A landscape of driver mutations in melanoma.

Despite recent insights into melanoma genetics, systematic surveys for driver mutations are challenged by an abundance of passenger mutations caused by carcinogenic UV light exposure. We developed a permutation-based framework to address this challenge, employing mutation data from intronic sequences to control for passenger mutational load on a per gene basis. Analysis of large-scale melanoma exome data by this approach discovered six novel melanoma genes (PPP6C, RAC1, SNX31, TACC1, STK19, and ARID2), three of which-RAC1, PPP6C, and STK19-harbored recurrent and potentially targetable mutations. Integration with chromosomal copy number data contextualized the landscape of driver mutations, providing oncogenic insights in BRAF- and NRAS-driven melanoma as well as those without known NRAS/BRAF mutations. The landscape also clarified a mutational basis for RB and p53 pathway deregulation in this malignancy. Finally, the spectrum of driver mutations provided unequivocal genomic evidence for a direct mutagenic role of UV light in melanoma pathogenesis.

Strengthening the clinical laboratory workforce in Cambodia: a case study of a mixed-method in-service training program to improve laboratory quality management system oversight.

BACKGROUND: Laboratory diagnostic testing service delivery and compliance with international standards for laboratory quality are directly influenced by laboratory workforce competency. Many hospital laboratories in constrained resource settings such as Cambodia struggle to cope with the training needs of laboratory professionals in an environment of competing healthcare development priorities. Resource-limited countries need an adaptable and effective approach to provide laboratory professionals with job-specific quality oversight training to ensure the accuracy, timeliness, and reliability of diagnostic services. CASE PRESENTATION: Here, we describe the results of an in-service training and mentoring program conducted with the Cambodia Ministry of Health at 12 tertiary-level hospital laboratories to drive improvements in laboratory quality management systems toward ISO 15189 accreditation, which demonstrated significant progress between baseline and outcome audits in a concurrent study. This case study describes the program, and evaluates how the four primary activities, including actionable gap assessments and planning, centralized and in situ training curriculum, in-person mentoring, and remote tele-mentoring via video communication technologies, contributed towards quality improvement in the participating laboratories. We evaluated participant responses to Likert scale and free response questions from program and training evaluation surveys, and we used thematic analysis to develop a model of best practices within the program's four primary activities to inform future training approaches. Of these activities, participants agreed most highly that in-person visits and planning based on gap assessments contributed to their learning and ability to improve laboratory operations. Tele-mentoring was rated lowest by participants, who were critical of excessive group dialogue and distraction during web-conferencing; however, feedback suggests both in-person and remote mentoring contribute to continuing education, accountability to action, and peer collaboration and problem solving to improve workforce efforts toward improved quality management systems. CONCLUSIONS: We recommend here a package of in-service training activities for laboratory quality management system improvement initiatives in resource constrained settings that includes needs-based curricula and personalized action plans for participants; interactive and on-site training workshops; and in-person mentoring, complemented with well managed and regular tele-mentoring that focuses on knowledge retention, accountability to goals, and collaborative problem solving. Our model presents an adaptable approach to human resource development for quality improvement in medical laboratories.

Structural and functional insights into asymmetric enzymatic dehydration of alkenols.

The asymmetric dehydration of alcohols is an important process for the direct synthesis of alkenes. We report the structure and substrate specificity of the bifunctional linalool dehydratase isomerase (LinD) from the bacterium Castellaniella defragrans that catalyzes in nature the hydration of ß-myrcene to linalool and the subsequent isomerization to geraniol. Enzymatic kinetic resolutions of truncated and elongated aromatic and aliphatic tertiary alcohols (C5-C15) that contain a specific signature motif demonstrate the broad substrate specificity of LinD. The three-dimensional structure of LinD from Castellaniella defragrans revealed a pentamer with active sites at the protomer interfaces. Furthermore, the structure of LinD in complex with the product geraniol provides initial mechanistic insights into this bifunctional enzyme. Site-directed mutagenesis confirmed active site amino acid residues essential for its dehydration and isomerization activity. These structural and mechanistic insights facilitate the development of hydrating catalysts, enriching the toolbox for novel bond-forming biocatalysis.

Mutational heterogeneity in cancer and the search for new cancer-associated genes.

Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.

Nozzle: a report generation toolkit for data analysis pipelines.

