Caroline Wright
Cambridge
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Articles by Caroline Wright
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The picornavirus foot-and-mouth disease virus (FMDV) is responsible for one of the most significant diseases of livestock, leading to large economic losses due to reduced productivity and trade embargoes for areas not certified as disease-free. The picornavirus non-structural protein 3A is involved in replication of the viral RNA genome and is implicated in host tropism of several picornaviruses.
A high-quality telomere-to-telomere lumpy skin disease virus genome assembly
Article metrics loading... /content/journal/jgv/10.1099/jgv.0.002348 Metrics Download as PowerPoint /deliver/fulltext/jgv/107/10/jgv002348.html?itemId=/content/journal/jgv/10.1099/jgv.0.002348&mimeType=html&fmt=ahah References Sereika M, Kirkegaard RH, Karst SM, Michaelsen TY, Sørensen EA et al. Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing.
Prevalence and penetrance of heritable retinoblastoma in two adult population cohorts: implications for genomic newborn screening
Abstract Retinoblastoma (Rb) is a rare childhood eye cancer. Almost half of cases are heritable, associated with germline RB1 pathogenic variants that pre-dispose to Rb and extraocular cancers. This study aimed to investigate the prevalence and penetrance of RB1-heritable Rb in two adult population cohorts.
Reducing the diagnostic odyssey in rare disease: why screening is not the only answer
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The timely detection of rare diseases is crucial, and using a range of approaches will be key to reducing the diagnostic odyssey.
By Caroline Wright, Amicia Phillips, Sarah Wynn Verified, Nick Meade, Emma L. Baple, Anneke Lucassen, Leigh Jackson
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Nature
Verified
Who and how we engage: A systemic mapping of stakeholder perspectives on genomic newborn screening
Abstract The use of genomic sequencing in newborn screening is increasingly being piloted through research programmes worldwide. In parallel, an expanding body of attitudinal studies has examined stakeholder views as jurisdictions consider whether and how to implement genomic newborn screening (gNBS).
Characterisation of the SMN1/2 locus using a highly specific variant caller on whole-genome sequence data from 500,000 individuals
Abstract Spinal muscular atrophy (SMA) is a rare autosomal recessive condition caused by biallelic loss of the SMN1 gene that results in severe lower motor neuron degeneration in childhood. Targeted pre-symptomatic treatments have been shown to dramatically improve outcomes, supporting the inclusion of SMA in newborn screening programmes.
Reduced penetrance of COL1A1/2 pathogenic variants linked with osteogenesis imperfecta: analysis of a large population cohort
Abstract Osteogenesis imperfecta (OI) is under consideration for inclusion in several genomic newborn screening initiatives, but its penetrance in clinically-unselected populations is currently unknown. It is an exemplar condition for evaluating penetrance in adult cohorts due to its relatively low mortality, variable expressivity and link to several large genes.
Revisiting penetrance in an era of genomic screening
Penetrance is widely understood to be “the conditional probability R(xg) that an individual with a given genotype g expresses the phenotype x” as defined in Ott’s 1985 textbook Analysis of Human Genetic Linkage. As described in the 2024 ACMG statement [1], this term had been overly simplified from its origins relating to specific alleles in an otherwise genetically homogenous background.
Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations - Nature Communications
Abstract GWAS have generally focused on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we use whole-genome sequencing data to evaluate the contribution to and architecture of rare non-coding variants for three commonly studied anthropometric traits: height, BMI and waist-hip ratio adjusted for BMI.
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Rinderpest, a once much feared livestock disease, was declared eradicated in 2011, however virus-containing material is still held in laboratories worldwide. Prior to the destruction of our institute’s stocks, we determined the full genome sequence of the distinct samples of rinderpest virus (RPV) in our repository. This data would decipher the historical epidemiology of RPV and allow for recovery of the virus should the need arise.
The LMSz method - an automatable scalable approach to constructing gene-specific growth charts in rare disorders - European Journal of Human Genetics
Abstract Children with monogenic neurodevelopmental disorders often grow abnormally. Gene-specific growth charts would be useful but require large samples to construct them using the conventional LMS method. We transformed anthropometry to British 1990 reference z-scores for 328 UK and 264 international individuals with ANKRD11, ARID1B, ASXL3, DDX3X, KMT2A, or SATB2-related disorders, and modelled mean and standard deviation (SD) of the z-scores as gene-specific linear age trends adjusted for sex.
Whole-genome sequencing analysis identifies rare, large-effect noncoding variants and regulatory regions associated with circulating protein levels - Nature Genetics
Abstract The contribution of rare noncoding genetic variation to common phenotypes is largely unknown, as a result of a historical lack of population-scale whole-genome sequencing data and the difficulty of categorizing noncoding variants into functionally similar groups.
