An app promoting weight gain prevention via healthy behaviours amongst young women with a family history of breast cancer: Acceptability and usability assessment.

BACKGROUND: Breast cancer is the most frequent female malignancy in the UK. Around 20% of cases are linked to weight gain, excess weight and health behaviours. We designed a weight gain prevention, health behaviour intervention for young women at increased risk. METHODS: The study comprised a single arm observational study over 2 months testing acceptability and usability of the intervention: online group welcome event, app and private Facebook group. Females aged 18-35 years at moderate or high risk of breast cancer (>17% lifetime risk) were recruited via invite letters and social media posts. The app included behaviour change techniques and education content. Online questionnaires were completed at baseline, as well as at 1 and 2 months. We also assessed feasibility of study procedures. RESULTS: Both recruitment methods were successful. Thirty-five women were recruited, 26% via social media posts. Median age was 33 (interquartile range = 28.2-34.5) years, the majority (94.1%) were of White ethnicity. Thirty-four participants were included in the analyses, of which 94% downloaded the app. Median self-monitoring logs per participant during the study period was 10.0 (interquartile range = 4.8-28.8). App quality mean (SD) score was 3.7 (0.6) at 1 and 2 months (scale: 1-5). Eighty-nine per cent rated the app at average or above at 1 month and 75.0% at 2 months. Nineteen women (55.9%) joined the Facebook group and there were 61 comments and 83 reactions and votes from participants during the study period. CONCLUSIONS: This first iteration of the app and intervention was well received and is suitable to progress to the next stage of refining and further testing.

Personalized, intuitive & visual QT-prolongation monitoring using patient-specific QTc threshold with pseudo-coloring and explainable AI.

BACKGROUND: Drug-induced QT-prolongation increases the risk of TdP arrhythmia attacks and sudden cardiac death. However, measuring the QT-interval and determining a precise cut-off QT/QTc value that could put a patient at risk of TdP is challenging and influenced by many factors including female sex, drug-free baseline, age, genetic predisposition, and bradycardia. OBJECTIVES: This paper presents a novel approach for intuitively and visually monitoring QT-prolongation showing a potential risk of TdP, which can be adjusted according to patient-specific risk factors, using a pseudo-coloring technique and explainable artificial intelligence (AI). METHODS: We extended the development and evaluation of an explainable AI-based technique- visualized using pseudo-color on the ECG signal, thus intuitively 'explaining' how its decision was made -to detect QT-prolongation showing a potential risk of TdP according to a cut-off personalized QTc value (using Bazett's ∆QTc > 60 ms relative to drug-free baseline and Bazett's QTc > 500 ms as examples), and validated its performance using a large number of ECGs (n = 5050), acquired from a clinical trial assessing the effects of four known QT-prolonging drugs versus placebo on healthy subjects. We compared this new personalized approach to our previous study that used a more general approach using the QT-nomogram. RESULTS AND CONCLUSIONS: The explainable AI-based algorithm can accurately detect QT-prolongation when adjusted to a personalized patient-specific cut-off QTc value showing a potential risk of TdP. Using ∆QTc > 60 ms relative to drug-free baseline and QTc > 500 ms as examples, the algorithm yielded a sensitivity of 0.95 and 0.79, and a specificity of 0.95 and 0.98, respectively. We found that adjusting pseudo-coloring according to Bazett's ∆QTc > 60 ms relative to a drug-free baseline personalized to each patient provides better sensitivity than using Bazett's QTc > 500 ms, which could underestimate a potentially clinically significant QT-prolongation with bradycardia.

Using interactive digital notebooks for bioscience and informatics education.

Interactive digital notebooks provide an opportunity for researchers and educators to carry out data analysis and report the results in a single digital format. Further to just being digital, the format allows for rich content to be created in order to interact with the code and data contained in such a notebook to form an educational narrative. This primer introduces some of the fundamental aspects involved in using Jupyter notebooks in an educational setting for teaching in the bio/health informatics disciplines. We also provide 2 case studies that detail how we used Jupyter notebooks to teach non-coders programming skills on a blended Master's degree module for a Health Informatics programme and a fully online distance learning unit on Programming for a postgraduate certificate (PG Cert) in Clinical Bioinformatics with a more technical audience.