SUMMARY: We have developed Nozzle, an R package that provides an Application Programming Interface to generate HTML reports with dynamic user interface elements. Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big datasets. The package can be applied to any project where user-friendly reports need to be created. AVAILABILITY: The R package is available on CRAN at http://cran.r-project.org/package=Nozzle.R1. Examples and additional materials are available at http://gdac.broadinstitute.org/nozzle. The source code is also available at http://www.github.com/parklab/Nozzle. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Improving drinking water quality through proficiency testing-the impact of testing method and accreditation status on Escherichia coli detection by Canadian environmental testing laboratories.

Water quality testing is crucial for protecting public health, especially considering the number of boil water advisories annually issued across Canada that impact daily life for residents in affected areas. To overcome these challenges, the development of drinking water safety plans and accessibility to regular testing using simple, rapid, and accurate materials are necessary. However, the significance of monitoring the accuracy of environmental microbiology testing laboratories cannot be overlooked. Participation in external quality assessment programs, such as those that include proficiency testing (PT), is a necessary risk management resource that ensures the effectiveness of these testing processes. Proficiency Testing Canada (PTC), in collaboration with the Canadian Microbiological Proficiency Testing (CMPT) program based at the University of British Columbia, have implemented a drinking-water microbiology PT program since 1996. Both PTC and CMPT are ISO/IEC 17043:2010-accredited EQA providers. The drinking water program provided PT challenges to subscribing testing laboratories twice per year. Each challenge consisted of four samples containing unknown concentrations of Escherichia coli (E. coli) and Enterobacter spp. Results from participants were assessed for accuracy based on the method of testing. This cross-sectional study evaluated 150 rural and metropolitan testing sites across Canada between 2016 and 2022. Multivariable logistic regression analysis was conducted to examine the impact of different testing methods and laboratory accreditation status on the proficiency scores. This approach enabled us to assess the association between multiple independent variables and the likelihood of achieving specific proficiency scores, providing insights into how testing methods and accreditation status affect overall performance. After adjusting for rural residence, testing time, and survey year, the membrane filtration method was positively associated with the likelihood of scoring satisfactory results compared to the enzyme-substrate method (OR: 1.75; CI: 1.37-2.24), as well as accreditation status (OR: 1.47; CI: 1.16-1.85). The potential for improvement in environmental laboratory testing performance through the implementation of regulated PT in drinking water safety plans is proposed, along with the need for reliable testing methods applicable to rapid drinking water microbiology testing.

Ensuring diagnostic testing accuracy for patient care and public health- COVID-19 testing scale-up from an EQA provider's perspective.

In response to the coronavirus pandemic (COVID-19) and scale up of diagnostic testing, the Canadian Microbiology Proficiency Testing program created a new proficiency testing (PT) program for the molecular and antigen detection of SARS-CoV-2. The program was geared to point of care testing (POCT) sites located in each of the eight provincial Health Authorities across British Columbia, Canada, with the intention to monitor testing quality. The PT program consisted of 6 shipments in a year, each containing a set of 4 samples either positive for SARS-CoV-2 virus or negative. The program began with initial 23 sites enrolling in March 2021, expanding to >100 participants by December 2021. After the first two surveys, it was observed that testing performance (accuracy) was consistently acceptable for sites using nucleic acid technology (NAT), however performance by sites using rapid antigen detection (RAD) methods was poor, especially when testing the weakly positive samples. A root cause investigation of poor testing performance revealed gaps in the execution of testing methods and also in results interpretation. These quality issues were most commonly associated with new testers who lacked experience with diagnostic testing. Tester training and mentoring was reinforced as was retraining of personnel; sample processing instructions were modified, and a training video was also created for testing sites. As a result of these interventions, sites improved their testing accuracy and the performance of POCT sites using RAD methods came to more closely match the performance of sites utilizing NAT. Overall, the PT program was highly successfully and improved quality of testing in the province. This work demonstrates the critical value of an external quality assessment (EQA) partner towards improving patient and public health and safety, especially when testing is conducted outside of an accredited medical laboratory setting.

Grand challenges in entomology: Priorities for action in the coming decades.