Phenotypic spectrum of dual diagnoses in developmental disorders
Introduction As exome and genome sequencing become widespread diagnostic tools, more and more patients and families with rare conditions are receiving genetic diagnoses.
Federated analysis of autosomal recessive coding variants in 29,745 developmental disorder patients from diverse populations - Nature Genetics
Abstract Autosomal recessive coding variants are well-known causes of rare disorders. We quantified the contribution of these variants to developmental disorders in a large, ancestrally diverse cohort comprising 29,745 trios, of whom 20.4% had genetically inferred non-European ancestries.
Genetic links between ovarian ageing, cancer risk and de novo mutation rates - Nature
Abstract Human genetic studies of common variants have provided substantial insight into the biological mechanisms that govern ovarian ageing1. Here we report analyses of rare protein-coding variants in 106,973 women from the UK Biobank study, implicating genes with effects around five times larger than previously found for common variants (ETAA1, ZNF518A, PNPLA8, PALB2 and SAMHD1).
Guidance for estimating penetrance of monogenic disease-causing variants in population cohorts - Nature Genetics
Abstract Penetrance is the probability that an individual with a pathogenic genetic variant develops a specific disease. Knowing the penetrance of variants for monogenic disorders is important for counseling of individuals. Until recently, estimates of penetrance have largely relied on affected individuals and their at-risk family members being clinically referred for genetic testing, a ‘phenotype-first’ approach.
De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome - Nature
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Abstract Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here we identify the non-coding RNA RNU4-2 as a syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2.
By Yuyang Chen, Ruebena Dawes, Hyung Chul Kim, Sarah Stenton, Susan Walker, Jenny Lord, Alexandra Martin-Geary, Erwan Delage, Elston N. D’Souza, Seth Berger, Jonathan Bernstein, David J. Coman, Alison G. Compton, Kerith-Rae Dias, Frances Elmslie, Jamie Fraser, Lyndon Gallacher, Anne Goriely, Christina L. Grant, Tobias B. Haack, Anjali G. Hinch, Matthew E Hurles, Elsa Leitão, Anna Le Fevre, Sarah J Lindsay, Paul J. Lockhart, Taylor Maurer, Hector Mendez, Stephen Montgomery, Serena M. Neumann, Melanie O’Leary, Nikhil Pattani, Nicole Revencu, Rocio Rius, Jill A. Rosenfeld, Cas Simons, Penny Snell, David Thorburn, Eloise Uebergang, Pradeep Vasudevan, Matthew Wheeler, Zoe Wolfenson, Caroline Wright, Sebastian M. Fica, Christel Depienne, Joanna M. M. Howson, Stephan Sanders, Anne H. O’Donnell-Luria
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Nature
Verified
Clustering of predicted loss-of-function variants in genes linked with monogenic disease can explain incomplete penetrance - Genome Medicine
Variants from exome sequencing (ES) data within the UK Biobank were called centrally by the UKB team using graphTyper [19]. We used the Ensembl VEP v104 [20] with the LOFTEE plugin [15] to annotate the variants with their predicted functional consequences. We excluded variants which were flagged for removal by UKB due to low depth based on 90% of calls having depth < 10.
Re: Challenges of using whole genome sequencing in population newborn screening
Dear Editor We thank the Generation Study team [1] for responding to our paper [2]. We questioned the proportionality of data collection – namely, sequencing and storing the entire genetic code, when only a tiny proportion (<0.01%) will be screened, and cheaper more targeted methods of data collection are available. Unfortunately, in their response, the Generation Study fails to address this issue.
Re: Challenges of using whole genome sequencing in population newborn screening
Dear Editor We thank Dr Izatt for engaging with our article. Our purpose in citing the example of the V804M variant in RET was to illustrate how understanding of the medical significance of variants continues to evolve, rather than to comment on whether the Genomics England Newborn Genomes Programme (Generation Study) intends to disclose this particular variant.
Primate-specific ZNF808 is essential for pancreatic development in humans - Nature Genetics
Abstract Identifying genes linked to extreme phenotypes in humans has the potential to highlight biological processes not shared with all other mammals. Here, we report the identification of homozygous loss-of-function variants in the primate-specific gene ZNF808 as a cause of pancreatic agenesis. ZNF808 is a member of the KRAB zinc finger protein family, a large and rapidly evolving group of epigenetic silencers which target transposable elements.
Penetrance of pathogenic genetic variants associated with premature ovarian insufficiency - Nature Medicine
Author notes These authors contributed equally: Saleh Shekari, Stasa Stankovic, John R. B. Perry, Anna Murray. Authors and Affiliations Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK Saleh Shekari, Gareth Hawkes, Robin N. Beaumont, Andrew R. Wood, Caroline F. Wright, Michael N. Weedon, Katherine S. Ruth & Anna Murray School of Public Health, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia Saleh Shekari & Gita D.
