CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.

In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network.

User testing of a diagnostic decision support system with machine-assisted chart review to facilitate clinical genomic diagnosis.

OBJECTIVES: There is a need in clinical genomics for systems that assist in clinical diagnosis, analysis of genomic information and periodic reanalysis of results, and can use information from the electronic health record to do so. Such systems should be built using the concepts of human-centred design, fit within clinical workflows and provide solutions to priority problems. METHODS: We adapted a commercially available diagnostic decision support system (DDSS) to use extracted findings from a patient record and combine them with genomic variant information in the DDSS interface. Three representative patient cases were created in a simulated clinical environment for user testing. A semistructured interview guide was created to illuminate factors relevant to human factors in CDS design and organisational implementation. RESULTS: Six individuals completed the user testing process. Tester responses were positive and noted good fit with real-world clinical genetics workflow. Technical issues related to interface, interaction and design were minor and fixable. Testers suggested solving issues related to terminology and usability through training and infobuttons. Time savings was estimated at 30%-50% and additional uses such as in-house clinical variant analysis were suggested for increase fit with workflow and to further address priority problems. CONCLUSION: This study provides preliminary evidence for usability, workflow fit, acceptability and implementation potential of a modified DDSS that includes machine-assisted chart review. Continued development and testing using principles from human-centred design and implementation science are necessary to improve technical functionality and acceptability for multiple stakeholders and organisational implementation potential to improve the genomic diagnosis process.

Views on genomic research result delivery methods and informed consent: a review.

There has been little discussion of the way genomic research results should be returned and how to obtain informed consent for this. We systematically searched the empirical literature, identifying 63 articles exploring stakeholder perspectives on processes for obtaining informed consent about return of results and/or result delivery. Participants, patients and members of the public generally felt they should choose which results are returned to them and how, ranging from direct (face-to-face, telephone) to indirect (letters, emails, web-based delivery) communication. Professionals identified inadequacies in result delivery processes in the research context. Our findings have important implications for ensuring participants are supported in deciding which results they wish to receive or, if no choice is offered, preparing them for potential research outcomes.

The Human Genome Organisation (HUGO) and the 2020 COVID-19 pandemic.

This letter is the Human Genome Organisation's summary reaction to the 2020 COVID-19 pandemic. It identifies key areas for genomics research, and areas in which genomic scientists can contribute to a global response to the pandemic. The letter has been reviewed and endorsed by the HUGO Committee on Ethics, Law and Society (CELS) and the HUGO Council.

The genomics workforce must become more diverse: a strategic imperative.

The National Human Genome Research Institute (NHGRI) recently published a new strategic vision for the future of human genomics, the product of an extensive, multi-year engagement with numerous research, medical, educational, and public communities. The theme of this 2020 vision-The Forefront of Genomics-reflects NHGRI's critical role in providing responsible stewardship of the field of human genomics, especially as genomic methods and approaches become increasingly disseminated throughout biomedicine. Embracing that role, the new NHGRI strategic vision features a set of guiding principles and values that provide an ethical and moral framework for the field. One principle emphasizes the need to champion a diverse genomics workforce because "the promise of genomics cannot be fully achieved without attracting, developing, and retaining a diverse workforce, which includes individuals from groups that are currently underrepresented in the genomics enterprise." To build on the remarkable metamorphosis of the field over the last three decades, enhancing the diversity of the genomics workforce must be embraced as an urgent priority. Toward that end, NHGRI recently developed an "action agenda" for training, employing, and retaining a genomics workforce that reflects the diversity of the US population.

COVID-19 Pandemic and Africa: From the Situation in Zimbabwe to a Case for Precision Herbal Medicine.

