MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates.

MOTIVATION: Current fusion detection tools use diverse calling approaches and provide varying results, making selection of the appropriate tool challenging. Ensemble fusion calling techniques appear promising; however, current options have limited accessibility and function. RESULTS: MetaFusion is a flexible metacalling tool that amalgamates outputs from any number of fusion callers. Individual caller results are standardized by conversion into the new file type Common Fusion Format. Calls are annotated, merged using graph clustering, filtered and ranked to provide a final output of high-confidence candidates. MetaFusion consistently achieves higher precision and recall than individual callers on real and simulated datasets, and reaches up to 100% precision, indicating that ensemble calling is imperative for high-confidence results. MetaFusion uses FusionAnnotator to annotate calls with information from cancer fusion databases and is provided with a Benchmarking Toolkit to calibrate new callers. AVAILABILITY AND IMPLEMENTATION: MetaFusion is freely available at https://github.com/ccmbioinfo/MetaFusion. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A Quality Improvement Project to Measure and Improve the Quality of Below-Knee Ankle Cast Application in Emergency Departments.

Background Ankle fractures are very common injuries seen in an emergency setting. Initial management involves the application of below-knee plaster casts. At our local trauma meetings, we have observed that below-knee casts are often applied incorrectly which can result in suboptimal outcomes for patients and increase the burden on plaster room services if re-application is required. This quality improvement project aimed to assess the quality of below-knee cast applications for ankle fractures in two local district general hospitals (DGHs). Methodology We performed a closed-loop audit utilising a retrospective analysis of patients who underwent casting for unstable ankle fractures. Two audit cycles were completed over a 90-day period across two DGHs. Working within our local orthopaedic unit, we created a targeted, multi-disciplinary educational programme led by experienced plaster technicians. Between audit cycles, we organised a single interactive session with specialist nurses in the urgent treatment centre (UTC) of our DGH while a second DGH did the same with junior doctors working in the emergency department. Both sessions demonstrated correct casting techniques and discussed the importance of a neutral ankle position for optimal patient recovery. Our audit criteria were based on AO Foundation guidance, which states that the ankle should be immobilised in a neutral plantigrade position. All patients with an unstable ankle fracture requiring immobilisation in a below-knee cast were included in the audit. We measured the angle of plantarflexion from neutral, with 90° representing a neutral angle. The angle between the axis of the tibia and the sole of the foot was measured and judged to be within an acceptable range if it was between 80° and 100°, representing a stable ankle position. The audit findings were presented in our local audit meeting. Results In our first audit cycle, we collected data from 65 patients across both sites (N = 32 for DGH 1 and N = 33 for DGH 2). The mean angle was 108.5° and 18 of the 65 (27.7%) patients had angles of ankle plantarflexion that were in the acceptable range (80°-100°). Following the intervention, we again collected data from 61 patients across both sites (N = 28 for DGH 1 and N = 33 for DGH 2). The mean angle was 106.2° and 23 of the 61 (37.7%) patients had an acceptable angle of ankle plantarflexion (80°-100°). Both of our outcome measures showed an improvement but were not statistically significant. The hospital that provided an educational session for the doctors showed an improvement in acceptable ankle casts of 3% while the hospital which provided an educational session for the UTC team improved by 22%. Conclusions We demonstrated a quantifiable approach to assess and improve the quality of below-knee cast application for ankle fractures via a single intervention that would be easily reproducible in other hospitals. We suggest further studies to investigate below-knee cast application quality and its association with patient outcomes as our data and other preliminary sources suggest that current standards are unsatisfactory.

Accurate isoform quantification by joint short- and long-read RNA-sequencing.

Accurate quantification of transcript isoforms is crucial for understanding gene regulation, functional diversity, and cellular behavior. Existing RNA sequencing methods have significant limitations: short-read (SR) sequencing provides high depth but struggles with isoform deconvolution, whereas long-read (LR) sequencing offers isoform resolution at the cost of lower depth, higher noise, and technical biases. Addressing this gap, we introduce Multi-Platform Aggregation and Quantification of Transcripts (MPAQT), a generative model that combines the complementary strengths of different sequencing platforms to achieve state-of-the-art isoform-resolved transcript quantification, as demonstrated by extensive simulations and experimental benchmarks. By applying MPAQT to an in vitro model of human embryonic stem cell differentiation into cortical neurons, followed by machine learning-based modeling of transcript abundances, we show that untranslated regions (UTRs) are major determinants of isoform proportion and exon usage; this effect is mediated through isoform-specific sequence features embedded in UTRs, which likely interact with RNA-binding proteins that modulate mRNA stability. These findings highlight MPAQT's potential to enhance our understanding of transcriptomic complexity and underline the role of splicing-independent post-transcriptional mechanisms in shaping the isoform and exon usage landscape of the cell.

Early mobilization following elective ankle lateral collateral ligament reconstruction in adults.

