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

A tool for subjective and interactive visual data exploration

We present SIDE, a tool for Subjective and Interactive Visual Data Exploration, which lets users explore high dimensional data via subjectively informative 2D data visualizations. Many existing visual analytics tools are either restricted to specific problems and domains or they aim to find visualizations that align with user’s belief about the data. In contrast, our generic tool computes data visualizations that are surprising given a user’s current understanding of the data. The user’s belief state is represented as a set of projection tiles. Hence, this user-awareness offers users an efficient way to interactively explore yet-unknown features of complex high dimensional datasets

Performance of health-status scales when used selectively or within multi-scale questionnaire

BACKGROUND: Little work has been done to investigate the suggestion that the use of selected scales from a multi-scale health-status questionnaire would compromise reliability and validity. The aim of this study was to compare the performance of three scales selected from the SF-36 generic health questionnaire when administered in isolation or within the entire SF-36 to patients with musculoskeletal disorders. METHODS: Two groups of patients referred to an orthopedic department completed a mailed questionnaire within 4 weeks prior to and a second questionnaire during their visit. The first group completed three SF-36 scales related to physical health (physical functioning, bodily pain, and general health perceptions) on one occasion and all eight SF-36 scales on the other occasion. The second group completed the entire SF-36 on two occasions. Results for patients who reported unchanged health status and had complete scores were analyzed; 80 patients in the first and 62 patients in the second group. RESULTS: The Cronbach alpha reliability and intraclass correlation coefficients exceeded 0.7 for all three scales for both groups. For the first group the mean difference between the scores was 0.4 point for physical functioning, 2.5 points for bodily pain, and 0.5 point for general health perceptions, which did not differ significantly from the corresponding differences for the second group (0.1, 1.9 and 1 point, respectively). CONCLUSION: The use of selected scales from a multi-scale health-status questionnaire seems to yield similar results compared to their use within the entire questionnaire

Exploring differential item functioning in the SF-36 by demographic, clinical, psychological and social factors in an osteoarthritis population

The SF-36 is a very commonly used generic measure of health outcome in osteoarthritis (OA). An important, but frequently overlooked, aspect of validating health outcome measures is to establish if items work in the same way across subgroup of a population. That is, if respondents have the same 'true' level of outcome, does the item give the same score in different subgroups or is it biased towards one subgroup or another. Differential item functioning (DIF) can identify items that may be biased for one group or another and has been applied to measuring patient reported outcomes. Items may show DIF for different conditions and between cultures, however the SF-36 has not been specifically examined in an osteoarthritis population nor in a UK population. Hence, the aim of the study was to apply the DIF method to the SF-36 for a UK OA population. The sample comprised a community sample of 763 people with OA who participated in the Somerset and Avon Survey of Health. The SF-36 was explored for DIF with respect to demographic, social, clinical and psychological factors. Well developed ordinal regression models were used to identify DIF items. Results: DIF items were found by age (6 items), employment status (6 items), social class (2 items), mood (2 items), hip v knee (2 items), social deprivation (1 item) and body mass index (1 item). Although the impact of the DIF items rarely had a significant effect on the conclusions of group comparisons, in most cases there was a significant change in effect size. Overall, the SF-36 performed well with only a small number of DIF items identified, a reassuring finding in view of the frequent use of the SF-36 in OA. Nevertheless, where DIF items were identified it would be advisable to analyse data taking account of DIF items, especially when age effects are the focus of interest

A mobile telehealth intervention for adults with insulin-requiring diabetes: early results of a mixed-methods randomized controlled trial

