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4 results on '"C. R. Boustred"'

1. Genome sequencing reveals underdiagnosis of primary ciliary dyskinesia in bronchiectasis

Author

Amelia, Shoemark, Helen, Griffin, Gabrielle, Wheway, Claire, Hogg, Jane S, Lucas, Carme, Camps, Jenny, Taylor, Mary, Carroll, Michael R, Loebinger, James D, Chalmers, Deborah, Morris-Rosendahl, Hannah M, Mitchison, Anthony, De Soyza, D, Brown, J C, Ambrose, P, Arumugam, R, Bevers, M, Bleda, F, Boardman-Pretty, C R, Boustred, H, Brittain, M J, Caulfield, G C, Chan, T, Fowler, A, Giess, A, Hamblin, S, Henderson, T J P, Hubbard, R, Jackson, L J, Jones, D, Kasperaviciute, M, Kayikci, A, Kousathanas, L, Lahnstein, S E A, Leigh, I U S, Leong, F J, Lopez, F, Maleady-Crowe, M, McEntagart, F, Minneci, L, Moutsianas, M, Mueller, N, Murugaesu, A C, Need, P, O'Donovan, C A, Odhams, C, Patch, D, Perez-Gil, M B, Pereira, J, Pullinger, T, Rahim, A, Rendon, T, Rogers, K, Savage, K, Sawant, R H, Scott, A, Siddiq, A, Sieghart, S C, Smith, A, Sosinsky, A, Stuckey, M, Tanguy, A L, Taylor Tavares, E R A, Thomas, S R, Thompson, A, Tucci, M J, Welland, E, Williams, K, Witkowska, and S M, Wood

Subjects
Pulmonary and Respiratory Medicine, Kartagener Syndrome, Mutation, Humans, Cilia, Ciliopathies, Bronchiectasis, Ciliary Motility Disorders
Abstract

BackgroundBronchiectasis can result from infectious, genetic, immunological and allergic causes. 60–80% of cases are idiopathic, but a well-recognised genetic cause is the motile ciliopathy, primary ciliary dyskinesia (PCD). Diagnosis of PCD has management implications including addressing comorbidities, implementing genetic and fertility counselling and future access to PCD-specific treatments. Diagnostic testing can be complex; however, PCD genetic testing is moving rapidly from research into clinical diagnostics and would confirm the cause of bronchiectasis.MethodsThis observational study used genetic data from severe bronchiectasis patients recruited to the UK 100,000 Genomes Project and patients referred for gene panel testing within a tertiary respiratory hospital. Patients referred for genetic testing due to clinical suspicion of PCD were excluded from both analyses. Data were accessed from the British Thoracic Society audit, to investigate whether motile ciliopathies are underdiagnosed in people with bronchiectasis in the UK.ResultsPathogenic or likely pathogenic variants were identified in motile ciliopathy genes in 17 (12%) out of 142 individuals by whole-genome sequencing. Similarly, in a single centre with access to pathological diagnostic facilities, 5–10% of patients received a PCD diagnosis by gene panel, often linked to normal/inconclusive nasal nitric oxide and cilia functional test results. In 4898 audited patients with bronchiectasis, ConclusionsPCD is underdiagnosed as a cause of bronchiectasis. Increased uptake of genetic testing may help to identify bronchiectasis due to motile ciliopathies and ensure appropriate management.

