The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest.

Model consent clauses for rare disease research.

BACKGROUND: Rare Disease research has seen tremendous advancements over the last decades, with the development of new technologies, various global collaborative efforts and improved data sharing. To maximize the impact of and to further build on these developments, there is a need for model consent clauses for rare diseases research, in order to improve data interoperability, to meet the informational needs of participants, and to ensure proper ethical and legal use of data sources and participants' overall protection. METHODS: A global Task Force was set up to develop model consent clauses specific to rare diseases research, that are comprehensive, harmonized, readily accessible, and internationally applicable, facilitating the recruitment and consent of rare disease research participants around the world. Existing consent forms and notices of consent were analyzed and classified under different consent themes, which were used as background to develop the model consent clauses. RESULTS: The IRDiRC-GA4GH MCC Task Force met in September 2018, to discuss and design model consent clauses. Based on analyzed consent forms, they listed generic core elements and designed the following rare disease research specific core elements; Rare Disease Research Introductory Clause, Familial Participation, Audio/Visual Imaging, Collecting, storing, sharing of rare disease data, Recontact for matching, Data Linkage, Return of Results to Family Members, Incapacity/Death, and Benefits. CONCLUSION: The model consent clauses presented in this article have been drafted to highlight consent elements that bear in mind the trends in rare disease research, while providing a tool to help foster harmonization and collaborative efforts.

Data Safe Havens in health research and healthcare.

MOTIVATION: The data that put the 'evidence' into 'evidence-based medicine' are central to developments in public health, primary and hospital care. A fundamental challenge is to site such data in repositories that can easily be accessed under appropriate technical and governance controls which are effectively audited and are viewed as trustworthy by diverse stakeholders. This demands socio-technical solutions that may easily become enmeshed in protracted debate and controversy as they encounter the norms, values, expectations and concerns of diverse stakeholders. In this context, the development of what are called 'Data Safe Havens' has been crucial. Unfortunately, the origins and evolution of the term have led to a range of different definitions being assumed by different groups. There is, however, an intuitively meaningful interpretation that is often assumed by those who have not previously encountered the term: a repository in which useful but potentially sensitive data may be kept securely under governance and informatics systems that are fit-for-purpose and appropriately tailored to the nature of the data being maintained, and may be accessed and utilized by legitimate users undertaking work and research contributing to biomedicine, health and/or to ongoing development of healthcare systems. RESULTS: This review explores a fundamental question: 'what are the specific criteria that ought reasonably to be met by a data repository if it is to be seen as consistent with this interpretation and viewed as worthy of being accorded the status of 'Data Safe Haven' by key stakeholders'? We propose 12 such criteria. CONTACT: paul.burton@bristol.ac.uk.

Data harmonization and federated analysis of population-based studies: the BioSHaRE project.

BACKGROUND: Individual-level data pooling of large population-based studies across research centres in international research projects faces many hurdles. The BioSHaRE (Biobank Standardisation and Harmonisation for Research Excellence in the European Union) project aims to address these issues by building a collaborative group of investigators and developing tools for data harmonization, database integration and federated data analyses. METHODS: Eight population-based studies in six European countries were recruited to participate in the BioSHaRE project. Through workshops, teleconferences and electronic communications, participating investigators identified a set of 96 variables targeted for harmonization to answer research questions of interest. Using each study's questionnaires, standard operating procedures, and data dictionaries, harmonization potential was assessed. Whenever harmonization was deemed possible, processing algorithms were developed and implemented in an open-source software infrastructure to transform study-specific data into the target (i.e. harmonized) format. Harmonized datasets located on server in each research centres across Europe were interconnected through a federated database system to perform statistical analysis. RESULTS: Retrospective harmonization led to the generation of common format variables for 73% of matches considered (96 targeted variables across 8 studies). Authenticated investigators can now perform complex statistical analyses of harmonized datasets stored on distributed servers without actually sharing individual-level data using the DataSHIELD method. CONCLUSION: New Internet-based networking technologies and database management systems are providing the means to support collaborative, multi-center research in an efficient and secure manner. The results from this pilot project show that, given a strong collaborative relationship between participating studies, it is possible to seamlessly co-analyse internationally harmonized research databases while allowing each study to retain full control over individual-level data. We encourage additional collaborative research networks in epidemiology, public health, and the social sciences to make use of the open source tools presented herein.