BACKGROUND: The role of technology in health care delivery has grown rapidly in the last decade. The potential of mobile telehealth (MTH) to support patient self-management is a key area of research. Providing patients with technological tools that allow for the recording and transmission of health parameters to health care professionals (HCPs) may promote behavior changes that result in improved health outcomes. Although for some conditions the evidence of the effectiveness of MTH is clear, to date the findings on the effects of MTH on diabetes management remain inconsistent. OBJECTIVE: This study aims to evaluate an MTH intervention among insulin-requiring adults with diabetes to establish whether supplementing standard care with MTH results in improved health outcomes-glycated hemoglobin (HbA1c), blood pressure (BP), health-related quality of life (HRQoL), diabetes self-management behaviors, diabetes health care utilization, and diabetes self-efficacy and illness beliefs. An additional objective was to explore the acceptability of MTH and patients' perceptions of, and experience, using it. METHODS: A mixed-method design consisting of a 9-month, two-arm, parallel randomized controlled trial (RCT) was used in combination with exit qualitative interviews. Quantitative data was collected at baseline, 3 months, and 9 months. Additional intervention fidelity data, such as participants' MTH transmissions and contacts with the MTH nurse during the study, were also recorded. RESULTS: Data collection for both the quantitative and qualitative components of this study has ended and data analysis is ongoing. A total of 86 participants were enrolled into the study. Out of 86 participants, 45 (52%) were randomized to the intervention group and 36 (42%) to the control group. Preliminary data on MTH training sessions and MTH usage by intervention participants are presented in this paper. We expect to publish complete study results in 2015. CONCLUSIONS: The range of data collected in this study will allow for a comprehensive evaluation of processes and outcomes. The early results presented suggest that MTH usage decreases over time and that MTH participants would benefit from attending more than one training session. TRIAL REGISTRATION: ClinicalTrials.gov NCT00922376; http://clinicaltrials.gov/ct2/show/NCT00922376 (Archived by WebCite at http://www.webcitation.org/6Vu4nhLI6)

Outcome and quality of life after aorto-bifemoral bypass surgery

<p>Abstract</p> <p>Background</p> <p>Aorto-bifemoral bypass (AFB) is commonly performed to treat aorto-iliac disease and a durable long-term outcome is achieved. Most studies documenting beneficial outcomes after AFB have been limited to mortality and morbidity rates, costs and length of hospital stay (LOS). Few studies have examined the dependency of patients and how their perception of their own health changes after surgery. The aim of the present study was to evaluate outcome after AFB and to study its determinants.</p> <p>Methods</p> <p>This retrospective study was carried out in the multidisciplinary Post-Anaesthesia Care Unit (PACU) with five intensive care beds. Out of 1597 intensive care patients admitted to the PACU, 75 were submitted to infrarenal AFB and admitted to these intensive care unit (ICU) beds over 2 years. Preoperative characteristics and outcome were evaluated by comparing occlusive disease with aneurysmatic disease patients. Six months after discharge, the patients were contacted to complete a Short Form-36 questionnaire (SF-36) and to have their dependency in Activities of Daily Living (ADL) evaluated. Patient's characteristics and postoperative follow-up data were compared using Mann-Whitney U test, t test for independent groups, chi-square or Fisher's exact test. Patient preoperative characteristics were evaluated for associations with mortality using a multiple logistic regression analysis.</p> <p>Results</p> <p>The mortality rate was 12% at six months. Multivariate analysis identified congestive heart disease and APACHE II as independent determinants for mortality. Patients submitted to AFB for occlusive disease had worse SF-36 scores in role physical and general health perception. Patients submitted to AFB had worse SF-36 scores for all domains than a comparable urban population and had similar scores to other PACU patients. Sixty-six percent and 23% of patients were dependent in at least one activity in instrumental and personal ADL, respectively, but 64% reported having better general health.</p> <p>Conclusion</p> <p>This study shows that congestive heart disease and APACHE II were risk factors for mortality after AFB surgery. Survivors who have undergone AFB perceive an improved quality of life although they are more dependent in ADL tasks and have worse scores in almost all SF-36 than the population to which they belong.</p

Risk Assessment of a Synthetic Pyrethroid, Bifenthrin on Pulses

This work was undertaken to determine the pre-harvest interval of bifenthrin and to minimize its residues in pulses and thereby ensure consumer safety and avoid non-compliance in terms of residues violations in export market. Furthermore the residue dynamics in the soil under pulses was explored to assess the environmental safety. The residues of bifenthrin dissipated following first order kinetics. The residues in harvest time grains were below the maximum residue limit (MRL) of 0.02 mg/kg applicable for European Union. In soil the degradation rate was fast with a half life of 2–3 days. This work is of high practical significance to the domestic and export pulse industry of India to ensure safety compliance in respect of bifenthrin residues, keeping in view the requirements of international trade

A bi-directional relationship between obesity and health-related quality of life : evidence from the longitudinal AusDiab study