Entomology is key to understanding terrestrial and freshwater ecosystems at a time of unprecedented anthropogenic environmental change and offers substantial untapped potential to benefit humanity in a variety of ways, from improving agricultural practices to managing vector-borne diseases and inspiring technological advances.We identified high priority challenges for entomology using an inclusive, open, and democratic four-stage prioritisation approach, conducted among the membership and affiliates (hereafter 'members') of the UK-based Royal Entomological Society (RES).A list of 710 challenges was gathered from 189 RES members. Thematic analysis was used to group suggestions, followed by an online vote to determine initial priorities, which were subsequently ranked during an online workshop involving 37 participants.The outcome was a set of 61 priority challenges within four groupings of related themes: (i) 'Fundamental Research' (themes: Taxonomy, 'Blue Skies' [defined as research ideas without immediate practical application], Methods and Techniques); (ii) 'Anthropogenic Impacts and Conservation' (themes: Anthropogenic Impacts, Conservation Options); (iii) 'Uses, Ecosystem Services and Disservices' (themes: Ecosystem Benefits, Technology and Resources [use of insects as a resource, or as inspiration], Pests); (iv) 'Collaboration, Engagement and Training' (themes: Knowledge Access, Training and Collaboration, Societal Engagement).Priority challenges encompass research questions, funding objectives, new technologies, and priorities for outreach and engagement. Examples include training taxonomists, establishing a global network of insect monitoring sites, understanding the extent of insect declines, exploring roles of cultivated insects in food supply chains, and connecting professional with amateur entomologists. Responses to different challenges could be led by amateur and professional entomologists, at all career stages.Overall, the challenges provide a diverse array of options to inspire and initiate entomological activities and reveal the potential of entomology to contribute to addressing global challenges related to human health and well-being, and environmental change.

The at-risk registers in severe asthma (ARRISA) study: a cluster-randomised controlled trial examining effectiveness and costs in primary care.

BACKGROUND: Patients at risk of severe exacerbations contribute disproportionally to asthma mortality, morbidity and costs. We evaluated the effectiveness and costs of using 'asthma risk registers' for these patients in primary care. METHODS: In a cluster-randomised trial, 29 primary care practices identified 911 at-risk asthma patients using British asthma guideline criteria (severe asthma plus adverse psychosocial characteristics). Intervention practices added electronic alerts to identified patients' records to flag their at-risk status and received practice-based training about using the alerts to improve patient access and opportunistic management. Control practices continued routine care. Numbers of patients experiencing the primary outcome of a moderate-severe exacerbation (resulting in death, hospitalisation, accident and emergency attendance, out-of-hours contact, or a course/boost in oral prednisolone for asthma), other healthcare and medication usage, and costs over 1 year were derived from practice-based records. RESULTS: There was no significant effect on exacerbations (control: 46.5%; intervention: 53.6%, OR, 95% CI 1.30, 0.93 to 1.80). However, this composite outcome masked relative reductions in intervention patients experiencing hospitalisations (OR 0.50, 95% CI 0.26 to 0.94), accident and emergency (OR 0.74, 95% CI 0.42 to 1.31) and out-of-hours contacts (OR 0.79, 95% CI 0.45 to 1.37); and a relative increase in prednisolone prescription for exacerbations (OR 1.31, 95% CI 0.92 to 1.85). Furthermore, prescription of nebulised short-acting ß-agonists reduced and long-acting ß-agonists increased for intervention relative to control patients. The adjusted mean per patient healthcare cost was £138.21 lower (p=0.837) among intervention practices. CONCLUSION: Using asthma risk registers in primary care did not reduce treated exacerbations, but reduced hospitalisations and increased prescriptions of recommended preventative therapies without increasing costs.

Respiratory syncytial virus-associated hospitalisation in children aged ≤5†years: a scoping review of literature from 2009 to 2021.

Introduction: Following the easing of COVID-19 restrictions in many countries, a surge in respiratory syncytial virus (RSV) hospitalisations was reported, surpassing yearly trends pre-pandemic. The changes to RSV epidemiology may have unforeseen effects on healthcare systems and populations globally, adding to the burden generated during the pandemic and placing increased demand on resources. Here we aim to identify recent global trends of RSV hospitalisation amongst children aged ≤5 years, to help inform policy makers in the planning of preventative interventions. Methods: We conducted a scoping review of published literature between January 2009 and May 2021. Using keywords "Hospital admissions, Respiratory syncytial virus, RSV, Bronchiolitis, Children" we located studies using Medline, EMCARE, CINAHL and HMIC. Studies were eligible if they reported on trends/data for RSV hospitalisation amongst children aged ≤5 years. The articles were reviewed by two independent reviewers. Findings: We assessed 3310 abstracts, reviewed 70 studies and included 56 studies in the final review. Findings were categorised into themes. The review highlighted that, although RSV incidence has been steadily increasing since 2009, the number of reported RSV hospitalisations decreased during lockdown. The highest numbers of hospitalisations were reported in children <1 year of age, particularly 0-2-month-old infants. Globally, RSV hospitalisations tend to peak in the winter months; however, since COVID-19 restrictions have eased, countries are reporting incidence peaks at different times, in contrast to the trends of previous years. Conclusion: With greater physical interactions due to the relaxation of COVID-19 restriction measures, RSV-related hospitalisations can be seen to increase amongst children aged ≤5 years, possibly surpassing the numbers reported in previous RSV seasons.

