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Karimi K, Mol MO, Haghshenas S, Relator R, Levy MA, Kerkhof J, McConkey H, Brooks A, Zonneveld-Huijssoon E, Gerkes EH, Tedder ML, Vissers L, Salzano E, Piccione M, Asaftei SD, Carli D, Mussa A, Shukarova-Angelovska E, Trajkova S, Brusco A, Merla G, Alders MM, Bouman A, Sadikovic B. Identification of DNA methylation episignature for the intellectual developmental disorder, autosomal dominant 21 syndrome, caused by variants in the CTCF gene. Genet Med 2024; 26:101041. [PMID: 38054406 DOI: 10.1016/j.gim.2023.101041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
PURPOSE The main objective of this study was to assess clinical features and genome-wide DNA methylation profiles in individuals affected by intellectual developmental disorder, autosomal dominant 21 (IDD21) syndrome, caused by variants in the CCCTC-binding factor (CTCF) gene. METHODS DNA samples were extracted from peripheral blood of 16 individuals with clinical features and genetic findings consistent with IDD21. DNA methylation analysis was performed using the Illumina Infinium Methylation EPIC Bead Chip microarrays. The methylation levels were fitted in a multivariate linear regression model to identify the differentially methylated probes. A binary support vector machine classification model was constructed to differentiate IDD21 samples from controls. RESULTS We identified a highly specific, reproducible, and sensitive episignature associated with CTCF variants. Six variants of uncertain significance were tested, of which 2 mapped to the IDD21 episignature and clustered alongside IDD21 cases in both heatmap and multidimensional scaling plots. Comparison of the genomic DNA methylation profile of IDD21 with that of 56 other neurodevelopmental disorders provided insights into the underlying molecular pathophysiology of this disorder. CONCLUSION The robust and specific CTCF/IDD21 episignature expands the growing list of neurodevelopmental disorders with distinct DNA methylation profiles, which can be applied as supporting evidence in variant classification.
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Affiliation(s)
- Karim Karimi
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Merel O Mol
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Alice Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Lisenka Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Emanuela Salzano
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy
| | - Maria Piccione
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy; Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Sebastian Dorin Asaftei
- Pediatric Onco-Hematology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | - Diana Carli
- Department of Medical Sciences, University of Turin, Turin, Italy; Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - Elena Shukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Children's Diseases, Medical Faculty, University Sv. Kiril i Metodij, Skopje, North Macedonia
| | - Slavica Trajkova
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Marielle M Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Canada.
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2
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Müller AR, van Silfhout NY, den Hollander B, Kampman DHC, Bakkum L, Brands MMMG, Haverman L, Terwee CB, Schuengel C, Daams J, Hessl D, Wijburg FA, Boot E, van Eeghen AM. Navigating the outcome maze: a scoping review of outcomes and instruments in clinical trials in genetic neurodevelopmental disorders and intellectual disability. THERAPEUTIC ADVANCES IN RARE DISEASE 2024; 5:26330040241245721. [PMID: 38681798 PMCID: PMC11047260 DOI: 10.1177/26330040241245721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/14/2024] [Indexed: 05/01/2024]
Abstract
Background Individuals with genetic neurodevelopmental disorders (GNDs) or intellectual disability (ID) are often affected by complex neuropsychiatric comorbidities. Targeted treatments are increasingly available, but due to the heterogeneity of these patient populations, choosing a key outcome and corresponding outcome measurement instrument remains challenging. Objectives The aim of this scoping review was to describe the research on outcomes and instruments used in clinical trials in GNDs and ID. Eligibility criteria Clinical trials in individuals with GNDs and ID for any intervention over the past 10 years were included in the review. Sources of evidence MEDLINE, PsycINFO, and Cochrane CENTRAL were searched. Titles and abstracts were independently screened for eligibility with a subsample of 10% double-screening for interrater reliability. Data from full texts were independently reviewed. Discrepancies were discussed until consensus was reached. Charting methods Information was recorded on patient populations, interventions, designs, outcomes, measurement instruments, and type of reporter when applicable. Qualitative and descriptive analyses were performed. Results We included 312 studies reporting 91 different outcomes, with cognitive function most frequently measured (28%). Various outcome measurement instruments (n = 457) were used, with 288 in only a single clinical trial. There were 18 genetic condition-specific instruments and 16 measures were designed ad-hoc for one particular trial. Types of report included proxy-report (39%), self-report (22%), clinician-report (16%), observer-report (6%), self-assisted report (1%), or unknown (16%). Conclusion This scoping review of current practice reveals a myriad of outcomes and outcome measurement instruments for clinical trials in GNDs and ID. This complicates generalization, evidence synthesis, and evaluation. It underlines the need for consensus on suitability, validity, and relevancy of instruments, ultimately resulting in a core outcome set. A series of steps is proposed to move from the myriad of measures to a more unified approach.