Integrating field and laboratory approaches for ripple development in mixed sand-clay-EPS.

The shape and size of sedimentary bedforms play a key role in the reconstruction of sedimentary processes in modern and ancient environments. Recent laboratory experiments have shown that bedforms in mixed sand-clay develop at a slower rate and often have smaller heights and wavelengths than equivalent bedforms in pure sand. This effect is generally attributed to cohesive forces that can be of physical origin, caused by electrostatic forces of attraction between clay minerals, and of biological origin, caused by 'sticky' extracellular polymeric substances (EPS) produced by micro-organisms, such as microalgae (microphytobenthos) and bacteria. The present study demonstrates, for the first time, that these laboratory experiments are a suitable analogue for current ripples formed by tidal currents on a natural mixed sand-mud-EPS intertidal flat in a macrotidal estuary. Integrated hydrodynamic and bed morphological measurements, collected during a spring tide under weak wave conditions near Hilbre Island (Dee Estuary, north-west England, UK), reveal a statistically significant decrease in current ripple wavelength for progressively higher bed mud and EPS contents, and a concurrent change from three-dimensional linguoid to two-dimensional straight-crested ripple planform morphology. These results agree well with observations in laboratory flumes, but the rate of decrease of ripple wavelength as mud content increased was found to be substantially greater for the field than the laboratory. Since the formation of ripples under natural conditions is inherently more complex than in the laboratory, four additional factors that might affect current ripple development in estuaries, but which were not accounted for in laboratory experiments, were explored. These were current forcing, clay type, pore water salinity and bed EPS content. These data illustrate that clay type alone cannot explain the difference in the rate of decrease in ripple wavelength, because the bed clay contents were too low for clay type to have had a measurable effect on bedform development. Accounting for the difference in current forcing between the field and experiments, and therefore the relative stage of development with respect to equilibrium ripples, increases the difference between the ripple wavelengths. The presence of strongly cohesive EPS in the current ripples on the natural intertidal flat might explain the majority of the difference in the rate of decrease in ripple wavelength between the field and the laboratory. The effect of pore water salinity on the rate of bedform development cannot be quantified at present, but salinity is postulated herein to have had a smaller influence on the ripple wavelength than bed EPS content. The common presence of clay and EPS in many aqueous sedimentary environments implies that a re-assessment of the role of current ripples and their primary current lamination in predicting and reconstructing flow regimes is necessary, and that models that are valid for pure sand are an inappropriate descriptor for more complex mixed sediment. This study proposes that this re-assessment is necessary at all bed clay contents above 3%.

Carrying out systematic literature reviews: an introduction.

Systematic reviews provide a synthesis of evidence for a specific topic of interest, summarising the results of multiple studies to aid in clinical decisions and resource allocation. They remain among the best forms of evidence, and reduce the bias inherent in other methods. A solid understanding of the systematic review process can be of benefit to nurses that carry out such reviews, and for those who make decisions based on them. An overview of the main steps involved in carrying out a systematic review is presented, including some of the common tools and frameworks utilised in this area. This should provide a good starting point for those that are considering embarking on such work, and to aid readers of such reviews in their understanding of the main review components, in order to appraise the quality of a review that may be used to inform subsequent clinical decision making.

Web Use for Symptom Appraisal of Physical Health Conditions: A Systematic Review.