Allelic variation in class I HLA determines CD8+ T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2.

Effective presentation of antigens by human leukocyte antigen (HLA) class I molecules to CD8+ T cells is required for viral elimination and generation of long-term immunological memory. In this study, we applied a single-cell, multiomic technology to generate a unified ex vivo characterization of the CD8+ T cell response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across four major HLA class I alleles. We found that HLA genotype conditions key features of epitope specificity, TCRα/ß sequence diversity, and the utilization of pre-existing SARS-CoV-2-reactive memory T cell pools. Single-cell transcriptomics revealed functionally diverse T cell phenotypes of SARS-CoV-2-reactive T cells, associated with both disease stage and epitope specificity. Our results show that HLA variations notably influence the CD8+ T cell repertoire shape and utilization of immune recall upon SARS-CoV-2 infection.

Predicting asthma-related crisis events using routine electronic healthcare data: a quantitative database analysis study.

BACKGROUND: There is no published algorithm predicting asthma crisis events (accident and emergency [A&E] attendance, hospitalisation, or death) using routinely available electronic health record (EHR) data. AIM: To develop an algorithm to identify individuals at high risk of an asthma crisis event. DESIGN AND SETTING: Database analysis from primary care EHRs of people with asthma across England and Scotland. METHOD: Multivariable logistic regression was applied to a dataset of 61 861 people with asthma from England and Scotland using the Clinical Practice Research Datalink. External validation was performed using the Secure Anonymised Information Linkage Databank of 174 240 patients from Wales. Outcomes were ≥1 hospitalisation (development dataset) and asthma-related hospitalisation, A&E attendance, or death (validation dataset) within a 12-month period. RESULTS: Risk factors for asthma-related crisis events included previous hospitalisation, older age, underweight, smoking, and blood eosinophilia. The prediction algorithm had acceptable predictive ability with a receiver operating characteristic of 0.71 (95% confidence interval [CI] = 0.70 to 0.72) in the validation dataset. Using a cut-point based on the 7% of the population at greatest risk results in a positive predictive value of 5.7% (95% CI = 5.3% to 6.1%) and a negative predictive value of 98.9% (95% CI = 98.9% to 99.0%), with sensitivity of 28.5% (95% CI = 26.7% to 30.3%) and specificity of 93.3% (95% CI = 93.2% to 93.4%); those individuals had an event risk of 6.0% compared with 1.1% for the remaining population. In total, 18 people would need to be followed to identify one admission. CONCLUSION: This externally validated algorithm has acceptable predictive ability for identifying patients at high risk of asthma-related crisis events and excluding those not at high risk.

Impact of age and treatment institution type on outcomes of patients treated for chronic lymphocytic leukemia in British Columbia, Canada.

Older age has been shown to adversely impact overall survival (OS) in chronic lymphocytic leukemia (CLL) however, prior population-based studies did not analyze the impact of cytogenetic abnormalities or were prior to the availability of ibrutinib. OBJECTIVES: i) We sought to compare outcomes of patients based on their age at treatment to examine if older age has an impact on OS in patients who were treated during the period when fludarabine-rituximab was the standard upfront therapy and when ibrutinib was first introduced and ii) compare outcomes based on whether the patient received primary treatment at an academic or community-based centre. METHODS: The BC Provincial CLL Database, a population-based databasewas used to include patients who have received treatment in British Columbia (BC), Canada between 2004 and 2016. RESULTS: A total of 1122 patients were included (<70 years at treatment, n = 589) with median age at diagnosis 66 years. Younger patients had higher Rai stage (55% vs. 44% stage I-II, p < 0.001), higher lymphocyte count at diagnosis (13 × 109/L vs. 10 × 109/L, p = 0.004), greater proportion with B-symptoms at diagnosis (15% vs 10%, p = 0.004), shorter time from diagnosis to treatment (13.9 months vs. 21.4 months, p = 0.001), higher proportion treated at an academic centre (79% vs. 69%, p < 0.001) and more were treated with fludarabine-rituximab or FCR (69% vs. 42%, p < 0.001) compared to older patients. Older patients had both a significantly (p < 0.001) shorter OS from treatment start (4.7 years) and disease specific survival (8.1 years) than younger patients (median OS and DSS not reached). Of interest, there was no difference in OS between patients treated at an academic centre or community centre (p = 0.087). First-line treatment with chemoimmunotherapy improved OS (HR 0.465, 95% CI: 0.381-.567). CONCLUSIONS: Older age but not treatment-institution type adversely impacts overall survival and CLL survival in treated patients in BC.