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Affiliation(s)
- Annelieke R. Müller
- Department of Pediatrics, Emma Children’s Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Advisium, ’s Heeren Loo, Amersfoort, Utrecht, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands
| | - Nadia Y. van Silfhout
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development, Child Development, Amsterdam, The Netherlands
- Emma Children’s Hospital, Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Bibiche den Hollander
- Department of Pediatrics, Emma Children’s Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands
- United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Dick H. C. Kampman
- Faculty of Science, Operational Management, ICT Department, Utrecht University, Utrecht, The Netherlands
| | - Lianne Bakkum
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Clinical Child and Family Studies, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marion M. M. G. Brands
- Department of Pediatrics, Emma Children’s Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development, Child Development, Amsterdam, The Netherlands
- United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Lotte Haverman
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development, Child Development, Amsterdam, The Netherlands
- Emma Children’s Hospital, Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Caroline B. Terwee
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Epidemiology and Data Science, Amsterdam UMC Location Vrije Universiteit, Amsterdam, The Netherlands
| | - Carlo Schuengel
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Clinical Child and Family Studies, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Joost Daams
- Medical Library, Research Support, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - David Hessl
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis, Sacramento, CA, USA
| | - Frits A. Wijburg
- Department of Pediatrics, Emma Children’s Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Erik Boot
- Advisium, ’s Heeren Loo, Amersfoort, Utrecht, The Netherlands
- The Dalglish Family 22q Clinic, Toronto, ON, Canada
- Department of Psychiatry & Neuropsychology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Agnies M. van Eeghen
- Emma Center for Personalized Medicine, Amsterdam UMC, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
- Advisium, ’s Heeren Loo, Berkenweg 11, 3818 LA, Amersfoort, The Netherlands
- Amsterdam Public Health Research Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development, Child Development, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
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3
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Smolen C, Jensen M, Dyer L, Pizzo L, Tyryshkina A, Banerjee D, Rohan L, Huber E, El Khattabi L, Prontera P, Caberg JH, Van Dijck A, Schwartz C, Faivre L, Callier P, Mosca-Boidron AL, Lefebvre M, Pope K, Snell P, Lockhart PJ, Castiglia L, Galesi O, Avola E, Mattina T, Fichera M, Luana Mandarà GM, Bruccheri MG, Pichon O, Le Caignec C, Stoeva R, Cuinat S, Mercier S, Bénéteau C, Blesson S, Nordsletten A, Martin-Coignard D, Sistermans E, Kooy RF, Amor DJ, Romano C, Isidor B, Juusola J, Girirajan S. Assortative mating and parental genetic relatedness contribute to the pathogenicity of variably expressive variants. Am J Hum Genet 2023; 110:2015-2028. [PMID: 37979581 PMCID: PMC10716518 DOI: 10.1016/j.ajhg.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/20/2023] Open
Abstract
We examined more than 97,000 families from four neurodevelopmental disease cohorts and the UK Biobank to identify phenotypic and genetic patterns in parents contributing to neurodevelopmental disease risk in children. We identified within- and cross-disorder correlations between six phenotypes in parents and children, such as obsessive-compulsive disorder (R = 0.32-0.38, p < 10-126). We also found that measures of sub-clinical autism features in parents are associated with several autism severity measures in children, including biparental mean Social Responsiveness Scale scores and proband Repetitive Behaviors Scale scores (regression coefficient = 0.14, p = 3.38 × 10-4). We further describe patterns of phenotypic similarity between spouses, where spouses show correlations for six neurological and psychiatric phenotypes, including a within-disorder correlation for depression (R = 0.24-0.68, p < 0.001) and a cross-disorder correlation between anxiety and bipolar disorder (R = 0.09-0.22, p < 10-92). Using a simulated population, we also found that assortative mating can lead to increases in disease liability over generations and the appearance of "genetic anticipation" in families carrying rare variants. We identified several families in a neurodevelopmental disease cohort where the proband inherited multiple rare variants in disease-associated genes from each of their affected parents. We further identified parental relatedness as a risk factor for neurodevelopmental disorders through its inverse relationship with variant pathogenicity and propose that parental relatedness modulates disease risk by increasing genome-wide homozygosity in children (R = 0.05-0.26, p < 0.05). Our results highlight the utility of assessing parent phenotypes and genotypes toward predicting features in children who carry rare variably expressive variants and implicate assortative mating as a risk factor for increased disease severity in these families.
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Affiliation(s)
- Corrine Smolen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Anastasia Tyryshkina
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Neuroscience Graduate Program, Pennsylvania State University, University Park, PA 16802, USA
| | - Deepro Banerjee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Rohan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Emily Huber
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laila El Khattabi
- Assistance Publique-Hôpitaux de Paris, Department of Medical Genetics, Armand Trousseau and Pitié-Salpêtrière Hospitals, Paris, France
| | - Paolo Prontera
- Medical Genetics Unit, Hospital "Santa Maria della Misericordia", Perugia, Italy
| | - Jean-Hubert Caberg
- Centre Hospitalier Universitaire de Liège. Domaine Universitaire du Sart Tilman, Liège, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | | | - Laurence Faivre
- Centre de Genetique et Cenre de Référence Anomalies du développement et syndromes malformatifs, Hôpital d'Enfants, CHU Dijon, Dijon, France; GAD INSERM UMR1231, FHU TRANSLAD, Université de Bourgogne Franche Comté, Dijon, France
| | - Patrick Callier
- Centre de Genetique et Cenre de Référence Anomalies du développement et syndromes malformatifs, Hôpital d'Enfants, CHU Dijon, Dijon, France; GAD INSERM UMR1231, FHU TRANSLAD, Université de Bourgogne Franche Comté, Dijon, France
| | | | - Mathilde Lefebvre
- GAD INSERM UMR1231, FHU TRANSLAD, Université de Bourgogne Franche Comté, Dijon, France
| | - Kate Pope
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Penny Snell
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Paul J Lockhart
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Bruce Lefroy Center, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Lucia Castiglia
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Ornella Galesi
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Emanuela Avola
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Teresa Mattina
- Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Marco Fichera
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy; Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | | | - Maria Grazia Bruccheri
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Olivier Pichon
- CHU Nantes, Department of Medical Genetics, Nantes, France
| | - Cedric Le Caignec
- CHU Toulouse, Department of Medical Genetics, Toulouse, France; ToNIC, Toulouse Neuro Imaging, Center, Inserm, UPS, Université de Toulouse, Toulouse, France
| | - Radka Stoeva
- Service de Cytogenetique, CHU de Le Mans, Le Mans, France
| | | | - Sandra Mercier
- CHU Nantes, Department of Medical Genetics, Nantes, France
| | | | - Sophie Blesson
- Department of Genetics, Bretonneau University Hospital, Tours, France
| | | | | | - Erik Sistermans
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, the Netherlands
| | - R Frank Kooy
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - David J Amor
- Bruce Lefroy Center, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Corrado Romano
- Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; Medical Genetics, ASP Ragusa, Ragusa, Italy
| | | | | | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA; Neuroscience Graduate Program, Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.
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4
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Kleberg JL, Hallman AEZ, Galazka MA, Riby DM, Bölte S, Willfors C, Fawcett C, Nordgren A. No transfer of arousal from other's eyes in Williams syndrome. Sci Rep 2023; 13:18397. [PMID: 37884631 PMCID: PMC10603144 DOI: 10.1038/s41598-023-45521-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
Typically developing humans automatically synchronize their arousal levels, resulting in pupillary contagion, or spontaneous adaptation of pupil size to that of others. This phenomenon emerges in infancy and is believed to facilitate social interaction. Williams syndrome (WS) is a genetic condition characterized by a hyper-social personality and social interaction challenges. Pupillary contagion was examined in individuals with WS (n = 44), age-parallel-matched typically developing children and adults (n = 65), and infants (n = 79). Bayesian statistics were used. As a group, people with WS did not show pupillary contagion (Bayes factors supporting the null: 25-50) whereas control groups did. This suggests a very early emerging atypical developmental trajectory. In WS, higher pupillary contagion was associated with lower autistic symptoms of social communication. Diminished synchronization of arousal may explain why individuals with WS have social challenges, whereas synchronization of arousal is not a necessary correlate of high social motivation.
