ORCID Profile
0000-0002-2218-6833
Current Organisations
Perth Children's Hospital
,
University of Sheffield
,
University of Notre Dame Australia
,
University of Western Australia
,
University of Melbourne
,
St Vincent's Institute of Medical Research
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Western Journal of Emergency Medicine
Date: 23-03-2015
Publisher: Elsevier BV
Date: 10-2015
Publisher: Springer Science and Business Media LLC
Date: 12-2019
DOI: 10.1186/S13059-019-1865-2
Abstract: Multiplexed single-cell RNA-seq analysis of multiple s les using pooling is a promising experimental design, offering increased throughput while allowing to overcome batch variation. To reconstruct the s le identify of each cell, genetic variants that segregate between the s les in the pool have been proposed as natural barcode for cell demultiplexing. Existing demultiplexing strategies rely on availability of complete genotype data from the pooled s les, which limits the applicability of such methods, in particular when genetic variation is not the primary object of study. To address this, we here present Vireo, a computationally efficient Bayesian model to demultiplex single-cell data from pooled experimental designs. Uniquely, our model can be applied in settings when only partial or no genotype information is available. Using pools based on synthetic mixtures and results on real data, we demonstrate the robustness of Vireo and illustrate the utility of multiplexed experimental designs for common expression analyses.
Publisher: Springer Science and Business Media LLC
Date: 07-11-2017
Publisher: Wiley
Date: 30-07-2019
DOI: 10.1002/AET2.10376
Publisher: BMJ
Date: 03-2017
Publisher: BMJ
Date: 26-09-2019
Publisher: Oxford University Press (OUP)
Date: 14-01-2017
DOI: 10.1093/BIOINFORMATICS/BTW777
Abstract: Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of in idual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for downstream analysis. scater provides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development. The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at ackages/scater. Supplementary data are available at Bioinformatics online.
Publisher: Elsevier BV
Date: 06-2018
Publisher: Oxford University Press (OUP)
Date: 11-11-2009
DOI: 10.1093/BIOINFORMATICS/BTP616
Abstract: Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (bioconductor.org). Contact: mrobinson@wehi.edu.au
Publisher: Wiley
Date: 26-08-2011
DOI: 10.1111/J.1440-1681.2011.05572.X
Abstract: 1. Aliskiren is a renin inhibitor with an IC(50) of 0.6 nmol/L for human renin, 4.5 nmol/L for mouse renin and 80 nmol/L for rat renin. 2. In the present study, we compared the effects of aliskiren (10 mg/kg per day), the angiotensin-converting enzyme inhibitor perindopril (0.2 mg/kg per day) and their combination on angiotensin and bradykinin peptides in female heterozygous (mRen-2)27 rats, transgenic for the mouse renin gene. 3. All three treatments produced similar reductions in systolic blood pressure, heart weight and plasma aldosterone levels and reduced angiotensin II levels in lung, but only perindopril and the combination reduced angiotensin II levels in kidney of (mRen-2)27 rats. In contrast, aliskiren and the combination, but not perindopril alone, increased cardiac bradykinin levels. Aliskiren increased immunostaining for tissue kallikrein in the heart and reduced cardiac fibrosis. 4. We investigated the mechanism underlying the increase in bradykinin levels following aliskiren treatment in Sprague-Dawley rats, in which aliskiren has a lower potency for renin inhibition. Aliskiren (10 mg/kg per day) reduced renal angiotensin levels within 24 h, but treatment for > 24 h was required to increase cardiac bradykinin levels. Moreover, 3 mg/kg per day aliskiren increased cardiac bradykinin levels, but did not reduce renal angiotensin levels. Aliskiren did not potentiate the hypotensive effects of bradykinin however, it increased tissue kallikrein, but not plasma kallikrein, mRNA levels in the heart. 5. These data demonstrate that the aliskiren-induced increase in cardiac bradykinin levels is independent of renin inhibition and changes in bradykinin metabolism, but is associated with increased tissue kallikrein gene expression.
Publisher: Springer Science and Business Media LLC
Date: 10-05-2017
DOI: 10.1038/NATURE22403
Publisher: Cambridge University Press (CUP)
Date: 04-2013
DOI: 10.1192/PB.37.4.146
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 05-2006
Publisher: Elsevier BV
Date: 06-2017
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 05-2006
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 05-2006
Publisher: Springer Science and Business Media LLC
Date: 03-07-2020
DOI: 10.1007/S00247-020-04738-6
Abstract: Multiple long-bone fractures, particularly bilateral fractures, are of moderate specificity for inflicted injury (physical abuse) in infants and young children. Bilateral healing fractures of the fibulae are rare and, depending on age, raise the suspicion of inflicted injury. We report healing undisplaced fractures of both fibulae, in almost identical positions, in a pre-ambulant infant. The caregivers reported that the infant repeatedly banged his legs against the metal frame of his playpen. A video of this mechanism was provided to the instructed radiology expert and showed that the point of impact of the infant’s legs against the metal frame was at a similar level to the radiographic abnormalities. This mechanism was therefore believed to be consistent with the injuries, resulting in a diagnosis of self-inflicted bilateral fibular fractures and not of inflicted injury.
Publisher: Springer Science and Business Media LLC
Date: 17-02-2016
Publisher: EduRad
Date: 26-04-2014
Abstract: We report the case of a previously well 18-year-old male who presented to the Emergency Department with lower limb pain. An ultrasound demonstrated extensive left sided deep vein thrombosis and computed tomography demonstrated inferior vena cava agenesis, leading to the diagnosis of inferior vena cava agenesis associated deep vein thrombosis. The aetiology of inferior vena cava agenesis is explored in depth.
Publisher: Cold Spring Harbor Laboratory
Date: 17-06-2021
DOI: 10.1101/2021.06.17.448806
Abstract: With improving technology and decreasing costs, single-cell RNA sequencing (scRNA-seq) at the population scale has become more viable, opening up the doors to study functional genomics at the single-cell level. This development has lead to a rush to adapt bulk methods and develop new single-cell-specific methods and tools for computational analysis of these studies. Many single-cell methods have been tested, developed, and benchmarked using simulated data. However, current scRNA-seq simulation frameworks do not allow for the simulation of population-scale scRNA-seq data. Here, we present splatPop, a new Splatter model, for flexible, reproducible, and well documented simulation of population-scale scRNA-seq data with known expression quantitative trait loci (eQTL) effects. The splatPop model also allows for the simulation of complex batch effects, cell group effects, and conditional effects between in iduals from different cohorts.
