It Is in Our DNA: Bringing Electronic Health Records and Genomic Data Together for Precision Medicine

Health care is at a turning point. We are shifting from protocolized medicine to precision medicine, and digital health systems are facilitating this shift. By providing clinicians with detailed information for each patient and analytic support for decision-making at the point of care, digital health technologies are enabling a new era of precision medicine. Genomic data also provide clinicians with information that can improve the accuracy and timeliness of diagnosis, optimize prescribing, and target risk reduction strategies, all of which are key elements for precision medicine. However, genomic data are predominantly seen as diagnostic information and are not routinely integrated into the clinical workflows of electronic medical records. The use of genomic data holds significant potential for precision medicine; however, as genomic data are fundamentally different from the information collected during routine practice, special considerations are needed to use this information in a digital health setting. This paper outlines the potential of genomic data integration with electronic records, and how these data can enable precision medicine.

A Taxonomy for Health Information Systems

The health sector is highly digitized, which is enabling the collection of vast quantities of electronic data about health and well-being. These data are collected by a diverse array of information and communication technologies, including systems used by health care organizations, consumer and community sources such as information collected on the web, and passively collected data from technologies such as wearables and devices. Understanding the breadth of IT that collect these data and how it can be actioned is a challenge for the significant portion of the digital health workforce that interact with health data as part of their duties but are not for informatics experts. This viewpoint aims to present a taxonomy categorizing common information and communication technologies that collect electronic data. An initial classification of key information systems collecting electronic health data was undertaken via a rapid review of the literature. Subsequently, a purposeful search of the scholarly and gray literature was undertaken to extract key information about the systems within each category to generate definitions of the systems and describe the strengths and limitations of these systems.

Toward an open access genomics database of South Africans: ethical considerations

Genomics research holds the potential to improve healthcare. Yet, a very low percentage of the genomic data used in genomics research internationally relates to persons of African origin. Establishing a large-scale, open access genomics database of South Africans may contribute to solving this problem. However, this raises various ethics concerns, including privacy expectations and informed consent. The concept of open consent offers a potential solution to these concerns by (a) being explicit about the research participant's data being in the public domain and the associated privacy risks, and (b) setting a higher-than-usual benchmark for informed consent by making use of the objective assessment of prospective research participants' understanding. Furthermore, in the South African context-where local culture is infused with Ubuntu and its relational view of personhood-community engagement is vital for establishing and maintaining an open access genomics database of South Africans. The South African National Health Research Ethics Council is called upon to provide guidelines for genomics researchers-based on open consent and community engagement-on how to plan and implement open access genomics projects.

Deep reinforcement learning-based pairwise DNA sequence alignment method compatible with embedded edge devices

Sequence alignment is an essential component of bioinformatics, for identifying regions of similarity that may indicate functional, structural, or evolutionary relationships between the sequences. Genome-based diagnostics relying on DNA sequencing have benefited hugely from the boom in computing power in recent decades, particularly due to cloud-computing and the rise of graphics processing units (GPUs) and other advanced computing platforms for running advanced algorithms. Translating the success of such breakthroughs in diagnostics to affordable solutions for low-cost healthcare requires development of algorithms that can operate on the edge instead of in the cloud, using low-cost and low-power electronic systems such as microcontrollers and field programmable gate arrays (FPGAs). In this work, we present EdgeAlign, a deep reinforcement learning based method for performing pairwise DNA sequence alignment on stand-alone edge devices. EdgeAlign uses deep reinforcement learning to train a deep Q-network (DQN) agent for performing sequence alignment on fixed length sub-sequences, using a sliding window that is scanned over the length of the entire sequence. The hardware resource-consumption for implementing this scheme is thus independent of the lengths of the sequences to be aligned, and is further optimized using a novel AutoML based method for neural network model size reduction. Unlike other algorithms for sequence alignment reported in literature, the model demonstrated in this work is highly compact and deployed on two edge devices (NVIDIA Jetson Nano Developer Kit and Digilent Arty A7-100T, containing Xilinx XC7A35T Artix-7 FPGA) for demonstration of alignment for sequences from the publicly available Influenza sequences at the National Center for Biotechnology Information (NCBI) Virus Data Hub.