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Affiliation(s)
- Johan Lundin Kleberg
- Department of Psychology, Stockholm University, Stockholm, Sweden.
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden.
| | - Astrid E Z Hallman
- Department of Psychology, Stockholm University, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Martyna A Galazka
- Department of Applied Information Technology, Division of Cognition and Communication, University of Gothenburg, Gothenburg, Sweden
| | | | - Sven Bölte
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet & Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Child and Adolescent Psychiatry, Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Curtin Autism Research Group, Curtin School of Allied Health, Curtin University, Perth, WA, Australia
| | - Charlotte Willfors
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Christine Fawcett
- Department of Psychology, Stockholm University, Stockholm, Sweden
- Department of Psychology, Uppsala University, Uppsala, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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5
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Mir A, Song Y, Lee H, Khanahmad H, Khorram E, Nasiri J, Tabatabaiefar MA. Whole exome sequencing revealed variants in four genes underlying X-linked intellectual disability in four Iranian families: novel deleterious variants and clinical features with the review of literature. BMC Med Genomics 2023; 16:239. [PMID: 37821930 PMCID: PMC10566173 DOI: 10.1186/s12920-023-01680-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/01/2023] [Indexed: 10/13/2023] Open
Abstract
AIM AND OBJECTIVE Intellectual disability (ID) is a heterogeneous condition affecting brain development, function, and/or structure. The X-linked mode of inheritance of ID (X-linked intellectual disability; XLID) has a prevalence of 1 out of 600 to 1000 males. In the last decades, exome sequencing technology has revolutionized the process of disease-causing gene discovery in XLIDs. Nevertheless, so many of them still remain with unknown etiology. This study investigated four families with severe XLID to identify deleterious variants for possible diagnostics and prevention aims. METHODS Nine male patients belonging to four pedigrees were included in this study. The patients were studied genetically for Fragile X syndrome, followed by whole exome sequencing and analysis of intellectual disability-related genes variants. Sanger sequencing, co-segregation analysis, structural modeling, and in silico analysis were done to verify the causative variants. In addition, we collected data from previous studies to compare and situate our work with existing knowledge. RESULTS In three of four families, novel deleterious variants have been identified in three different genes, including ZDHHC9 (p. Leu189Pro), ATP2B3 (p. Asp847Glu), and GLRA2 (p. Arg350Cys) and also with new clinical features and in another one family, a reported pathogenic variant in the L1CAM (p. Glu309Lys) gene has been identified related to new clinical findings. CONCLUSION The current study's findings expand the existing knowledge of variants of the genes implicated in XLID and broaden the spectrum of phenotypes associated with the related conditions. The data have implications for genetic diagnosis and counseling.
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Affiliation(s)
- Atefeh Mir
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
| | - Yongjun Song
- Division of Medical Genetics, 3Billion Inc, Seoul, South Korea
| | - Hane Lee
- Division of Medical Genetics, 3Billion Inc, Seoul, South Korea
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Erfan Khorram
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
| | - Jafar Nasiri
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran.
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.
- Deputy of Research and Technology, GenTArget Corp (GTAC), Isfahan University of Medical Sciences, Isfahan, Iran.
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6
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Smolen C, Jensen M, Dyer L, Pizzo L, Tyryshkina A, Banerjee D, Rohan L, Huber E, El Khattabi L, Prontera P, Caberg JH, Van Dijck A, Schwartz C, Faivre L, Callier P, Mosca-Boidron AL, Lefebvre M, Pope K, Snell P, Lockhart PJ, Castiglia L, Galesi O, Avola E, Mattina T, Fichera M, Mandarà GML, Bruccheri MG, Pichon O, Le Caignec C, Stoeva R, Cuinat S, Mercier S, Bénéteau C, Blesson S, Nordsletten A, Martin-Coignard D, Sistermans E, Kooy RF, Amor DJ, Romano C, Isidor B, Juusola J, Girirajan S. Assortative mating and parental genetic relatedness drive the pathogenicity of variably expressive variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.18.23290169. [PMID: 37292616 PMCID: PMC10246151 DOI: 10.1101/2023.05.18.23290169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We examined more than 38,000 spouse pairs from four neurodevelopmental disease cohorts and the UK Biobank to identify phenotypic and genetic patterns in parents associated with neurodevelopmental disease risk in children. We identified correlations between six phenotypes in parents and children, including correlations of clinical diagnoses such as obsessive-compulsive disorder (R=0.31-0.49, p<0.001), and two measures of sub-clinical autism features in parents affecting several autism severity measures in children, such as bi-parental mean Social Responsiveness Scale (SRS) scores affecting proband SRS scores (regression coefficient=0.11, p=0.003). We further describe patterns of phenotypic and genetic similarity between spouses, where spouses show both within- and cross-disorder correlations for seven neurological and psychiatric phenotypes, including a within-disorder correlation for depression (R=0.25-0.72, p<0.001) and a cross-disorder correlation between schizophrenia and personality disorder (R=0.20-0.57, p<0.001). Further, these spouses with similar phenotypes were significantly correlated for rare variant burden (R=0.07-0.57, p<0.0001). We propose that assortative mating on these features may drive the increases in genetic risk over generations and the appearance of "genetic anticipation" associated with many variably expressive variants. We further identified parental relatedness as a risk factor for neurodevelopmental disorders through its inverse correlations with burden and pathogenicity of rare variants and propose that parental relatedness drives disease risk by increasing genome-wide homozygosity in children (R=0.09-0.30, p<0.001). Our results highlight the utility of assessing parent phenotypes and genotypes in predicting features in children carrying variably expressive variants and counseling families carrying these variants.