Biobanking and deceased persons.

Early biomedical research focused primarily on the study of specific diseases or sets of diseases within small groups of living research participants. Accordingly, the first ethical frameworks governing biomedical research addressed short-term, limited-scope research involving living research participants. Due to recent interest in longitudinal population studies and biobanking, research is increasingly long term. This shift raises several ethical and legal issues concerning the impact of a participant's death on research. This paper offers an overview of these issues in the context of longitudinal biobanking genetic research. Our first part outlines the legal and ethical frameworks that govern the effect of the participants' death on consent. This will be followed by an analysis of the legal and ethical frameworks that govern the secondary use of deceased participants' data and samples and the return of deceased participants' individual research results to biological family members. In our second part, we will review the current literature and discuss the above mentioned issues using the bioethics "principlism" theory before concluding.

Regulatory approval for new pharmacogenomic tests: a comparative overview.

Pharmacogenomics is the study of how genetic variants affect the way in which an individual or subgroup responds to drugs. This developing field aims to inform individual drug therapy and to minimize adverse drug reactions (ADRs). It also promises great benefits in the drug development process. Innovation in pharmacogenomics and its translation into clinical practice is desirable, but appropriate regulation of the safety and effectiveness of pharmacogenomics testing is necessary. This article will describe the current regulatory framework applicable to pharmacogenomic tests in Canada, the United States and Europe. In particular, it will examine the different regulatory pathways for pharmacogenomic tests marketed as test kits and for laboratory-developed tests (LDTs). Recent and upcoming changes to the regulation of pharmacogenomic tests will also be discussed. For example, FDA's proposal to regulate LDTs could have a major impact on the development and availability of pharmacogenomic tests. This review will lead to an evaluation of the issues raised by the regulatory framework and the impact of regulatory changes in relation to meeting the goals of ensuring public safety and promoting the advancement of pharmacogenomics. Regulatory policies which successfully achieve the dual objectives of ensuring public safety and promoting innovation in health technology are imperative in order to reap the benefits of this emerging field.

European recommendations integrating genetic testing into multidisciplinary management of sudden cardiac death.

Sudden cardiac death (SCD) accounts for 10-20% of total mortality, i.e., one in five individuals will eventually die suddenly. Given the substantial genetic component of SCD in younger cases, postmortem genetic testing may be particularly useful in elucidating etiological factors in the cause of death in this subset. The identification of genes responsible for inherited cardiac diseases have led to the organization of cardiogenetic consultations in many countries worldwide. Expert recommendations are available, emphasizing the importance of genetic testing and appropriate information provision of affected individuals, as well as their relatives. However, the context of postmortem genetic testing raises some particular ethical, legal, and practical (including economic or financial) challenges. The Public and Professional Policy Committee of the European Society of Human Genetics (ESHG), together with international experts, developed recommendations on management of SCD after a workshop sponsored by the Brocher Foundation and ESHG in November 2016. These recommendations have been endorsed by the ESHG Board, the European Council of Legal Medicine, the European Society of Cardiology working group on myocardial and pericardial diseases, the ERN GUARD-HEART, and the Association for European Cardiovascular Pathology. They emphasize the importance of increasing the proportion of both medical and medicolegal autopsies and educating the professionals. Multidisciplinary collaboration is of utmost importance. Public funding should be allocated to reach these goals and allow public health evaluation.

Barriers and Opportunities in Consent and Access Procedures in Low- and Middle-Income Country Biobanks: Meeting Notes from the BCNet Training and General Assembly.

As biobanking research in low- and middle-income countries (LMICs) continues to grow, novel legal and policy considerations have arisen. Also, while an expansive literature has developed around these issues, the views and concerns of individual researchers in these contexts have been less actively studied. These meeting notes aim to contribute to the growing literature on biobanking in LMICs by communicating a number of challenges and opportunities identified by biobank researchers themselves. Specifically, we describe concerns that emerge in consent and access policy domains. First, we present a review of the literature on distinct policy and legal concerns faced in LMICs, giving special attention to the general absence of practitioner perspectives. From there, we outline and discuss considerations that were raised by meeting participants at a Biobank and Cohort Building Network (BCNet) Ethical, Legal, and Social Issues training program. We conclude by proposing that the unique perspectives of biobank researchers in LMICs should be given serious attention and further research on these perspectives should be conducted.

