Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.

Incidence and significance of the JAK2 V617F mutation in patients with chronic myeloproliferative disorders

BACKGROUND: The chronic myeloproliferative disorders (MPD) are clonal haemopoietic stem cell disorders.

AIMS: The incidence of JAK2 V617F mutation was sought in a population of patients with MPD.

METHODS: The JAK2 V617 mutation status was determined in 79 patients with known MPD and 59 patients with features suggestive of MPD.

RESULTS: The mutation was found in patients with polycythaemia vera, essential thrombocythaemia, idiopathic myelofibrosis and in patients with other chronic myeloproliferative disorders. Eight JAK2 V617F positive cases were identified amongst those patients with features suggestive of MPD.

CONCLUSIONS: The incidence of the JAK2 V617F mutation in MPD patients is similar to that reported by other groups. The assay confirmed and refined the diagnosis of several patients with features indicative of MPD. We suggest screening for this mutation in all patients with known and suspected MPD as identification is valuable in classification and is a potential target for signal transduction therapy.

The use of patient experience survey data by out-of-hours primary care services: a qualitative interview study

Background English National Quality Requirements mandate out-of-hours primary care services to routinely audit patient experience, but do not state how it should be done.

Objectives We explored how providers collect patient feedback data and use it to inform service provision. We also explored staff views on the utility of out-of-hours questions from the English General Practice Patient Survey (GPPS).

Methods A qualitative study was conducted with 31 staff (comprising service managers, general practitioners and administrators) from 11 out-of-hours primary care providers in England, UK. Staff responsible for patient experience audits within their service were sampled and data collected via face-to-face semistructured interviews.

Results Although most providers regularly audited their patients’ experiences by using patient surveys, many participants expressed a strong preference for additional qualitative feedback. Staff provided examples of small changes to service delivery resulting from patient feedback, but service-wide changes were not instigated. Perceptions that patients lacked sufficient understanding of the urgent care system in which out-of-hours primary care services operate were common and a barrier to using feedback to enable change. Participants recognised the value of using patient experience feedback to benchmark services, but perceived weaknesses in the out-of-hours items from the GPPS led them to question the validity of using these data for benchmarking in its current form.

Conclusions The lack of clarity around how out-of-hours providers should audit patient experience hinders the utility of the National Quality Requirements. Although surveys were common, patient feedback data had only a limited role in service change. Data derived from the GPPS may be used to benchmark service providers, but refinement of the out-of-hours items is needed.

Good Practice in Achieving Best Evidence Interview with Child Witnesses in Northern Ireland – Criminal Justice Perspectives

This report outlines the findings from a research project examining what works well in investigative interviews (ABE interviews) with child witnesses in Northern Ireland. The project was developed in collaboration with key stakeholders and was joint funded by the Department of Justice NI, NSPCC, SBNI and PSNI. While there is substantial a research literature examining the practice of forensic interview both internationally and within the UK there has been little in the way of exploration of this issue in Northern Ireland. Equally, the existing literature has tended to focus on a ‘deficit’ approach, identifying areas of poor practice with limited recognition of the practical difficulties interview practitioners face or what works well for them in practice. This study aimed to address these gaps by adopting an ‘appreciative inquiry’ approach to explore stakeholder perspectives on what is working well within ABE current practice and identify what can be built on to deliver optimal practice.

An interview with Manuel Salto-Tellez on diagnostic pathology: the future is morphomolecular

Professor Manuel Salto-Tellez of Queen’s University, Belfast, Northern Ireland is an expert histopathologist and molecular diagnostician. Professor Salto-Tellez is a lead investigator at the Northern Ireland Molecular Pathology Laboratory and also serves as a member of the Editorial Advisory Board for Expert Review of Molecular Diagnostics. In this interview, he proposes directions for the future of molecular pathology and molecular diagnostics, integrating all aspects of pathology toward a common goal.

LNK mutations and myeloproliferative disorders

The lymphocyte adaptor protein (LNK) is one of a family of adaptor proteins involved cell signalling and control of B cell populations. It has a critical role in regulation of signalling in hematopoiesis. Lnk negatively regulates cytokine initiated cell signalling and it functions as a negative regulator of the mutant protein in myeloproliferative neoplasms JAK2V617F. A number of mutations in LNK have been described in a variety of myeloproliferative neoplasms some of which have been demonstrated to cause increased cellular proliferation. The majority of mutations occur in exon 2. In a small number of cases idiopathic erythrocytosis with subnormal erythropoietin levels LNK mutations have been found which may account for the clinical phenotype. Thus investigation for LNK mutations should be considered in the investigation of idiopathic erythrocytosis and perhaps other myeloproliferative neoplasms.

Evaluation of Restorative Dentistry Specialty Registrars’ Clinical Experience of Developmental Disorders: A Survey

Background

Specialty Registrars in Restorative Dentistry (StRs) should be competent in the independent restorative management of patients with developmental disorders including hypodontia and cleft lip/palate upon completion of their specialist training.1 Knowledge and management may be assessed via the Intercollegiate Specialty Fellowship Examination (ISFE) in Restorative Dentistry.2

Objective

The aim of this study was to collate and compare data on the training and experience of StRs in the management of patients with developmental disorders across different training units within the British Isles.

Methods

Questionnaires were distributed to all StRs attending the Annual General Meeting of the Specialty Registrars in Restorative Dentistry Group, Belfast, in October 2015. Participants were asked to rate their confidence and experience of assessing and planning treatment for patients with developmental disorders, construction of appropriate prostheses, and provision of dental implants. Respondents were also asked to record clinical supervision and didactic teaching at their unit, and to rate their confidence of passing a future ISFE station assessing knowledge of developmental disorders.

Results

Responses were obtained from 32 StRs (n=32) training within all five countries of the British Isles. The majority of respondents were based in England (72%) with three in Wales, and two in each of Scotland, Northern Ireland, and the Republic of Ireland. Approximately one third of respondents (34%) were in the final years of training (years 4-6). Almost half of the StRs reported that they were not confident of independently assessing (44%) new patients with a developmental disorder, with larger numbers (72%) indicating a lack of confidence in treatment planning. Six respondents rated their experience of treating obturator patients as ‘poor’ or ‘very poor’. The majority (56%) rated their experience of implant provision in these cases as ‘good’ or ‘excellent’ with three-quarters (75%) rating clinical supervision at their unit as ‘good’ or ‘excellent’. Less than half (41%) rated the didactic teaching at their unit as ‘good’ or ‘excellent’, and only 8 StRs indicated that they were confident of passing an ISFE station focused on developmental disorders.

Conclusion

Experience and training regarding patients with developmental disorders is inconsistent for StRs across the British Isles with a number of trainees reporting a lack of clinical exposure.