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Affiliation(s)
- Corrine Smolen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Anastasia Tyryshkina
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Neuroscience Graduate program, Pennsylvania State University, University Park, PA 16802
| | - Deepro Banerjee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Rohan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Emily Huber
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laila El Khattabi
- Assistance Publique–Hôpitaux de Paris, Department of Medical Genetics, Armand Trousseau and Pitié-Salpêtrière Hospitals, Paris, France
| | - Paolo Prontera
- Medical Genetics Unit, Hospital “Santa Maria della Misericordia”, Perugia, Italy
| | - Jean-Hubert Caberg
- Centre Hospitalier Universitaire de Liège. Domaine Universitaire du Sart Tilman, Liège, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | | | - Laurence Faivre
- Centre de Genetique et Cenre de Référence Anomalies du développement et syndromes malformatifs, Hôpital d’Enfants, CHU Dijon, Dijon, France
- GAD INSERM UMR1231, FHU TRANSLAD, Université de Bourgogne Franche Comté, Dijon, France
| | - Patrick Callier
- Centre de Genetique et Cenre de Référence Anomalies du développement et syndromes malformatifs, Hôpital d’Enfants, CHU Dijon, Dijon, France
- GAD INSERM UMR1231, FHU TRANSLAD, Université de Bourgogne Franche Comté, Dijon, France
| | | | - Mathilde Lefebvre
- GAD INSERM UMR1231, FHU TRANSLAD, Université de Bourgogne Franche Comté, Dijon, France
| | - Kate Pope
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Penny Snell
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Paul J. Lockhart
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Bruce Lefroy Center, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Lucia Castiglia
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Ornella Galesi
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Emanuela Avola
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Teresa Mattina
- Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Marco Fichera
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
- Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | | | - Maria Grazia Bruccheri
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Olivier Pichon
- CHU Nantes, Department of Medical Genetics, Nantes, France
| | - Cedric Le Caignec
- CHU Toulouse, Department of Medical Genetics, Toulouse, France
- ToNIC, Toulouse Neuro Imaging, Center, Inserm, UPS, Université de Toulouse, Toulouse, France
| | - Radka Stoeva
- Service de Cytogenetique, CHU de Le Mans, Le Mans, France
| | | | - Sandra Mercier
- CHU Nantes, Department of Medical Genetics, Nantes, France
| | | | - Sophie Blesson
- Department of Genetics, Bretonneau University Hospital, Tours, France
| | | | | | - Erik Sistermans
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - R. Frank Kooy
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - David J. Amor
- Bruce Lefroy Center, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Corrado Romano
- Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
- Medical Genetics, ASP Ragusa, Ragusa, Italy
| | | | | | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
- Neuroscience Graduate program, Pennsylvania State University, University Park, PA 16802
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
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7
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Mohd FN, Said AH, Mat Naji AS. Perceptions Toward Healthcare and Dental Care Services among Parents and Caretakers of People with Intellectual Disability (PWID)-A Questionnaire Study. J Int Soc Prev Community Dent 2023; 13:54-61. [PMID: 37153925 PMCID: PMC10155881 DOI: 10.4103/jispcd.jispcd_157_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/12/2022] [Accepted: 01/14/2023] [Indexed: 05/10/2023] Open
Abstract
Aim and Objective In Malaysia, there was lack of local evidence on the perception of parents/caretakers of people with intellectual disabilities (PWID) about healthcare. Thus, this study aims to assess the perceptions toward healthcare services of parents or caretakers for PWID. Materials and Methods Online survey using Google Forms was conducted on parents/caretakers of PWID who attended the special care dentistry clinic and special community centers in Kuantan, Pahang. A questionnaire was developed for data collection. Cronbach alpha was conducted to measure the reliability. Content and face validation was performed to establish the validity. Data entry and analysis were done using IBM statistical package for social sciences (SPSS) version 24. This study only involved univariate (descriptive) data analysis in which categorical data were summarized in actual numbers and percentages. Results The respondents' perceptions toward healthcare access and services were reasonably good; about 50% disagreed and strongly disagreed on having difficulty accessing healthcare facilities. 65% and 55% of parents/caretakers brought PWID for regular health and dental checkups. The majority agreed and strongly agreed (about 73%) that healthcare staff gave equal services and good support and showed positive attitudes toward PWID under their care. Insufficient healthcare information and below-par communication skills remained the main barriers faced by the parents/caretakers of PWID. About 13% of the respondents reported experiencing discrimination in receiving health and dental services for PWID under their care. The Cronbach alpha scores for sections 2 and 4 were 0.892 and 0.681, respectively. Conclusion Most of the respondents felt that Malaysia's healthcare services for PWID were fairly good. However, it was intriguing to find that some still experienced discrimination. This shows that education about intellectual disability is salient for healthcare workers and should be embedded in the current curriculum.
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Affiliation(s)
- Farah N Mohd
- Special Care Dentistry Unit, Department of Oral Diagnosis and Oral Maxillofacial Surgery, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Malaysia
| | - Abdul H Said
- Department of Family Medicine, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan, Malaysia
- Address for correspondence: Dr. Abdul Hadi Said, Department of Family Medicine, International Islamic University Malaysia, Kuantan 25200, Malaysia. E-mail:
| | - Ahmad Syahir Mat Naji
- Dental Clinic Pekan, Pekan District, Dental Health Unit, Oral Health Department, Ministry of Health, Kuantan, Malaysia
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8
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The diagnostic yield, candidate genes, and pitfalls for a genetic study of intellectual disability in 118 middle eastern families. Sci Rep 2022; 12:18862. [PMID: 36344539 PMCID: PMC9640568 DOI: 10.1038/s41598-022-22036-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022] Open
Abstract
Global Developmental Delay/Intellectual disability (ID) is the term used to describe various disorders caused by abnormal brain development and characterized by impairments in cognition, communication, behavior, or motor skills. In the past few years, whole-exome sequencing (WES) has been proven to be a powerful, robust, and scalable approach for candidate gene discoveries in consanguineous populations. In this study, we recruited 215 patients affected with ID from 118 Middle Eastern families. Whole-exome sequencing was completed for 188 individuals. The average age at which WES was completed was 8.5 years. Pathogenic or likely pathogenic variants were detected in 32/118 families (27%). Variants of uncertain significance were seen in 33/118 families (28%). The candidate genes with a possible association with ID were detected in 32/118 (27%) with a total number of 64 affected individuals. These genes are novel, were previously reported in a single family, or cause strikingly different phenotypes with a different mode of inheritance. These genes included: AATK, AP1G2, CAMSAP1, CCDC9B, CNTROB, DNAH14, DNAJB4, DRG1, DTNBP1, EDRF1, EEF1D, EXOC8, EXOSC4, FARSB, FBXO22, FILIP1, INPP4A, P2RX7, PRDM13, PTRHD1, SCN10A, SCYL2, SMG8, SUPV3L1, TACC2, THUMPD1, XPR1, ZFYVE28. During the 5 years of the study and through gene matching databases, several of these genes have now been confirmed as causative of ID. In conclusion, understanding the causes of ID will help understand biological mechanisms, provide precise counseling for affected families, and aid in primary prevention.