Genomic medicine in Africa: a need for molecular genetics and pharmacogenomics experts

The large-scale implementation of genomic medicine in Africa has not been actualized. This overview describes how routine molecular genetics and advanced protein engineering/structural biotechnology could accelerate the implementation of genomic medicine. By using data-mining and analysis approaches, we analyzed relevant information obtained from public genomic databases on pharmacogenomics biomarkers and reviewed published studies to discuss the ideas. The results showed that only 68 very important pharmacogenes currently exist, while 867 drug label annotations, 201 curated functional pathways, and 746 annotated drugs have been catalogued on the largest pharmacogenomics database (PharmGKB). Only about 5009 variants of the reported ∼25,000 have been clinically annotated. Predominantly, the genetic variants were derived from 43 genes that contribute to 2318 clinically relevant variations in 57 diseases. Majority (∼60%) of the clinically relevant genetic variations in the pharmacogenes are missense variants (1390). The enrichment analysis showed that 15 pharmacogenes are connected biologically and are involved in the metabolism of cardiovascular and cancer drugs. The review of studies showed that cardiovascular diseases are the most frequent non-communicable diseases responsible for approximately 13% of all deaths in Africa. Also, warfarin pharmacogenomics is the most studied drug on the continent, while CYP2D6, CYP2C9, DPD, and TPMT are the most investigated pharmacogenes with allele activities indicated in African and considered to be intermediate metaboliser for DPD and TPMT (8.4% and 11%). In summary, we highlighted a framework for implementing genomic medicine starting from the available resources on ground.

Implementation of Public Health Genomics in Africa: Lessons from the COVID-19 pandemic, challenges, and recommendations

Public Health Genomics (PHG) is a relatively new field. The wide application of genomic technologies played a pivotal role in elucidating the full genomic sequence of the SARS-CoV-2 virus. This breakthrough proved to be the starting point in the manufacture of diagnostic kits and the subsequent making of vaccines. Beyond the COVID-19 pandemic, many African countries can take advantage of the various investments in genomic technologies to introduce and intensify the use of genomics for public health gain. Public Health Genomics effectively monitors, prevents, and manages non-communicable and infectious diseases. However, there are several challenges to implementing PHG in Africa. In this perspective article, we discuss the utilization of PHG during the COVID-19 pandemic, the lessons learned from using PHG to manage and contain the COVID-19 pandemic, as well as potential challenges Africa may face when putting PHG into practice compared to challenges of other regions. We also discuss our recommendations for overcoming these challenges.

A systematic review of geographical inequities for accessing clinical genomic and genetic services for non-cancer related rare disease

Place plays a significant role in our health. As genetic/genomic services evolve and are increasingly seen as mainstream, especially within the field of rare disease, it is important to ensure that where one lives does not impede access to genetic/genomic services. Our aim was to identify barriers and enablers of geographical equity in accessing clinical genomic or genetic services. We undertook a systematic review searching for articles relating to geographical access to genetic/genomic services for rare disease. Searching the databases Medline, EMBASE and PubMed returned 1803 papers. Screening led to the inclusion of 20 articles for data extraction. Using inductive thematic analysis, we identified four themes (i) Current service model design, (ii) Logistical issues facing clinicians and communities, (iii) Workforce capacity and capability and iv) Rural culture and consumer beliefs. Several themes were common to both rural and urban communities. However, many themes were exacerbated for rural populations due to a lack of clinician access to/relationships with genetic specialist staff, the need to provide more generalist services and a lack of genetic/genomic knowledge and skill. Additional barriers included long standing systemic service designs that are not fit for purpose due to historically ad hoc approaches to delivery of care. There were calls for needs assessments to clarify community needs. Enablers of geographically equitable care included the uptake of new innovative models of care and a call to raise both community and clinician knowledge and awareness to demystify the clinical offer from genetics/genomics services.

