ORCID Profile
0000-0003-0212-6443
Current Organisation
University of Oxford
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Publisher: Springer Science and Business Media LLC
Date: 03-2023
DOI: 10.1038/S41588-023-01314-0
Abstract: Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. In idual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of intervening in pathways underlying lung function. We highlight new putative causal variants, genes, proteins and pathways, including those targeted by existing drugs. These findings bring us closer to understanding the mechanisms underlying lung function and COPD, and should inform functional genomics experiments and potentially future COPD therapies.
Publisher: Elsevier BV
Date: 2019
DOI: 10.1016/J.JPEDS.2018.08.033
Abstract: Infants in the Australian and UK Benefits of Oxygen Saturation Targeting-II trials treated using revised oximeters spent more time within their planned pulse oximeter saturation target ranges than infants treated using the original oximeters (P < .001). This may explain the larger mortality difference seen with revised oximeters. If so, average treatment effects from the Neonatal Oxygen Prospective Meta-analysis trials may be underestimates.
Publisher: Springer Science and Business Media LLC
Date: 04-04-2017
Publisher: MDPI AG
Date: 18-05-2021
Abstract: Telehealth interventions offer a practical platform to support adolescent and young adult (AYA) cancer survivors’ mental health needs after treatment, yet efficacy data are lacking. We evaluated an online, group-based, videoconferencing-delivered cognitive-behavioral therapy (CBT) intervention (‘Recapture Life’) in a 3-arm randomized-controlled trial comparing Recapture Life with an online peer-support group, and a waitlist control, with the aim of testing its impact on quality of life, emotional distress and healthcare service use. Forty AYAs (Mage = 20.6 years) within 24-months of completing treatment participated, together with 18 support persons. No groupwise impacts were measured immediately after the six-week intervention. However, Recapture Life participants reported using more CBT skills at the six-week follow-up (OR = 5.58, 95% CI = 2.00–15.56, p = 0.001) than peer-support controls. Recapture Life participants reported higher perceived negative impact of cancer, anxiety and depression at 12-month follow-up, compared to peer-support controls. Post-hoc analyses suggested that AYAs who were further from completing cancer treatment responded better to Recapture Life than those who had completed treatment more recently. While online telehealth interventions hold promise, recruitment to this trial was challenging. As the psychological challenges of cancer survivorship are likely to evolve with time, different support models may prove more or less helpful for different sub-groups of AYA survivors at different times.
Publisher: Cold Spring Harbor Laboratory
Date: 08-05-2022
DOI: 10.1101/2022.05.07.490900
Abstract: Highly multiplexed quantitative subcellular imaging holds enormous promise for understanding how spatial context shapes the activity of our genome and its products at multiple scales. Yet unbiased analysis of subcellular organisation across experimental conditions remains challenging, because differences in molecular profiles between conditions confound differences in molecular profiles across space. Here, we introduce a deep-learning framework called CAMPA (Conditional Autoencoder for Multiplexed Pixel Analysis), which uses a variational autoencoder conditioned on cellular states and perturbations to learn consistent molecular signatures. Clustering the learned representations into subcellular landmarks allows quantitative comparisons of landmark sizes, shapes, molecular compositions and relative spatial organisation between conditions. By performing high-resolution multiplexed immunofluorescence on human cells, we use CAMPA to reveal how subnuclear organisation changes upon different perturbations of RNA production or processing, and how different membraneless organelles scale with cell size. Furthermore, by integrating information across the cellular and subcellular scales, we uncover new links between the molecular composition of membraneless organelles and bulk RNA synthesis rates of single cells. We anticipate that CAMPA will greatly accelerate the systematic mapping of multiscale atlases of biological organisation to identify the rules by which context shapes physiology and disease.
Publisher: Springer Science and Business Media LLC
Date: 31-10-2019
DOI: 10.1038/S41467-019-12283-6
Abstract: In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients ( F ROH ) for .4 million in iduals, we show that F ROH is significantly associated ( p 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: F ROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44–66%] in the odds of having children. Finally, the effects of F ROH are confirmed within full-sibling pairs, where the variation in F ROH is independent of all environmental confounding.
Publisher: MDPI AG
Date: 09-11-2021
Abstract: We conducted a three-armed trial to assess Cascade, a four-module group videoconferencing cognitive behavior therapy (CBT) intervention for parents of childhood cancer survivors currently aged years. We allocated parents to Cascade, an attention control (peer-support group), or a waitlist. The primary outcome was parents’ health-related quality of life (PedsQL-Family Impact/EQ-5D-5L) six months post-intervention. Parents also reported their anxiety/depression, parenting self-agency, fear of recurrence, health service and psychotropic medication use, engagement in productive activities, confidence to use, and actual use of, CBT skills, and their child’s quality of life. Seventy-six parents opted in 56 commenced the trial. Cascade achieved good parent engagement and most Cascade parents were satisfied and reported benefits. Some parents expressed concerns about the time burden and the group format. Most outcomes did not differ across trial arms. Cascade parents felt more confident to use more CBT skills than peer-support and waitlisted parents, but this did not lead to more use of CBT. Cascade parents reported lower psychosocial health scores for their child than waitlisted parents. Cascade parents’ health service use, psychotropic medication use, and days engaged in productive activities did not improve, despite some improvements in waitlisted parents. Our trial was difficult to implement, but participants were largely satisfied. Cascade did not improve most outcomes, possibly because many parents were functioning well pre-enrolment. We used these findings to improve Cascade and will trial the new version in future.