BACKGROUND: The Web has become an important information source for appraising symptoms. We need to understand the role it currently plays in help seeking and symptom evaluation to leverage its potential to support health care delivery. OBJECTIVE: The aim was to systematically review the literature currently available on Web use for symptom appraisal. METHODS: We searched PubMed, EMBASE, PsycINFO, ACM Digital Library, SCOPUS, and Web of Science for any empirical studies that addressed the use of the Web by lay people to evaluate symptoms for physical conditions. Articles were excluded if they did not meet minimum quality criteria. Study findings were synthesized using a thematic approach. RESULTS: A total of 32 studies were included. Study designs included cross-sectional surveys, qualitative studies, experimental studies, and studies involving website/search engine usage data. Approximately 35% of adults engage in Web use for symptom appraisal, but this proportion varies between 23% and 75% depending on sociodemographic and disease-related factors. Most searches were symptom-based rather than condition-based. Users viewed only the top search results and interacted more with results that mentioned serious conditions. Web use for symptom appraisal appears to impact on the decision to present to health services, communication with health professionals, and anxiety. CONCLUSIONS: Web use for symptom appraisal has the potential to influence the timing of help seeking for symptoms and the communication between patients and health care professionals during consultations. However, studies lack suitable comparison groups as well as follow-up of participants over time to determine whether Web use results in health care utilization and diagnosis. Future research should involve longitudinal follow-up so that we can weigh the benefits of Web use for symptom appraisal (eg, reductions in delays to diagnosis) against the disadvantages (eg, unnecessary anxiety and health care use) and relate these to health care costs.

The role of biophysical cohesion on subaqueous bed form size.

Biologically active, fine-grained sediment forms abundant sedimentary deposits on Earth's surface, and mixed mud-sand dominates many coasts, deltas, and estuaries. Our predictions of sediment transport and bed roughness in these environments presently rely on empirically based bed form predictors that are based exclusively on biologically inactive cohesionless silt, sand, and gravel. This approach underpins many paleoenvironmental reconstructions of sedimentary successions, which rely on analysis of cross-stratification and bounding surfaces produced by migrating bed forms. Here we present controlled laboratory experiments that identify and quantify the influence of physical and biological cohesion on equilibrium bed form morphology. The results show the profound influence of biological cohesion on bed form size and identify how cohesive bonding mechanisms in different sediment mixtures govern the relationships. The findings highlight that existing bed form predictors require reformulation for combined biophysical cohesive effects in order to improve morphodynamic model predictions and to enhance the interpretations of these environments in the geological record.

جِین(Gene): A Co-Designed Smartphone App for Genetics Education and Empowerment in the Pakistani Community.

In the Pakistani/British Pakistani community in England it is quite common for people to marry close cousin relatives, which can increase the chances of certain genetic problems in their children. Families in these situations often have little knowledge of genetics and encounter difficulties accessing genetic counselling services and culturally appropriate genetics information is needed to support these families. We describe the co-design of a prototype culturally sensitive smart phone app with the British Pakistani community, to improve understanding of genetics and genetic services.

The relationship of within-individual and between-individual variation in mental health with bodyweight: An exploratory longitudinal study.

BACKGROUND: Poor mental health is associated with obesity, but existing studies are either cross-sectional or have long time periods between measurements of mental health and weight. It is, therefore, unclear how small fluctuations in mental wellbeing within individuals predict bodyweight over short time periods, e.g. within the next month. Studying this could identify modifiable determinants of weight changes and highlight opportunities for early intervention. METHODS: 2,133 UK adults from a population-based cohort completed monthly mental health and weight measurements using a mobile app over a period of 6-9 months. We used random intercept regression models to examine longitudinal associations of depressive symptoms, anxiety symptoms and stress with subsequent weight. In sub-group analyses, we included interaction terms of mental health variables with baseline characteristics. Mental health variables were split into "between-individual" measurements (= the participant's median score across all timepoints) and "within-individual" measurements (at each timepoint, the difference between the participant's current score and their median). RESULTS: Within-individual variation in depressive symptoms predicted subsequent weight (0.045kg per unit of depressive symptom severity, 95% CI 0.021-0.069). We found evidence of a moderation effect of baseline BMI on the association between within-individual fluctuation in depressive symptoms and subsequent weight: The association was only apparent in those with overweight/obesity, and it was stronger in those with obesity than those with overweight (BMI<25kg/m2: 0.011kg per unit of depressive symptom severity [95% CI -0.017 to 0.039]; BMI 25-29.9kg/m2: 0.052kg per unit of depressive symptom severity [95%CI 0.010-0.094kg]; BMI≥30kg/m2: 0.071kg per unit of depressive symptom severity [95%CI 0.013-0.129kg]). We found no evidence for other interactions, associations of stress and anxiety with weight, or for a reverse direction of association. CONCLUSION: In this exploratory study, individuals with overweight or obesity were more vulnerable to weight gain following higher-than-usual (for that individual) depressive symptoms than individuals with a BMI<25kg/m2.

