To investigate public willingness to share sensitive health information for research, health policy and clinical practice. A total of 1,003 Australian respondents answered an online, ...attribute-driven, survey in which participants were asked to accept or reject hypothetical choice sets based on a willingness to share their health data for research and frontline-medical support as part of an integrated health system. The survey consisted of 5 attributes: Stakeholder access for analysis (Analysing group); Type of information collected; Purpose of data collection; Information governance; and Anticipated benefit; the results of which were analysed using logistic regression. When asked about their preference for sharing their health data, respondents had no preference between data collection for the purposes of clinical practice, health policy or research, with a slight preference for having government organisations manage, govern and curate the integrated datasets from which the analysis was being conducted. The least preferred option was for personal health records to be integrated with insurance records or for their data collected by privately owned corporate organisations. Individuals preferred their data to be analysed by a public healthcare provider or government staff and expressed a dislike for any private company involvement. The findings from this study suggest that Australian consumers prefer to share their health data when there is government oversight, and have concerns about sharing their anonymised health data for clinical practice, health policy or research purposes unless clarity is provided pertaining to its intended purpose, limitations of use and restrictions to access. Similar findings have been observed in the limited set of existing international studies utilising a stated preference approach. Evident from this study, and supported by national and international research, is that the establishment and preservation of a social license for data linkage in health research will require routine public engagement as a result of continuously evolving technological advancements and fluctuating risk tolerance. Without more work to understand and address stakeholder concerns, consumers risk being reluctant to participate in data-sharing and linkage programmes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
An outbreak of tuberculosis occurred over a 3-year period in a medium-size community in British Columbia, Canada. The results of mycobacterial interspersed repetitive unit–variable-number ...tandem-repeat (MIRU-VNTR) genotyping suggested the outbreak was clonal. Traditional contact tracing did not identify a source. We used whole-genome sequencing and social-network analysis in an effort to describe the outbreak dynamics at a higher resolution.
Mycobacterium tuberculosis
is an important infectious disease even in developed countries with extensive control programs. This is the case in British Columbia, Canada, where the 2007 incidence rate of 6.4 cases per 100,000 population exceeded the national average of 4.7 cases per 100,000 population.
1
In May 2006, a case of smear-negative pleural tuberculosis was diagnosed in an adult in a medium-size community in British Columbia. A second case, manifested as disseminated tuberculosis, was reported in an infant in July 2006. Reverse contact tracing identified nine additional cases between August and October 2006, when the British Columbia Centre for Disease Control . . .
We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors ...in vivo. We used ChIP-seq to map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes. By ChIP-seq, using 15.1 and 12.9 million uniquely mapped sequence reads, and an estimated false discovery rate of less than 0.001, we identified 41,582 and 11,004 putative STAT1-binding regions in stimulated and unstimulated cells, respectively. Of the 34 loci known to contain STAT1 interferon-responsive binding sites, ChIP-seq found 24 (71%). ChIP-seq targets were enriched in sequences similar to known STAT1 binding motifs. Comparisons with two ChIP-PCR data sets suggested that ChIP-seq sensitivity was between 70% and 92% and specificity was at least 95%.
Abstract
Objective
The potential for data collected in general practice to be linked and used to address health system challenges of maintaining quality care, accessibility and safety, including ...pandemic support, has led to an increased interest in public acceptability of data sharing, however practitioners have rarely been asked to share their opinions on the topic. This paper attempts to gain an understanding of general practitioner’s perceptions on sharing routinely collected data for the purposes of healthcare planning and research. It also compares findings with data sharing perceptions in an international context.
Materials and methods
A mixed methods approach combining an initial online survey followed by face-to-face interviews (before and during COVID-19), designed to identify the barriers and facilitators to sharing data, were conducted on a cross sectional convenience sample of general practitioners across Western Australia (WA).
Results
Eighty online surveys and ten face-to-face interviews with general practitioners were conducted from November 2020 – May 2021. Although respondents overwhelmingly identified the importance of population health research, their willingness to participate in data sharing programs was determined by a perception of trust associated with the organisation collecting and analysing shared data; a clearly defined purpose and process of collected data; including a governance structure providing confidence in the data sharing initiative simultaneously enabling a process of data sovereignty and autonomy.
Discussion
Results indicate strong agreement around the importance of sharing patient’s medical data for population and health research and planning. Concerns pertaining to lack of trust, governance and secondary use of data continue to be a setback to data sharing with implications for primary care business models being raised.