Teamwork in clinical genomics: A dynamic sociotechnical healthcare setting

RATIONALE, AIMS AND OBJECTIVES

Teamworking across sociotechnical boundaries in healthcare is growing as technological advances in medicine abound. With this progress, teams need to find new ways of working together in non-traditional settings. The novel field of clinical genomics provides the opportunity to rethink the existing approach to teamworking and how it needs to evolve. Our aim was to identify the key factors influencing teamworking in the emerging field of clinical genomics and how can they be applied in practice.

METHOD

We drew on three qualitative datasets from interviews undertaken in Australia, 2018/2019, that explored determinants of implementation of clinical genomics with laboratory scientists (n = 7), service and programme leads (n = 21), project officers (n = 2), clinical genetics staff (n = 26) and other medical specialists (n = 21). Data were analysed using a theory-informed matrix approach to identify themes related to teamworking.

RESULTS

We identify that teams in clinical genomics work in an elongated adaptive context where there is rapid evolution of the knowledge base, shifting expectations of staff roles, and fast changes of technology. Delivering care in this setting brings additional challenges to teamworking as members strive to stay abreast of current knowledge and technology. We identify four themes: (a) the role of the team in keeping knowledge up-to-date; (b) professional identity; (c) team adaptability, and (d) practical/organisational considerations.

CONCLUSION

Challenges to teamworking that arise in the elongated adaptive context do not always fit traditional ways of working, and innovative strategies will need to be adopted to ensure the diagnostic advances of clinical genomics are realised. Provision of time and permission for team members to share knowledge and evolve, promoting capacity building, nurturing trustful relationships and establishing boundaries are amongst the practice recommendations for organisational and team leaders, even though these activities may disrupt existing ways of working or hierarchical structures.

Genetics and pediatric hospital admissions, 1985 to 2017

PURPOSE

To determine the prevalence and sociodemographic and hospitalization history of genetic conditions in a sample of inpatients in a pediatric hospital in 2017, and to compare results with unpublished studies from 1985, 1995, and 2007.

METHODS

Two weeks of admissions were classified according to a pre-existing categorization, based on genetic etiology, encompassing chromosomal and monogenic conditions, multifactorial (MF) conditions, and no known genetic cause.

RESULTS

In 2017, 299 (16%) patients had chromosomal or monogenic conditions, 6-7% more than 2007 and 1995, but similar to 1985. Autosomal dominant (AD) conditions increased from <2% previously to 6% in 2017 (p < 0.001). MF conditions comprised the majority throughout, increasing from 45% to 54%. Age at admission was highest in autosomal recessive (AR) and X-linked categories in 1995, 2007, and 2017, reflected in their high number of previous admissions, while the AD, MF, and nongenetic categories were the youngest with similar lengths of stay and previous admissions.

CONCLUSION

Conditions with a genetic contribution account for over half of pediatric inpatients. Since 1985, there have been many changes in age at admission and length of stay, but it is the increasing prevalence of AR, AD, and MF conditions that is important when considering future service provision.

Vitalism in contemporary chiropractic: a help or a hinderance?

BACKGROUND

Chiropractic emerged in 1895 and was promoted as a viable health care substitute in direct competition with the medical profession. This was an era when there was a belief that one cause and one cure for all disease would be discovered. The chiropractic version was a theory that most diseases were caused by subluxated (slightly displaced) vertebrae interfering with "nerve vibrations" (a supernatural, vital force) and could be cured by adjusting (repositioning) vertebrae, thereby removing the interference with the body's inherent capacity to heal. DD Palmer, the originator of chiropractic, established chiropractic based on vitalistic principles. Anecdotally, the authors have observed that many chiropractors who overtly claim to be "vitalists" cannot define the term. Therefore, we sought the origins of vitalism and to examine its effects on chiropractic today.

DISCUSSION

Vitalism arose out of human curiosity around the biggest questions: Where do we come from? What is life? For some, life was derived from an unknown and unknowable vital force. For others, a vital force was a placeholder, a piece of knowledge not yet grasped but attainable. Developments in science have demonstrated there is no longer a need to invoke vitalistic entities as either explanations or hypotheses for biological phenomena. Nevertheless, vitalism remains within chiropractic. In this examination of vitalism within chiropractic we explore the history of vitalism, vitalism within chiropractic and whether a vitalistic ideology is compatible with the legal and ethical requirements for registered health care professionals such as chiropractors.