Published
2022

2. Comparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders

Author

Augusto Rendon, A. Kousathanas, S. E. A. Leigh, D. Kasperaviciute, R. Jackson, J. Pullinger, Richard H. Scott, T. Rahim, Graeme C.M. Black, C. A. Odhams, Simon C Ramsden, A. Siddiq, L. Lahnstein, S. R. Thompson, Huw B. Thomas, Jenny Lord, M. Bleda, M. J. Welland, L. Moutsianas, A. Giess, Jill Clayton-Smith, A. Stuckey, Panagiotis I. Sergouniotis, H. Brittain, K. Sawant, Arianna Tucci, A. Sosinsky, I. U. S. Leong, Nicole Gossan, William G. Newman, Christopher Campbell, Mark J. Caulfield, T. Rogers, Diana Baralle, Andrew G. L. Douglas, A. L. Taylor Tavares, N. Murugaesu, Gavin Arno, S. M. Wood, Louise J. Jones, Robert A. Hirst, Htoo A Wai, A. Hamblin, Glenda M. Beaman, P. O’Donovan, A. Sieghart, F. Maleady-Crowe, S. Henderson, M. Tanguy, Claire Hardcastle, C. R. Boustred, G. C. Chan, M. McEntagart, Beatriz Gomes-Silva, E. Williams, Andrew R. Webster, Ellen R A Thomas, T. Fowler, Christine Patch, Raymond T. O'Keefe, Elizabeth A. Jones, D. Perez-Gil, M. B. Pereira, R. Bevers, F. J. Lopez, Jamie M Ellingford, Kevin Webb, M. Kayikci, S. C. Smith, F. Boardman-Pretty, Charlie Rowlands, K. Witkowsa, P. Arumugam, A. C. Need, Tim Hubbard, J. C. Ambrose, M. Mueller, Christopher O'Callaghan, F. Minneci, and K. Savage

Subjects
Prioritization, Genetic testing, Science, RNA Splicing, In silico, Computational biology, Biology, Article, Diagnosis, Differential, Human disease, Databases, Genetic, Diagnosis, RNA Precursors, Genetics, Humans, Disease, Clinical genetics, Medical diagnosis, Uncertain significance, Diagnostic Techniques and Procedures, Multidisciplinary, Disease genetics, Computational Biology, Genetic Variation, Diagnostic test, Exons, Genomics, Pathogenicity, Mutation, RNA splicing, Medicine, RNA Splice Sites, Algorithms
Abstract

The development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 250 variants of uncertain significance (VUSs) that underwent splicing functional analyses. It is the capability of algorithms to differentiate VUSs away from the immediate splice site as being ‘pathogenic’ or ‘benign’ that is likely to have the most substantial impact on diagnostic testing. We show that SpliceAI is the best single strategy in this regard, but that combined usage of tools using a weighted approach can increase accuracy further. We incorporated prioritization strategies alongside diagnostic testing for rare disorders. We show that 15% of 2783 referred individuals carry rare variants expected to impact splicing that were not initially identified as ‘pathogenic’ or ‘likely pathogenic’; 1 in 5 of these cases could lead to new or refined diagnoses.

Published
2020
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3. De novo SOX6 variants cause a neurodevelopmental syndrome associated with ADHD, craniosynostosis, and osteochondromas