Conclusion
To further increase general practitioner’s confidence in sharing their clinical data, efforts should be directed towards implementing a robust data governance structure with an emphasis on transparency and representative stakeholder inclusion as well as identifying the role of government and government funded organisations, as well as building trust with the entities collecting and analysing the data.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics ...research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom ‘WIG’ track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads. Availability: The FindPeaks 3.1 package and manual, containing algorithm descriptions, usage instructions and examples, are available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks Source files for FindPeaks 3.1 are available for academic use. Contact: afejes@bcgsc.ca
Sequence-based methods for transcriptome characterization have typically relied on generation of either serial analysis of gene expression tags or expressed sequence tags. Although such approaches ...have the potential to enumerate transcripts by counting sequence tags derived from them, they typically do not robustly survey the majority of transcripts along their entire length. Here we show that massively parallel sequencing of randomly primed cDNAs, using a next-generation sequencing-by-synthesis technology, offers the potential to generate relative measures of mRNA and individual exon abundance while simultaneously profiling the prevalence of both annotated and novel exons and exon-splicing events. This technique identifies known single nucleotide polymorphisms (SNPs) as well as novel single-base variants. Analysis of these variants, and previously unannotated splicing events in the HeLa S3 cell line, reveals an overrepresentation of gene categories including those previously implicated in cancer.
Virtual healthcare solutions are proposed as a way to combat the inequity of access to healthcare in rural and remote areas, and to better support the front-line providers who work in these areas. ...Rural provider-to-provider telehealth (RPPT) connects rural and remote clinicians to a 'hub' of healthcare specialists who can increase access to emergency and specialised healthcare via an integrated model. Reported benefits for the place-based provider include enhanced knowledge, expanded professional development opportunities, improved scope of practice, and increased confidence in treating more complex cases. These reported benefits could have implications for supporting and futureproofing our health workforce in terms of productivity, burnout, recruitment, and retention.
The research uses an explanatory sequential mixed methods approach across multiple phases to evaluate the current implementation of Western Australia Country Health Service's (WACHS) Command Centre (CC) services and explore factors associated with their differential use. The primary population of interest and participants in this study are the place-based providers in country Western Australia (WA). Patient data constitutes the secondary population, informing the access and reach of CC services into country WA. Data collection will include service data, an online survey, and semi-structured interviews with the primary population. The data will be interpreted to inform evidence-based strategies and recommendations to improve the implementation and sustainment of RPPT.
Innovative and sustained workforce models and solutions are needed globally. Virtual healthcare, including provider-to-provider models, demonstrate potential, especially in rural and remote areas, designed to increase access to specialised expertise for patients and to support the local workforce. This research will generate new data around behaviour, perceptions, and value from the WACHS rural and remote workforce about provider-to-provider telehealth, to explore the implementation and investigate strategies for the long-term sustainment of RPPT services.
Foxa2 (HNF3β) is a one of three, closely related transcription factors that are critical to the development and function of the mouse liver. We have used chromatin immunoprecipitation and massively ...parallel Illumina 1G sequencing (ChIP-Seq) to create a genome-wide profile of in vivo Foxa2-binding sites in the adult liver. More than 65% of the ~11.5 k genomic sites associated with Foxa2 binding, mapped to extended gene regions of annotated genes, while more than 30% of intragenic sites were located within first introns. 20.5% of all sites were further than 50 kb from any annotated gene, suggesting an association with novel gene regions. QPCR analysis demonstrated a strong positive correlation between peak height and fold enrichment for Foxa2-binding sites. We measured the relationship between Foxa2 and liver gene expression by overlapping Foxa2-binding sites with a SAGE transcriptome profile, and found that 43.5% of genes expressed in the liver were also associated with Foxa2 binding. We also identified potential Foxa2-interacting transcription factors whose motifs were enriched near Foxa2-binding sites. Our comprehensive results for in vivo Foxa2-binding sites in the mouse liver will contribute to resolving transcriptional regulatory networks that are important for adult liver function.
General practice is often a patient’s first point of contact with the health system and the gateway to specialist services. In Australia different aspects of the health system are managed by the ...Commonwealth Government and individual state/territory governments. Although there is a long history of research using administrative data in Australia, this split in the management and funding of services has hindered whole-system research. Additionally, the administrative data typically available for research are often collected for reimbursement purposes and lack clinical information.
General practices collect a range of patient information including diagnoses, medications prescribed, results of pathology tests ordered and so on. Practices are increasingly using clinical information systems and data extraction tools to make use of this information. This paper describes approaches used on several research projects to access clinical, as opposed to administrative, general practice data which to date has seen little use as a resource for research.
This information was accessed in three ways. The first was by working directly with practices to access clinical and management data to support research. The second involved accessing general practice data through collaboration with Primary Health Networks, recently established in Australia to increase the efficiency and effectiveness of health services for patients. The third was via NPS MedicineWise’s MedicineInsight program, which collects data from consenting practices across Australia and makes these data available to researchers.
We describe each approach including data access requirements and the advantages and challenges of each method. All approaches provide the opportunity to better understand data previously unavailable for research in Australia. The challenge of linking general practice data to other sources, currently being explored for general practice data, is discussed.
Finally, we describe some general practice data collections used for research internationally and how these compare to collections available in Australia.
Keywords:
General practice; administrative data; big data, health information systems, medical records systems
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