Publisher: Oxford University Press (OUP)
Date: 28-01-2012
DOI: 10.1093/NAR/GKS042
Publisher: BMJ
Date: 17-02-2022
DOI: 10.1136/ARCHDISCHILD-2021-323444
Abstract: Rate and severity of radiological features of physical abuse in children during the first UK-wide COVID-19 enforced national lockdown. To assess the number, type and outcome of radiological investigations for children presenting to hospital with suspected physical abuse (SPA including abusive head trauma) during the first national COVID-19 enforced lockdown compared with the prelockdown period. Multicentre, retrospective, observational, interrupted time series analysis. Eight secondary/tertiary paediatric centres between January 2018 and July 2020 inclusive. 1587 hospital assessed children undergoing radiographic skeletal surveys (SkS) and head CT imaging performed for SPA/child protection concerns. Incidence and severity of fractures identified on SkS head injury (composed of incidence rates and ratios of skull fracture, intracranial haemorrhage (ICH) and hypoxic ischaemic injury (HII)) on head CT imaging and ratio of antemortem and postmortem SkS. 1587 SkS were performed: 1282 (81%) antemortem, 762 (48%) male, and positive findings in 582 (37%). Median patient age was 6 months. There were 1.7 fractures/child prelockdown versus 1.1 fractures/child during lockdown. There was no difference between positive/negative SkS rates, the absolute ratio of antemortem ostmortem SkS or absolute numbers of head injury occurring between January 2018 and February 2020 and the lockdown period April–July 2020. Likewise, prelockdown incidence and rates of skull fracture 30/244 (12%), ICH 28/220 (13%) and HIE 10/205 (5%) were similar to lockdown, 142/1304 (11%), 171/1152 (15%) and 68/1089 (6%), respectively. The first UK COVID-19 lockdown did not lead to an increase in either the number of antemortem or postmortem radiological investigations performed for SPA, or the number or severity of fractures and intracranial injuries identified by these investigations.
Publisher: Walter de Gruyter GmbH
Date: 22-10-2012
Abstract: Next generation sequencing technology provides a powerful tool for measuring gene expression (mRNA) levels in the form of RNA-sequence data. Method development for identifying differentially expressed (DE) genes from RNA-seq data, which frequently includes many low-count integers and can exhibit severe overdispersion relative to Poisson or binomial distributions, is a popular area of ongoing research. Here we present quasi-likelihood methods with shrunken dispersion estimates based on an adaptation of Smyth's (2004) approach to estimating gene-specific error variances for microarray data. Our suggested methods are computationally simple, analogous to ANOVA and compare favorably versus competing methods in detecting DE genes and estimating false discovery rates across a variety of simulations based on real data.
Publisher: Springer Science and Business Media LLC
Date: 11-07-2016
DOI: 10.1038/NATURE18642
Publisher: Figshare
Date: 2014
Publisher: SAGE Publications
Date: 12-2010
Publisher: Elsevier BV
Date: 05-2017
Publisher: Elsevier BV
Date: 12-2016
DOI: 10.1016/J.ANNEMERGMED.2016.02.018
Abstract: Since 2014, Academic Life in Emergency Medicine (ALiEM) has used the Approved Instructional Resources (AIR) score to critically appraise online content. The primary goals of this study are to determine the interrater reliability (IRR) of the ALiEM AIR rating score and determine its correlation with expert educator gestalt. We also determine the minimum number of educator-raters needed to achieve acceptable reliability. Eight educators each rated 83 online educational posts with the ALiEM AIR scale. Items include accuracy, usage of evidence-based medicine, referencing, utility, and the Best Evidence in Emergency Medicine rating score. A generalizability study was conducted to determine IRR and rating variance contributions of facets such as rater, blogs, posts, and topic. A randomized selection of 40 blog posts previously rated through ALiEM AIR was then rated again by a blinded group of expert medical educators according to their gestalt. Their gestalt impression was subsequently correlated with the ALiEM AIR score. The IRR for the ALiEM AIR rating scale was 0.81 during the 6-month pilot period. Decision studies showed that at least 9 raters were required to achieve this reliability. Spearman correlations between mean AIR score and the mean expert gestalt ratings were 0.40 for recommendation for learners and 0.35 for their colleagues. The ALiEM AIR scale is a moderately to highly reliable, 5-question tool when used by medical educators for rating online resources. The score displays a fair correlation with expert educator gestalt in regard to the quality of the resources. The score displays a fair correlation with educator gestalt.
Publisher: Elsevier BV
Date: 07-2019
DOI: 10.1016/J.CRAD.2019.04.016
Abstract: One of the most challenging areas of radiological imaging in children is the diagnosis of physical abuse. There is a dearth of paediatric radiologists willing to act as expert witnesses, particularly in the family courts. There are a number of reasons why radiologists may not be interested or willing to put themselves forward to work as expert witnesses in this field. A group of imaging experts recently formed the "British Society of Paediatric Radiology (BSPR) Working Group on Imaging in Suspected Physical Abuse (SPA)". The group comprises radiologists and neuroradiologists with current or previous experience of providing expert witness reports to the court in cases of SPA. The group met in January 2019 to explore pragmatic solutions to the chronic inefficiencies in both medical and legal practices and the challenges that arise from working in a legal arena with different structures, goals, and assessment criteria. Key issues concerned organisational inefficiencies, variable support from National Health Service Trusts and the Royal College of Radiologists to conduct this work, and the risk/benefit of involvement. This work is important for the patient, parents, and society in general, and highly rewarding for clinical practitioners who are involved, but there are several issues with current practices that discourage active participation. With several members of the group either retired or close to retirement, the shortage of experts is becoming a pressing issue within the UK, which requires an engaged multidisciplinary group to come up with creative solutions. Here, the group provide a consensus opinion highlighting the current barriers and potential facilitators to increasing the number of radiologists willing to provide opinions to the court.
Publisher: Springer Science and Business Media LLC
Date: 11-11-2021
DOI: 10.1038/S41366-021-01002-1
Abstract: Lipedema, a poorly understood chronic disease of adipose hyper-deposition, is often mistaken for obesity and causes significant impairment to mobility and quality-of-life. To identify molecular mechanisms underpinning lipedema, we employed comprehensive omics-based comparative analyses of whole tissue, adipocyte precursors (adipose-derived stem cells (ADSCs)), and adipocytes from patients with or without lipedema. We compared whole-tissues, ADSCs, and adipocytes from body mass index–matched lipedema ( n = 14) and unaffected ( n = 10) patients using comprehensive global lipidomic and metabolomic analyses, transcriptional profiling, and functional assays. Transcriptional profiling revealed significant differences in lipedema tissue, with altered levels of mRNAs involved in critical signaling and cell function-regulating pathways (e.g., lipid metabolism and cell-cycle roliferation). Functional assays showed accelerated ADSC proliferation and differentiation in lipedema. Profiling lipedema adipocytes revealed changes in lipid composition and differentially altered metabolites. Transcriptional profiling of lipedema ADSCs and non-lipedema ADSCs revealed significant differential expression of genes including some involved in extracellular matrix and cell-cycle roliferation signaling pathways. One upregulated gene in lipedema ADSCs, Bub1 , encodes a cell-cycle regulator, central to the kinetochore complex, which regulates several histone proteins involved in cell proliferation. Downstream signaling analysis of lipedema ADSCs demonstrated enhanced activation of histone H2A, a key cell proliferation driver and Bub1 target. Critically, hyperproliferation exhibited by lipedema ADSCs was inhibited by the small molecule Bub1 inhibitor 2OH-BNPP1 and by CRISPR/Cas9-mediated Bub1 gene depletion. We found significant differences in gene expression, and lipid and metabolite profiles, in tissue, ADSCs, and adipocytes from lipedema patients compared to non-affected controls. Functional assays demonstrated that dysregulated Bub1 signaling drives increased proliferation of lipedema ADSCs, suggesting a potential mechanism for enhanced adipogenesis in lipedema. Importantly, our characterization of signaling networks driving lipedema identifies potential molecular targets, including Bub1, for novel lipedema therapeutics.