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9
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Levy MA, Relator R, McConkey H, Pranckeviciene E, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Ferilli M, Fletcher RS, Cherick F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Plomp AS, Poulton C, Reilly J, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, John MS, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci TB, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Campion D, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Heron D, Husson T, Kernohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vincent M, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. Hum Mutat 2022; 43:1609-1628. [PMID: 35904121 DOI: 10.1002/humu.24446] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022]
Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Erinija Pranckeviciene
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Mariet W Elting
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Marco Ferilli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Florian Cherick
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, The Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000, Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | | | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | | | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Delphine Heron
- AP-HP, Département de Génétique Médicale, Groupe Hospitalier Pitié Salpétrière, Paris, France
| | - Thomas Husson
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, UK, and Sheffield Children's Hospital NHS Foundation Trust
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Dept of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Marie Vincent
- Service de génétique Médicale, CHU Nantes, France.,Institut du thorax, INSERM, CNRS, UNIV Nantes, 44007, Nantes, France
| | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
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10
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Williams syndrome: reduced orienting to other's eyes in a hypersocial phenotype. J Autism Dev Disord 2022:10.1007/s10803-022-05563-6. [PMID: 35445369 PMCID: PMC9020553 DOI: 10.1007/s10803-022-05563-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2022] [Indexed: 11/08/2022]
Abstract
Williams syndrome (WS) is a rare genetic condition associated with high sociability, intellectual disability, and social cognitive challenges. Attention to others’ eyes is crucial for social understanding. Orienting to, and from other’s eyes was studied in WS (n = 37, mean age = 23, age range 9–53). The WS group was compared to a typically developing comparison participants (n = 167) in stratified age groups from infancy to adulthood. Typically developing children and adults were quicker and more likely to orient to eyes than the mouth. This bias was absent in WS. The WS group had reduced peak saccadic velocities, indicating hypo-arousal. The current study indicates reduced orienting to others’ eyes in WS, which may affect social interaction skills.
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11
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Levy MA, McConkey H, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Fletcher RS, Cherik F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Pizzi S, Plomp AS, Poulton C, Reilly J, Relator R, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, St John M, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci T, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Kerrnohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders. HGG ADVANCES 2022; 3:100075. [PMID: 35047860 PMCID: PMC8756545 DOI: 10.1016/j.xhgg.2021.100075] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, UK
| | | | - Mariet W Elting
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Florian Cherik
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, the Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Kristin D Kerrnohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
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12
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Sáenz SS, Arias B, Hosomichi K, Romero VI. The limits of clinical findings in similar phenotypes, from Carpenter to ATRX syndrome using a whole exome sequencing approach: a case review. Hum Genomics 2021; 15:49. [PMID: 34348791 PMCID: PMC8336023 DOI: 10.1186/s40246-021-00348-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The diagnostic process for uncommon disorders with similar manifestations is complicated and requires newer technology, like gene sequencing for a correct diagnosis. MAIN BODY We described two brothers clinically diagnosed with Carpenter syndrome, which is a condition characterized by the premature fusion of certain skull bones (craniosynostosis), abnormalities of the fingers and toes, and other developmental problems, for which they underwent craniotomies. However, whole exome sequencing analysis concluded a novel pathological variation in the ATRX chromatin remodeler gene and protein remodeling demonstrated structural variations that decreased the function, giving a completely different diagnosis to these patients. CONCLUSION Our study focuses on the importance of using newer technologies, such as whole exome sequencing analysis, in patients with ambiguous phenotypes.
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Affiliation(s)
- Samantha S Sáenz
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Kanazawa University, Kanazawa, Japan
| | - Vanessa I Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador.
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13
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Milone R, Scalise R, Pasquariello R, Berloffa S, Ricca I, Battini R. De Novo 1q21.3q22 Duplication Revaluation in a "Cold" Complex Neuropsychiatric Case with Syndromic Intellectual Disability. Genes (Basel) 2021; 12:genes12040511. [PMID: 33807234 PMCID: PMC8066010 DOI: 10.3390/genes12040511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 11/26/2022] Open
Abstract
Syndromic intellectual disability often obtains a genetic diagnosis due to the combination of first and next generation sequencing techniques, although their interpretation may require revaluation over the years. Here we report on a composite neuropsychiatric case whose phenotype includes moderate intellectual disability, spastic paraparesis, movement disorder, and bipolar disorder, harboring a 1.802 Mb de novo 1q21.3q22 duplication. The role of this duplication has been reconsidered in the light of negativity of many other genetic exams, and of the possible pathogenic role of many genes included in this duplication, potentially configuring a contiguous gene-duplication syndrome.
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Affiliation(s)
- Roberta Milone
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Roberta Scalise
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
- Tuscan PhD Program of Neuroscience, University of Florence, Pisa and Siena, 50139 Florence, Italy
| | - Rosa Pasquariello
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Stefano Berloffa
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Ivana Ricca
- Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56125 Pisa, Italy
- Correspondence: ; Tel.: +39-050886229; Fax: +39-050886247
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14
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Mary L, Nourisson E, Feger C, Laugel V, Chaigne D, Keren B, Afenjar A, Billette T, Trost D, Cieuta-Walti C, Gerard B, Piton A, Schaefer E. Pathogenic variants in KCNQ2 cause intellectual deficiency without epilepsy: Broadening the phenotypic spectrum of a potassium channelopathy. Am J Med Genet A 2021; 185:1803-1815. [PMID: 33754465 DOI: 10.1002/ajmg.a.62181] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/19/2021] [Accepted: 03/11/2021] [Indexed: 12/22/2022]
Abstract
High-throughput sequencing (HTS) improved the molecular diagnosis in individuals with intellectual deficiency (ID) and helped to broaden the phenotype of previously known disease-causing genes. We report herein four unrelated patients with isolated ID, carriers of a likely pathogenic variant in KCNQ2, a gene usually implicated in benign familial neonatal seizures (BFNS) or early onset epileptic encephalopathy (EOEE). Patients were diagnosed by targeted HTS or exome sequencing. Pathogenicity of the variants was assessed by multiple in silico tools. Patients' ID ranged from mild to severe with predominance of speech disturbance and autistic features. Three of the four variants disrupted the same amino acid. Compiling all the pathogenic variants previously reported, we observed a strong overlap between variants causing EOEE, isolated ID, and BFNS and an important intra-familial phenotypic variability, although missense variants in the voltage-sensing domain and the pore are significantly associated to EOEE (p < 0.01, Fisher test). Thus, pathogenic variants in KCNQ2 can be associated with isolated ID. We did not highlight strong related genotype-phenotype correlations in KCNQ2-related disorders. A second genetic hit, a burden of rare variants, or other extrinsic factors may explain such a phenotypic variability. However, it is of interest to study encephalopathy genes in non-epileptic ID patients.