This opinion commentary on the coronavirus disease 2019 (COVID-19) pandemic brings together observations from Zimbabwe specifically, and Africa broadly, drawing from the fields of pharmacogenomics, precision herbal medicine, and responsible innovation so as to respond to the pandemic in ways that are efficient, critically informed, principled, and responsive to needs in rural and urban communities across Africa. With new findings suggesting that COVID-19 is a systemic disease, impacting the respiratory system and beyond in some individuals, we need new molecular targets for therapeutics innovation more than ever. We argue that the current pandemic will likely strip the limited resources from other diseases such as malaria, human immunodeficiency virus (HIV) infection, and among others affecting the African continent. Hence, we need to address not only COVID-19 but also its broader health care and societal impacts in Africa. Extensive diagnostic testing to trace and isolate the COVID-19 cases as well as basic income and economic support for those who are unable to work will be needed. A critically informed and democratic governance that builds on transparency and trust for the elected leaders is crucial. Finally, the pandemic offers a silver lining for Africa: the prospects to integrate omics research with long-standing expertise in herbal medicine in Africa, thus accelerating the advances toward novel molecular therapeutic targets for COVID-19 and precision herbal medicine worldwide.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021.

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching its core database resources through big data deposition, integration and translation. In the past year, considerable efforts have been devoted to 2019nCoVR, a newly established resource providing a global landscape of SARS-CoV-2 genomic sequences, variants, and haplotypes, as well as Aging Atlas, BrainBase, GTDB (Glycosyltransferases Database), LncExpDB, and TransCirc (Translation potential for circular RNAs). Meanwhile, a series of resources have been updated and improved, including BioProject, BioSample, GWH (Genome Warehouse), GVM (Genome Variation Map), GEN (Gene Expression Nebulas) as well as several biodiversity and plant resources. Particularly, BIG Search, a scalable, one-stop, cross-database search engine, has been significantly updated by providing easy access to a large number of internal and external biological resources from CNCB-NGDC, our partners, EBI and NCBI. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.

Establishment and implementation of Cancer Genomic Medicine in Japan.

Approximately 1 in 2 Japanese people are estimated to be diagnosed with cancer during their lifetime. Cancer still remains the leading cause of death in Japan, therefore the government of Japan has decided to develop a better cancer control policy and launched the Cancer Genomic Medicine (CGM) program. The Ministry of Health, Labour, and Welfare (MHLW) held a consortium at their headquarters with leading academic authorities and the representatives of related organizations to discuss ways to advance CGM in Japan. Based on the report of the consortium, the CGM system under the national health insurance system has gradually been realized. Eleven hospitals were designated in February 2018 as core hospitals for CGM; subsequently, the MHLW built the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) as an institution to aggregate and manage genomic and clinical information on cancer patients, and support appropriate secondary use of the aggregated information to develop research aimed at medical innovation. As the first step in Japan's CGM in routine practice, in June 2019 the MHLW started reimbursement of 2 types of tumor profiling tests for advanced solid cancer patients using the national insurance system. Japan's CGM has swiftly been spreading nationwide with the collaboration of 167 hospitals and patients. The health and research authorities are expected to embody personalized cancer medicine and promote CGM utilizing state-of-the-art technologies.

Inauguration of the Tanzania Society of Human Genetics: Biomedical Research in Tanzania with Emphasis on Human Genetics and Genomics.

Human genetics research and applications are rapidly growing areas in health innovations and services. African populations are reported to be highly diverse and carry the greatest number of variants per genome. Exploring these variants is key to realize the genomic medicine initiative. However, African populations are grossly underrepresented in various genomic databases, which has alerted scientists to address this issue with urgency. In Tanzania, human genetics research and services are conducted in different institutions on both communicable and noncommunicable diseases. However, there is poor coordination of the research activities, often leading to limited application of the research findings and poor utilization of available resources. In addition, contributions from Tanzanian human genetics research and services are not fully communicated to the government, national, and international communities. To address this scientific gap, the Tanzania Society of Human Genetics (TSHG) has been formed to bring together all stakeholders of human genetics activities in Tanzania and to formally bring Tanzania as a member to the African Society of Human Genetics. This article describes the inauguration event of the TSHG, which took place in November 2019. It provides a justification for its establishment and discusses presentations from invited speakers who took part in the inauguration of the TSHG.

Demonstrating the influence of HTA: INAHTA member stories of HTA impact.