CONCLUSION

Vitalism has had many meanings throughout the centuries of recorded history. Though only vaguely defined by chiropractors, vitalism, as a representation of supernatural force and therefore an untestable hypothesis, sits at the heart of the divisions within chiropractic and acts as an impediment to chiropractic legitimacy, cultural authority and integration into mainstream health care.

Scoping the Scene: What Do Nurses, Midwives, and Allied Health Professionals Need and Want to Know About Genomics?

Introduction: Rapid changes in genomic technology are transforming healthcare delivery. Although it has been well established that many health professionals lack the adequate knowledge, skills, and confidence to adapt to these changes, the specific educational needs of Australian allied health professionals, nurses, and midwives are not well understood. This diverse group of health professionals is primarily involved in the management of symptoms and psychosocial care of patients with genetic conditions, rather than risk assessment and diagnosis. The relevance of genetics and genomics to their clinical practice may therefore differ from medical practitioners and specialists.

Materials and Methods: This paper reports on a study undertaken to identify the perceived genetic knowledge and education needs for this group of health professionals. Allied health professionals, nurses, and midwives were recruited from throughout New South Wales (NSW) and invited to participate in semi-structured telephone or face to face interviews.

Results: A total of 24 geographically and professionally diverse individuals (14 allied health, 6 nurses, and 4 midwives) were interviewed. Interview recordings were transcribed and using thematic qualitative analysis recurring themes were identified. The results show that this is a diverse group that is keen to know more about genomics and genetic services but unsure of reliable sources.

Discussion: The need for a generic update from a trustworthy source was identified and suggested topics to be covered included genetic fundamentals, recognizing common genetic conditions, and psychosocial/ethical aspects of genetics/testing including informed consent. In addition, the challenge of incorporating education into highly clinical roles was identified as a key barrier and having a readily accessible, accredited learning resource would help overcome this. Findings from this study are informing the development of a targeted, interactive e-learning resource for allied health professionals, nurses, and midwives.

Lessons learned from a health authority research capacity-building initiative

Health systems worldwide are under pressure to deliver better care to more people with increasingly complex needs within constrained budgets. Research capacity building has been shown to help alleviate these challenges and is underway at hospitals and health authorities across the country; however, approaches vary widely and little exists in the Canadian literature to share experience and best practices. This article describes how a health authority in British Columbia, Canada, implemented and evaluated a 5-year research capacity-building program in partnership with a provincial health research funder. We offer lessons learned for those leading similar innovation-focused change management initiatives, including vision and buy in, complexity thinking, infrastructure, leadership, and coalition development. We suggest that collective learning and building a more robust research capacity-building literature can help health organizations and their partners take significant steps toward integrating research and care for a more effective, efficient, and patient-centred health system.

The future of health systems to 2030: a roadmap for global progress and sustainability

Most research on health systems examines contemporary problems within one, or at most a few, countries. Breaking with this tradition, we present a series of case studies in a book written by key policymakers, scholars and experts, looking at health systems and their projected successes to 2030. Healthcare Systems: Future Predictions for Global Care includes chapters on 52 individual countries and five regions, covering a total of 152 countries. Synthesised, two key contributions are made in this compendium. First, five trends shaping the future healthcare landscape are analysed: sustainable health systems; the genomics revolution; emerging technologies; global demographics dynamics; and new models of care. Second, nine main themes arise from the chapters: integration of healthcare services; financing, economics and insurance; patient-based care and empowering the patient; universal healthcare; technology and information technology; aging populations; preventative care; accreditation, standards, and policy; and human development, education and training. These five trends and nine themes can be used as a blueprint for change. They can help strengthen the efforts of stakeholders interested in reform, ranging from international bodies such as the World Health Organization, the International Society for Quality in Health Care and the World Bank, through to national bodies such as health departments, quality and safety agencies, non-government organisations (NGO) and other groups with an interest in improving healthcare delivery systems. This compendium offers more than a glimpse into the future of healthcare-it provides a roadmap to help shape thinking about the next generation of caring systems, extrapolated over the next 15 years.

