Societies, including medical students and healthcare practitioners. All data were anonymous; no personal identifiable information was collected. Consent was implied by participation in the survey, which was on a voluntary basis.

Results

We collated 527 responses from 111 institutions across 26 countries. Globally, 93.5% of medical student placements were affected by the first wave of COVID-19, with examination restructuring and alternative teaching methods employed by 87.8% of medical schools. Trainee redeployment was common in both surgical (61.5%) and non-surgical (77.1%) disciplines. Surgical services were significantly affected, with reduced elective procedures in 93% of institutions. On an individual level, COVID-19 resulted in prolonged absence from clinical duties and mental health concerns at all levels of training.

Conclusions

Our data highlight drastic changes in medical and surgical education and practice as a result of the first wave of COVID-19. These changes are significant at all levels of training, both institutionally and individually. The pandemic is likely to have persistent consequences for future trainees in terms of education and career progression.

Enhancing the Impact of Genomics Research in Autism through Integration of Research Results into Routine Care Pathways-A Case Series

The return of genetic results (RoR) to participants, enrolled as children, in autism research remains a complex process. Existing recommendations offer limited guidance on the use of genetic research results for clinical care. We highlight current challenges with RoR and illustrate how the use of a guiding framework drawn from existing literature facilitates RoR and the clinical integration of genetic research results. We report a case series (n = 16) involving the return of genetic results to participants in large genomics studies in Autism Spectrum Disorders (ASD). We outline the framework that guided RoR and facilitated integration into clinical care pathways. We highlight specific cases to illustrate challenges that were, or could have been, resolved through this framework. The case series demonstrates the ethical, clinical and practical difficulties of RoR in ASD genomic studies for participants enrolled as children. Challenges were resolved using pre-established framework to guide RoR and incorporate research genetic results into clinical care. We suggest that optimal use of genetic research results relies on their integration into individualized care pathways for participants. We offer a framework that attempts to bridge the gap between research and healthcare in ASD.

Knowledge, perceptions and experiences of nurses in antimicrobial optimization or stewardship in the intensive care unit

There is an urgent and recognized need for an interprofessional collaborative approach to support global action in addressing antimicrobial resistance (AMR). Antimicrobial stewardship (AMS) refers to systematic approaches for antimicrobial optimization within healthcare organizations. In areas with high antimicrobial utilization such as intensive care units (ICUs), specific roles for nurses in AMS are not clearly defined. This review aimed to identify and to critically evaluate primary studies that examined knowledge, perspectives and experiences of nurses associated with antimicrobial use and optimization in ICUs. A systematic search of Medline, CINAHL, PsychINFO, EMBASE, PubMed, SCOPUS, Cochrane Library and Web of Science databases for primary studies published from 1^st January 2000 to 20^th March 2020 was performed. A convergent synthesis design was used to synthesize quantitative and qualitative data. Of the 898 studies initially screened, 26 were included. Most (18/26) studies were quantitative. All qualitative studies (6/26) were of high methodological quality. Studies where interventions were used (10/26) identified significant potential for ICU nurses to reduce antimicrobial use, time-to-antibiotic administration, and error rates. Barriers to nursing engagement included knowledge deficits in antimicrobial use, interprofessional dissonance and the culture of deference to physicians. Enhancing education, technology utilization, strong nursing leadership and robust organizational structures that support nurses were perceived as enablers to strengthen their roles in optimizing antimicrobial use. This review showed that nursing initiatives have significant potential to strengthen antimicrobial optimization in ICUs. Barriers and enablers to active engagement were identified.

The drivers of antimicrobial use across institutions, stakeholders and economic settings: a paradigm shift is required for effective optimization

OBJECTIVES

Significant antimicrobial overuse persists worldwide, despite overwhelming evidence of antimicrobial resistance and knowledge that optimization of antimicrobial use will slow the development of resistance. It is critical to understand why this occurs. This study aims to consider the social influences on antimicrobial use within hospitals in Australia, via an in-depth, multisite analysis.