A central function of health technology assessment (HTA) agencies is the production of HTA reports to support evidence-informed policy and decision making. HTA agencies are interested in understanding the mechanisms of HTA impact, which can be understood as the influence or impact of HTA report findings on decision making at various levels of the health system. The members of the International Network of Agencies for HTA (INAHTA) meet at their annual Congress where impact story sharing is one important activity. This paper summarizes four stories of HTA impact that were finalists for the David Hailey Award for Best Impact Story.The methods to measure impact include: document review; claims analysis and review of reimbursement status; citation analysis; qualitative evaluation of stakeholders' views; and review of media response. HTA agency staff also observed changes in government activities and priorities based on the HTA. Impact assessment can provide information to improve the HTA process, for example, the value of patient and clinician engagement in the HTA process to better define the assessment question and literature reviews in a more holistic and balanced way.HTA reports produced by publicly funded HTA agencies are valued by health systems around the globe as they support decision making regarding the appropriate use, pricing, reimbursement, and disinvestment of health technologies. HTAs can also have a positive impact on information sharing between different levels of government and across stakeholder groups. These stories show how HTA can have a significant impact, irrespective of the health system and health technology being assessed.

Roadmap for Establishing Large-Scale Genomic Medicine Initiatives in Low- and Middle-Income Countries.

In the post-genomic era, genomic medicine interventions as a key component of personalized medicine and tailored-made health care are greatly anticipated following recent scientific and technological advances. Indeed, large-scale sequencing efforts that explore human genomic variation have been initiated in several, mostly developed, countries across the globe, such as the United States, the United Kingdom, and a few others. Here, we highlight the successful implementation of large-scale national genomic initiatives, namely the Genome of Greece (GoGreece) and the DNA do Brasil (DNABr), aiming to emphasize the importance of implementing such initiatives in developing countries. Based on this experience, we also provide a roadmap for replicating these projects in other low-resource settings, thereby bringing genomic medicine in these countries closer to clinical fruition.

The Genome3D Consortium for Structural Annotations of Selected Model Organisms.

Genome3D consortium is a collaborative project involving protein structure prediction and annotation resources developed by six world-leading structural bioinformatics groups, based in the United Kingdom (namely Blundell, Murzin, Gough, Sternberg, Orengo, and Jones). The main objective of Genome3D serves as a common portal to provide both predicted models and annotations of proteins in model organisms, using several resources developed by these labs such as CATH-Gene3D, DOMSERF, pDomTHREADER, PHYRE, SUPERFAMILY, FUGUE/TOCATTA, and VIVACE. These resources primarily use SCOP- and/or CATH-based protein domain assignments. Another objective of Genome3D is to compare structural classifications of protein domains in CATH and SCOP databases and to provide a consensus mapping of CATH and SCOP protein superfamilies. CATH/SCOP mapping analyses led to the identification of total of 1429 consensus superfamilies.Currently, Genome3D provides structural annotations for ten model organisms, including Homo sapiens, Arabidopsis thaliana, Mus musculus, Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Plasmodium falciparum, Staphylococcus aureus, and Schizosaccharomyces pombe. Thus, Genome3D serves as a common gateway to each structure prediction/annotation resource and allows users to perform comparative assessment of the predictions. It, thus, assists researchers to broaden their perspective on structure/function predictions of their query protein of interest in selected model organisms.

A Roadmap for Global Acceleration of Genomics Integration Across Nursing.

PURPOSE: The changes needed to accelerate integration of genomics across nursing are complex, with significant challenges faced globally. Common themes lend themselves to a coordinated and collaborative strategic approach to sustained change. We aim to synthesize the outputs of a research program to present a roadmap for nursing leadership to guide integration of genomics across practice. DESIGN: Mixed methods involving a purposive sample of global nursing leaders and nursing organizations in a sustained, highly interactive program. METHODS: Experts in nursing, health care and healthcare services, policy, and leadership were recruited. Online surveys preceded a 3-day residential meeting utilizing participatory methods and techniques to gain consensus on the essential elements of a roadmap to promote genomics integration. FINDINGS: Twenty-three leaders representing 19 countries and seven organizations participated overall. Data on the scope and status of nursing, genomics health care, and resources have been synthesized. Participants identified 117 facilitators to genomics integration across diverse sources. Barriers and priorities identified were mapped to the constructs of the Consolidated Framework for Implementation Research. The roadmap is underpinned by a maturity matrix created by participants to guide and benchmark progress in genomics integration. CONCLUSIONS: Nurse leaders seeking to accelerate change can access practical guidance with the roadmap, underpinned by support through the Global Genomics Nursing Alliance and its strategic priorities. CLINICAL RELEVANCE: Genomics is shaping the future of healthcare, but change is needed for integration across nursing. This practical roadmap, adaptable to local health systems and clinical and educational contexts, is relevant to nurse leaders aiming to accelerate change.