Reporting quality of published reviews of commercial and publicly available mobile health apps (mHealth app reviews): a scoping review protocol.

INTRODUCTION: Reviews of commercial and publicly available smartphone (mobile) health applications (mHealth app reviews) are being undertaken and published. However, there is variation in the conduct and reporting of mHealth app reviews, with no existing reporting guidelines. Building on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we aim to develop the Consensus for APP Review Reporting Items (CAPPRRI) guidance, to support the conduct and reporting of mHealth app reviews. This scoping review of published mHealth app reviews will explore their alignment, deviation, and modification to the PRISMA 2020 items for systematic reviews and identify a list of possible items to include in CAPPRRI. METHOD AND ANALYSIS: We are following the Joanna Briggs Institute approach and Arksey and O'Malley's five-step process. Patient and public contributors, mHealth app review, digital health research and evidence synthesis experts, healthcare professionals and a specialist librarian gave feedback on the methods. We will search SCOPUS, CINAHL Plus, AMED, EMBASE, Medline, APA PsycINFO and the ACM Digital Library for articles reporting mHealth app reviews and use a two-step screening process to identify eligible articles. Information on whether the authors have reported, or how they have modified the PRISMA 2020 items in their reporting, will be extracted. Data extraction will also include the article characteristics, protocol and registration information, review question frameworks used, information about the search and screening process, how apps have been evaluated and evidence of stakeholder engagement. This will be analysed using a content synthesis approach and presented using descriptive statistics and summaries. This protocol is registered on OSF (https://osf.io/5ahjx). ETHICS AND DISSEMINATION: Ethical approval is not required. The findings will be disseminated through peer-reviewed journal publications (shared on our project website and on the EQUATOR Network website where the CAPPRRI guidance has been registered as under development), conference presentations and blog and social media posts in lay language.

How do automated reasoning features impact the usability of a clinical task management system? Development and usability testing of a prototype.

BACKGROUND: Electronic clinical task management systems (ECTMSs) have been developed and adopted by care providers to improve care coordination. Some systems utilised automated reasoning (AR) to enable more intelligent task management functionalities, such as automated task allocation. Yet, the impact of such features on usability remains unclear. Poor usability of health information systems has been described to cause frustration and contribute to patient safety incidents. AIM: To design AR features for an ECTMS and to evaluate their impact on usability. METHODS: In this mixed methods study, four ECTMS feature prototypes were co-designed with two clinicians. For each prototype, one AR variant and one non-AR variant with equivalent functionalities were developed. A moderated usability testing was conducted with seven clinicians to obtain ease-of-use ratings of prototypes and measure task durations. Parameters related to demographics and attitudes of participants were obtained via a questionnaire. A framework analysis was performed to summarise qualitative feedback. To determine statistical relationships of study variables, Spearmans rank coefficients were calculated and presented as a correlation matrix. RESULTS: Three out of four prototypes received higher median ease-of-use ratings for AR variants and were associated with shorter average task durations. Multiple clinical use cases suitable for AR were identified. Preference for AR was found to moderately correlate with digital proficiency and prior experience with ECTMSs. Insufficient trust in automation, alert fatigue, and system customisation were identified as challenges in the adoption of AR features. CONCLUSIONS: This study provides evidence for the potential of AR to enhance usability in ECTMSs. Consideration of psychological and organisational context of users in the feature design was found to be decisive for usability. Future research should explore implications for operational and clinical outcomes.

