Genomics knowledge and attitudes among European public health professionals. Results of a cross-sectional survey

Background The international public health (PH) community is debating the opportunity to incorporate genomic technologies into PH practice. A survey was conducted to assess attitudes of the European Public Health Association (EUPHA) members towards their role in the implementation of public health genomics (PHG), and their knowledge and attitudes towards genetic testing and the delivery of genetic services. Methods EUPHA members were invited via monthly newsletter and e-mail to take part in an online survey from February 2017 to January 2018. A descriptive analysis of knowledge and attitudes was conducted, along with a univariate and multivariate analysis of their determinants. Results Five hundred and two people completed the questionnaire, 17.9% were involved in PHG activities. Only 28.9% correctly identified all medical conditions for which there is (or not) evidence for implementing genetic testing; over 60% thought that investing in genomics may divert economic resources from social and environmental determinants of health. The majority agreed that PH professionals may play different roles in incorporating genomics into their activities. Better knowledge was associated with positive attitudes towards the use of genetic testing and the delivery of genetic services in PH (OR = 1.48; 95% CI 1.01–2.18). Conclusions Our study revealed quite positive attitudes, but also a need to increase awareness on genomics among European PH professionals. Those directly involved in PHG activities tend to have a more positive attitude and better knowledge; however, gaps are also evident in this group, suggesting the need to harmonize practice and encourage greater exchange of knowledge among professionals

The emergence of commercial genomics: analysis of the rise of a biotechnology subsector during the Human Genome Project, 1990 to 2004.

BackgroundDevelopment of the commercial genomics sector within the biotechnology industry relied heavily on the scientific commons, public funding, and technology transfer between academic and industrial research. This study tracks financial and intellectual property data on genomics firms from 1990 through 2004, thus following these firms as they emerged in the era of the Human Genome Project and through the 2000 to 2001 market bubble.MethodsA database was created based on an early survey of genomics firms, which was expanded using three web-based biotechnology services, scientific journals, and biotechnology trade and technical publications. Financial data for publicly traded firms was collected through the use of four databases specializing in firm financials. Patent searches were conducted using firm names in the US Patent and Trademark Office website search engine and the DNA Patent Database.ResultsA biotechnology subsector of genomics firms emerged in parallel to the publicly funded Human Genome Project. Trends among top firms show that hiring, capital improvement, and research and development expenditures continued to grow after a 2000 to 2001 bubble. The majority of firms are small businesses with great diversity in type of research and development, products, and services provided. Over half the public firms holding patents have the majority of their intellectual property portfolio in DNA-based patents.ConclusionsThese data allow estimates of investment, research and development expenditures, and jobs that paralleled the rise of genomics as a sector within biotechnology between 1990 and 2004

Development of usable grid services for the biomedical community

The BRIDGES project was funded by the UK Department of Trade and Industry to directly address the needs of the cardiovascular research scientists investigating the genetic causes of hypertension as part of the Wellcome Trust funded (£4.34M) Cardiovascular Functional Genomics (CFG) project. Specifically, the BRIDGES project developed a compute Grid and a data Grid with security at its heart. This paper presents the experiences in developing usable Grid services for the bio-community and the different phases of prototypes that were refined based upon user requirements and feedback

Towards data grids for microarray expression profiles

The UK DTI funded Biomedical Research Informatics Delivered by Grid Enabled Services (BRIDGES) project developed a Grid infrastructure through which research into the genetic causes of hypertension could be supported by scientists within the large Wellcome Trust funded Cardiovascular Functional Genomics project. The BRIDGES project had a focus on developing a compute Grid and a data Grid infrastructure with security at its heart. Building on the work within BRIDGES, the BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project plans to provide an enhanced data Grid infrastructure to support richer queries needed for the discovery and analysis of microarray data sets, also based upon a fine-grained security infrastructure. This paper outlines the experiences gained within BRIDGES and outlines the status of the GEMEPS project, the open challenges that remain and plans for the future

Design and evaluation of a genomics variant analysis pipeline using GATK Spark tools

Scalable and efficient processing of genome sequence data, i.e. for variant discovery, is key to the mainstream adoption of High Throughput technology for disease prevention and for clinical use. Achieving scalability, however, requires a significant effort to enable the parallel execution of the analysis tools that make up the pipelines. This is facilitated by the new Spark versions of the well-known GATK toolkit, which offer a black-box approach by transparently exploiting the underlying Map Reduce architecture. In this paper we report on our experience implementing a standard variant discovery pipeline using GATK 4.0 with Docker-based deployment over a cluster. We provide a preliminary performance analysis, comparing the processing times and cost to those of the new Microsoft Genomics Services

How genomic information is accessed in clinical practice: an electronic survey of UK general practitioners.