Author

M. Zarowiecki, A. Devereau, S.M. Wood, J. M. Boissiere, G. Elgar, Cara Forster, Liesbeth Keldermans, A. Sieghart, Allyn McConkie-Rosell, Augusto Rendon, S. R. Thompson, D. Polychronopoulos, Alexandre Arkader, Julien Thevenon, D. Kasperaviciute, Alma Kuechler, Bryan L. Krock, Dominique Martin-Coignard, Damian Smedley, T. Rahim, Barbara Mikat, Amber Begtrup, Priya Prasad, Lindsay B. Henderson, A. Stuckey, Mathilde Nizon, Tim Hubbard, I. U. S. Leong, M. Bleda, L. Lahnstein, C. E. H. Craig, Bertrand Isidor, Sarah Leigh, Joanne Mason, L. Moutsianas, T. Fowler, A. Siddiq, J. Pullinger, Marco Angelozzi, J. Ambrose, S. A. Watters, Saadet Mercimek-Andrews, K. Lawson, Claudia A. L. Ruivenkamp, Ian D. Krantz, J. E. Holman, Solveig Heide, Christel Depienne, Elizabeth T. DeChene, L. C. Daugherty, Alvaro Serrano Russi, Arianna Tucci, Mark J. Caulfield, Marie T. McDonald, Boris Keren, A. C. Need, Damara Ortiz, Nicola Foulds, William Spooner, Dara Tolchin, Eduardo Calpena, C. R. Boustred, Abdul Haseeb, Rudolf Gorazd, Charles Coutton, Alona Sosinsky, D. Perez-Gil, Sarah Stewart, J. M. Hackett, Giada Melistaccio, Andrew O.M. Wilkie, Radka Stoeva, Cédric Le Caignec, Pauline Le Tanno, Benjamin Cogné, Martina Mueller, Naghmeh Dorrani, Pedro Furió-Tarí, Gijs W. E. Santen, Hermann-Josef Lüdecke, Jessica P. Yeager, Julian A. Martinez-Agosto, Damien Haye, Kieran B. Pechter, Mohnish Suri, Livija Medne, M. J. Welland, Patrick Reed, K. Savage, G. C. Chan, Anne C.H. Tsai, F. Maleady-Crowe, A. de Burca, Ellen M. McDonagh, T. Rogers, F. Boardman-Pretty, Emily Lancaster, Katherine R. Smith, Christopher A. Odhams, Véronique Lefebvre, M. Ryten, Olivier Pichon, D. Halai, Aleš Maver, Christine Patch, R. E. Foulger, Frédéric Bilan, Helen Stevens, Hilde Van Esch, Eleanor Williams, Brigitte Gilbert-Dussardier, C. Tregidgo, K. Witkowska, F. J. Lopez, Gwenaël Le Guyader, Richard H Scott, M. Kayikci, Ellen Thomas, and E. Walsh

Subjects
0301 basic medicine, Male, Osteochondroma, Adolescent, Transcription, Genetic, media_common.quotation_subject, Nonsense, Medizin, Active Transport, Cell Nucleus, Mutation, Missense, Biology, Cell fate determination, Translocation, Genetic, Article, Craniosynostosis, 03 medical and health sciences, Craniosynostoses, 0302 clinical medicine, Intellectual disability, Genetics, medicine, Missense mutation, Humans, Computer Simulation, Amino Acid Sequence, RNA-Seq, Child, Gene, Genetics (clinical), media_common, Base Sequence, Brain, Infant, Syndrome, medicine.disease, 030104 developmental biology, Attention Deficit Disorder with Hyperactivity, Neurodevelopmental Disorders, Child, Preschool, Genomic Structural Variation, Autism, Female, Haploinsufficiency, Transcriptome, SOXD Transcription Factors, 030217 neurology & neurosurgery
Abstract

SOX6 belongs to a family of 20 SRY-related HMG-box-containing (SOX) genes that encode transcription factors controlling cell fate and differentiation in many developmental and adult processes. For SOX6, these processes include, but are not limited to, neurogenesis and skeletogenesis. Variants in half of the SOX genes have been shown to cause severe developmental and adult syndromes, referred to as SOXopathies. We here provide evidence that SOX6 variants also cause a SOXopathy. Using clinical and genetic data, we identify 19 individuals harboring various types of SOX6 alterations and exhibiting developmental delay and/or intellectual disability; the individuals are from 17 unrelated families. Additional, inconstant features include attention-deficit/hyperactivity disorder (ADHD), autism, mild facial dysmorphism, craniosynostosis, and multiple osteochondromas. All variants are heterozygous. Fourteen are de novo, one is inherited from a mosaic father, and four offspring from two families have a paternally inherited variant. Intragenic microdeletions, balanced structural rearrangements, frameshifts, and nonsense variants are predicted to inactivate the SOX6 variant allele. Four missense variants occur in residues and protein regions highly conserved evolutionarily. These variants are not detected in the gnomAD control cohort, and the amino acid substitutions are predicted to be damaging. Two of these variants are located in the HMG domain and abolish SOX6 transcriptional activity in vitro. No clear genotype-phenotype correlations are found. Taken together, these findings concur that SOX6 haploinsufficiency leads to a neurodevelopmental SOXopathy that often includes ADHD and abnormal skeletal and other features.