Digital interventions for genomics and genetics education, empowerment, and service engagement: A systematic review.

BACKGROUND: Patient-facing digital technologies may reduce barriers to and alleviate the burden on genetics services. However, no work has synthesised the evidence for patient-facing digital interventions for genomics/genetics education and empowerment, or to facilitate service engagement more broadly. It is also unclear which groups have been engaged by digital interventions. AIM: This systematic review explores which existing patient-facing digital technologies have been used for genomics/genetics education and empowerment, or to facilitate service engagement, and for whom and for which purposes the interventions have been developed. METHODS: The review adhered to the Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Eight databases were searched for literature. Information was extracted into an Excel sheet and analysed in a narrative manner. Quality assessments were conducted using the Mixed Methods Appraisal Tool. RESULTS: Twenty-four studies were included, of which 21 were moderate or high quality. The majority (88%) were conducted in the United States of America or within a clinical setting (79%). More than half (63%) of the interventions were web-based tools, and almost all focussed on educating users (92%). There were promising results regarding educating patients and their families and facilitating engagement with genetics services. Few of the studies focussed on empowering patients or were community-based. CONCLUSION: Digital interventions may be used to deliver information about genetics concepts and conditions, and positively impact service engagement. However, there is insufficient evidence related to empowering patients and engaging underserved communities or consanguineous couples. Future work should focus on co-developing content with end users and incorporating interactive features.

Correction: Evaluating the Acceptance and Usability of an App Promoting Weight Gain Prevention and Healthy Behaviors Among Young Women With a Family History of Breast Cancer: Protocol for an Observational Study.

[This corrects the article DOI: 10.2196/41246.].

Creation of a core competency framework for clinical informatics: From genesis to maintaining relevance.

BACKGROUND: The United Kingdom's Faculty of Clinical Informatics (FCI) embarked on the creation of a core competency framework in response to the need to provide support to those working in clinical and health and social care that also hold informatics roles. METHODS: The work spanned several phases and utilised a mixed-methods approach consisting of interviews, surveys, job listing analysis, expert discussions and a systematic literature review. The work presented here explores the lessons learnt from the process of creating the framework and the next steps for ensuring its use and continued relevance. RESULTS: A core competency framework was generated with six domains, 36 sub-domains and 111 individual competency statements. A discussion and eight key recommendations are presented based on the development of this framework. CONCLUSION: Definition of the target audience is important to manage scope and define purpose. The use of robust reproducible methods helps to establish a strong evidence base. Competency frameworks should be living documents, ideally presented in an accessible digital form to enable easy use and embedding in other tools (e.g. for accreditation or to search competencies).

Applying Co-Design Principles for the Development of Health Education and Workforce Development.

The digital transformation of the UK's healthcare system necessitates the development of digital capabilities across the workforce. This ranges from basic digital literacy through to advanced skills with data and analytic methods. We present two projects that apply co-design to work with end-users and other stakeholders to produce a digital healthcare technologies capability framework aimed at the wider NHS workforce and a post graduate Clinical Data Science course aimed at bridging the gap between clinicians and the data-centric professions (e.g. analysts, data scientists, informaticians) to aid in digital transformation projects.

Patient-facing genetic and genomic mobile apps in the UK: a systematic review of content, functionality, and quality.