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Affiliation(s)
- Laura Mary
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Elsa Nourisson
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Claire Feger
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Vincent Laugel
- Service de Neuropédiatrie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Denys Chaigne
- Service de Neuropédiatrie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Boris Keren
- Département de Génétique, Centre de Référence des Déficiences Intellectuelles de Causes Rares, Groupe de Recherche Clinique "Déficiences Intellectuelles et Autisme," Université Pierre et Marie Curie, Hôpital de la Pitié-Salpêtrière, Paris, France.,Institut du Cerveau et de la Moelle Épinière, Sorbonne Universités, Université Pierre et Marie Curie (Université Paris 06), UMRS 1127, INSERM U 1127, CNRS UMR 7225, Paris, France
| | - Alexandra Afenjar
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Département de Génétique et Embryologie Médicale, Hôpital Trousseau, Sorbonne Universités, Paris, France
| | - Thierry Billette
- Assistance Publique-Hôpitaux de Paris, Service de Neuropédiatrie, Hôpital Armand Trousseau, Paris, France
| | | | | | - Bénédicte Gerard
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Amélie Piton
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR-7104, Inserm U964, Université de Strasbourg, Strasbourg, France
| | - Elise Schaefer
- Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
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15
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Sadikovic B, Levy MA, Kerkhof J, Aref-Eshghi E, Schenkel L, Stuart A, McConkey H, Henneman P, Venema A, Schwartz CE, Stevenson RE, Skinner SA, DuPont BR, Fletcher RS, Balci TB, Siu VM, Granadillo JL, Masters J, Kadour M, Friez MJ, van Haelst MM, Mannens MMAM, Louie RJ, Lee JA, Tedder ML, Alders M. Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders. Genet Med 2021; 23:1065-1074. [PMID: 33547396 PMCID: PMC8187150 DOI: 10.1038/s41436-020-01096-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 01/23/2023] Open
Abstract
Purpose We describe the clinical implementation of genome-wide DNA methylation analysis in rare disorders across the EpiSign diagnostic laboratory network and the assessment of results and clinical impact in the first subjects tested. Methods We outline the logistics and data flow between an integrated network of clinical diagnostics laboratories in Europe, the United States, and Canada. We describe the clinical validation of EpiSign using 211 specimens and assess the test performance and diagnostic yield in the first 207 subjects tested involving two patient subgroups: the targeted cohort (subjects with previous ambiguous/inconclusive genetic findings including genetic variants of unknown clinical significance) and the screening cohort (subjects with clinical findings consistent with hereditary neurodevelopmental syndromes and no previous conclusive genetic findings). Results Among the 207 subjects tested, 57 (27.6%) were positive for a diagnostic episignature including 48/136 (35.3%) in the targeted cohort and 8/71 (11.3%) in the screening cohort, with 4/207 (1.9%) remaining inconclusive after EpiSign analysis. Conclusion This study describes the implementation of diagnostic clinical genomic DNA methylation testing in patients with rare disorders. It provides strong evidence of clinical utility of EpiSign analysis, including the ability to provide conclusive findings in the majority of subjects tested.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Andrea Venema
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Victoria Mok Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Jennefer Masters
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Mike Kadour
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | | | - Mieke M van Haelst
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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16
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Oliva-Teles N, de Stefano MC, Gallagher L, Rakic S, Jorge P, Cuturilo G, Markovska-Simoska S, Borg I, Wolstencroft J, Tümer Z, Harwood AJ, Kodra Y, Skuse D. Rare Pathogenic Copy Number Variation in the 16p11.2 (BP4-BP5) Region Associated with Neurodevelopmental and Neuropsychiatric Disorders: A Review of the Literature. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E9253. [PMID: 33321999 PMCID: PMC7763014 DOI: 10.3390/ijerph17249253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/24/2020] [Accepted: 12/05/2020] [Indexed: 11/17/2022]
Abstract
Copy number variants (CNVs) play an important role in the genetic underpinnings of neuropsychiatric/neurodevelopmental disorders. The chromosomal region 16p11.2 (BP4-BP5) harbours both deletions and duplications that are associated in carriers with neurodevelopmental and neuropsychiatric conditions as well as several rare disorders including congenital malformation syndromes. The aim of this article is to provide a review of the current knowledge of the diverse neurodevelopmental disorders (NDD) associated with 16p11.2 deletions and duplications reported in published cohorts. A literature review was conducted using the PubMed/MEDLINE electronic database limited to papers published in English between 1 January 2010 and 31 July 2020, describing 16p11.2 deletions and duplications carriers' cohorts. Twelve articles meeting inclusion criteria were reviewed from the 75 articles identified by the search. Of these twelve papers, eight described both deletions and duplications, three described deletions only and one described duplications only. This study highlights the heterogeneity of NDD descriptions of the selected cohorts and inconsistencies concerning accuracy of data reporting.
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Affiliation(s)
- Natália Oliva-Teles
- Centro de Genética Médica Doutor Jacinto Magalhães/Centro Hospitalar Universitário do Porto, 4099-001 Porto, Portugal;
- Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto (UMIB/ICBAS/UP), 4050-313 Porto, Portugal
| | - Maria Chiara de Stefano
- Italian National Transplant Center, Italian National Institute of Health, 00161 Rome, Italy;
| | - Louise Gallagher
- Trinity Institute of Neurosciences, Trinity College Dublin, University of Dublin, 152-160 Dublin, Ireland;
| | - Severin Rakic
- Public Health Institute of Republic of Srpska, 78000 Banja Luka, Bosnia and Herzegovina;
| | - Paula Jorge
- Centro de Genética Médica Doutor Jacinto Magalhães/Centro Hospitalar Universitário do Porto, 4099-001 Porto, Portugal;
- Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto (UMIB/ICBAS/UP), 4050-313 Porto, Portugal
| | - Goran Cuturilo
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
- Department of Medical Genetics, University Children’s Hospital, Tirsova 10, 11000 Belgrade, Serbia
| | | | - Isabella Borg
- Department of Pathology, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
- Medical Genetics Unit, Mater Dei Hospital, MSD 2090 L-Imsida, Malta
| | - Jeanne Wolstencroft
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (J.W.); (D.S.)