Genomic Interventions in Medicine

Lately, the term "genomics" has become ubiquitous in many scientific articles. It is a rapidly growing aspect of the biomedical sciences that studies the genome. The human genome contains a torrent of information that gives clues about human origin, evolution, biological function, and diseases. In a bid to demystify the workings of the genome, the Human Genome Project (HGP) was initiated in 1990, with the chief goal of sequencing the approximately 3 billion nucleotide base pairs of the human DNA. Since its completion in 2003, the HGP has opened new avenues for the application of genomics in clinical practice. This review attempts to overview some milestone discoveries that paved way for the initiation of the HGP, remarkable revelations from the HGP, and how genomics is influencing a paradigm shift in routine clinical practice. It further highlights the challenges facing the implementation of genomic medicine, particularly in Africa. Possible solutions are also discussed.

Drivers of Orphan Drug Development

Previously neglected by the pharmaceutical industry, rare diseases and orphan drugs are rapidly becoming mainstream. Both market forces and technology enablers are responsible for this migration and combine to create multiple business approaches. This viewpoint discusses the drivers that attract different companies into this booming orphan drug space.

Discovery of biomarkers in rare diseases: innovative approaches by predictive and personalized medicine

There are more than 8000 rare diseases (RDs) that affect >5 % of the world’s population. Many of the RDs have no effective treatment and lack of knowledge creates delayed diagnosis making management difficult. The emerging concept of the personalized medicine allows for early screening, diagnosis, and individualized treatment of human diseases. In this context, the discovery of biomarkers in RDs will be of prime importance to enable timely prevention and effective treatment. Since 80 % of RDs are of genetic origin, identification of new genes and causative mutations become valuable biomarkers. Furthermore, dynamic markers such as expressed genes, metabolites, and proteins are also very important to follow prognosis and response the therapy. Recent advances in omics technologies and their use in combination can define pathophysiological pathways that can be drug targets. Biomarker discovery and their use in diagnosis in RDs is a major pillar in RD research.

Genetic education, knowledge and experiences between nurses and physicians in primary care in Brazil: A cross-sectional study

Recent advances in genomics and related technologies have the potential to improve health care throughout the world. In this cross-sectional study, we examine genetics education, knowledge, and genetics-related experiences among the nurses and physicians who provide primary care in a Brazilian city. Fifty-four healthcare professionals from family health units participated in the study (response rate: 90%). Data were collected using a structured 36-item questionnaire divided into five axes: sociodemographic data and academic background; genetics education; genetics knowledge; genetics-related experiences in family practice; and knowledge regarding the National Policy for Comprehensive Care in Clinical Genetics in the Unified Health System. Although most participants (85.2%) acknowledged receiving some genetic content during their undergraduate education, the majority (77.8%) advised that they did not feel prepared to deliver genomics-based health care in primary care. The results suggest that nurses and physicians often lack the knowledge to provide genomics-based health care in primary care. Therefore, continuing education in genetics/genomics should be provided to primary healthcare professionals in order to enhance family practice and compliance with national policies.

Genomics in research and health care with Aboriginal and Torres Strait Islander peoples

Genomics is increasingly becoming an integral component of health research and clinical care. The perceived difficulties associated with genetic research involving Aboriginal and Torres Strait Islander people mean that they have largely been excluded as research participants. This limits the applicability of research findings for Aboriginal and Torres Strait Islander patients. Emergent use of genomic technologies and personalised medicine therefore risk contributing to an increase in existing health disparities unless urgent action is taken. To allow the potential benefits of genomics to be more equitably distributed, and minimise potential harms, we recommend five actions: (1) ensure diversity of participants by implementing appropriate protocols at the study design stage; (2) target diseases that disproportionately affect disadvantaged groups; (3) prioritise capacity building to promote Indigenous leadership across research professions; (4) develop resources for consenting patients or participants from different cultural and linguistic backgrounds; and (5) integrate awareness of issues relating to Indigenous people into the governance structures, formal reviews, data collection protocols and analytical pipelines of health services and research projects.