METHODS

We used a qualitative multisite design, involving 222 individual semi-structured interviews and thematic analysis. Participants (85 doctors, 79 nurses, 31 pharmacists and 27 hospital managers) were recruited from five hospitals in Australia, including four public hospitals (two metropolitan, one regional and one remote) and one private hospital.

RESULTS

Analysis of the interviews identified social relationships and institutional structures that may have a strong influence on antimicrobial use, which must be addressed concurrently. (i) Social relationships that exist across settings: these include the influence of personal risk, hierarchies, inter- and intraprofessional dynamics and sense of futility in making a difference long term in relation to antimicrobial resistance. (ii) Institutional structures that offer context-specific influences: these include patient population factors (including socioeconomic factors, geographical isolation and local infection patterns), proximity and resource issues.

CONCLUSIONS

The success of antimicrobial optimization rests on adequate awareness and incorporation of multilevel influences. Analysis of the problem has tended to emphasize individual 'behaviour improvement' in prescribing rather than incorporating the problem of overuse as inherently multidimensional and necessarily incorporating personal, interpersonal and institutional variables. A paradigm shift is urgently needed to incorporate these critical factors in antimicrobial optimization strategies.

How Can We Not Waste Legacy Genomic Research Data?

Enabling genomic and biomedical data to be shared for secondary research purposes is not always straightforward for existing “legacy” data sets. Researchers may not know whether their data meet ethical and regulatory requirements for sharing. As a result, these data, collected using public funds and the good will and efforts of the donors and investigators, may not be used beyond their original purpose. Single-use plastics are now being banned in many countries; single-use research should be avoided if possible. This paper describes a filter developed through the driver projects of the Global Alliance for Genomics and Health that can be used by researchers to help them determine the extent of sharing possible for their legacy data and actions to be taken to enable further sharing.

Ethical, Legal, and Regulatory Issues for the Implementation of Omics-Based Risk Prediction of Women's Cancer: Points to Consider

BACKGROUND AND OBJECTIVE

Advances in omics open new opportunities for cancer risk prediction and risk-based screening interventions. However, implementation of risk prediction in clinical practice may impact the ethical, legal, and regulatory aspects of current cancer screening programs. In order to support decision-making, we analyzed the ethical, legal, and regulatory issues and developed a set of Points to Consider to support management of these issues.

METHODS

We analyzed the legal and policy frameworks applicable to breast and cervical cancer screening programs in 7 European countries. We identified the most relevant issues to be considered, and we developed considerations for their management, based on the literature, the legal and policy frameworks, and our experience with similar issues.

RESULTS

The considerations focus on five topics: (A) health services planning, (B) information and invitation, (C) consent and data/sample collection, (D) risk calculation and communication of results, and (E) storage of data and residual samples.

CONCLUSION

Current frameworks might not be adequate to implement a risk prediction approach using omics factors due to the different characteristics of such approaches.

Responsible sharing of biomedical data and biospecimens via the "Automatable Discovery and Access Matrix" (ADA-M)

Given the data-rich nature of modern biomedical research, there is a pressing need for a systematic, structured, computer-readable way to capture, communicate, and manage sharing rules that apply to biomedical resources. This is essential for responsible recording, versioning, communication, querying, and actioning of resource sharing plans. However, lack of a common “information model” for rules and conditions that govern the sharing of materials, methods, software, data, and knowledge creates a fundamental barrier. Without this, it can be virtually impossible for Research Ethics Committees (RECs), Institutional Review Boards (IRBs), Data Access Committees (DACs), biobanks, and end users to confidently track, manage, and interpret applicable legal and ethical requirements. This raises costs and burdens of data stewardship and decreases efficient and responsible access to data, biospecimens, and other resources. To address this, the GA4GH and IRDiRC organizations sponsored the creation of the Automatable Discovery and Access Matrix (ADA-M, read simply as “Adam”). ADA-M is a comprehensive information model that provides the basis for producing structured metadata “Profiles” of regulatory conditions, thereby enabling efficient application of those conditions across regulatory spheres. Widespread use of ADA-M will aid researchers in globally searching and prescreening potential data and/or biospecimen resources for compatibility with their research plans in a responsible and efficient manner, increasing likelihood of timely DAC approvals while also significantly reducing time and effort DACs, RECs, and IRBs spend evaluating resource requests and research proposals. Extensive online documentation, software support, video guides, and an Application Programming Interface (API) for ADA-M have been made available.

Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder

We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10^-4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.

Optimizing antibiotic usage in hospitals: a qualitative study of the perspectives of hospital managers

BACKGROUND

Antibiotic optimization in hospitals is an increasingly critical priority in the context of proliferating resistance. Despite the emphasis on doctors, optimizing antibiotic use within hospitals requires an understanding of how different stakeholders, including non-prescribers, influence practice and practice change.

AIM

This study was designed to understand Australian hospital managers' perspectives on antimicrobial resistance, managing antibiotic governance, and negotiating clinical vis-à-vis managerial priorities.

METHODS

Twenty-three managers in three hospitals participated in qualitative semi-structured interviews in Australia in 2014 and 2015. Data were systematically coded and thematically analysed.

FINDINGS

The findings demonstrate, from a managerial perspective: (1) competing demands that can hinder the prioritization of antibiotic governance; (2) ineffectiveness of audit and monitoring methods that limit rationalization for change; (3) limited clinical education and feedback to doctors; and (4) management-directed change processes are constrained by the perceived absence of a 'culture of accountability' for antimicrobial use amongst doctors.

CONCLUSION

Hospital managers report considerable structural and interprofessional challenges to actualizing antibiotic optimization and governance. These challenges place optimization as a lower priority vis-à-vis other issues that management are confronted with in hospital settings, and emphasize the importance of antimicrobial stewardship (AMS) programmes that engage management in understanding and addressing the barriers to change.

Developing an Ethical and Legal Interoperability Assessment Process for Retrospective Studies

The past decade has witnessed the creation of major international research consortia, aiming to facilitate the sharing of data from different studies to maximize health benefits. However, combining heterogeneous data across existing studies requires addressing issues related to both data harmonization and ethical and legal interoperability. This article proposes a rigorous interoperability assessment process to assess whether different data sets are sufficiently ethically and legally interoperable to allow for a given proposed research use. The methodology used to develop this process is based on a comprehensive analysis of the international ethical and legal framework governing the use of retrospective data in research, and includes the following steps: (I) finding existing processes; (II) comparing processes to identify similarities and differences and determining the limits of the "consistent whole"; (III) establishing common principles and procedures; and, (IV) changing or removing processes that do not contribute to the consistent whole. Each of these four steps were examined using step-specific methodologies, including (a) literature and policy reviews; (b) consultations with international ethical, legal and social implications (ELSI) experts; and (c) a case study piloting the proposed framework in an actual international research consortium. This assessment process takes into account key legal and ethical components such as consent, recontact, and waiver of consent. As a result, this analysis allows the development of a comprehensive filter used to verify the legal and ethical restrictions pertaining to a data set. This in turns helps in determining whether the given data set can to be used for a proposed research project, or is ethically and legally interoperable for use in research collaborations. By integrating this filter to the regular data access processes used by cohorts, not only will researchers be able to create virtual "mega-cohorts" of research participants, but it will also ensure that these cohorts respect basic legal and ethical precepts.

Synthesis of cold-insoluble globulin by cultured calf endothelial cells

Radiolabeled amino acids were incorporated into nondialyzable protein by cultures of endothelial cells derived from calf aorta. Antibody prepared against purified bovine plasma cold-insoluble globulin (CIG) formed a strong precipitin line upon immunodiffusion against 3H-labeled proteins from endothelial cell culture media. This precipitin line formed a line of identity with the precipitin line formed by anti-CIG and purified CIG. Double-antibody immunoprecipitation of 3H-labeled protein showed that 36.3% of the radioactivity was specifically precipitated by the anti-CIG antibody. Gel filtration and polyacrylamide gel electrophoresis of the immunoprecipitate indicated that it contained a single protein species whose molecular weight was consistent with that of CIG isolated from plasma. When cultured cells were examined by indirect immunofluorescence microscopy, the endothelial cells stained specifically with anti-CIG antibody. These data indicate that cultured endothelial cells derived from calf aorta synthesize and secrete a protein antigenically similar to CIG.