Genomic technologies are having an increasing impact across medicine, including primary care. To enable their wider adoption and realize their potential, education of primary health-care practitioners will be required. To enable the development of such resources, understanding where GPs currently access genomic information is needed. One-hundred fifty-nine UK GPs completed the survey in response to an open invitation, between September 2017 and September 2018. Questions were in response to 4 clinical genomic scenarios, with further questions exploring resources used for rare disease patients, direct-to-consumer genetic testing and collecting a family history. Respondents were most commonly GP principals (independent GPs who own their clinic) (64.8%), aged 35-49 years (54%), worked as a GP for more than 15 years (44%) and practiced within suburban locations (typically wealthier) (50.3%). The most popular 'just in time' education source for all clinical genomic scenarios were online primary care focussed resources with general Internet search engines also popular. For genomic continuous medical education, over 70% of respondents preferred online learning. Considering specific scenarios, local guidelines were a popular resource for the familial breast cancer scenario. A large proportion (41%) had not heard of Genomics England's 100,000 genome project. Few respondents (4%) would access rare disease specific Internet resources (Orphanet, OMIM). Twenty-five percent of respondents were unsure how to respond to a direct-to-consumer commercial genetic test query, with 41% forwarding such queries to local genetic services. GPs require concise, relevant, primary care focussed resources in trusted and familiar online repositories of information. Inadequate genetic education of GPs could increase burden on local genetic services

Counseling Customers: Emerging Roles for Genetic Counselors in the Direct-to-Consumer Genetic Testing Market

Individuals now have access to an increasing number of internet resources offering personal genomics services. As the direct-to-consumer genetic testing (DTC GT) industry expands, critics have called for pre- and post-test genetic counseling to be included with the product. Several genetic testing companies offer genetic counseling. There has been no examination to date of this service provision, whether it meets critics’ concerns and implications it may have for the genetic counseling profession. Considering the increasing relevance of genetics in healthcare, the complexity of genetic information provided by DTC GT, the mediating role of the internet in counseling, and potential conflicts of interest, this is a topic which deserves further attention. In this paper we offer a discourse analysis of ways in which genetic counseling is represented on DTC GT websites, blogs and other online material. This analysis identified four types of genetic counseling represented on the websites: the integrated counseling product; discretionary counseling; independent counseling; and product advice. Genetic counselors are represented as having the following roles: genetics educator; mediator; lifestyle advisor; risk interpreter; and entrepreneur. We conclude that genetic counseling as represented on DTC GT websites demonstrates shifting professional roles and forms of expertise in genetic counseling. Genetic counselors are also playing an important part in how the genetic testing market is taking shape. Our analysis offers important and timely insights into recent developments in the genetic counseling profession, which have relevance for practitioners, researchers and policy makers concerned with the evolving field of personal genomics. Keywords Genetic counseling Internet Direct-to-consumer genetic testing Discourse analysis

Identification of delivery models for the provision of predictive genetic testing in Europe: protocol for a multicentre qualitative study and a systematic review of the literature

Introduction: The appropriate application of genomic technologies in healthcare is surrounded by many concerns. In particular, there is a lack of evidence on what constitutes an optimal genetic service delivery model, which depends on the type of genetic test and healthcare context considered. The present project aims to identify, classify, and evaluate delivery models for the provision of predictive genetic testing in Europe and in selected Anglophone extra-European countries (the USA, Canada, Australia, and New Zealand). It also sets out to survey the European public health community’s readiness to incorporate public health genomics into their practice. Materials and equipment: The project consists of (i) a systematic review of published literature and selected country websites, (ii) structured interviews with health experts on the genetic service delivery models in their respective countries, and (iii) a survey of European Public Health Association (EUPHA) members’ knowledge and attitudes toward genomics applications in clinical practice. The inclusion criteria for the systematic review are that articles be published in the period 2000–2015; be in English or Italian; and be from European countries or from Canada, the USA, Australia, or New Zealand. Additional policy documents will be retrieved from represented countries’ government-affiliated websites. The results of the research will be disseminated through the EUPHA network, the Italian Network for Genomics in Public Health (GENISAP), and seminars and workshops. Expected impact of the study on public health: The transfer of genomic technologies from research to clinical application is influenced not only by several factors inherent to research goals and delivery of healthcare but also by external and commercial interests that may cause the premature introduction of genetic tests in the public and private sectors. Furthermore, current genetic services are delivered without a standardized set of process and outcome measures, which makes the evaluation of healthcare services difficult. The present study will identify and classify delivery models and, subsequently, establish which are appropriate for the provision of predictive genetic testing in Europe by comparing sets of process and outcome measures. In this way, the study will provide a basis for future recommendations to decision makers involved in the financing, delivery, and consumption of genetic services

Computational Strategies for Scalable Genomics Analysis.

The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions to mine the big genomics data. In this review, we survey some of these exciting developments in the applications of parallel distributed computing and special hardware to genomics. We comment on the pros and cons of each strategy in the context of ease of development, robustness, scalability, and efficiency. Although this review is written for an audience from the genomics and bioinformatics fields, it may also be informative for the audience of computer science with interests in genomics applications

Genomic Nutritional Profiling:Innovation and Regulation in Nutrigenomics

Castle, David. (2007). Genomic Nutritional Profiling: Innovation and Regulation in Nutrigenomics. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/155613