Publisher: Cold Spring Harbor Laboratory
Date: 04-04-2019
DOI: 10.1101/598748
Abstract: The joint analysis of multiple s les using single-cell RNA-seq is a promising experimental design, offering both increased throughput while allowing to account for batch variation. To achieve multi-s le designs, genetic variants that segregate between the s les in the pool have been proposed as natural barcodes for cell demultiplexing. Existing demultiplexing strategies rely on access to complete genotype data from the pooled s les, which greatly limits the applicability of such methods, in particular when genetic variation is not the primary object of study. To address this, we here present Vireo, a computationally efficient Bayesian model to demultiplex single-cell data from pooled experimental designs. Uniquely, our model can be applied in settings when only partial or no genotype information is available. Using simulations based on synthetic mixtures and results on real data, we demonstrate the robustness of our model and illustrate the utility of multi-s le experimental designs for common expression analyses.
Publisher: Wiley
Date: 29-11-2016
DOI: 10.1002/PD.4961
Abstract: Interpretation of magnetic resonance (MR) imaging of the fetal brain in utero is primarily undertaken using 2D images to provide anatomical information about structural abnormalities. It is now possible to obtain 3D image acquisitions that allow measurement of fetal brain volumes that are potentially useful clinically. The aim of our current work is to provide reference values of total brain volumes obtained from a cohort of low risk fetuses with no abnormalities on ante-natal ultrasonography and in utero MR imaging. Images from volume MR acquisitions of 132 fetuses were used to extract brain volumes by manual segmentation. Reproducibility and reliability were assessed by analysis of the results of two subgroups who had repeated measurements made by the primary and a secondary observer. Intra-observer and inter-observer agreement was high with no statistically significant differences between and within observers (p = 0.476 and p = 0.427, respectively). The results of the brain volume assessments are presented graphically with mean and 95% prediction limits alongside estimates of normal growth rates. We have shown that fetal brain volumes can be reliably extracted from in utero MR (iuMR) imaging 3D datasets with a high degree of reproducibility. The resultant data could potentially be used as a reference tool in the clinical setting. © 2016 John Wiley & Sons, Ltd.
Publisher: Elsevier BV
Date: 12-2018
DOI: 10.1016/J.ANNEMERGMED.2018.05.003
Abstract: Online educational resources such as blogs are increasingly used for education by emergency medicine clinicians. The Social Media Index was developed to quantify their relative impact. The Medical Education Translational Resources: Indicators of Quality (METRIQ) study was conducted in part to determine the association between the Social Media Index score and quality as measured by gestalt and previously derived quality instruments. Ten blogs were randomly selected from a list of emergency medicine and critical care Web sites. The 2 most recent clinically oriented blog posts published on these blogs were evaluated with gestalt, the Academic Life in Emergency Medicine Approved Instructional Resources (ALiEM AIR) score, and the METRIQ-8 score. Volunteer raters (including medical students, emergency medicine residents, and emergency medicine attending physicians) were identified with a multimodal recruitment methodology. The Social Media Index was calculated in February 2016, November 2016, April 2017, and December 2017. Pearson's correlations were calculated between the Social Media Index and the average rater gestalt, ALiEM AIR score, and METRIQ-8 score. A total of 309 of 330 raters completed all ratings (93.6%). The Social Media Index correlated moderately to strongly with the mean rater gestalt ratings (range 0.69 to 0.76) and moderately with the mean rater ALiEM AIR score (range 0.55 to 0.61) and METRIQ-8 score (range 0.53 to 0.57) during the month of the blog post's selection and for 2 years after. The Social Media Index's correlation with multiple quality evaluation instruments over time supports the hypothesis that it is associated with overall Web site quality. It can play a role in guiding in iduals to high-quality resources that can be reviewed with critical appraisal techniques.
Publisher: Cold Spring Harbor Laboratory
Date: 10-05-2022
DOI: 10.1101/2022.05.09.490241
Abstract: The development of single-cell RNA sequencing (scRNA-seq) has enabled scientists to catalogue and probe the transcriptional heterogeneity of in idual cells in unprecedented detail. A common step in the analysis of scRNA-seq data is the selection of so-called marker genes, most commonly to enable annotation of the biological cell types present in the s le. In this paper we benchmarked 56 computational methods for selecting marker genes in scRNA-seq data. The performance of the methods was compared using 10 real scRNA-seq datasets and over 170 additional simulated datasets. Methods were compared on their ability to recover simulated and expert-annotated marker genes, the predictive performance and characteristics of the gene sets they select, their memory usage and speed and their implementation quality. In addition, various case studies were used to scrutinise the most commonly used methods, highlighting issues and inconsistencies. Overall, we present a comprehensive evaluation of methods for selecting marker genes in scRNA-seq data. Our results highlight the efficacy of simple methods, especially the Wilcoxon rank-sum test, Student’s t-test and logistic regression. All code used in the evaluation, including an extensible Snakemake pipeline, is available at: gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking .
Publisher: Cold Spring Harbor Laboratory
Date: 25-10-2023
Publisher: Cold Spring Harbor Laboratory
Date: 17-06-2022
DOI: 10.1101/2022.06.16.496499
Abstract: Meiotic crossovers are required for accurate chromosome segregation and to produce new allelic combinations. Meiotic crossover numbers are tightly regulated within a narrow range, despite an excess of initiating DNA double-strand breaks. Here, we describe the tumour suppressor FANCM as a meiotic anti-crossover factor in mammals. Crossover analyses with single-gamete and pedigree datasets both reveal a genome-wide increase in crossover frequencies in Fancm -deficient mice. Gametogenesis is heavily perturbed in Fancm loss of function mice, which is consistent with the reproductive defects reported in humans with biallelic FANCM mutations. A portion of the gametogenesis defects can be attributed to the cGAS-STING pathway. Despite the gametogenesis phenotypes in Fancm mutants both sexes were capable of producing offspring. We propose that the anti-crossover function and role in gametogenesis of Fancm are separable and will inform diagnostic pathways for human genomic instability disorders.
Publisher: BMJ
Date: 11-2019
Abstract: We present the case of an 11-year-old girl who was presented to the Emergency Department with right elbow pain and swelling following a fall. Radiography demonstrated intra-articular displacement of an avulsed medial epicondyle ossification centre, which was not readily identified at presentation. She proceeded to an uncomplicated open reduction and internal fixation.
Publisher: Ferrata Storti Foundation (Haematologica)
Date: 11-07-2014
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1038/MI.2017.74
Publisher: Walter de Gruyter GmbH
Date: 29-06-2020
Publisher: Springer Science and Business Media LLC
Date: 10-02-2020
DOI: 10.1038/S41467-020-14457-Z
Abstract: Recent developments in stem cell biology have enabled the study of cell fate decisions in early human development that are impossible to study in vivo. However, understanding how development varies across in iduals and, in particular, the influence of common genetic variants during this process has not been characterised. Here, we exploit human iPS cell lines from 125 donors, a pooled experimental design, and single-cell RNA-sequencing to study population variation of endoderm differentiation. We identify molecular markers that are predictive of differentiation efficiency of in idual lines, and utilise heterogeneity in the genetic background across in iduals to map hundreds of expression quantitative trait loci that influence expression dynamically during differentiation and across cellular contexts.
Publisher: Elsevier BV
Date: 10-2020
Publisher: Springer Science and Business Media LLC
Date: 2014
DOI: 10.1186/GM543
Publisher: Springer Science and Business Media LLC
Date: 18-05-2201
DOI: 10.1038/NG.3304
Publisher: Springer Science and Business Media LLC
Date: 19-12-2017
Abstract: To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European in iduals and exome sequencing of 12,940 in iduals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1–5%) non-coding variants in the whole-genome sequenced in iduals and 99.7% of low-frequency coding variants in the whole-exome sequenced in iduals. Each variant was tested for association with T2D in the sequenced in iduals, and, to increase power, most were tested in larger numbers of in iduals ( % of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.