Simplifying research access to genomics and health data with Library Cards.

The volume of genomics and health data is growing rapidly, driven by sequencing for both research and clinical use. However, under current practices, the data is fragmented into many distinct datasets, and researchers must go through a separate application process for each dataset. This is time-consuming both for the researchers and the data stewards, and it reduces the velocity of research and new discoveries that could improve human health. We propose to simplify this process, by introducing a standard Library Card that identifies and authenticates researchers across all participating datasets. Each researcher would only need to apply once to establish their bona fides as a qualified researcher, and could then use the Library Card to access a wide range of datasets that use a compatible data access policy and authentication protocol.

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.

Epigenome-based cancer risk prediction: rationale, opportunities and challenges.

The incidence of cancer is continuing to rise and risk-tailored early diagnostic and/or primary prevention strategies are urgently required. The ideal risk-predictive test should: integrate the effects of both genetic and nongenetic factors and aim to capture these effects using an approach that is both biologically stable and technically reproducible; derive a score from easily accessible biological samples that acts as a surrogate for the organ in question; and enable the effectiveness of risk-reducing measures to be monitored. Substantial evidence has accumulated suggesting that the epigenome and, in particular, DNA methylation-based tests meet all of these requirements. However, the development and implementation of DNA methylation-based risk-prediction tests poses considerable challenges. In particular, the cell type specificity of DNA methylation and the extensive cellular heterogeneity of the easily accessible surrogate cells that might contain information relevant to less accessible tissues necessitates the use of novel methods in order to account for these confounding issues. Furthermore, the engagement of the scientific community with health-care professionals, policymakers and the public is required in order to identify and address the organizational, ethical, legal, social and economic challenges associated with the routine use of epigenetic testing.

Consent Processes for Mobile App Mediated Research: Systematic Review.

BACKGROUND: Since the launch of ResearchKit on the iOS platform in March 2015 and ResearchStack on the Android platform in June 2016, many academic and commercial institutions around the world have adapted these frameworks to develop mobile app-based research studies. These studies cover a wide variety of subject areas including melanoma, cardiomyopathy, and autism. Additionally, these app-based studies target a variety of participant populations, including children and pregnant women. OBJECTIVE: The aim of this review was to document the variety of self-administered remote informed consent processes used in app-based research studies available between May and September 2016. Remote consent is defined as any consenting process with zero in-person steps, when a participant is able to join a study without ever seeing a member of the research team. This type of review has not been previously conducted. The research community would benefit from a rigorous interrogation of the types of consent taken as part of the seismic shift to entirely mobile meditated research studies. METHODS: This review examines both the process of information giving and specific content shared, with special attention to data privacy, aggregation, and sharing. RESULTS: Consistency across some elements of the app-based consent processes was found; for example, informing participants about how data will be curated from the phone. Variations in other elements were identified; for example, where specific information is shared and the level of detail disclosed. Additionally, several novel elements present in eConsent not typically seen in traditional consent for research were highlighted. CONCLUSIONS: This review advocates the importance of participant informedness in a novel and largely unregulated research setting.

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.

A Comparative Analysis of the Legal and Bioethical Frameworks Governing the Secondary Use of Data for Research Purposes.

The secondary use of research and health data for purposes that differ from the original purpose of the collection is becoming a major trend in research, since it allows for the optimal use of already available resources, and reduces the costs of research activities. However, the consent provided at the time of the initial data collection might not have foreseen these new uses of the data. This is especially true for biobanks having collected data under a restricted or a disease-specific consent, and for data linkage, which allows researchers to combine research data with information from the medical record of participants. To protect the participants' privacy, confidentiality, and autonomy, the use of identifiable research and clinical data for secondary research purposes is governed by a rather complex legal and ethical framework. This article aims to: (1) provide a comprehensive analysis of the legal and bioethical framework governing the secondary use of data at the international level, and; (2) identify points of convergence and divergence with regard to the secondary use of data for research purposes, in five countries (Australia, Canada, France, United Kingdom, and United States). While the secondary use of already collected data carries benefits and drawbacks, the international and national legal framework provide guidance to promote a wider (although limited) secondary use of data, while protecting research participants' rights and interests. Despite some differences, the similarities between international and national regulations and norms reveal the emergence of a common set of criteria for the secondary use of data in international research.

