Now showing 1 - 10 of 14
  • Publication
    Combining linkage data sets for meta-analysis and mega-analysis: the GAW15 rheumatoid arthritis data set
    We have used the genome-wide marker genotypes from Genetic Analysis Workshop 15 Problem 2 to explore joint evidence for genetic linkage to rheumatoid arthritis across several samples. The data consisted of four high-density genome scans on samples selected for rheumatoid arthritis. We cleaned the data, removed intermarker linkage disequilibrium, and assembled the samples onto a common genetic map using genome sequence positions as a reference for map interpolation. The individual studies were combined first at the genotype level (mega-analysis) prior to a multipoint linkage analysis on the combined sample, and second using the genome scan meta-analysis method after linkage analysis of each sample. The two approaches were compared, and give strong support to the HLA locus on chromosome 6 as a susceptibility locus. Other regions of interest include loci on chromosomes 11, 2, and 12.
      308
  • Publication
    Large-scale linkage analysis of 1302 affected relative pairs with rheumatoid arthritis
    Rheumatoid arthritis is the most common systematic autoimmune disease and its etiology is believed to have both strong genetic and environmental components. We demonstrate the utility of including genetic and clinical phenotypes as covariates within a linkage analysis framework to search for rheumatoid arthritis susceptibility loci. The raw genotypes of 1302 affected relative pairs were combined from four large family-based samples (North American Rheumatoid Arthritis Consortium, United Kingdom, European Consortium on Rheumatoid Arthritis Families, and Canada). The familiality of the clinical phenotypes was assessed. The affected relative pairs were subjected to autosomal multipoint affected relative-pair linkage analysis. Covariates were included in the linkage analysis to take account of heterogeneity within the sample. Evidence of familiality was observed with age at onset (p << 0.001) and rheumatoid factor (RF) IgM (p << 0.001), but not definite erosions (p = 0.21). Genome-wide significant evidence for linkage was observed on chromosome 6. Genome-wide suggestive evidence for linkage was observed on chromosomes 13 and 20 when conditioning on age at onset, chromosome 15 conditional on gender, and chromosome 19 conditional on RF IgM after allowing for multiple testing of covariates.
      509
  • Publication
    Reference ranges for fetal volumes in the late first trimester, obtained using 9-degree rotational steps
    Objectives: In the course of another study, we calculated fetal volume centile values for each week of gestation from 11 to 14 weeks using nine-degree rotation steps.
      61
  • Publication
    Community first responders for out-of-hospital cardiac arrest in adults and children
    Background: Mobilization of community first responders (CFRs) to the scene of an out-of-hospital cardiac arrest (OHCA) event has been proposed as a means of shortening the interval from occurrence of cardiac arrest to performance of cardiopulmonary resuscitation (CPR) and defibrillation, thereby increasing patient survival. Objectives: To assess the effect of mobilizing community first responders (CFRs) to out-of-hospital cardiac arrest events in adults and children older than four weeks of age, in terms of survival and neurological function. Search methods We searched the following databases for relevant trials in January 2019: CENTRAL, MEDLINE (Ovid SP), Embase (Ovid SP), and Web of Science. We also searched the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) and ClinicalTrials.gov, and we scanned the abstracts of conference proceedings of the American Heart Association and the European Resuscitation Council. Selection criteria We included randomized and quasi-randomized trials (RCTs and q-RCTs) that compared routine emergency medical services (EMS) care versus EMS care plus mobilization of CFRs in instances of OHCA.Trials with randomization by cluster were eligible for inclusion, including cluster-design studies with intervention cross-over. In some communities, the statutory ambulance service/EMS is routinely provided by the local fire service. For the purposes of this review, this group represents the statutory ambulance service/EMS, as distinct from CFRs, and was not included as an eligible intervention. We did not include studies primarily focused on opportunistic bystanders. Individuals who were present at the scene of an OHCA event and who performed CPR according to telephone instruction provided by EMS call takers were not considered to be CFRs. Studies primarily assessing the impact of specific additional interventions such as administration of naloxone in narcotic overdose or adrenaline in anaphylaxis were also excluded. We included adults and children older than four weeks of age who had experienced an OHCA. Data collection and analysis Two review authors independently reviewed all titles and abstracts received to assess potential eligibility, using set inclusion criteria. We obtained and examined in detail full-text copies of all papers considered potentially eligible, and we approached authors of trials for additional information when necessary. We summarized the process of study selection in a PRISMA flowchart. Three review authors independently extracted relevant data using a standard data extraction form and assessed the validity of each included trial using the Cochrane ’Risk of bias’ tool. We resolved disagreements by discussion and consensus. We synthesized findings in narrative fashion due to the heterogeneity of the included studies. We used the principles of the GRADE system to assess the certainty of the body of evidence associated with specific outcomes and to construct a ’Summary of findings’ table. Main results: We found two completed studies involving a total of 1136 participants that ultimately met our inclusion criteria. We also found one ongoing study and one planned study. We noted significant heterogeneity in the characteristics of interventions and outcomes measured or reported across these studies, thus we could not pool study results. One completed study considered the dispatch of police and fire service CFRs equipped with automatic external defibrillators (AEDs) in an EMS system in