Publisher: Oxford University Press (OUP)
Date: 15-09-2022
DOI: 10.1093/NAR/GKAC764
Abstract: Profiling gametes of an in idual enables the construction of personalised haplotypes and meiotic crossover landscapes, now achievable at larger scale than ever through the availability of high-throughput single-cell sequencing technologies. However, high-throughput single-gamete data commonly have low depth of coverage per gamete, which challenges existing gamete-based haplotype phasing methods. In addition, haplotyping a large number of single gametes from high-throughput single-cell DNA sequencing data and constructing meiotic crossover profiles using existing methods requires intensive processing. Here, we introduce efficient software tools for the essential tasks of generating personalised haplotypes and calling crossovers in gametes from single-gamete DNA sequencing data (sgcocaller), and constructing, visualising, and comparing in idualised crossover landscapes from single gametes (comapr). With additional data pre-possessing, the tools can also be applied to bulk-sequenced s les. We demonstrate that sgcocaller is able to generate impeccable phasing results for high-coverage datasets, on which it is more accurate and stable than existing methods, and also performs well on low-coverage single-gamete sequencing datasets for which current methods fail. Our tools achieve highly accurate results with user-friendly installation, comprehensive documentation, efficient computation times and minimal memory usage.
Publisher: Cold Spring Harbor Laboratory
Date: 28-11-2022
DOI: 10.1101/2022.11.23.22282646
Abstract: Artificial intelligence (AI) readers, derived from applying deep learning models to medical image analysis, hold great promise for improving population breast cancer screening. However, previous evaluations of AI readers for breast cancer screening have mostly been conducted using cancer-enriched cohorts and have lacked assessment of the potential use of AI readers alongside radiologists in multi-reader screening programs. Here, we present a new AI reader for detecting breast cancer from mammograms in a large-scale population screening setting, and a novel analysis of the potential for human-AI reader collaboration in a well-established, high-performing population screening program. We evaluated the performance of our AI reader and AI-integrated screening scenarios using a two-year, real-world, population dataset from Victoria, Australia, a screening program in which two radiologists independently assess each episode and disagreements are arbitrated by a third radiologist. We used a retrospective full-field digital mammography image and non-image dataset comprising 808,318 episodes, 577,576 clients and 3,404,326 images in the period 2013 to 2019. Screening episodes from 2016, 2017 and 2018 were sequential population cohorts containing 752,609 episodes, 565,087 clients and 3,169,322 images. The dataset was split by screening date into training, development, and testing sets. All episodes from 2017 and 2018 were allocated to the testing set (509,109 episodes 3,651 screen-detected cancer episodes). Eight distinct AI models were trained on subsets of the training set (which included a validation set) and combined into our ensemble AI reader. Operating points were selected using the development set. We evaluated our AI reader on our testing set and on external datasets previously unseen by our models. The AI reader outperformed the mean in idual radiologist on this large retrospective testing dataset with an area under the receiver operator characteristic curve of 0.92 (95% CI 0.91, 0.92). The AI reader generalised well across screening round, client demographics, device manufacturer and cancer type, and achieved state-of-the-art performance on external datasets compared to recently published AI readers. Our simulations of AI-integrated screening scenarios demonstrated that a reader-replacement human-AI collaborative system could achieve better sensitivity and specificity (82.6%, 96.1%) compared to the current two-reader consensus system (79.9%, 96.0%), with reduced human reading workload and cost. Our band-pass AI-integrated scenario also enabled both higher sensitivity and specificity (80.6%, 96.2%) with larger reductions in human reading workload and cost. This study demonstrated that human-AI collaboration in a population breast cancer screening program has potential to improve accuracy and lower radiologist workload and costs in real world screening programs. The next stage of validation is to undertake prospective studies that can also assess the effects of the AI systems on human performance and behaviour.
Publisher: Cold Spring Harbor Laboratory
Date: 08-05-2019
DOI: 10.1101/630996
Abstract: Recent developments in stem cell biology have enabled the study of cell fate decisions in early human development that are impossible to study in vivo . However, understanding how development varies across in iduals and, in particular, the influence of common genetic variants during this process has not been characterised. Here, we exploit human iPS cell lines from 125 donors, a pooled experimental design, and single-cell RNA-sequencing to study population variation of endoderm differentiation. We identify molecular markers that are predictive of differentiation efficiency, and utilise heterogeneity in the genetic background across in iduals to map hundreds of expression quantitative trait loci that influence expression dynamically during differentiation and across cellular contexts.
Publisher: Elsevier BV
Date: 11-2018
Publisher: Cold Spring Harbor Laboratory
Date: 10-09-2018
DOI: 10.1101/413047
Abstract: Decoding the clonal substructures of somatic tissues sheds light on cell growth, development and differentiation in health, ageing and disease. DNA-sequencing, either using bulk or using single-cell assays, has enabled the reconstruction of clonal trees from frequency and co-occurrence patterns of somatic variants. However, approaches to systematically characterize phenotypic and functional variations between in idual clones are not established. Here we present cardelino ( github.com/PMBio/cardelino ), a computational method for inferring the clone of origin of in idual cells that have been assayed using single-cell RNA-seq (scRNA-seq). After validating our model using simulations, we apply cardelino to matched scRNA-seq and exome sequencing data from 32 human dermal fibroblast lines, identifying hundreds of differentially expressed genes between cells from different somatic clones. These genes are frequently enriched for cell cycle and proliferation pathways, indicating a key role for cell ision genes in non-neutral somatic evolution. A novel approach for integrating DNA-seq and single-cell RNA-seq data to reconstruct clonal substructure for single-cell transcriptomes. Evidence for non-neutral evolution of clonal populations in human fibroblasts. Proliferation and cell cycle pathways are commonly distorted in mutated clonal populations.
Publisher: Proceedings of the National Academy of Sciences
Date: 14-04-2015
Abstract: The body is patterned in the anterior–posterior axis by the correct spatial and temporal expression of Hox genes during embryonic development. One mechanism critical for the precise spatiotemporal expression of Hox genes is the chromatin state. While changes in chromatin conformation during the activation of Hox genes have been well described, the importance of the factors that in turn regulate chromatin remains enigmatic and controversial. In the current study, we investigate the role of two critical chromatin regulators, MOZ and BMI1, during Hox gene activation and in specifying body segment identity. We establish the importance of MOZ and BMI1 during the initial activation of Hox genes in ES cells and in correctly specifying body segment identity during embryonic development.
Publisher: Cold Spring Harbor Laboratory
Date: 22-05-2018
DOI: 10.1101/328138
Abstract: Alternative splicing is a key regulatory mechanism in eukaryotic cells and increases the effective number of functionally distinct gene products. Using bulk RNA sequencing, splicing variation has been studied across human tissues and in genetically erse populations. This has identified disease-relevant splicing events, as well as associations between splicing and genomic variations, including sequence composition and conservation. However, variability in splicing between single cells from the same tissue or cell type and its determinants remain poorly understood. We applied parallel DNA methylation and transcriptome sequencing to differentiating human induced pluripotent stem cells to characterize splicing variation (exon skipping) and its determinants. Our results shows that variation in single-cell splicing can be accurately predicted based on local sequence composition and genomic features. We observe moderate but consistent contributions from local DNA methylation profiles to splicing variation across cells. A combined model that is built based on sequence as well as DNA methylation information accurately predicts different splicing modes of in idual cassette exons (AUC=0.85). These categories include the conventional inclusion and exclusion patterns, but also more subtle modes of cell-to-cell variation in splicing. Finally, we identified and characterized associations between DNA methylation and splicing changes during cell differentiation. Our study yields new insights into alternative splicing at the single-cell level and reveals a previously underappreciated link between DNA methylation variation and splicing.