BACKGROUND: Emergency departments in the UK are overwhelmed with musculoskeletal trauma, 50 % of which resulting from ligamentous injuries. Of these, ankle sprains are the most prevalent, however with poor rehabilitation in the recovery period, 20 % of patients may develop chronic instability that may necessitate operative reconstruction. At present, there are no national guidelines or protocols to help direct postoperative rehabilitation and determine weightbearing status. Our aim is to review the existing literature that investigated postoperative outcomes following different rehabilitation protocols in patients with Chronic Lateral Collateral Ligament (CLCL) instability. METHODS: A literature search was performed via Medline, Embase and Pubmed databases using the terms 'ankle', 'lateral ligament', 'repair'. 'reconstruction' and 'early mobilisation'. A total of 19 studies were identified after filtering that they were English language papers. A gray literature search was also performed using the Google search engine. RESULTS: Based on the literature reviewed, patients undergoing early mobilisation and Range Of Movement (ROM) following lateral ligament reconstruction for chronic instability seem to have better functional outcomes and earlier return to work and sports. This is however in the short-term, and there are no medium to long-term studies evaluating the effects of early mobilisation on ankle stability. Furthermore, there may be an increased risk of postoperative complications, mainly wound related, with early mobilization compared to delayed mobilization. CONCLUSION: Further randomized studies and long-term prospective studies with larger cohorts of patients are required to improve the level of evidence available but based on current literature it would appear that controlled early ROM and weight-bearing is advisable in patients undergoing surgery for CLCL instability.

Clinical Implementation of MetaFusion for Accurate Cancer-Driving Fusion Detection from RNA Sequencing.

Oncogenic fusion genes may be identified from next-generation sequencing data, typically RNA-sequencing. However, in a clinical setting, identifying these alterations is challenging against a background of nonrelevant fusion calls that reduce workflow precision and specificity. Furthermore, although numerous algorithms have been developed to detect fusions in RNA-sequencing, there are variations in their individual sensitivities. Here this problem was addressed by introducing MetaFusion into clinical use. Its utility was illustrated when applied to both whole-transcriptome and targeted sequencing data sets. MetaFusion combines ensemble fusion calls from eight individual fusion-calling algorithms with practice-informed identification of gene fusions that are known to be clinically relevant. In doing so, it allows oncogenic fusions to be identified with near-perfect sensitivity and high precision and specificity, significantly outperforming the individual fusion callers it uses as well as existing clinical-grade software. MetaFusion enhances clinical yield over existing methods and is able to identify fusions that have patient relevance for the purposes of diagnosis, prognosis, and treatment.

The presence of the ossific nucleus and its relation to avascular necrosis rates and the number of secondary procedures in late-presenting developmental dysplasia of the hip.

Late-presenting developmental dysplasia of the hip (DDH) has an incidence reported between 0.07 and 2:1000 live births. Avascular necrosis (AVN) of the femoral head secondary to treatment of DDH is a feared complication and may lead to adverse long-term sequelae. This study aims to investigate the relationship between the ossific nucleus (ON) presence and AVN in late-presenting DDH. This is a retrospective study of prospectively collected data over a 24-year period, at a single UK centre. Late-presenting DDH who were treated surgically with a closed or open reduction were included in the series. The presence of ON was monitored, and outcomes measured included AVN and whether delaying surgery affected the number of secondary procedures. Seventy-six patients with 79 hips (mean age at presentation 13.8 months) were included in the analysis. The mean age at presentation was 13.8 months. About 45.5% of hips with no ON present developed clinically significant AVN (Kalamchi and MacEwen grades 2-4, P = 0.12), compared to 20.6% of hips with the ON present. Delaying surgery did not affect AVN rates or the number of secondary procedures. Looking at long-term outcomes, 86.7% of hips had a Severin grade of I or II and 13.3% had a grade ≥III. Factors that affected long-term outcomes were absent ON (P = 0.04) and open reduction (P = 0.03). In the multiple logistic regression model, only open reduction could increase AVN rates (P value 0.027). The presence of ON at the time of surgery may have an impact on the rate and significance of AVN. Absence of the ON at the time of reduction negatively affects long-term outcomes in late-presenting DDH.

Early outcomes of patients undergoing total hip arthroplasty for trauma during COVID-19.

AIMS: This study aimed to identify patients receiving total hip arthroplasty (THA) for trauma during the peak of the COVID-19 pandemic in the UK and quantify the risks of contracting SARS-CoV-2 virus, the proportion of patients requiring treatment in an intensive care unit (ICU), and rate of complications including mortality. METHODS: All patients receiving a primary THA for trauma in four regional hospitals were identified for analysis during the period 1 March to 1 June 2020, which covered the current peak of the COVID-19 pandemic in the UK. RESULTS: Overall, one of 48 patients (2%) contracted COVID-19 during their admission. Although they required a protracted stay in hospital, they did not require ICU treatment. Two patients did require ICU support for medical problems but not relating to COVID-19. Complications were no greater than expected given the short follow-up. There were no mortalities. CONCLUSION: There is a paucity of evidence to guide restarting elective joint arthroplasties following the COVID-19 pandemic. Although THAs for trauma are by no means a perfect surrogate, the results of this study show a low incidence of contracting COVID-19 virus during admission and no significant sequalae during this period.Cite this article: Bone Joint Open 2020;1-7:438-442.