IMPROVE-DD: Integrating multiple phenotype resources optimizes variant evaluation in genetically determined developmental disorders
Main text The importance of phenotype to ranking candidate disease-causing genes is established in research and increasingly so in clinical practice. The primary data resource used in computational phenotype analyses is the Human Phenotype Ontology (HPO). 1 Köhler S. Gargano M. Matentzoglu N. Carmody L.C. Lewis-Smith D. Vasilevsky N.A. Danis D. Balagura G. Baynam G. Brower A.M. et al. The human phenotype ontology in 2021. Despite promising results, 2 Aitken S. Firth H.V. McRae J. Halachev M. Kini U.
Reduced penetrance of MODY-associated HNF1A/HNF4A variants but not GCK variants in clinically unselected cohorts
Introduction Maturity-onset diabetes of the young (MODY [MIM: 606391 ]) is the most common subtype of monogenic diabetes. It is an autosomal-dominant form of the monogenic disease and classically presents with diabetes before 25 years of age. 1 Maturity onset diabetes of the young: identification and diagnosis. , 2 Hattersley A.T. Patel K.A. Precision diabetes: learning from monogenic diabetes.
Gain-of-function mutations in KCNK3 cause a developmental disorder with sleep apnea - Nature Genetics
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Genetics Four probands were identified through the United Kingdom-based DDD study, which has been described previously58,59. Briefly, probands with severe, undiagnosed developmental disorders and their parents were recruited and phenotyped by referring clinical geneticists in 24 regional genetics services across the National Health Service in the United Kingdom and Ireland.
By Janina Sörmann, Marcus Schewe, Shanlin Rao, Paul Mark, Volker Straub, Thomas Muller Verified, Thomas Müller Verified, Matthew E Hurles, Caroline Wright, Thibault Jouen-Tachoire, Elena B. Riel, Amber Begtrup
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Nature
Verified
Optimising diagnostic yield in highly penetrant genomic disease
Abstract Background: Pediatric disorders include a range of highly genetically heterogeneous conditions that are amenable to genome-wide diagnostic approaches. Finding a molecular diagnosis is challenging but can have profound lifelong benefits. Methods: The Deciphering Developmental Disorders (DDD) study recruited >33,500 individuals from families with severe, likely monogenic developmental disorders from 24 regional genetics services around the UK and Ireland.
Effects of brief exposure to misinformation about e-cigarette harms on twitter: a randomised controlled experiment
Abstract Objectives To assess the effect of exposure to misinformation about e-cigarette harms found on Twitter on adult current smokers’ intention to quit smoking cigarettes, intention to purchase e-cigarettes and perceived relative harm of e-cigarettes compared with regular cigarettes. Setting An online randomised controlled experiment conducted in November 2019 among USA and UK current smokers.
Effects of brief exposure to misinformation about e-cigarette harms on twitter: a randomised controlled experiment
Wright C, Williams P, Elizarova O, et al Effects of brief exposure to misinformation about e-cigarette harms on twitter: a randomised controlled experiment BMJ Open 2021;11:e045445. doi: 10.1136/bmjopen-2020-045445
Unreliability of genotyping arrays for detecting very rare variants in human genetic studies: Example from a recent study of MC4R
Michael N. Weedon Michael N. Weedon Correspondence Corresponding author Affiliations Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK Search for articles by this author Caroline F. Wright Caroline F.
Tremendous Teamwork
Tremendous Teamwork By Caroline Wright Posted in: Remodel • Renovating While many older homes have undeniable charms, they weren’t always built to take advantage of the natural gifts of their surroundings. That was certainly the case with a home Graham Builders rebuilt for a Pauoa family this past year. Created in 1958, the original single-wall home lacked the views of the neighborhood’s peaceful forests and the gentle breezes that channel through the valley.
Assessing the Pathogenicity, Penetrance, and Expressivity of Putative Disease-Causing Variants in a Population Setting
More than 100,000 genetic variants are classified as disease causing in public databases. However, the true penetrance of many of these rare alleles is uncertain and might be over-estimated by clinical ascertainment. Here, we use data from 379,768 UK Biobank (UKB) participants of European ancestry to assess the pathogenicity and penetrance of putatively clinically important rare variants.
Wellcome Open Research Article: Genomic variant sharing: a position statement.