Objective: To assess the prospective relationship between obesity and health-related quality of life, including a novel assessment of the impact of health-related quality of life on weight gain.Design and setting: Longitudinal, national, population-based Australian Diabetes, Obesity and Lifestyle (AusDiab) study, with surveys conducted in 1999/2000 and 2004/2005.Participants: A total of 5985 men and women aged 25 years at study entry.Main outcome measure(s): At both time points, height, weight and waist circumference were measured and self-report data on health-related quality of life from the SF-36 questionnaire were obtained. Cross-sectional and bi-directional, prospective associations between obesity categories and health-related quality of life were assessed.Results: Higher body mass index (BMI) at baseline was associated with deterioration in health-related quality of life over 5 years for seven of the eight health-related quality of life domains in women (all P0.01, with the exception of mental health, P&gt;0.05), and six out of eight in men (all P&lt;0.05, with the exception of role-emotional, P=0.055, and mental health, P&gt;0.05). Each of the quality-of-life domains related to mental health as well as the mental component summary were inversely associated with BMI change (all P&lt;0.0001 for women and P0.01 for men), with the exception of vitality, which was significant in women only (P=0.008). For the physical domains, change in BMI was inversely associated with baseline general health in women only (P=0.023).Conclusions: Obesity was associated with a deterioration in health-related quality of life (including both physical and mental health domains) in this cohort of Australian adults followed over 5 years. Health-related quality of life was also a predictor of weight gain over 5 years, indicating a bi-directional association between obesity and health-related quality of life. The identification of those with poor health-related quality of life may be important in assessing the risk of future weight gain, and a focus on health-related quality of life may be beneficial in weight management strategies.<br /

Influence of an outpatient multidisciplinary pain management program on the health-related quality of life and the physical fitness of chronic pain patients

BACKGROUND: Approximately 10 to 20 percent of the population is suffering from chronic pain. Since this represents a major contribution to the costs of the health care system, more efficient measures and interventions to treat these patients are sought. RESULTS: The development of general health and physical activity of patients with chronic pain was assessed in an interdisciplinary outpatient pain management program (IOPP). 36 patients with an average age of 48 years were included in the IOPP. Subjective assessment of well-being was performed at five time points (baseline, post intervention and 3, 6, and 12 months thereafter) by using standardized questionnaires. The study focused on the quality of life survey Medical Outcomes Study Short Form-36, which is a validated instrument with established reliability and sensitivity. In addition, the patients participated in physical assessment testing strength, power, endurance, and mobility. Prior to therapy a substantial impairment was found on different levels. Marked improvements in the psychological parameters were obtained by the end of the program. No success was achieved with regard to the physical assessments. CONCLUSION: Although many different studies have evaluated similar programs, only few of them have attained positive results such as improvements of general quality of life or of physical strength. Often no difference from the control group could be detected only some months after the intervention. In the present study no significant persistent improvement of well-being occurred. Possible reasons are either wrong instruments, wrong selection of patients or wrong interventions

Preoperative Plasma Club (Clara) Cell Secretory Protein Levels Are Associated With Primary Graft Dysfunction After Lung Transplantation

Inherent recipient factors, including pretransplant diagnosis, obesity and elevated pulmonary pressures, are established primary graft dysfunction (PGD) risks. We evaluated the relationship between preoperative lung injury biomarkers and PGD to gain further mechanistic insight in recipients. We performed a prospective cohort study of recipients in the Lung Transplant Outcomes Group enrolled between 2002 and 2010. Our primary outcome was Grade 3 PGD on Day 2 or 3. We measured preoperative plasma levels of five biomarkers (CC‐16, sRAGE, ICAM‐1, IL‐8 and Protein C) that were previously associated with PGD when measured at the postoperative time point. We used multivariable logistic regression to adjust for potential confounders. Of 714 subjects, 130 (18%) developed PGD. Median CC‐16 levels were elevated in subjects with PGD (10.1 vs. 6.0, p < 0.001). CC‐16 was associated with PGD in nonidiopathic pulmonary fibrosis (non‐IPF) subjects (OR for highest quartile of CC‐16: 2.87, 95% CI: 1.37, 6.00, p = 0.005) but not in subjects with IPF (OR 1.38, 95% CI: 0.43, 4.45, p = 0.59). After adjustment, preoperative CC‐16 levels remained associated with PGD (OR: 3.03, 95% CI: 1.26, 7.30, p = 0.013) in non‐IPF subjects. Our study suggests the importance of preexisting airway epithelial injury in PGD. Markers of airway epithelial injury may be helpful in pretransplant risk stratification in specific recipients. The authors demonstrate a relationship between perioperative CC‐16 blood levels and an increased risk of primary lung allograft dysfunction, particularly in those without idiopathic pulmonary fibrosis as a pretransplant diagnosis.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102697/1/ajt12541.pd