Publisher: BMJ
Date: 18-03-2015
DOI: 10.1136/BMJ.H1437
Publisher: Springer Science and Business Media LLC
Date: 12-2021
DOI: 10.1186/S13059-021-02546-1
Abstract: Population-scale single-cell RNA sequencing (scRNA-seq) is now viable, enabling finer resolution functional genomics studies and leading to a rush to adapt bulk methods and develop new single-cell-specific methods to perform these studies. Simulations are useful for developing, testing, and benchmarking methods but current scRNA-seq simulation frameworks do not simulate population-scale data with genetic effects. Here, we present splatPop, a model for flexible, reproducible, and well-documented simulation of population-scale scRNA-seq data with known expression quantitative trait loci. splatPop can also simulate complex batch, cell group, and conditional effects between in iduals from different cohorts as well as genetically-driven co-expression.
Publisher: Elsevier BV
Date: 09-2019
Publisher: BMJ
Date: 11-2020
Abstract: We report an unusual complication of COVID-19 infection in a 53-year-old Caucasian man. He presented with shortness of breath, fever and pleuritic chest pain. A CT pulmonary angiogram (CTPA) demonstrated acute bilateral pulmonary embolism and bilateral multifocal parenchymal ground glass change consistent with COVID-19 (SARS-CoV-2) infection. Right adrenal haemorrhage was suspected on the CTPA which was confirmed on triple-phase abdominal CT imaging. A short Synacthen test revealed normal adrenal function. He was treated initially with an intravenous heparin infusion, which was changed to apixaban with a planned outpatient review in 3 months’ time. He made an uncomplicated recovery and was discharged. Follow-up imaging nearly 5 months later showed near complete resolution of the right adrenal haemorrhage with no CT evidence of an underlying adrenal lesion.
Publisher: Elsevier BV
Date: 03-2021
DOI: 10.1016/J.PEDIATRNEUROL.2020.11.004
Abstract: Cerebral cavernous malformations are the second most common vascular malformations in the central nervous system, and over one-third are found in children. Lesions may be solitary or multiple, be discovered incidentally, be sporadic, or be secondary to familial cavernomatosis or radiation therapy. Children may present with focal seizures, intracranial hemorrhage, or focal neurological deficits without radiological evidence of recent hemorrhage. We present several children with cerebral cavernous malformations and explore the challenges of their diagnosis in children, their key imaging features, the role of follow-up imaging, and their subsequent management including stereotactic radiosurgery and microsurgical resection. In idual patient risk stratification is advocated for all affected children and their families.
Publisher: Springer Science and Business Media LLC
Date: 29-01-2022
Publisher: Public Library of Science (PLoS)
Date: 29-09-2022
DOI: 10.1371/JOURNAL.PONE.0275168
Abstract: We developed a simple and reliable method for the isolation of haploid nuclei from fresh and frozen testes. The described protocol uses readily available reagents in combination with flow cytometry to separate haploid and diploid nuclei. The protocol can be completed within 1 hour and the resulting in idual haploid nuclei have intact morphology. The isolated nuclei are suitable for library preparation for high-throughput DNA and RNA sequencing using bulk or single nuclei. The protocol was optimised with mouse testes and we anticipate that it can be applied for the isolation of mature sperm from other mammals including humans.
Publisher: Radiological Society of North America (RSNA)
Date: 03-2023
DOI: 10.1148/RYAI.220072
Publisher: Elsevier BV
Date: 09-2015
Publisher: Cold Spring Harbor Laboratory
Date: 10-02-2022
DOI: 10.1101/2022.02.10.479822
Abstract: Profiling gametes of an in idual enables the construction of personalised haplotypes and meiotic crossover landscapes, now achievable at larger scale than ever through the availability of high-throughput single-cell sequencing technologies. However, high-throughput single-gamete data commonly have low depth of coverage per gamete, which challenges existing gametebased haplotype phasing methods. In addition, haplotyping a large number of single gametes from high-throughput singlecell DNA sequencing data and constructing meiotic crossover profiles using existing methods requires intensive processing. Here, we introduce efficient software tools for the essential tasks of generating personalised haplotypes and calling crossovers in gametes from single-gamete DNA sequencing data (sgcocaller), and constructing, visualising, and comparing in idualised crossover landscapes from single gametes (comapr). With additional data pre-possessing, the tools can also be applied to bulk-sequenced s les. We demonstrate that sgcocaller is able to generate impeccable phasing results for high-coverage datasets, on which it is more accurate and stable than existing methods, and also performs well on low-coverage single-gamete sequencing datasets for which current methods fail. Our tools achieve highly accurate results with user-friendly installation, comprehensive documentation, efficient computation times and minimal memory usage.
Publisher: Springer New York
Date: 22-09-2012
Publisher: Springer Science and Business Media LLC
Date: 07-02-2020
DOI: 10.1186/S13059-020-1926-6
Abstract: The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands—or even millions—of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.
Publisher: Cold Spring Harbor Laboratory
Date: 12-05-2022
DOI: 10.1101/2022.05.12.491598
Abstract: Macrophages coordinate the initial host inflammatory response to tissue infection, as well as mediating the reparative phase, by producing growth factors that promote tissue repair. One model of this functional dichotomy is that peripherally recruited monocyte-derived macrophages drive acute inflammatory responses to infection, whereas tissue-resident macrophages are responsible for tissue repair. Alternatively, inflammation and repair may be inter-dependent molecular programs, such that both recruited and resident cells have equivalent capacity to contribute. Repeated exposure to pathogenic challenge results in innate tolerance, which may also alter the contributions of discrete macrophage populations to inflammation or repair. In this study a village model of tissue resident and recruited macrophages was created using induced pluripotent stem cell-derived macrophages and peripheral blood monocyte-derived macrophages, respectively. Population responses to repeated exposure to lipopolysaccharide were assessed with single-cell RNA sequencing and donors demultiplexed with Vireo. A subset of genes escaped classical tolerance programs in the iPSC, but not monocyte-derived macrophages, and this was associated with differences in their proliferative capacity. This suggests that targeting the proliferative resident macrophages would be most effective to limit inflammatory signaling.