Open Letter Genomic variant sharing: a position statement [version 1; referees: awaiting peer review] Caroline F. Wright https://orcid.org/0000-0003-2958-5076 1, James S. Ware https://orcid.org/0000-0002-6110-5880 2, Anneke M. Lucassen3, [...] Alison Hall4, Anna Middleton https://orcid.org/0000-0003-3103-8098 5,6, Nazneen Rahman7, Sian Ellard https://orcid.org/0000-0002-7620-5526 1, Helen V. Firth8,9 Caroline F. Wright https://orcid.org/0000-0003-2958-5076 1, James S.
Assessing the pathogenicity, penetrance and expressivity of putative disease-causing variants in a population setting
Assessing the pathogenicity, penetrance and expressivity of putative disease-causing variants in a population setting Caroline F Wright, Ben West, Marcus Tuke, Samuel E Jones, Kashyap Patel, Thomas W Laver, Robin N Beaumont, Jessica Tyrrell, Andrew R Wood, Timothy M Frayling, Andrew T Hattersley, Michael N Weedon bioRxiv 407981; doi: https://doi.org/10.1101/407981
Phenotyping patients with chronic cough: Evaluating the ability to predict the response to anti-inflammatory therapy
To view the full text, please login as a subscribed user or purchase a subscription. Click here to view the full text on ScienceDirect. FiguresFigure?1Consort flow diagram. FeNO indicates fraction of exhaled nitric oxide.Figure?2Measurements of fraction of exhaled nitric oxide (FeNO), 24-hour cough count, Hull Airways Reflux Questionnaire (HARQ), and Leicester Cough Questionnaire (LCQ) in 3 treatment groups during 3 visits (visits 1, 3, and 5).
Paediatric genomics: diagnosing rare disease in children
In Figure 2a of the above article, the resolution of microarrays was originally stated to be 50-100 Mb. The actual resolution is 50-100 kb. In addition, the key for Figure 2b referred to 30,000 coding variants instead of 20,000. These errors have been corrected online. Nature Reviews Genetics apologizes for these errors.
Paediatric genomics: diagnosing rare disease in children
1.European Organisation for Rare Diseases. Rare Diseases: Understanding this Public Health Priority. (Eurodis, 2005).2.Boycott, K. M. et al. International cooperation to enable the diagnosis of all rare genetic diseases. Am. J. Hum. Genet. 100, 695–705 (2017).3.Quintana-Murci, L. Understanding rare and common diseases in the context of human evolution. Genome Biol. 17, 225 (2016).4.Amberger, J., Bocchini, C. A., Scott, A. F. & Hamosh, A. Mckusick's online mendelian inheritance in man (OMIM). Nucleic Acids Res.
Watercress reduces risk from carcinogens, Pitt Cancer Institute study finds
Watercress appears to improve the body's response to some of the carcinogens in cigarettes, suggesting it could reduce cancer risk in smokers, according to a new University of Pittsburgh Cancer Institute study. When taken four times a day, an extract of the aquatic plant species slightly inhibited the activation of a tobacco-specific carcinogen known as NNK in smokers, according to study results.
Live Reactions: Party workers celebrate as trends project win for Nitish Kumar
As results come in, leaders and party supporters celebrate what appears to be a win for the Grand Alliance, while BJP leaders remain optimistic about a victory in the state. Photo credit: IANS Crowds celebrate Maha Gathbandhan lead outside the BJP office in Patna. 10.30 am: BJP leader Prakash Javadekat tells NDTV, "Let us wait a few hours.
Live: Trends now suggesting comfortable majority for the Grand Alliance in Bihar
The BJP-led National Democratic Alliance had taken an early lead, before the Maha Gathbandhan fought back. Photo credit: AFP All the channels are now not only showing leads for the Grand Alliance, but are even suggesting that the JDU-RJD-Congress combine will comfortably cross the 122-seat halfway mark. Some are even suggesting that the Grand Alliance will come close to touching 150 seats in the 243-seat assembly.
Live: Grand Alliance takes the lead, according to EC trends
Workers of the BJP had started celebrating with crackers after the National Democratic Alliance took a lead in the early trends before 9am. Photo credit: AFP 9.35am: ANI reports that the Grand Alliance has taken the lead according to the latest data from the Election Commission: #BiharResults FLASH: Mahagathbandan is leading now according to latest EC data.
Despite attempts at damage control, Badals face further setbacks in Punjab
Despite attempts at damage control, Badals face further setbacks in Punjab The proposed Sikh congregation of November 10, whether or not it is officially sanctified as Sarbat Khalsa, would still leave the ruling establishment red faced.
On a train in Bengal, listen to the music of the bauls
Laltoo Baul didn’t much like being asked to pose for a photograph. “I am working now”, he said, smiling lightly through his irritation. “I need to get off soon at Sainthia. That’s where I live”. Bauls are the wandering minstrels of Bengal, mendicants who live a life of holy detachment away from the material world.
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