Bayesian models for syndrome- and gene-specific probabilities of novel variant pathogenicity

BACKGROUND: With the advent of affordable and comprehensive sequencing technologies, access to molecular genetics for clinical diagnostics and research applications is increasing. However, variant interpretation remains challenging, and tools that close the gap between data generation and data interpretation are urgently required. Here we present a transferable approach to help address the limitations in variant annotation. METHODS: We develop a network of Bayesian logistic regression models that integrate multiple lines of evidence to evaluate the probability that a rare variant is the cause of an individual's disease. We present models for genes causing inherited cardiac conditions, though the framework is transferable to other genes and syndromes. RESULTS: Our models report a probability of pathogenicity, rather than a categorisation into pathogenic or benign, which captures the inherent uncertainty of the prediction. We find that gene- and syndrome-specific models outperform genome-wide approaches, and that the integration of multiple lines of evidence performs better than individual predictors. The models are adaptable to incorporate new lines of evidence, and results can be combined with familial segregation data in a transparent and quantitative manner to further enhance predictions. Though the probability scale is continuous, and innately interpretable, performance summaries based on thresholds are useful for comparisons. Using a threshold probability of pathogenicity of 0.9, we obtain a positive predictive value of 0.999 and sensitivity of 0.76 for the classification of variants known to cause long QT syndrome over the three most important genes, which represents sufficient accuracy to inform clinical decision-making. A web tool APPRAISE [http://www.cardiodb.org/APPRAISE] provides access to these models and predictions. CONCLUSIONS: Our Bayesian framework provides a transparent, flexible and robust framework for the analysis and interpretation of rare genetic variants. Models tailored to specific genes outperform genome-wide approaches, and can be sufficiently accurate to inform clinical decision-making

Experimental Testing of Door Panel Boundary Conditions to Determine NVH Variability

The variability of measured frequency response functions (FRFs) from nominally identical structures is a well-known phenomenon and trying to eradicate it increases the design challenge for automotive manufacturers. In this paper a vehicle door is experimentally tested in order to assess the effect of variability in the attachment boundary conditions between the door structure and trim components upon measured FRF data. Plastic clips can be used to hold the trim to the door panel, so individual clips were systematically removed and then replaced in order to generate a set of measured FRFs that demonstrate how individual property changes can influence the global structure. Point and transfer FRFs, with corresponding normalised standard deviations, were measured by exciting the door panel and measuring the response both on the door panel and on the attached trim. The door response was found to vary by up to 10% over all clip combinations, and this is compared to the test variability. A newly developed function that predicts the FRF variability due to measurement test error was also applied. The results of this prediction match closely with the normalised standard deviation calculated from repeat FRF measurements taken on the structure. This will therefore enable test-to-test variability to be separated from structure-to-structure variabilit

A study of vehicle and measurement NVH variability

A range of nominally identical automotive vehicles have been tested for NVH variability by exciting the engine mount with an impact hammer and measuring the responses at different points on the vehicle. Normalised standard deviations were calculated from the mobility, which fell well within the boundaries of previous comparable measurements. The measurement variability was determined by taking repeat measurements on a single vehicle, which were found to be very repeatable, varying by up to 2.9%. A function that uses the coherence to determine the random error was applied to the data to determine the variability due to the measurement taking process. This was compared with repeat measurements taken on a single vehicle and was shown to agree well with one another. A design of experiments has also been created that determines the effect of each variable such as the temperature and angle of impact on the overall vehicle to vehicle variability

Evaluating the design and reporting of pragmatic trials in osteoarthritis research

Objectives. Among the challenges in health research is translating interventions from controlled experimental settings to clinical and community settings where chronic disease is managed daily. Pragmatic trials offer a method for testing interventions in real-world settings but are seldom used in OA research. The aim of this study was to evaluate the literature on pragmatic trials in OA research up to August 2016 in order to identify strengths and weaknesses in the design and reporting of these trials. Methods. We used established guidelines to assess the degree to which 61 OA studies complied with pragmatic trial design and reporting. We assessed design according to the pragmatic–explanatory continuum indicator summary and reporting according to the pragmatic trials extension of the CONsolidated Standards of Reporting Trials guidelines. Results. None of the pragmatic trials met all 11 criteria evaluated and most of the trials met between 5 and 8 of the criteria. Criteria most often unmet pertained to practitioner expertise (by requiring specialists) and criteria most often met pertained to primary outcome analysis (by using intention-to-treat analysis). Conclusion. Our results suggest a lack of highly pragmatic trials in OA research. We identify this as a point of opportunity to improve research translation, since optimizing the design and reporting of pragmatic trials can facilitate implementation of evidence-based interventions for OA care

A new Mississippian tetrapod from Fife, Scotland, and its environmental context.

