Developing data governance standards for using free-text data in research (TexGov)

Background Free-text data represent a vast, untapped source of rich information to guide research and public service delivery. Free-text data contain a wealth of additional detail that, if more accessible, would clarify and supplement information coded in structured data fields. Personal data usually need to be de-identified or anonymised before they can be used for purposes such as audit and research, but there are major challenges in finding effective methods to de-identify free-text that do not damage data utility as a by-product. The main aim of the TexGov project is to work towards data governance standards to enable free-text data to be used safely for public benefit. Methods We conducted: a rapid literature review to explore the data governance models used in working with free-text data, plus case studies of systems making de-identified free-text data available for research; we engaged with text mining researchers and the general public to explore barriers and solutions in working with free-text; and we outlined (UK) data protection legislation and regulations for context. Results We reviewed 50 articles and the models of 4 systems providing access to de-identified free-text. The main emerging themes were: i) patient involvement at identifiable and de-identified data stages; ii) questions of consent and notification for the reuse of free-text data; iii) working with identifiable data for Natural Language Processing algorithm development; and iv) de-identification methods and thresholds of reliability. Conclusion We have proposed a set of recommendations, including: ensuring public transparency in data flows and uses; adhering to the principles of minimal data extraction; treating de-identified blacklisted free-text as potentially identifiable with use limited to accredited data safe-havens; and, the need to commit to a culture of continuous improvement to understand the relationships between accuracy of de-identification and re-identification risk, so this can be communicated to all stakeholders

The potential of research drawing on clinical free text to bring benefits to patients in the United Kingdom: a systematic review of the literature

Background: The analysis of clinical free text from patient records for research has potential to contribute to the medical evidence base but access to clinical free text is frequently denied by data custodians who perceive that the privacy risks of data-sharing are too high. Engagement activities with patients and regulators, where views on the sharing of clinical free text data for research have been discussed, have identified that stakeholders would like to understand the potential clinical benefits that could be achieved if access to free text for clinical research were improved. We aimed to systematically review all UK research studies which used clinical free text and report direct or potential benefits to patients, synthesizing possible benefits into an easy to communicate taxonomy for public engagement and policy discussions. Methods: We conducted a systematic search for articles which reported primary research using clinical free text, drawn from UK health record databases, which reported a benefit or potential benefit for patients, actionable in a clinical environment or health service, and not solely methods development or data quality improvement. We screened eligible papers and thematically analyzed information about clinical benefits reported in the paper to create a taxonomy of benefits. Results: We identified 43 papers and derived five themes of benefits: health-care quality or services improvement, observational risk factor-outcome research, drug prescribing safety, case-finding for clinical trials, and development of clinical decision support. Five papers compared study quality with and without free text and found an improvement of accuracy when free text was included in analytical models. Conclusions: Findings will help stakeholders weigh the potential benefits of free text research against perceived risks to patient privacy. The taxonomy can be used to aid public and policy discussions, and identified studies could form a public-facing repository which will help the health-care text analysis research community better communicate the impact of their work

Pembrolizumab for locally advanced or metastatic urothelial cancer where cisplatin is unsuitable: an evidence review group perspective of a NICE single technology appraisal

As part of its Single Technology Appraisal (STA) process, the National Institute for Health and Care Excellence (NICE) invited the manufacturer (Merck Sharp & Dohme) of pembrolizumab (Keytruda®) to submit evidence of its clinical and cost effectiveness for the treatment of locally advanced or metastatic urothelial cancer where cisplatin is unsuitable. The School of Health and Related Research Technology Appraisal Group at the University of Sheffield was commissioned to act as the independent Evidence Review Group (ERG). The ERG produced a detailed review of the evidence for the clinical and cost effectiveness of the technology, based on the company’s submission (CS) to NICE. The clinical effectiveness evidence in the CS for pembrolizumab was based on one phase II, single-arm, open-label, non-randomised study (KEYNOTE-052), while the evidence for the comparator (carboplatin plus gemcitabine) was based on four studies, including one randomised controlled trial and three cohort studies. In the absence of head-to-head trials, the company conducted an indirect treatment comparison for both progression-free survival (PFS) and overall survival (OS), by firstly adjusting cross-study differences using a simulated treatment comparison approach and then synthesizing the evidence based on an assumption of constant hazard ratios using a standard meta-analysis model and time-varying hazard ratios using fractional polynomial models. The treatment effect of pembrolizumab was more favourable in the adjusted population compared with the observed effect in the KEYNOTE-052 study. The company submitted a de novo partitioned survival cohort simulation model, which partitions the OS time into PFS and post-progression survival. The probabilistic incremental cost-effectiveness ratio (ICER) for pembrolizumab compared with carboplatin plus gemcitabine was estimated to be £37,081 per quality-adjusted life-year (QALY) gained, based on the results within the company’s health economic model. Following a critique of the model, for their preferred base case the ERG corrected some minor model errors, chose a progression approach for estimating utilities, and revised the extrapolation of PFS and OS. The ERG’s probabilistic base case ICER was estimated to be £67,068 per QALY gained. The ERG also undertook a range of exploratory sensitivity analyses which suggested that the ICER was highly uncertain. In particular, the choices of extrapolation for the OS of pembrolizumab and the stopping rule for pembrolizumab had the largest impacts on the ICER. The NICE Appraisal Committee recommended pembrolizumab for use within the Cancer Drugs Fund as an option for treating locally advanced or metastatic urothelial carcinoma in adults who have had platinum-containing chemotherapy, provided that pembrolizumab was stopped at 2 years of uninterrupted treatment, or earlier if the disease progresses, and the conditions of the managed access agreement for pembrolizumab are followed