Amsterdam and surrounding areas. This study was an RCT with allocation made by cluster according to non-overlapping geographical regions. It was conducted between 5 January 2000 and 5 January 2002. All participants were 18 years of age or older and had experienced witnessed OHCA. The study found no difference in survival at hospital discharge (odds ratio (OR) 1.3, 95% confidence interval (CI) 0.8 to 2.2; 1 RCT; 469 participants; low-certainty evidence), despite the observation that all 72 incidences of defibrillation performed before EMS arrival occurred in the intervention group (OR and 95% CI-not applicable; 1 RCT; 469 participants; moderate-certainty evidence). This study reported increased survival to hospital admission in the intervention group (OR 1.5, 95% CI 1.1 to 2.0; 1 RCT; 469 participants; moderate-certainty evidence). The second completed study considered the dispatch of nearby lay volunteers in Stockholm, Sweden, who were trained to perform cardiopulmonary resuscitation (CPR). This represented a supplementary CFR intervention in an EMS system where police and fire services were already routinely dispatched to OHCA in addition to EMS ambulances. This study, an RCT, included both witnessed and unwitnessed OHCA and was conducted between 1 April 2012 and 1 December 2013. Participants included adults and children eight years of age and older. Researchers found no difference in 30-day survival (OR 1.34, 95% CI 0.79 to 2.29; 1 RCT; 612 participants; low-certainty evidence), despite a significant increase in CPR performed before EMS arrival (OR 1.49, 95% CI 1.09 to 2.03; 1 RCT; 665 participants; moderate-certainty evidence). Neither of the included completed studies considered neurological function at hospital discharge or at 30 days, measured by cerebral performance category or by any other means. Neither of the included completed studies considered health-related quality of life. The overall certainty of evidence for the outcomes of included studies was low to moderate. Authors’ conclusions Moderate-certainty evidence shows that context-specific CFR interventions result in increased rates of CPR or defibrillation performed before EMS arrival. It remains uncertain whether this can translate to significantly increased rates of overall patient survival. When possible, further high-quality RCTs that are adequately powered to measure changes in survival should be conducted. The included studies did not consider survival with good neurological function. This outcome is likely to be important to patients and should be included routinely wherever survival is measured. We identified one ongoing study and one planned trial whose results once available may change the results of this review. As this review was limited to randomized and quasi-randomized trials, we may have missed some important data from other study types.
      241Scopus© Citations 4
  • Publication
    Evidence that common variation in NEDD9 is associated with susceptibility to late-onset Alzheimer's and Parkinson's disease
    Late-onset Alzheimer's disease (LOAD) and Parkinson's disease (PD) are the most common neurodegenerative disorders and in both diseases susceptibility is known to be influenced by genes. We set out to identify novel susceptibility genes for LOAD by performing a large scale, multi-tiered association study testing 4692 single nucleotide polymorphism (SNPs). We identified a SNP within a putative transcription factor binding site in the NEDD9 gene (neural precursor cell expressed, developmentally down-regulated), that shows good evidence of association with disease risk in four out of five LOAD samples [N = 3521, P = 5.38x10(-6), odds ratio (OR) = 1.38 (1.20-1.59)] and in addition, we observed a similar pattern of association in two PD sample sets [N = 1464, P = 0.0145, OR =1.31 (1.05-1.62)]. In exploring a potential mechanism for the association, we observed that expression of NEDD9 and APOE show a strong inverse correlation in the hippocampus of Alzheimer's cases. These data implicate NEDD9 as a novel susceptibility gene for LOAD and possibly PD.
      343Scopus© Citations 38
  • Publication
    Contact tracing during the COVID-19 outbreak: a protocol for enabling rapid learning from experiences and exploring the psychological impact on contact tracers
    Background: Given the unprecedented nature of the COVID-19 pandemic, the Irish health system required the redeployment of public sector staff and the recruitment of dedicated contact tracing staff in the effort to contain the spread of the virus. Contact tracing is crucial for effective disease control and is normally a role carried out by public health teams. Contact tracing staff are provided with rapid intensive training but are operating in a dynamic environment where processes and advice are adapting continuously. Real-time data is essential to inform strategy, coordinate interconnected processes, and respond to needs. Given that many contact tracers have been newly recruited or redeployed, they may not have significant experience in healthcare and may experience difficulties in managing the anxieties and emotional distress of members of the public. Aim: This research aims to: (i) identify emerging needs and issues and feed this information back to the Health Service Executive for updates to the COVID-19 Contact Management Programme (CMP); (ii) understand the psychological impact on contact tracers and inform the development of appropriate supports. Methods: We will use a mixed-methods approach. A brief online survey will be administered at up to three time points during 2021 to measure emotional exhaustion, anxiety, general health, and stress of contact tracing staff, identify tracing systems or processes issues, as well as issues of concern and confusion among the public. Interviews will also be conducted with a subset of participants to achieve a more in-depth understanding of these experiences. Observations may be conducted in contact tracing centres to document processes, practices, and explore any local contextual issues. Impact: Regular briefs arising from this research with data, analysis, and recommendations will aim to support the work of the CMP to identify problems and implement solutions. We will deliver regular feedback on systems issues; challenges; and the psychological well-being of contact tracing staff.