Improving laboratory quality and capacity through leadership and management training: Lessons from Zambia 2016-2018.

BACKGROUND: Competent leadership and management are imperative for delivering quality laboratory services; however, few laboratory managers receive job-specific training in organisational management and leadership. OBJECTIVE: To develop and evaluate participants' competencies in organisational leadership and management as measured through learner and laboratory quality improvement assessments. METHODS: This professional development programme employed a mentored, blended learning approach, utilising in-person didactic and online training, with the practical application of a capstone project in the laboratories. Programme impact was evaluated through a series of pre- and post-laboartory assessments using the Stepwise Laboratory Improvement Process Towards Accreditation checklist, as well as learner-competency assessments through online quizzes and discussions. RESULTS: From 2016 to 2018, 31 managers and quality officers from 16 individual laboratories graduated from the programme having completed capstone projects addressing areas in the entire laboratory testing process. Laboratories increased their compliance with the International Organization for Standardization 15189 standard and all but two laboratories significantly increased their accreditation scores. Two laboratories gained three stars, two laboratories gained two stars, and five laboratories gained one star. Five laboratories subsequently achieved International Organization for Standardization 15189 accreditation in 2019. CONCLUSION: This programme taught leadership theory to laboratory managers and allowed them to implement leadership and management practices in the laboratory setting. Programmes such as this complement existing laboratory quality management training programmes such as Strengthening Laboratory Management Toward Accreditation.

Comparison of real-world treatment patterns in chronic lymphocytic leukemia management before and after availability of ibrutinib in the province of British Columbia, Canada.

We performed a retrospective study comparing treatment patterns and overall survival (OS) in chronic lymphocytic leukemia (CLL) patients with the advent of ibrutinib to provide current real-world data. METHODS: Using a provincial population-based database, we analyzed CLL patients who received upfront treatment in British Columbia before ibrutinib availability (1984-2014), during ibrutinib access for: relapse only (2014-2015) and for upfront treatment of patients (with 17p deletion or unfit for chemotherapy) (2015-2016). Analysis included up to third-line treatment. RESULTS: Of 1729 patients meeting inclusion criteria (median age, 66 years; 1466, period 1; 140, period 2; 123, period 3), FR was the most common first-line therapy (35.8 %, 54.3 % and 40.7 %, periods 1-3, respectively) and 18.7 % received ibrutinib upfront in period 3. The most common therapies in relapse were chemoimmunotherapy (36.1 % and 55.6 %, periods 1 and 2, second-line; 29.2 %, period 1, third-line) and ibrutinib (69.8 %, period 3, second-line; 46.4 % and 70.3 %, periods 2 and 3, third-line). OS improved for patients treated in periods 2-3 over period 1 (median OS not reached vs. 11.9 years, p < 0.001; no difference in OS for periods 2-3, p = 0.385). CONCLUSION: Ibrutinib has replaced chemoimmunotherapy as the preferred therapy in relapse. Overall survival has improved over time with access to ibrutinib.

Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data.

We present a systematic analysis of the effects of synchronizing a large-scale, deeply characterized, multi-omic dataset to the current human reference genome, using updated software, pipelines, and annotations. For each of 5 molecular data platforms in The Cancer Genome Atlas (TCGA)-mRNA and miRNA expression, single nucleotide variants, DNA methylation and copy number alterations-comprehensive sample, gene, and probe-level studies were performed, towards quantifying the degree of similarity between the 'legacy' GRCh37 (hg19) TCGA data and its GRCh38 (hg38) version as 'harmonized' by the Genomic Data Commons. We offer gene lists to elucidate differences that remained after controlling for confounders, and strategies to mitigate their impact on biological interpretation. Our results demonstrate that the hg19 and hg38 TCGA datasets are very highly concordant, promote informed use of either legacy or harmonized omics data, and provide a rubric that encourages similar comparisons as new data emerge and reference data evolve.

Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda(6)-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 5: Exploration of pyridazinones containing 6-amino-substituents.

The synthesis of 4-(1',1'-dioxo-1',4'-dihydro-1'lambda(6)-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones bearing 6-amino substituents as potent inhibitors of the HCV RNA-dependent RNA polymerase (NS5B) is described. Several of these agents also display potent antiviral activity in cell culture experiments (EC(50)<0.10 microM). In vitro DMPK data (microsome t(1/2), Caco-2 P(app)) for many of the compounds are also disclosed, and a crystal structure of a representative inhibitor complexed with the NS5B protein is discussed.

Laboratory error reporting rates can change significantly with year-over-year examination.

BACKGROUND: Incident reporting systems are useful tools to raise awareness of patient safety issues associated with healthcare error, including errors associated with the medical laboratory. METHODS: Previously, we presented the analysis of data compiled by the British Columbia Patient Safety & Learning System over a 3-year period. A second comparable set was collected and analyzed to determine if reported error rates would tend to remain stable or change. RESULTS: Compared to the original set, the second set presented changes that were both materially and statistically significant. Overall, the total number of reports increased by 297% with substantial changes between the pre-examination, examination and post-examination phases (χ2: 993.925, DF=20; p<0.00001). While the rate of change for pre-examination (clerical and collection) errors were not significantly different than the total year results, the rate of change for reporting examination errors rose by 998%. While the exact reason for dramatic change is not clear, possible explanations are provided. CONCLUSIONS: Longitudinal error rate tracking is a useful approach to monitor for laboratory quality improvement.

At-risk registers integrated into primary care to stop asthma crises in the UK (ARRISA-UK): study protocol for a pragmatic, cluster randomised trial with nested health economic and process evaluations.

BACKGROUND: Despite effective treatments and long-standing management guidelines, there are approximately 1400 hospital admissions for asthma weekly in the United Kingdom (UK), many of which could be avoided. In our previous research, a secondary analysis of the intervention (ARRISA) suggested an improvement in the management of at-risk asthma patients in primary care. ARRISA involved identifying individuals at risk of adverse asthma events, flagging their electronic health records, training practice staff to develop and implement practice-wide processes of care when alerted by the flag, plus motivational reminders. We now seek to determine the effectiveness and cost-effectiveness of ARRISA in reducing asthma-related crisis events. METHODS: We are undertaking a pragmatic, two-arm, multicentre, cluster randomised controlled trial, plus health economic and process evaluation. We will randomise 270 primary care practices from throughout the UK covering over 10,000 registered patients with 'at-risk asthma' identified according to a validated algorithm. Staff in practices randomised to the intervention will complete two 45-min eLearning modules (an individually completed module giving background to ARRISA and a group-completed module to develop practice-wide pathways of care) plus a 30-min webinar with other practices. On completion of training at-risk patients' records will be coded so that a flag appears whenever their record is accessed. Practices will receive a phone call at 4 weeks and a reminder video at 6 weeks and 6 months. Control practices will continue to provide usual care. We will extract anonymised routine patient data from primary care records (with linkage to secondary care data) to determine the percentage of at-risk patients with an asthma-related crisis event (accident and emergency attendances, hospitalisations and deaths) after 12 months (primary outcome). We will also capture the time to crisis event, all-cause hospitalisations, asthma control and any changes in practice asthma management for at-risk and all patients with asthma. Cost-effectiveness analysis and mixed-methods process evaluations will also be conducted. DISCUSSION: This study is novel in terms of using a practice-wide intervention to target and engage with patients at risk from their asthma and is innovative in the use of routinely captured data with record linkage to obtain trial outcomes. TRIAL REGISTRATION: ISRCTN95472706 . Registered on 5 December 2014.

Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups.

There is a pressing need to identify therapeutic targets in tumors with low mutation rates such as the malignant pediatric brain tumor medulloblastoma. To address this challenge, we quantitatively profiled global proteomes and phospho-proteomes of 45 medulloblastoma samples. Integrated analyses revealed that tumors with similar RNA expression vary extensively at the post-transcriptional and post-translational levels. We identified distinct pathways associated with two subsets of SHH tumors, and found post-translational modifications of MYC that are associated with poor outcomes in group 3 tumors. We found kinases associated with subtypes and showed that inhibiting PRKDC sensitizes MYC-driven cells to radiation. Our study shows that proteomics enables a more comprehensive, functional readout, providing a foundation for future therapeutic strategies.