Close relative (consanguineous) marriage is widely practised globally, and it increases the risk of genetic disorders. Mobile apps may increase awareness and education regarding the associated risks in a sensitive, engaging, and accessible manner. This systematic review of patient-facing genetic/genomic mobile apps explores content, function, and quality. We searched the NHS Apps Library and the UK Google Play and Apple App stores for patient-facing genomic/genetic smartphone apps. Descriptive information and information on content was extracted and summarized. Readability was examined using the Flesch-Kincaid metrics. Two raters assessed each app, using the Mobile App Rating Scale (MARS) and the IMS Institute for Healthcare Informatics functionality score. A total of 754 apps were identified, of which 22 met the eligibility criteria. All apps intended to inform/educate users, while 32% analyzed genetic data, and 18% helped to diagnose genetic conditions. Most (68%) were clearly about genetics, but only 14% were affiliated with a medical/health body or charity, and only 36% had a privacy strategy. Mean reading scores were 35 (of 100), with the average reading age being equivalent to US grade 12 (UK year 13). On average, apps had 3.3 of the 11 IMS functionality criteria. The mean MARS quality score was 3.2 ± 0.7. Half met the minimum acceptability score (3 of 5). None had been formally evaluated. It was evident that there are few high-quality genomic/genetic patient-facing apps available in the UK. This demonstrates a need for an accessible, culturally sensitive, evidence-based app to improve genetic literacy within patient populations and specific communities.

Educating the Healthcare Workforce to Support Digital Transformation.

Digital transformation of the healthcare workforce is a priority if we are to leverage the potential of digital technologies, artificial intelligence in clinical decision support and the potential of data captured within electronic health records. Educational programmes need to be diverse and support the digital novices through to the champions whom will be responsible for procuring and implementing digital solutions. In order to professionalise the workforce in this area, digital competencies need to be built into training from early on and be underpinned by frameworks that help to guide regulators and professional bodies and support educational providers to deliver them. Here we describe Manchester's involvement in the development of digital competency frameworks and our digital transformation education programmes that we have created, including a Massive Online Open Course and a professional development course for England's Topol Digital Fellows.

Evaluating the Acceptance and Usability of an App Promoting Weight Gain Prevention and Healthy Behaviors Among Young Women With a Family History of Breast Cancer: Protocol for an Observational Study.

BACKGROUND: Breast cancer is the most common form of cancer in women, and around 20% of cases are associated with factors such as adult weight gain, overweight and obesity, and potentially modifiable health behaviors including high alcohol intake, smoking, lack of physical activity, and breastfeeding. Significant weight gain occurs between the ages of 18 and 35 years; hence, this age group could benefit from weight gain prevention interventions. Population studies have reported that women at increased risk of breast cancer account for a disproportionate amount of cases. Thus, there is a particular need to target weight gain prevention and other health behavior interventions for women at increased risk. A literature review identified no evidence-based apps that cover all relevant health behaviors. With patient and participant involvement from the target population, we have developed a new app to promote healthy behaviors among young women at increased risk of breast cancer. Alongside the app, a Facebook group provides peer support, and a virtual welcome event provides an overview of the project and the opportunity to meet the research team and other study participants. The aim of the intervention is to prevent weight gain via changes to eating habits and physical activity levels, and improve other health behaviors associated with breast cancer. The app includes goal setting and self-monitoring of health behaviors and provides education about breast cancer. OBJECTIVE: This study aims to assess the acceptability and usability of the app in young women at increased risk of breast cancer, and the feasibility of the study procedures for a future, larger efficacy study. METHODS: Young women (n=35, age 18-35 years) at increased risk of breast cancer (>17% lifetime risk) will be recruited via 2 recruitment procedures: mailed invite from the local breast cancer family history, risk and prevention clinic, and advertisements on social media and websites. Participants will have access to the app and the private Facebook group for 2 months. They will complete questionnaires regarding their health behaviors and breast cancer risk belief at the start and end of the study, complete app rating scales in the middle and at the end of the study, and be invited to give feedback on the app during the study period. Approximately 20 participants will have a semistructured interview at the end of the study regarding their views on the app and trial procedures. RESULTS: The trial is ongoing, and the publication of results is anticipated in 2023. CONCLUSIONS: The trial will provide evidence regarding the acceptability and usability of the newly developed app for young women at increased risk of breast cancer. Feedback obtained will be used to improve the app. The trial will also assess the feasibility of the study procedures and how these can be refined for a future efficacy study. TRIAL REGISTRATION: ClinicalTrials.gov NCT05460650; https://clinicaltrials.gov/ct2/show/NCT05460650. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/41246.