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhangen, Denmark;
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Adrian J. Harwood
- Neuroscience and Mental Health Research Institute (NMHRI), & School of Biosciences, Cardiff University, Cardiff CF24 4HQ, UK;
| | - Yllka Kodra
- National Centre for Rare Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - David Skuse
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (J.W.); (D.S.)
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17
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Assenza C, Cacciatore D, Manica M, Iosa M, Foti C, Gobbetti T, Paolucci S, Morelli D. Assistive products and childhood neurodisability: a retrospective study on factors associated with aids/orthoses prescription. Eur J Phys Rehabil Med 2020; 56:412-420. [PMID: 32406225 DOI: 10.23736/s1973-9087.20.06224-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Children affected by pathologies causing neurodisability go through motor, cognitive, sensory and other limitations. The selection of assistive products can influence their level of independence and quality of life. AIM The present study investigated the possibility to assess the equipment needs of children with neurodisabilities, based on their clinical characteristics. DESIGN A retrospective observational study. SETTING Outpatients. POPULATION Inclusion criteria: diagnosis of cerebral palsy or genetic/chromosomal/syndromic disorders, age range 0-18 years, intelligence quotient evaluation, medical history of positive or negative presence of epilepsy and of communication disorders, admission at our neurorehabilitation service between 2007 and 2017, and registration of all equipment prescribed to each child. METHODS In 192 children (111 males, 57.81%) we evaluated the relationship between several independent variables (diagnosis, sex, Gross Motor Function Classification System level, intelligence quotient, history of epilepsy and communication disorders) and equipment prescription by means of logistic regression models. RESULTS Our data showed significant correlation between the Gross Motor Function Classification System level and the equipment prescribed. A history of seizures was negatively correlated with walker prescriptions (the log odds of prescription decreases by -2.156; CI: -4.16 to -0.65) and positively with those of stroller (the log odds increases by 1.427; CI: 0.22 to 2.69). Stroller and knee-ankle-foot orthoses and hip-knee-ankle-foot orthoses prescriptions were negatively correlated with the cerebral palsy diagnosis. The prescription of foot orthoses was positively correlated with mental retardation (the log odds increases by 0.358; CI: 0.12 to 0.61). A negative correlation between communication disorders and the prescription of ankle-foot orthoses and communication/learning devices was also found (the log odds decreases by -0.833; CI -1.66 to -0.01). CONCLUSIONS Several clinical characteristics correlate with specific equipment needs. CLINICAL REHABILITATION IMPACT The definition of the clinical characteristics with a potential predicting value, may facilitate the task of physician on choosing what is more appropriate to prescribe, as well as the authorizing office responsible for evaluating the appropriateness of prescriptions. Furthermore, it could be possible to foresee the care needs in terms of type and number of aids/orthoses and to guarantee every disabled child the possibility to take advantage of the same opportunities.
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Affiliation(s)
- Carla Assenza
- Department of Pediatric Neurorehabilitation, Scientific Institute for Research and Health Care Santa Lucia Foundation, Rome, Italy - .,Physical and Rehabilitation Medicine, Tor Vergata University, Rome, Italy -
| | - Denise Cacciatore
- Department of Pediatric Neurorehabilitation, Scientific Institute for Research and Health Care Santa Lucia Foundation, Rome, Italy
| | | | - Marco Iosa
- Clinical Laboratory of Experimental Neurorehabilitation, Scientific Institute for Research and Health Care Santa Lucia Foundation, Rome, Italy
| | - Calogero Foti
- Physical and Rehabilitation Medicine, Tor Vergata University, Rome, Italy
| | - Tiziana Gobbetti
- Department of Pediatric Neurorehabilitation, Scientific Institute for Research and Health Care Santa Lucia Foundation, Rome, Italy
| | - Stefano Paolucci
- Clinical Laboratory of Experimental Neurorehabilitation, Scientific Institute for Research and Health Care Santa Lucia Foundation, Rome, Italy
| | - Daniela Morelli
- Department of Pediatric Neurorehabilitation, Scientific Institute for Research and Health Care Santa Lucia Foundation, Rome, Italy
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18
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Kerr K, McAneney H, Smyth LJ, Bailie C, McKee S, McKnight AJ. A scoping review and proposed workflow for multi-omic rare disease research. Orphanet J Rare Dis 2020; 15:107. [PMID: 32345347 PMCID: PMC7189570 DOI: 10.1186/s13023-020-01376-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/07/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Patients with rare diseases face unique challenges in obtaining a diagnosis, appropriate medical care and access to support services. Whole genome and exome sequencing have increased identification of causal variants compared to single gene testing alone, with diagnostic rates of approximately 50% for inherited diseases, however integrated multi-omic analysis may further increase diagnostic yield. Additionally, multi-omic analysis can aid the explanation of genotypic and phenotypic heterogeneity, which may not be evident from single omic analyses. MAIN BODY This scoping review took a systematic approach to comprehensively search the electronic databases MEDLINE, EMBASE, PubMed, Web of Science, Scopus, Google Scholar, and the grey literature databases OpenGrey / GreyLit for journal articles pertaining to multi-omics and rare disease, written in English and published prior to the 30th December 2018. Additionally, The Cancer Genome Atlas publications were searched for relevant studies and forward citation searching / screening of reference lists was performed to identify further eligible articles. Following title, abstract and full text screening, 66 articles were found to be eligible for inclusion in this review. Of these 42 (64%) were studies of multi-omics and rare cancer, two (3%) were studies of multi-omics and a pre-cancerous condition, and 22 (33.3%) were studies of non-cancerous rare diseases. The average age of participants (where known) across studies was 39.4 years. There has been a significant increase in the number of multi-omic studies in recent years, with 66.7% of included studies conducted since 2016 and 33% since 2018. Fourteen combinations of multi-omic analyses for rare disease research were returned spanning genomics, epigenomics, transcriptomics, proteomics, phenomics and metabolomics. CONCLUSIONS This scoping review emphasises the value of multi-omic analysis for rare disease research in several ways compared to single omic analysis, ranging from the provision of a diagnosis, identification of prognostic biomarkers, distinct molecular subtypes (particularly for rare cancers), and identification of novel therapeutic targets. Moving forward there is a critical need for collaboration of multi-omic rare disease studies to increase the potential to generate robust outcomes and development of standardised biorepository collection and reporting structures for multi-omic studies.