Publisher: Springer Science and Business Media LLC
Date: 11-02-2019
Publisher: Cold Spring Harbor Laboratory
Date: 08-03-2022
DOI: 10.1101/2022.03.07.483367
Abstract: Recent innovations in droplet-based single-cell RNA-sequencing (scRNA-seq) have provided the technology necessary to investigate biological questions at cellular resolution. With the ability to assay thousands of cells in a single capture, pooling cells from multiple in iduals has become a common strategy. Droplets can subsequently be assigned to a specific in idual by leveraging their inherent genetic differences, and numerous computational methods have been developed to address this problem. However, another challenge implicit with droplet-based scRNA-seq is the occurrence of doublets - droplets containing two or more cells. The inaccurate assignment of cells to in iduals or failure to remove doublets contribute unwanted noise to the data and result in erroneous scientific conclusions. Therefore, it is essential to assign cells to in iduals and remove doublets accurately. We present a new framework to improve in idual singlet classification and doublet removal through a multi-method intersectional approach. We developed a framework to evaluate the enhancement in donor assignment and doublet removal through the consensus intersection of multiple demultiplexing and doublet detecting methods. The accuracy was assessed using scRNA-seq data of ∼1.4 million peripheral blood mononucleated cells from 1,034 unrelated in iduals and ∼90,000 fibroblast cells from 81 unrelated in iduals. We show that our approach significantly improves droplet assignment by separating singlets from doublets and classifying the correct in idual compared to any single method. We show that the best combination of techniques varies under different biological and experimental conditions, and we present a framework to optimise cell assignment for a given experiment. We offer Demuxafy ( demultiplexing-doublet-detecting-docs.readthedocs.io/en/latest/index.html ) - a framework built-in Singularity to provide clear, consistent documentation of each method and additional tools to simplify and improve demultiplexing and doublet removal. Our results indicate that leveraging multiple demultiplexing and doublet detecting methods improves accuracy and, consequently, downstream analyses in multiplexed scRNA-seq experiments.
Publisher: BMJ
Date: 17-02-2023
DOI: 10.1136/ARCHDISCHILD-2020-321378
Abstract: Palpable cervical lymph nodes are common in children and are a frequent reason for presentation to both primary and secondary care. Enlarged lymph nodes are most commonly the result of self-limiting infection, and in children, are rarely the first indicator of a malignant process. This article presents an evidenced-based approach to evaluating these patients.
Publisher: Springer Science and Business Media LLC
Date: 03-12-2019
DOI: 10.1007/S00330-019-06579-W
Abstract: To assess whether head CT with 3D reconstruction can replace skull radiographs (SXR) in the imaging investigation of suspected physical abuse (SPA)/abusive head trauma (AHT). PACS was interrogated for antemortem skeletal surveys performed for SPA, patients younger than 2 years, SXR and CT performed within 4 days of each other. Paired SXR and CT were independently reviewed. One reviewer analysed CT without and (3 months later) with 3D reconstructions. SXR and CT expert consensus review formed the gold standard. Observer reliability was calculated. A total of 104 SXR/CT examination pairs were identified, mean age 6.75 months (range 4 days to 2 years) 21 (20%) had skull fractures two fractures on CT were missed on SXR. There were no fractures on SXR that were not seen on CT. For SXR and CT, respectively: PPV reviewer 1, 95% confidence interval (CI) 48–82% and 85–100% reviewer 2, 67–98% and 82–100% and NPV reviewer 1, 95%, CI 88–98% and 96–100% reviewer 2, 88–97% and 88–98%. Inter- and intra-observer reliability were respectively the following: SXR, excellent (kappa = 0.831) and good (kappa = 0.694) CT, excellent (kappa = 0.831) and perfect (kappa = 1). All results were statistically significant ( p 0.001). CT has greater diagnostic accuracy than SXR in detecting skull fractures which is increased on concurrent review of 3D reconstructions and should be performed in every case of SPA/AHT. SXR does not add further diagnostic information and can be omitted from the skeletal survey when CT with 3D reconstruction is going to be, or has been, performed. • Head CT with 3D reconstruction is more sensitive and specific for the diagnosis of skull fractures. • Skull radiographs can be safely omitted from the initial skeletal survey performed for suspected physical abuse when head CT with 3D reconstruction is going to be, or has been, performed .
Publisher: Elsevier BV
Date: 11-2020
Publisher: Informa UK Limited
Date: 30-01-2018
DOI: 10.1080/10401334.2017.1414609
Abstract: Construct: We investigated the quality of emergency medicine (EM) blogs as educational resources. Online medical education resources such as blogs are increasingly used by EM trainees and clinicians. However, quality evaluations of these resources using gestalt are unreliable. We investigated the reliability of two previously derived quality evaluation instruments for blogs. Sixty English-language EM websites that published clinically oriented blog posts between January 1 and February 24, 2016, were identified. A random number generator selected 10 websites, and the 2 most recent clinically oriented blog posts from each site were evaluated using gestalt, the Academic Life in Emergency Medicine (ALiEM) Approved Instructional Resources (AIR) score, and the Medical Education Translational Resources: Impact and Quality (METRIQ-8) score, by a s le of medical students, EM residents, and EM attendings. Each rater evaluated all 20 blog posts with gestalt and 15 of the 20 blog posts with the ALiEM AIR and METRIQ-8 scores. Pearson's correlations were calculated between the average scores for each metric. Single-measure intraclass correlation coefficients (ICCs) evaluated the reliability of each instrument. Our study included 121 medical students, 88 EM residents, and 100 EM attendings who completed ratings. The average gestalt rating of each blog post correlated strongly with the average scores for ALiEM AIR (r = .94) and METRIQ-8 (r = .91). Single-measure ICCs were fair for gestalt (0.37, IQR 0.25-0.56), ALiEM AIR (0.41, IQR 0.29-0.60) and METRIQ-8 (0.40, IQR 0.28-0.59). The average scores of each blog post correlated strongly with gestalt ratings. However, neither ALiEM AIR nor METRIQ-8 showed higher reliability than gestalt. Improved reliability may be possible through rater training and instrument refinement.
Publisher: Elsevier BV
Date: 03-2017
DOI: 10.1016/J.CRAD.2016.11.016
Abstract: Recognising the skeletal manifestations of inflicted injury (II) in infants and young children is of crucial importance. There are specific fracture patterns which are highly suspicious of II in addition to common differential diagnoses with which radiologists should be familiar. Our objective is to provide a non-exhaustive review of the important factors relevant to the imaging and reporting of II as a platform for further learning. Part 1 encompasses important initial considerations and fracture patterns of the appendicular skeleton.
Publisher: Springer Science and Business Media LLC
Date: 16-03-2021
DOI: 10.1007/S00330-021-07775-3
Abstract: To assess the diagnostic performance of chest CT in the detection of rib fractures in children investigated for suspected physical abuse (SPA). Medline, Web of Science and Cochrane databases were searched from January 1980 to April 2020. The QUADAS-2 tool was used to assess the quality of the eligible English-only studies following which a formal narrative synthesis was constructed. Studies reporting true-positive, false-positive, true-negative, and false-negative results were included in the meta-analysis. Overall sensitivity and specificity of chest CT for rib fracture detection were calculated, irrespective of fracture location, and were pooled using a univariate random-effects meta-analysis. The diagnostic accuracy of specific locations along the rib arc (anterior, lateral or posterior) was assessed separately. Of 242 identified studies, 4 met the inclusion criteria. Of these, 2 were included in the meta-analysis. Chest CT identified 142 rib fractures compared to 79 detected by initial skeletal survey chest radiographs in live children with SPA. Post-mortem CT (PMCT) has low sensitivity (34%) but high specificity (99%) in the detection of rib fractures when compared to the autopsy reference standard. PMCT has low sensitivity (45%, 21% and 42%) but high specificity (99%, 97% and 99%) at anterior, lateral and posterior rib locations, respectively. Chest CT detects more rib fractures than initial skeletal survey chest radiographs in live children with SPA. PMCT has low sensitivity but high specificity for detecting rib fractures in children investigated for SPA. • PMCT has low sensitivity (34%) but high specificity (99%) in the detection of rib fractures extrapolation to CT in live children is difficult. • No studies have compared chest CT with the current accepted practice of initial and follow-up skeletal survey chest radiographs in the detection of rib fractures in live children investigated for SPA.