Toward the development of data governance standards for using clinical free-text data in health research: position paper

Background: Clinical free-text data (eg, outpatient letters or nursing notes) represent a vast, untapped source of rich information that, if more accessible for research, would clarify and supplement information coded in structured data fields. Data usually need to be deidentified or anonymized before they can be reused for research, but there is a lack of established guidelines to govern effective deidentification and use of free-text information and avoid damaging data utility as a by-product. Objective: This study aimed to develop recommendations for the creation of data governance standards to integrate with existing frameworks for personal data use, to enable free-text data to be used safely for research for patient and public benefit. Methods: We outlined data protection legislation and regulations relating to the United Kingdom for context and conducted a rapid literature review and UK-based case studies to explore data governance models used in working with free-text data. We also engaged with stakeholders, including text-mining researchers and the general public, to explore perceived barriers and solutions in working with clinical free-text. Results: We proposed a set of recommendations, including the need for authoritative guidance on data governance for the reuse of free-text data, to ensure public transparency in data flows and uses, to treat deidentified free-text data as potentially identifiable with use limited to accredited data safe havens, and to commit to a culture of continuous improvement to understand the relationships between the efficacy of deidentification and reidentification risks, so this can be communicated to all stakeholders. Conclusions: By drawing together the findings of a combination of activities, we present a position paper to contribute to the development of data governance standards for the reuse of clinical free-text data for secondary purposes. While working in accordance with existing data governance frameworks, there is a need for further work to take forward the recommendations we have proposed, with commitment and investment, to assure and expand the safe reuse of clinical free-text data for public benefit

The Pictorial Fit-Frail Scale: developing a visual scale to assess frailty

Background: Standardized frailty assessments are needed for early identification and treatment. We aimed to develop a frailty scale using visual images, the Pictorial Fit-Frail Scale (PFFS), and to examine its feasibility and content validity. Methods: In Phase 1, a multidisciplinary team identified domains for measurement, operationalized impairment levels, and re-viewed visual languages for the scale. In Phase 2, feedback was sought from health professionals and the general public. In Phase 3, 366 participants completed preliminary testing on the revised draft, including 162 UK paramedics, and rated the scale on feasibility and usability. In Phase 4, following translation into Malay, the final prototype was tested in 95 participants in Peninsular Malaysia and Borneo. Results: The final scale incorporated 14 domains, each conceptualized with 3–6 response levels. All domains were rated as “understood well” by most participants (range 64–94%). Percentage agreement with positive statements regarding appearance, feasibility, and usefulness ranged from 66% to 95%. Overall feedback from health-care professionals supported its content validity. Conclusions: The PFFS is comprehensive, feasible, and appears generalizable across countries, and has face and content validity. Investigation into the reliability and predictive validity of the scale is currently underway

Discourses of integration and exclusion: Equal opportunities for university students with dependent children?

Despite the growth and diversification of the student population, many British universities are still organised to cater for young students without caring responsibilities. Drawing on feminist frameworks of gender equality, this paper explores the ways in which governmental discourse of equal opportunities is articulated, sustained and resisted by staff and studying parents in a 1960s university. While many respondents attempt to comply with the prevailing learner norms entrenched in government policy, some also articulate an alternative discourse justifying the 'special treatment' of non-traditional students. However, this paper extends a third narrative that attempts to re-imagine university as an inclusive space

The Concise Guide to PHARMACOLOGY 2023/24:Introduction and Other Protein Targets

The Concise Guide to PHARMACOLOGY 2023/24 is the sixth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of approximately 1800 drug targets, and about 6000 interactions with about 3900 ligands. There is an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes almost 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.16176. In addition to this overview, in which are identified 'Other protein targets' which fall outside of the subsequent categorisation, there are six areas of focus: G protein-coupled receptors, ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2023, and supersedes data presented in the 2021/22, 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.</p

Prevalence and architecture of de novo mutations in developmental disorders.

The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. Here we have sequenced the exomes of 4,293 families containing individuals with developmental disorders, and meta-analysed these data with data from another 3,287 individuals with similar disorders. We show that the most important factors influencing the diagnostic yield of DNMs are the sex of the affected individual, the relatedness of their parents, whether close relatives are affected and the parental ages. We identified 94 genes enriched in damaging DNMs, including 14 that previously lacked compelling evidence of involvement in developmental disorders. We have also characterized the phenotypic diversity among these disorders. We estimate that 42% of our cohort carry pathogenic DNMs in coding sequences; approximately half of these DNMs disrupt gene function and the remainder result in altered protein function. We estimate that developmental disorders caused by DNMs have an average prevalence of 1 in 213 to 1 in 448 births, depending on parental age. Given current global demographics, this equates to almost 400,000 children born per year