Published
2020

4. Human and mouse essentiality screens as a resource for disease gene discovery

Author

Cacheiro, Pilar, Muñoz-Fuentes, Violeta, Westerberg, Henrik, Scott, R. H., Siddiq, A., Sieghart, A., Smith, K. R., Sosinsky, A., Spooner, W., Stevens, H. E., Stuckey, A., Sultana, R., Thomas, E. R. A., Konopka, Tomasz, Thompson, S. R., Tregidgo, C., Tucci, A., Walsh, E., Watters, S. A., Welland, M. J., Williams, E., Witkowska, K., Wood, S. M., Zarowiecki, M., Hsu, Chih-Wei, Marschall, Susan, Lengger, Christoph, Maier, Holger, Seisenberger, Claudia, Bürger, Antje, Kühn, Ralf, Schick, Joel, Hörlein, Andreas, Oritz, Oskar, Giesert, Florian, Christiansen, Audrey, Beig, Joachim, Kenyon, Janet, Codner, Gemma, Fray, Martin, Johnson, Sara J, Cleak, James, Szoke-Kovacs, Zsombor, Lafont, David, Vancollie, Valerie E, McLaren, Robbie S B, Lanza, Denise G, Hughes-Hallett, Lena, Rowley, Christine, Sanderson, Emma, Galli, Antonella, Tuck, Elizabeth, Green, Angela, Tudor, Catherine, Siragher, Emma, Dabrowska, Monika, Mazzeo, Cecilia Icoresi, Beaudet, Arthur L, Griffiths, Mark, Gannon, David, Doe, Brendan, Cockle, Nicola, Kirton, Andrea, Bottomley, Joanna, Ingle, Catherine, Ryder, Edward, Gleeson, Diane, Ramirez-Solis, Ramiro, Heaney, Jason D, Birling, Marie-Christine, Pavlovic, Guillaume, Ayadi, Abdel, Hamid, Meziane, About, Ghina Bou, Champy, Marie-France, Jacobs, Hugues, Wendling, Olivia, Leblanc, Sophie, Vasseur, Laurent, Fuchs, Helmut, Chesler, Elissa J, Kumar, Vivek, White, Jacqueline K, Svenson, Karen L, Wiegand, Jean-Paul, Anderson, Laura L, Wilcox, Troy, Clark, James, Ryan, Jennifer, Denegre, James, Gailus-Durner, Valerie, Stearns, Tim, Philip, Vivek, Witmeyer, Catherine, Bates, Lindsay, Seavey, Zachary, Stanley, Pamela, Willet, Amelia, Roper, Willson, Creed, Julie, Moore, Michayla, Sorg, Tania, Dorr, Alex, Fraungruber, Pamelia, Presby, Rose, Mckay, Matthew, Nguyen-Bresinsky, Dong, Goodwin, Leslie, Urban, Rachel, Kane, Coleen, Murray, Stephen A, Prochazka, Jan, Novosadova, Vendula, Lelliott, Christopher J, Wardle-Jones, Hannah, Wells, Sara, Teboul, Lydia, Cater, Heather, Stewart, Michelle, Hough, Tertius, Wurst, Wolfgang, Dickinson, Mary E, Sedlacek, Radislav, Adams, David J, Seavitt, John R, Tocchini-Valentini, Glauco, Mammano, Fabio, Braun, Robert E, McKerlie, Colin, Herault, Yann, de Angelis, Martin Hrabě, Mallon, Ann-Marie, Bucan, Maja, Lloyd, K C Kent, Brown, Steve D M, Parkinson, Helen, Meehan, Terrence F, Smedley, Damian, Consortium, Genomics England Research, Consortium, International Mouse Phenotyping, Ambrose, J. C., Arumugam, P., Baple, E. L., Nutter, Lauryl M J, Bleda, M., Boardman-Pretty, F., Boissiere, J. M., Boustred, C. R., Brittain, H., Caulfield, M. J., Chan, G. C., Craig, C. E. H., Daugherty, L. C., de Burca, A., Peterson, Kevin A, Devereau, A., Elgar, G., Foulger, R. E., Fowler, T., Furió-Tarí, P., Hackett, J. M., Halai, D., Hamblin, A., Henderson, S., Holman, J. E., Haselimashhadi, Hamed, Hubbard, T. J. P., Ibáñez, K., Jackson, R., Jones, L. J., Kasperaviciute, D., Kayikci, M., Lahnstein, L., Lawson, K., Leigh, S. E. A., Leong, I. U. S., Flenniken, Ann M, Lopez, F. J., Maleady-Crowe, F., Mason, J., McDonagh, E. M., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A. C., Odhams, C. A., Patch, C., Morgan, Hugh, Perez-Gil, D., Polychronopoulos, D., Pullinger, J., Rahim, T., Rendon, A., Riesgo-Ferreiro, P., Rogers, T., Ryten, M., Savage, K., Sawant, K., Cacheiro, Pilar [0000-0002-6335-8208], Muñoz-Fuentes, Violeta [0000-0003-3574-546X], Nutter, Lauryl MJ [0000-0001-9619-146X], Peterson, Kevin A [0000-0001-8353-3694], Haselimashhadi, Hamed [0000-0001-7334-2421], Konopka, Tomasz [0000-0003-3042-4712], Hsu, Chih-Wei [0000-0002-9591-9567], Lanza, Denise G [0000-0001-8750-6933], Heaney, Jason D [0000-0001-8475-8828], Fuchs, Helmut [0000-0002-5143-2677], Gailus-Durner, Valerie [0000-0002-6076-0111], Lelliott, Christopher J [0000-0001-8087-4530], Adams, David J [0000-0001-9490-0306], Mammano, Fabio [0000-0003-3751-1691], McKerlie, Colin [0000-0002-2232-0967], Herault, Yann [0000-0001-7049-6900], de Angelis, Martin Hrabě [0000-0002-7898-2353], Lloyd, KC Kent [0000-0002-5318-4144], Smedley, Damian [0000-0002-5836-9850], Apollo - University of Cambridge Repository, Queen Mary University of London (QMUL), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, The Jackson Laboratory [Bar Harbor] (JAX), Baylor College of Medicine (BCM), Baylor University, University of Pennsylvania, The Hospital for sick children [Toronto] (SickKids), Mount Sinai Hospital [Toronto, Canada] (MSH), MRC Harwell Institute [UK], Helmholtz Zentrum München = German Research Center for Environmental Health, Institut Clinique de la Souris (ICS), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), French National Infrastructure for Mouse Phenogenomics (PHENOMIN), Institute of Molecular Genetics of the Czech Academy of Sciences (IMG / CAS), Czech Academy of Sciences [Prague] (CAS), The Wellcome Trust Sanger Institute [Cambridge], Technische Universität München = Technical University of Munich (TUM), Ludwig-Maximilians-Universität München (LMU), CNR - Italian National Research Council (CNR), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), German Center for Diabetes Research - Deutsches Zentrum für Diabetesforschung [Neuherberg] (DZD), University of California [Davis] (UC Davis), University of California (UC), J C Ambrose, P Arumugam, E L Baple, M Bleda, F Boardman-Pretty, J M Boissiere, C R Boustred, H Brittain, M J Caulfield, G C Chan, C E H Craig, L C Daugherty, A de Burca, A Devereau, G Elgar, R E Foulger, T Fowler, P Furió-Tarí, J M Hackett, D Halai, A Hamblin, S Henderson, J E Holman, T J P Hubbard, K Ibáñez, R Jackson, L J Jones, D Kasperaviciute, M Kayikci, L Lahnstein, K Lawson, S E A Leigh, I U S Leong, F J Lopez, F Maleady-Crowe, J Mason, E M McDonagh, L Moutsianas, M Mueller, N Murugaesu, A C Need, C A Odhams, C Patch, D Perez-Gil, D Polychronopoulos, J Pullinger, T Rahim, A Rendon, P Riesgo-Ferreiro, T Rogers, M Ryten, K Savage, K Sawant, R H Scott, A Siddiq, A Sieghart, K R Smith, A Sosinsky, W Spooner, H E Stevens, A Stuckey, R Sultana, E R A Thomas, S R Thompson, C Tregidgo, A Tucci, E Walsh, S A Watters, M J Welland, E Williams, K Witkowska, S M Wood, M Zarowiecki, Susan Marschall, Christoph Lengger, Holger Maier, Claudia Seisenberger, Antje Bürger, Ralf Kühn, Joel Schick, Andreas Hörlein, Oskar Oritz, Florian Giesert, Joachim Beig, Janet Kenyon, Gemma Codner, Martin Fray, Sara J Johnson, James Cleak, Zsombor Szoke-Kovacs, David Lafont, Valerie E Vancollie, Robbie S B McLaren, Lena Hughes-Hallett, Christine Rowley, Emma Sanderson, Antonella Galli, Elizabeth Tuck, Angela Green, Catherine Tudor, Emma Siragher, Monika Dabrowska, Cecilia Icoresi Mazzeo, Mark Griffiths, David Gannon, Brendan Doe, Nicola Cockle, Andrea Kirton, Joanna Bottomley, Catherine Ingle, Edward Ryder, Diane Gleeson, Ramiro Ramirez-Solis, Marie-Christine Birling, Guillaume Pavlovic, Abdel Ayadi, Meziane Hamid, Ghina Bou About, Marie-France Champy, Hugues Jacobs, Olivia Wendling, Sophie Leblanc, Laurent Vasseur, Elissa J Chesler, Vivek Kumar, Jacqueline K White, Karen L Svenson, Jean-Paul Wiegand, Laura L Anderson, Troy Wilcox, James Clark, Jennifer Ryan, James Denegre, Tim Stearns, Vivek Philip, Catherine Witmeyer, Lindsay Bates, Zachary Seavey, Pamela Stanley, Amelia Willet, Willson Roper, Julie Creed, Michayla Moore, Alex Dorr, Pamelia Fraungruber, Rose Presby, Matthew Mckay, Dong Nguyen-Bresinsky, Leslie Goodwin, Rachel Urban, Coleen Kane, Herault, Yann, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)