Publisher: Elsevier BV
Date: 03-2017
DOI: 10.1016/J.CRAD.2016.11.015
Abstract: Recognising the skeletal manifestations of inflicted injury (II) in infants and young children is of crucial importance. There are specific fracture patterns which are highly suspicious of II in addition to common differential diagnoses with which radiologists should be familiar. Our objective is to provide a non-exhaustive review of the important factors relevant to the imaging and reporting of II as a platform for further learning. Part 2 encompasses fracture patterns of the axial skeleton and important differential diagnoses.
Publisher: PeerJ
Date: 23-08-2019
DOI: 10.7287/PEERJ.PREPRINTS.27885V3
Abstract: The recent upswing of microfluidics and combinatorial indexing strategies, further enhanced by very low sequencing costs, have turned single cell sequencing into an empowering technology analyzing thousands—or even millions—of cells per experimental run is becoming a routine assignment in laboratories worldwide. As a consequence, we are witnessing a data revolution in single cell biology. Although some issues are similar in spirit to those experienced in bulk sequencing, many of the emerging data science problems are unique to single cell analysis together, they give rise to the new realm of 'Single-Cell Data Science'. Here, we outline twelve challenges that will be central in bringing this new field forward. For each challenge, the current state of the art in terms of prior work is reviewed, and open problems are formulated, with an emphasis on the research goals that motivate them. This compendium is meant to serve as a guideline for established researchers, newcomers and students alike, highlighting interesting and rewarding problems in 'Single-Cell Data Science' for the coming years.
Publisher: PeerJ
Date: 07-08-2019
DOI: 10.7287/PEERJ.PREPRINTS.27885V2
Abstract: The recent upswing of microfluidics and combinatorial indexing strategies, further enhanced by very low sequencing costs, have turned single cell sequencing into an empowering technology analyzing thousands—or even millions—of cells per experimental run is becoming a routine assignment in laboratories worldwide. As a consequence, we are witnessing a data revolution in single cell biology. Although some issues are similar in spirit to those experienced in bulk sequencing, many of the emerging data science problems are unique to single cell analysis together, they give rise to the new realm of 'Single Cell Data Science'. Here, we outline twelve challenges that will be central in bringing this new field forward. For each challenge, the current state of the art in terms of prior work is reviewed, and open problems are formulated, with an emphasis on the research goals that motivate them. This compendium is meant to serve as a guideline for established researchers, newcomers and students alike, highlighting interesting and rewarding problems in 'Single Cell Data Science' for the coming years.
Publisher: BMJ
Date: 26-10-2020
Publisher: Springer Science and Business Media LLC
Date: 06-04-2020
Publisher: Cold Spring Harbor Laboratory
Date: 21-03-2023
DOI: 10.1101/2023.03.17.533161
Abstract: Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis (PF). Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA-sequencing of lung tissue from 67 PF and 49 unaffected donors. Employing a pseudo-bulk approach, we mapped expression quantitative trait loci (eQTL) across 38 cell types, observing both shared and cell type-specific regulatory effects. Further, we identified disease-interaction eQTL and demonstrated that this class of associations is more likely to be cell-type specific and linked to cellular dysregulation in PF. Finally, we connected PF risk variants to their regulatory targets in disease-relevant cell types. These results indicate that cellular context determines the impact of genetic variation on gene expression, and implicates context-specific eQTL as key regulators of lung homeostasis and disease.
Publisher: Elsevier BV
Date: 05-2017
DOI: 10.1016/J.CRAD.2016.12.004
Abstract: To assess fetal brain growth over the third trimester in pregnant women with diabetes using in utero magnetic resonance imaging (iuMRI) to determine if greater brain growth occurs in type 1 (T1DM) when compared to gestational (GDM) diabetes mellitus. Each consented participant was scanned at three fixed times during the third trimester using iuMRI. One hundred and fifty-seven patients were approached, 48 participants were recruited, and 36 complete data sets were analysed. Three-dimensional (3D) iuMRI volume data sets were manually segmented using software to construct models of the fetal brain from which brain volumes could be calculated. Inter-rater analysis was performed, and volume differences and growth rates were compared between T1DM and GDM. Recruitment proved difficult with low uptake and high attrition rates (77.1%). Inter-rater analysis revealed excellent correlation (intraclass correlation coefficient=0.93, p<0.001) and agreement with no significant difference between operators (p=0.194). There was no evidence of increased brain volume in the T1DM group. Growth rates between visit 1 and 3 for T1DM and GDM were not significantly different (p=0.095). T1DM brain volumes were not significantly larger than GDM volumes and there was no significant ergence of brain growth over the third trimester. Constructing volume models from 3D iuMRI acquisitions is a novel technique that can be used to assess fetal brain growth. No specialist software or knowledge is required. Larger studies attempting to recruit pregnant women in the later stages of pregnancy should employ multicentre recruitment to overcome recruitment difficulties and high attrition rates.
Publisher: Springer Science and Business Media LLC
Date: 23-03-2020
DOI: 10.1038/S41467-020-15098-Y
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher: Springer Science and Business Media LLC
Date: 07-12-2020
DOI: 10.1038/S41596-020-00409-W
Abstract: Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows you to profile the whole transcriptome of a large number of in idual cells. However, the analysis of the large volumes of data generated from these experiments requires specialized statistical and computational methods. Here we present an overview of the computational workflow involved in processing scRNA-seq data. We discuss some of the most common tasks and the tools available for addressing central biological questions. In this article and our companion website ( scrnaseq-course.cog.sanger.ac.uk/website/index.html ), we provide guidelines regarding best practices for performing computational analyses. This tutorial provides a hands-on guide for experimentalists interested in analyzing their data as well as an overview for bioinformaticians seeking to develop new computational methods.
Publisher: Springer Science and Business Media LLC
Date: 19-04-2021
DOI: 10.1186/S13059-021-02327-W
Abstract: Genetic maps have been fundamental to building our understanding of disease genetics and evolutionary processes. The gametes of an in idual contain all of the information required to perform a de novo chromosome-scale assembly of an in idual’s genome, which historically has been performed with populations and pedigrees. Here, we discuss how single-cell gamete sequencing offers the potential to merge the advantages of short-read sequencing with the ability to build personalized genetic maps and open up an entirely new space in personalized genetics.
Publisher: Springer Science and Business Media LLC
Date: 22-08-2013
Abstract: RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially expressed genes across different conditions (e.g., tissues, perturbations) while optionally adjusting for other systematic factors that affect the data-collection process. There are a number of subtle yet crucial aspects of these analyses, such as read counting, appropriate treatment of biological variability, quality control checks and appropriate setup of statistical modeling. Several variations have been presented in the literature, and there is a need for guidance on current best practices. This protocol presents a state-of-the-art computational and statistical RNA-seq differential expression analysis workflow largely based on the free open-source R language and Bioconductor software and, in particular, on two widely used tools, DESeq and edgeR. Hands-on time for typical small experiments (e.g., 4-10 s les) can be <1 h, with computation time <1 d using a standard desktop PC.