The Visean stage of the Mississippian was a time of rapid tetrapod diversification which marks the earliest appearance of temnospondyls, microsaurs and the limbless aïstopods. Tetrapod finds from this stage are very rare and only a dozen sites are known worldwide. Here we announce the discovery of a new Visean site in Fife, Scotland, of Asbian age, and from it describe a new species of the baphetoid Spathicephalus. These specimens represent the oldest known baphetoid by three million years, yet belong to the most specialized members of the clade. Unlike typical baphetoids with large marginal teeth and palatal fangs characteristic of early tetrapods, spathicephalids had very broad flattened heads with a dentition consisting of a large number of small, uniform teeth. Spathicephalids were probably one of the earliest tetrapod groups to use suction feeding on small, aquatic prey. Palynological and sedimentological analysis indicates that the new fossil bed was deposited in a large, stratified, freshwater lake that became increasingly saline.Natural Environment Research Council. Grant Numbers: NE/J020621/1, NE/J020729/1, NE/J021091/1, NE/J022713/1, NEJ021067/

Histiocytoid cardiomyopathy and microphthalmia with linear skin defects syndrome: phenotypes linked by truncating variants in NDUFB11

Variants in NDUFB11, which encodes a structural component of complex I of the mitochondrial respiratory chain (MRC), were recently independently reported to cause histiocytoid cardiomyopathy (histiocytoid CM) and microphthalmia with linear skin defects syndrome (MLS syndrome). Here we report an additional case of histiocytoid CM, which carries a de novo nonsense variant in NDUFB11 (ENST00000276062.8: c.262C > T; p.[Arg88*]) identified using whole-exome sequencing (WES) of a family trio. An identical variant has been previously reported in association with MLS syndrome. The case we describe here lacked the diagnostic features of MLS syndrome, but a detailed clinical comparison of the two cases revealed significant phenotypic overlap. Heterozygous variants in HCCS (which encodes an important mitochondrially targeted protein) and COX7B, which, like NDUFB11, encodes a protein of the MRC, have also previously been identified in MLS syndrome including a case with features of both MLS syndrome and histiocytoid CM. However, a systematic review of WES data from previously published histiocytoid CM cases, alongside four additional cases presented here for the first time, did not identify any variants in these genes. We conclude that NDUFB11 variants play a role in the pathogenesis of both histiocytoid CM and MLS and that these disorders are allelic (genetically related)

Relationship between fibroblastic foci profusion and high resolution CT morphology in fibrotic lung disease

Background Fibroblastic foci profusion on histopathology and severity of traction bronchiectasis on highresolution computed tomography (HRCT) have been shown to be predictors of mortality in patients with idiopathic pulmonary fibrosis (IPF). The aim of this study was to investigate the relationship between fibroblastic foci (FF) profusion and HRCT patterns in patients with a histopathologic diagnosis of usual interstitial pneumonia (UIP), fibrotic non-specific interstitial pneumonia (NSIP) and chronic hypersensitivity pneumonitis (CHP). Methods The HRCT scans of 162 patients with a histopathologic diagnosis of UIP or fibrotic NSIP (n = 162) were scored on extent of groundglass opacification, reticulation, honeycombing, emphysema and severity of traction bronchiectasis. For each patient, a fibroblastic foci profusion score based on histopathologic appearances was assigned. Relationships between extent of fibroblastic foci and individual HRCT patterns were investigated using univariate correlation analysis and multivariate linear regression. Results Increasing extent of reticulation (P < 0.0001) and increasing severity of traction bronchiectasis (P < 0.0001) were independently associated with increasing FF score within the entire cohort. Within individual multidisciplinary team diagnosis subgroups, the only significant independent association with FF score was severity of traction bronchiectasis in patients with idiopathic pulmonary fibrosis (IPF)/UIP (n = 66, r2 = 0.19, P < 0.0001) and patients with chronic hypersensitivity pneumonitis (CHP) (n = 49, r2 = 0.45, P < 0.0001). Furthermore, FF score had the strongest association with severity of traction bronchiectasis in patients with IPF (r2 = 0.34, P < 0.0001) and CHP (r2 = 0.35, P < 0.0001). There was no correlation between FF score and severity of traction bronchiectasis in patients with fibrotic NSIP. Global disease extent had the strongest association with severity of traction bronchiectasis in patients with fibrotic NSIP (r2 = 0.58, P < 0.0001). Conclusion In patients with fibrotic lung disease, profusion of fibroblastic foci is strikingly related to the severity of traction bronchiectasis, particularly in IPF and CHP. This may explain the growing evidence that traction bronchiectasis is a predictor of mortality in several fibrotic lung diseases

Bluecap: A geospatial model to assess regional economic-viability for mineral resource development

© 2020 Frontier mineral exploration is often exclusively focused on assessing geological potential without consideration for the economic viability of resource development. This strategy may overlook potentially prosperous zones for more geologically-favoured but financially-disadvantageous regions, or conversely, may introduce implicit biases against potential developments without due regard to underlying economies of scale or proximity to infrastructure. Accordingly, in this paper, we introduce a numerical model aimed at identifying economic fairways, i.e. areas permissive to mineral development from an economic perspective. The model, Bluecap, combines large-scale infrastructure and geological datasets to conduct geospatial analysis of the economic-viability of mining operations across Australia. We provide a detailed description of the inputs and assumptions that underlie the cost models employed in Bluecap, outlining the methods used to evaluate mining, processing, administrative and infrastructure expenses. We also describe the databases used by the model to evaluate available infrastructure, transportation distances and depth of cover. Finally, we present examples that demonstrate the use of the Bluecap model on regions around Mount Isa and the Murray Basin to verify its ability to evaluate commercially feasible mineral prospects. While the immediate utility of this model stands to benefit mineral explorers, its ability to map mineral economic fairways also provides an objective, evidence base to underpin government decision making with respect to position of new infrastructure and consideration of competing land use claims