Publisher: Wiley
Date: 12-04-2016
DOI: 10.1002/SIM.6960
Abstract: Rate differences are an important effect measure in biostatistics and provide an alternative perspective to rate ratios. When the data are event counts observed during an exposure period, adjusted rate differences may be estimated using an identity-link Poisson generalised linear model, also known as additive Poisson regression. A problem with this approach is that the assumption of equality of mean and variance rarely holds in real data, which often show overdispersion. An additive negative binomial model is the natural alternative to account for this however, standard model-fitting methods are often unable to cope with the constrained parameter space arising from the non-negativity restrictions of the additive model. In this paper, we propose a novel solution to this problem using a variant of the expectation-conditional maximisation-either algorithm. Our method provides a reliable way to fit an additive negative binomial regression model and also permits flexible generalisations using semi-parametric regression functions. We illustrate the method using a placebo-controlled clinical trial of fenofibrate treatment in patients with type II diabetes, where the outcome is the number of laser therapy courses administered to treat diabetic retinopathy. An R package is available that implements the proposed method. Copyright © 2016 John Wiley & Sons, Ltd.
Publisher: American Medical Association (AMA)
Date: 22-07-2009
Publisher: Springer Science and Business Media LLC
Date: 25-11-2020
DOI: 10.1038/S41467-020-19742-5
Abstract: Miscarriage is a common, complex trait affecting ~15% of clinically confirmed pregnancies. Here we present the results of large-scale genetic association analyses with 69,054 cases from five different ancestries for sporadic miscarriage, 750 cases of European ancestry for multiple (≥3) consecutive miscarriage, and up to 359,469 female controls. We identify one genome-wide significant association (rs146350366, minor allele frequency (MAF) 1.2%, P = 3.2 × 10 −8 , odds ratio (OR) = 1.4) for sporadic miscarriage in our European ancestry meta-analysis and three genome-wide significant associations for multiple consecutive miscarriage (rs7859844, MAF = 6.4%, P = 1.3 × 10 −8 , OR = 1.7 rs143445068, MAF = 0.8%, P = 5.2 × 10 −9 , OR = 3.4 rs183453668, MAF = 0.5%, P = 2.8 × 10 −8 , OR = 3.8). We further investigate the genetic architecture of miscarriage with biobank-scale Mendelian randomization, heritability, and genetic correlation analyses. Our results show that miscarriage etiopathogenesis is partly driven by genetic variation potentially related to placental biology, and illustrate the utility of large-scale biobank data for understanding this pregnancy complication.
Publisher: Elsevier BV
Date: 09-2023
Publisher: Springer Science and Business Media LLC
Date: 29-05-2023
DOI: 10.1038/S41592-023-01894-Z
Abstract: Highly multiplexed imaging holds enormous promise for understanding how spatial context shapes the activity of the genome and its products at multiple length scales. Here, we introduce a deep learning framework called CAMPA (Conditional Autoencoder for Multiplexed Pixel Analysis), which uses a conditional variational autoencoder to learn representations of molecular pixel profiles that are consistent across heterogeneous cell populations and experimental perturbations. Clustering these pixel-level representations identifies consistent subcellular landmarks, which can be quantitatively compared in terms of their size, shape, molecular composition and relative spatial organization. Using high-resolution multiplexed immunofluorescence, this reveals how subcellular organization changes upon perturbation of RNA synthesis, RNA processing or cell size, and uncovers links between the molecular composition of membraneless organelles and cell-to-cell variability in bulk RNA synthesis rates. By capturing interpretable cellular phenotypes, we anticipate that CAMPA will greatly accelerate the systematic mapping of multiscale atlases of biological organization to identify the rules by which context shapes physiology and disease.
Publisher: Springer Science and Business Media LLC
Date: 19-09-2023
Publisher: MDPI AG
Date: 28-10-2022
Abstract: Precision medicine is changing the treatment of childhood cancer globally, however little is known about quality of life (QoL) in children and adolescents participating in precision medicine trials. We examined QoL among patients enrolled in PRISM, the Zero Childhood Cancer Program’s precision medicine trial for high-risk childhood cancer. We assessed patient QoL via self-report (aged 12–17 years) and parent-proxy (aged 4–17 years) completion of the EQ-5D-Y. We analysed data using descriptive statistics and regression models. Patients (n = 23) and parents (n = 136) provided data after trial enrolment and following receipt of trial results and treatment recommendations (n = 8 patients, n = 84 parents). At enrolment, most patients were experiencing at least some difficulty across more than one QoL domain (81% patient self-report, 83% parent report). We did not find strong evidence of a change in QoL between timepoints, or of demographic or disease factors that predicted parent-reported patient QoL (EQ-VAS) at enrolment. There was strong evidence that receiving a treatment recommendation but not a change in cancer therapy was associated with poorer parent-reported patient QoL (EQ-VAS Mdiff = −22.5, 95% CI: −36.5 to −8.5, p = 0.006). Future research needs to better understand the relationship between treatment decisions and QoL and would benefit from integrating assessment of QoL into routine clinical care.
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Mark Donoghoe.