The Implementation Chasm Hindering Genome-informed Health Care.

The promises of precision medicine are often heralded in the medical and lay literature, but routine integration of genomics in clinical practice is still limited. While the "last mile' infrastructure to bring genomics to the bedside has been demonstrated in some healthcare settings, a number of challenges remain - both in the receptivity of today's health system and in its technical and educational readiness to respond to this evolution in care. To improve the impact of genomics on health and disease management, we will need to integrate both new knowledge and new care processes into existing workflows. This change will be onerous and time-consuming, but hopefully valuable to the provision of high quality, economically feasible care worldwide.

Introducing "Precision Health Promotion": The Convergence of Genomics, Health Education, and Lived Experience.

The prospect that modifying just one mutated letter in a genomic sequence could save millions of lives has spawned a growing discipline called personalized medicine (PM). Where PM focuses on bringing greater precision to individual treatments, the genetics revolution also invites questions about how genetics testing and genetics reference panels can be applied in a public health context. Some voice concerns that the growth of PM will shift us back to an emphasis on the medical model for health advancement with undue focus and investment on individual rather than societal solutions. This editorial introduces precision health promotion and defines it as "the personalized design of lived experiences that foster improved health and well-being for individuals within the context of their families, organizations and communities."

ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.

High-throughput sequencing has become ubiquitous in biomedical sciences. As new technologies emerge and sequencing costs decline, the diversity and volume of available data increases exponentially, and successfully navigating the data becomes more challenging. Though datasets are often hosted by public repositories, scientists must rely on inconsistent annotation to identify and interpret meaningful data. Moreover, the experimental heterogeneity and wide-ranging quality of high-throughput biological data means that even data with desired cell lines, tissue types, or molecular targets may not be readily interpretable or integrated. We have developed ORSO (Online Resource for Social Omics) as an easy-to-use web application to connect life scientists with genomics data. In ORSO, users interact within a data-driven social network, where they can favorite datasets and follow other users. In addition to more than 30,000 datasets hosted from major biomedical consortia, users may contribute their own data to ORSO, facilitating its discovery by other users. Leveraging user interactions, ORSO provides a novel recommendation system to automatically connect users with hosted data. In addition to social interactions, the recommendation system considers primary read coverage information and annotated metadata. Similarities used by the recommendation system are presented by ORSO in a graph display, allowing exploration of dataset associations. The topology of the network graph reflects established biology, with samples from related systems grouped together. We tested the recommendation system using an RNA-seq time course dataset from differentiation of embryonic stem cells to cardiomyocytes. The ORSO recommendation system correctly predicted early data point sources as embryonic stem cells and late data point sources as heart and muscle samples, resulting in recommendation of related datasets. By connecting scientists with relevant data, ORSO provides a critical new service that facilitates wide-ranging research interests.

Ten Years of the International Parkinson Disease Genomics Consortium: Progress and Next Steps.

In June 2009 a small group of investigators met at the annual Movement Disorders Society meeting in Paris. The explicit goal of this meeting was to discuss a potential research alliance focused on the genetics of Parkinson disease (PD). The outcome of this informal meeting was the creation of the International Parkinson Disease Genomics Consortium (IPDGC), a group focused on collaborative genetics research, enabled by trust, sharing, and as little paperwork as possible. The IPDGC has grown considerably since its inception, including over 100 scientists from around the World. The focus has also grown, to include clinical and functional investigation of PD at scale. Most recently, the IPDGC has expanded to initiate major research efforts in East Asia and Africa, and has prioritized collaborations with ongoing major efforts in India and South America. Here we summarize the efforts of the IPDGC thus far and place these in the context of a decade of progress in PD genomics. We also discuss the future direction of IPDGC and our stated research priorities for the next decade.