Association between patient activation, self-management behaviours and clinical outcomes in adults with diabetes or related metabolic disorders: a systematic review and meta-analysis protocol.

INTRODUCTION: Diabetes and related metabolic disorders such as obesity and cardiovascular diseases (CVD) are a growing global issue. Equipping individuals with the necessary 'knowledge, skills and confidence to self-manage their health' (ie, patient activation (PAct)) may lead to improvements in health outcomes. It is unclear whether existing evidence allows us to assume a causal relationship. We aim to synthesise and critically appraise evidence on the relationship between PAct and self-management behaviours and clinical outcomes of people living with diabetes and related metabolic disorders. METHODS AND ANALYSIS: The protocol is based on guidance on Preferred Reporting Items for Systematic Review and Meta-analysis Protocols. We will search Medline, Embase, CENTRAL, PsycInfo, Web of Science and CINAHL using search terms related to PAct, diabetes, pre-diabetes, obesity and CVD. Any quantitative study design is eligible provided studies assess the association between PAct and clinical outcomes and/or self-management behaviours of diabetes and related metabolic disorders. Outcomes include behavioural (eg, diet) and clinical (eg, blood pressure) outcomes. Two reviewers will independently screen titles/abstracts and full texts and assess risk of bias using the revised Cochrane risk-of-bias tool for randomised trials or the Risk of Bias Assessment Tool for Nonrandomised Studies (RoBANS).One reviewer will extract data, with independent checking by a second reviewer. We will critically assess the level of evidence available for assuming a causal association between PAct and outcomes. Data permitting, we will use the Hunter-Schmidt random-effects method to meta-analyse correlations across studies. ETHICS AND DISSEMINATION: Ethical approval is not required. The review will be disseminated in the form of a peer-reviewed journal article, at conferences and other presentations. The findings of the review will be of interest to clinical commissioning groups, policymakers and intervention deliverers/developers. PROSPERO REGISTRATION NUMBER: CRD42021230727.

Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding.

The ascomycete, Sclerotinia sclerotiorum, has a broad host range and causes yield loss in dicotyledonous crops world wide. Genomic diversity was determined in a population of 127 isolates obtained from individual canola (Brassica napus) fields in western Canada. Genotyping with 39 simple sequence repeat (SSR) markers revealed each isolate was a unique haplotype. Analysis of molecular variance showed 97% was due to isolate and 3% due to geographical location. Testing of mycelium compatibility among 133 isolates identified clones of mutually compatible isolates with 86-95% similar SSR haplotype, whereas incompatible isolates were highly diverse. In the Province of Manitoba, 61% of isolates were compatible forming clones and stings of pairwise compatible isolates not described before. In contrast, only 35% of isolates were compatible in Alberta without forming clones and strings, while 39% were compatible in Saskatchewan with a single clone, but no strings. These difference can be explained by wetter growing seasons and more susceptible crop species in Manitoba favouring frequent mycelium interaction and more life cycles over time, which might also explain similar differences observed in other geographical areas and host crops. Analysis of linkage disequilibrium rejected random recombination, consistent with a self-fertile fungus, restricted outcrossing due to mycelium incompatibility, and only a single annual opportunity for genomic recombination during meiosis in the ascospore stage between non-sister chromatids in the rare event nuclei from different isolates come together. More probable sources of genomic diversity is slippage during DNA replication and point mutation affecting single nucleotides that accumulate and likely increase mycelium incompatibility in a population over time. A phylogenetic tree based on SSR haplotype grouped isolates into 17 sub-populations. Aggressiveness was tested by inoculating one isolate from each sub-population onto B. napus lines with quantitative resistance. Analysis of variance was significant for isolate, line, and isolate by line interaction. These isolates represent the genomic and pathogenic diversity in western Canada, and are suitable for resistance screening in canola breeding programs.