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.

Next-Generation Sequencing and the Return of Results.

The impact of next-generation sequencing (NGS) on the issue of return of results is defying clear policy guidance and creating international confusion. Limiting ourselves to the return of results revealed by NGS (including incidental findings) in adults, children, family members of deceased individuals, and population studies, we describe and contrast emerging policy positions in Europe, Canada, and the United States. Until there are clear, scientific, and professional standards and practical policy, both researchers and clinicians cannot be faulted for being either hesitant or pressured to return NGS results.

Access Governance for Biobanks: The Case of the BioSHaRE-EU Cohorts.

Currently, researchers have to apply separately to individual biobanks if they want to carry out studies that use samples and data from multiple biobanks. This article analyzes the access governance arrangements of the original five biobank members of the Biobank Standardisation and Harmonisation for Research Excellence in the European Union (BioSHaRE-EU) project in Finland, Germany, the Netherlands, Norway, and the United Kingdom to identify similarities and differences in policies and procedures, and consider the potential for internal policy "harmonization." Our analysis found differences in the range of researchers and organizations eligible to access biobanks; application processes; requirements for Research Ethics Committee approval; and terms of Material Transfer Agreements relating to ownership and commercialization. However, the main elements of access are the same across biobanks; access will be granted to bona fide researchers conducting research in the public interest, and all biobanks will consider the scientific merit of the proposed use and it's compatibility with the biobank's objectives. These findings suggest potential areas for harmonization across biobanks. This could be achieved through a single centralized application to a number of biobanks or a system of mutual recognition that places a presumption in favor of access to one biobank if already approved by another member of the same consortium. Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortia (BBMRI-ERIC), a European consortium of biobanks and bioresources with its own ethical, legal, and social implications (ELSI) common service, could provide a platform by developing guidelines for harmonized internal processes.

Recontacting Pediatric Research Participants for Consent When They Reach the Age of Majority.

Because children are presumed to have insufficient cognitive ability to consent to participate in research, pediatric research raises particular ethical and legal issues. For children who have not reached the age of consent stipulated by law or policy, parents (or legal guardians) must authorize their participation. This paper explores the issue of whether, to satisfy the ethical and legal norms of consent for research, participants in pediatric studies who attain the age of majority after their parents or guardians enrolled them in a study should be "recontacted" to obtain their consent to remain in the study. Using three different contexts (longitudinal studies, clinical trials, and newborn screening), we argue that distinctions should be made between the risks and benefits involved in recontacting for consent before determining the potential duties of researchers. An obligation to recontact should always be balanced with the feasibility and cost of such efforts in each particular research context and with consideration for the existence or lack of an ongoing relationship with the participant.

Genomic cloud computing: legal and ethical points to consider.

The biggest challenge in twenty-first century data-intensive genomic science, is developing vast computer infrastructure and advanced software tools to perform comprehensive analyses of genomic data sets for biomedical research and clinical practice. Researchers are increasingly turning to cloud computing both as a solution to integrate data from genomics, systems biology and biomedical data mining and as an approach to analyze data to solve biomedical problems. Although cloud computing provides several benefits such as lower costs and greater efficiency, it also raises legal and ethical issues. In this article, we discuss three key 'points to consider' (data control; data security, confidentiality and transfer; and accountability) based on a preliminary review of several publicly available cloud service providers' Terms of Service. These 'points to consider' should be borne in mind by genomic research organizations when negotiating legal arrangements to store genomic data on a large commercial cloud service provider's servers. Diligent genomic cloud computing means leveraging security standards and evaluation processes as a means to protect data and entails many of the same good practices that researchers should always consider in securing their local infrastructure.

P(3)G - 10 years of toolbuilding: From the population biobank to the clinic.

Over the past ten years, the Public Population Project in Genomics and Society ("P(3)G") has grown as a consortium. It has expanded its range of services and resources to adapt to the ever-evolving needs of the research community. From its outset - when P(3)G first tackled the building of biobanks as resources as well as data cataloguing and harmonization for data integration - to its new mission and vision, it has continually developed the tools for the conceptualization and design of population biobanks from their inception to their use to their closure. In so doing, P(3)G has become key in fostering research infrastructures to facilitate transition to the clinic. The consortium has become a crucial stakeholder in the international scientific, ethical, legal, and social research communities.