    Scopus© Citations 3  458
  • Publication
    Functional impact of global rare copy number variation in autism spectrum disorders
    The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours1. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability2. Although ASDs are known to be highly heritable (~90%)3, the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 × 10-4). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53–PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
      546Scopus© Citations 1589
  • Publication
    Analyses of single marker and pairwise effects of candidate loci for rheumatoid arthritis using logistic regression and random forests
    Using parametric and nonparametric techniques, our study investigated the presence of single locus and pairwise effects between 20 markers of the Genetic Analysis Workshop 15 (GAW15) North American Rheumatoid Arthritis Consortium (NARAC) candidate gene data set (Problem 2), analyzing 463 independent patients and 855 controls. Specifically, our work examined the correspondence between logistic regression (LR) analysis of single-locus and pairwise interaction effects, and random forest (RF) single and joint importance measures. For this comparison, we selected small but stable RFs (500 trees), which showed strong correlations (r~0.98) between their importance measures and those by RFs grown on 5000 trees. Both RF importance measures captured most of the LR single-locus and pairwise interaction effects, while joint importance measures also corresponded to full LR models containing main and interaction effects. We furthermore showed that RF measures were particularly sensitive to data imputation. The most consistent pairwise effect on rheumatoid arthritis was found between two markers within MAP3K7IP2/SUMO4 on 6q25.1, although LR and RFs assigned different significance levels.Within a hypothetical two-stage design, pairwise LR analysis of all markers with significant RF single importance would have reduced the number of possible combinations in our small data set by 61%, whereas joint importance measures would have been less efficient for marker pair reduction. This suggests that RF single importance measures, which are able to detect a wide range of interaction effects and are computationally very efficient, might be exploited as pre-screening tool for larger association studies. Follow-up analysis, such as by LR, is required since RFs do not indicate high-risk genotype combinations.
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  • Publication
    Community first responders for out-of-hospital cardiac arrest (Protocol)
    This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: To assess the impact of mobilizing community first responders (CFRs) to out-of-hospital cardiac arrest events in the community.
      198Scopus© Citations 26
  • Publication
    Feasibility cluster randomised controlled trial evaluating a theory-driven group-based complex intervention versus usual physiotherapy to support self-management of osteoarthritis and low back pain (SOLAS)
    Background: The self-management of osteoarthritis (OA) and low back pain (LBP) through activity and skills (SOLAS) theory-driven group-based complex intervention was developed primarily for the evaluation of its acceptability to patients and physiotherapists and the feasibility of trial procedures, to inform the potential for a definitive trial. Methods: This assessor-blinded multicentre two-arm parallel cluster randomised controlled feasibility trial compared the SOLAS intervention to usual individual physiotherapy (UP; pragmatic control group). Patients with OA of the hip, knee, lumbar spine and/or chronic LBP were recruited in primary care physiotherapy clinics (i.e. clusters) in Dublin, Ireland, between September 2014 and November 2015. The primary feasibility objectives were evaluated using quantitative methods and individual telephone interviews with purposive samples of participants and physiotherapists. A range of secondary outcomes were collected at baseline, 6 weeks (behaviour change only), 2 months and 6 months to explore the preliminary effects of the intervention. Analysis was by intention-to-treat according to participants' cluster allocation and involved descriptive analysis of the quantitative data and inductive thematic analysis of the qualitative interviews. A linear mixed model was used to contrast change over time in participant secondary outcomes between treatment arms, while adjusting for study waves and clusters. Results: Fourteen clusters were recruited (7 per trial arm), each cluster participated in two waves of recruitment, with the average cluster size below the target of six participants (intervention: mean (SD) = 4.92 (1.31), range 2-7; UP: mean (SD) = 5.08 (2.43), range 1-9). One hundred twenty participants (83.3% of n = 144 expected) were recruited (intervention n = 59; UP n = 61), with follow-up data obtained from 80.8% (n = 97) at 6 weeks, 84.2% (n = 101) at 2 months and 71.7% (n = 86) at 6 months. Most participants received treatment as allocated (intervention n = 49; UP n = 54). The qualitative interviews (12 participants; 10 physiotherapists (PTs) found the intervention and trial procedures acceptable and appropriate, with minimal feasible adaptations required. Linear mixed methods showed improvements in most secondary outcomes at 2 and 6 months with small between-group effects. Conclusions: While the SOLAS intervention and trial procedures were acceptable to participants and PTs, the recruitment of enough participants is the biggest obstacle to a definitive trial.
      84Scopus© Citations 7