Publisher: Annual Reviews
Date: 20-07-2018
DOI: 10.1146/ANNUREV-BIODATASCI-080917-013424
Abstract: The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices. This includes learning how to effectively integrate automated analysis with high–data density visualizations that clearly express complex phenomena. In this review, we summarize key principles and resources from data visualization research that help address this difficult challenge. We then survey how visualization is being used in a selection of emerging biomedical research areas, including three-dimensional genomics, single-cell RNA sequencing (RNA-seq), the protein structure universe, phosphoproteomics, augmented reality–assisted surgery, and metagenomics. While specific research areas need highly tailored visualizations, there are common challenges that can be addressed with general methods and strategies. Also common, however, are poor visualization practices. We outline ongoing initiatives aimed at improving visualization practices in biomedical research via better tools, peer-to-peer learning, and interdisciplinary collaboration with computer scientists, science communicators, and graphic designers. These changes are revolutionizing how we see and think about our data.
Publisher: Springer Science and Business Media LLC
Date: 29-04-2014
DOI: 10.1038/NCOMMS4756
Abstract: Bladder cancers are a leading cause of death from malignancy. Molecular markers might predict disease progression and behaviour more accurately than the available prognostic factors. Here we use whole-genome sequencing to identify somatic mutations and chromosomal changes in 14 bladder cancers of different grades and stages. As well as detecting the known bladder cancer driver mutations, we report the identification of recurrent protein-inactivating mutations in CDKN1A and FAT1. The former are not mutually exclusive with TP53 mutations or MDM2 lification, showing that CDKN1A dysfunction is not simply an alternative mechanism for p53 pathway inactivation. We find strong positive associations between higher tumour stage/grade and greater clonal ersity, the number of somatic mutations and the burden of copy number changes. In principle, the identification of sub-clones with greater ersity and/or mutation burden within early-stage or low-grade tumours could identify lesions with a high risk of invasive progression.
Publisher: Springer Science and Business Media LLC
Date: 15-12-2022
DOI: 10.1007/S00247-022-05561-X
Abstract: The knowledge, awareness and professionalism of health care providers in the field of child protection are crucial in identifying and reporting suspected child abuse. Radiologic technologists and radiologists play a vital role in the diagnosis of suspected physical child abuse. To assess current practice, knowledge and awareness of child abuse among radiologic technologists and radiologists in Saudi Arabia. We distributed an internet-based questionnaire to radiologic technologists and radiologists working in Saudi Arabia via national radiology societies and social media channels over a 6-week period (27 October to 8 December 2021). Survey questions covered knowledge regarding child abuse, professional practice in radiology departments in Saudi Arabia in cases of suspected physical abuse (SPA), and knowledge of the national legislation and reporting and acting procedures in child abuse. A total of 315 respondents (224 radiologic technologists and 91 radiologists) participated in this study. The median score for knowledge of abuse was higher amongst radiologists (4.8) than radiologic technologists (4.0) P 0.001. In total, 210 (93.8%) radiologic technologists and 61 (67.0%) radiologists reported that there was no protocol (i.e. skeletal survey) at their hospital for imaging children with SPA. Most radiologic technologists had no training in paediatric radiology (165/224, 73.7%) and most radiologists had received no training in evaluating imaging performed for SPA (73/91, 80.2%). More than half of respondents — 131 (58.5%) radiologic technologists and 44 (48.4%) radiologists — were not familiar with the reporting and acting procedures at their hospitals in cases of child abuse. Although radiologic technologists and radiologists in Saudi Arabia have good knowledge and awareness of child abuse in general, they lack specific knowledge of the reporting and acting procedures at their hospitals in cases of suspected child abuse. National imaging guidelines and training courses are needed to develop appropriate skills in the recognition, imaging and reporting of SPA in infants and young children in Saudi Arabia.
Publisher: Elsevier BV
Date: 07-2018
Publisher: Springer Science and Business Media LLC
Date: 07-03-2023
DOI: 10.1007/S00247-023-05618-5
Abstract: This second roundtable discussion was convened at the 56th European Society of Paediatric Radiology (ESPR) 2022 Annual Meeting in Marseille, France, to discuss controversial aspects of imaging in child abuse. The following topics were discussed: Fracture dating—the published literature is broadly similar with respect to the identification of the radiographic stages of bony healing. The non-expert/general radiologist is encouraged to use broad descriptors of fracture healing (acute, healing or old) within their reports, rather than attempting to date fractures. The more experienced/expert radiologist, who may provide a timeframe/range to assist the courts, should be aware that any published timeframes are not absolute and that recent research indicates that the rate of healing may differ according to the bone affected and the age of the patient. Whole spine imaging in suspected abusive head trauma—this is recommended to enable a complete assessment of the neuraxis when abusive head trauma is suspected or diagnosed, particularly in the presence of intracranial and cervical subdural haemorrhage and cervical ligamentous injury. Cranial imaging in suspected physical abuse—both computed tomography (CT) and magnetic resonance imaging (MRI) remain complimentary depending on the clinical context in which they are used with CT remaining first-line in the assessment of children with (suspected abusive) head trauma prior to an early MRI. MRI is superior in its assessment of parenchymal injury and may be employed as first-line in age appropriate asymptomatic siblings of a child with suspected physical abuse.
Publisher: Springer Science and Business Media LLC
Date: 16-03-2020
Publisher: F1000 Research Ltd
Date: 31-10-2016
DOI: 10.12688/F1000RESEARCH.9501.2
Abstract: Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of in idual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise. This article describes a computational workflow for low-level analyses of scRNA-seq data, based primarily on software packages from the open-source Bioconductor project. It covers basic steps including quality control, data exploration and normalization, as well as more complex procedures such as cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. Analyses were demonstrated on gene-level count data from several publicly available datasets involving haematopoietic stem cells, brain-derived cells, T-helper cells and mouse embryonic stem cells. This will provide a range of usage scenarios from which readers can construct their own analysis pipelines.
Publisher: Cold Spring Harbor Laboratory
Date: 21-01-2021
DOI: 10.1101/2021.01.20.427401
Abstract: Single-cell RNA-sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states. With the cost of scRNA-seq decreasing and techniques for s le multiplexing improving, population-scale scRNA-seq, and thus single-cell expression quantitative trait locus (sc-eQTL) mapping, is increasingly feasible. Mapping of sc-eQTL provides additional resolution to study the regulatory role of common genetic variants on gene expression across a plethora of cell types and states, and promises to improve our understanding of genetic regulation across tissues in both health and disease. While previously established methods for bulk eQTL mapping can, in principle, be applied to sc-eQTL mapping, there are a number of open questions about how best to process scRNA-seq data and adapt bulk methods to optimise sc-eQTL mapping. Here, we evaluate the role of different normalisation and aggregation strategies, covariate adjustment techniques, and multiple testing correction methods to establish best practice guidelines. We use both real and simulated datasets across single-cell technologies to systematically assess the impact of these different statistical approaches and provide recommendations for future single-cell eQTL studies that can yield up to twice as many eQTL discoveries as default approaches ported from bulk studies.
Publisher: BMJ
Date: 04-07-2017
Publisher: BMJ
Date: 24-07-2020
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 05-2006
Publisher: Springer Science and Business Media LLC
Date: 27-01-2013
DOI: 10.1038/NG.2531
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: Australia
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Start Date: 2019
End Date: 2025
Funder: National Health and Medical Research Council
View Funded ActivityStart Date: 2021
End Date: 2022
Funder: Ramaciotti Foundations
View Funded ActivityStart Date: 2021
End Date: 2025
Funder: National Health and Medical Research Council
View Funded ActivityStart Date: 2020
End Date: 2022
Funder: National Health and Medical Research Council
View Funded ActivityStart Date: 2016
End Date: 2020
Funder: National Health and Medical Research Council
View Funded Activity