Subjects
0301 basic medicine, Mutation rate, Cancer Research, [SDV]Life Sciences [q-bio], General Physics and Astronomy, methods [Genetic Association Studies], Disease, VARIANTS, Mice, Essential, 0302 clinical medicine, IMPC, Genetics research, Lethal allele, 2.1 Biological and endogenous factors, Aetiology, lcsh:Science, Organism, ComputingMilieux_MISCELLANEOUS, Disease gene, Mice, Knockout, 0303 health sciences, Multidisciplinary, Genes, Essential, genetics [Disease], Genomics, R/BIOCONDUCTOR PACKAGE, DATABASE, UPDATE, GENOME, [SDV] Life Sciences [q-bio], Knockout mouse, Identification (biology), ddc:500, International Mouse Phenotyping Consortium, Technology Platforms, Biotechnology, Knockout, Science, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Genetics, medicine, Animals, Humans, Genetic variation, Clinical genetics, Gene, Genetic Association Studies, 030304 developmental biology, Disease model, Prevention, Human Genome, General Chemistry, medicine.disease, Developmental disorder, Good Health and Well Being, 030104 developmental biology, Genomics England Research Consortium, Genes, lcsh:Q, Generic health relevance, 030217 neurology & neurosurgery, Rare disease
Abstract

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery., Discovery of causal variants for monogenic disorders has been facilitated by whole exome and genome sequencing, but does not provide a diagnosis for all patients. Here, the authors propose a Full Spectrum of Intolerance to Loss-of-Function (FUSIL) categorization that integrates gene essentiality information to aid disease gene discovery.

Published
2020
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