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Affiliation(s)
- Katie Kerr
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland
| | - Helen McAneney
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland
| | - Laura J Smyth
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland
| | - Caitlin Bailie
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland
| | - Shane McKee
- Regional Genetics Centre, Belfast City Hospital, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB, Northern Ireland
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland.
- Regional Genetics Centre, Belfast City Hospital, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB, Northern Ireland.
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19
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Coffman KA, Borgatti R. Finding a common path to the assessment of persons with intellectual development disorders. Neurology 2020; 94:507-508. [DOI: 10.1212/wnl.0000000000009132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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20
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Phenotypic and genotypic characterization of families with complex intellectual disability identified pathogenic genetic variations in known and novel disease genes. Sci Rep 2020; 10:968. [PMID: 31969655 PMCID: PMC6976666 DOI: 10.1038/s41598-020-57929-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/03/2020] [Indexed: 12/04/2022] Open
Abstract
Intellectual disability (ID), which presents itself during childhood, belongs to a group of neurodevelopmental disorders (NDDs) that are clinically widely heterogeneous and highly heritable, often being caused by single gene defects. Indeed, NDDs can be attributed to mutations at over 1000 loci, and all type of mutations, ranging from single nucleotide variations (SNVs) to large, complex copy number variations (CNVs), have been reported in patients with ID and other related NDDs. In this study, we recruited seven different recessive NDD families with comorbidities to perform a detailed clinical characterization and a complete genomic analysis that consisted of a combination of high throughput SNP-based genotyping and whole-genome sequencing (WGS). Different disease-associated loci and pathogenic gene mutations were identified in each family, including known (n = 4) and novel (n = 2) mutations in known genes (NAGLU, SLC5A2, POLR3B, VPS13A, SYN1, SPG11), and the identification of a novel disease gene (n = 1; NSL1). Functional analyses were additionally performed in a gene associated with autism-like symptoms and epileptic seizures for further proof of pathogenicity. Lastly, detailed genotype-phenotype correlations were carried out to assist with the diagnosis of prospective families and to determine genomic variation with clinical relevance. We concluded that the combination of linkage analyses and WGS to search for disease genes still remains a fruitful strategy for complex diseases with a variety of mutated genes and heterogeneous phenotypic manifestations, allowing for the identification of novel mutations, genes, and phenotypes, and leading to improvements in both diagnostic strategies and functional characterization of disease mechanisms.
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21
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Pravata VM, Gundogdu M, Bartual SG, Ferenbach AT, Stavridis M, Õunap K, Pajusalu S, Žordania R, Wojcik MH, van Aalten DMF. A missense mutation in the catalytic domain of O-GlcNAc transferase links perturbations in protein O-GlcNAcylation to X-linked intellectual disability. FEBS Lett 2019; 594:717-727. [PMID: 31627256 PMCID: PMC7042088 DOI: 10.1002/1873-3468.13640] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 06/25/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023]
Abstract
X‐linked intellectual disabilities (XLID) are common developmental disorders. The enzyme O‐GlcNAc transferase encoded by OGT, a recently discovered XLID gene, attaches O‐GlcNAc to nuclear and cytoplasmic proteins. As few missense mutations have been described, it is unclear what the aetiology of the patient phenotypes is. Here, we report the discovery of a missense mutation in the catalytic domain of OGT in an XLID patient. X‐ray crystallography reveals that this variant leads to structural rearrangements in the catalytic domain. The mutation reduces in vitro OGT activity on substrate peptides/protein. Mouse embryonic stem cells carrying the mutation reveal reduced O‐GlcNAcase (OGA) and global O‐GlcNAc levels. These data suggest a direct link between changes in the O‐GlcNAcome and intellectual disability observed in patients carrying OGT mutations.
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Affiliation(s)
- Veronica M Pravata
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, UK
| | - Mehmet Gundogdu
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, UK
| | - Sergio G Bartual
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, UK
| | - Andrew T Ferenbach
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, UK
| | - Marios Stavridis
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, UK
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Estonia
| | - Riina Žordania
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Estonia
| | - Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, UK
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22
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Pekeles H, Accogli A, Boudrahem-Addour N, Russell L, Parente F, Srour M. Diagnostic Yield of Intellectual Disability Gene Panels. Pediatr Neurol 2019; 92:32-36. [PMID: 30581057 DOI: 10.1016/j.pediatrneurol.2018.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Recent technological advances have improved the understanding and identification of the genetic basis of intellectual disability (ID) and global developmental delay (GDD). Next-generation sequencing panels of ID genes are now available for clinical testing; however, their overall yield in clinical practice has not yet been investigated. AIM We determined the diagnostic yield of ID gene panels in a clinical setting and explored whether any clinical features are associated with an increased diagnostic yield. METHODS We performed a systematic retrospective chart review of all patients with ID/GDD who underwent an ID gene panel between April 2014 and July 2017 at our institution. Chi-square analysis assessed whether any specific clinical features were significantly associated with a positive diagnostic yield. RESULTS Forty-eight subjects (18 females, 30 males; median age: 7.5 years) were included. Consanguinity was present in 17%, autism in 38%, seizures in 42%, nonspecific dysmorphic features in 67%, and abnormalities on neurological examination in 56%; furthermore, 29% of the cohort was nonverbal and 4% was nonambulatory. Four different gene panels were used. The diagnostic yield was 21% (10/48) overall, and 38% with the more recent trio-based panel. Eight of 10 patients had de novo pathogenic dominant mutations, one had an inherited pathogenic autosomal dominant mutation, and one had compound heterozygous pathogenic recessive mutations. No clinical feature was significantly associated with an increased diagnostic yield. CONCLUSIONS Our study suggests that ID gene panels have a high yield and are a valuable diagnostic tool in the evaluation of children with ID/GDD.
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Affiliation(s)
| | - Andrea Accogli
- Division of Pediatric Neurology, Departments of Pediatrics and Neurology & Neurosurgery, McGill University, Montreal, Canada; Scientific Institute for Research and Healthcare, Istituto Giannina Gaslini, Genova, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Children's Sciences, Università degli Studi di Genova, Italy
| | - Nassima Boudrahem-Addour
- Child Health and Human Development Program, McGill University Health Center (MUHC) Research Institute, Montreal, Canada
| | - Laura Russell
- Division of Medical Genetics, Department of Medicine, McGill University, Montreal, Canada
| | - Fabienne Parente
- Division of Medical Genetics, Department of Medicine, McGill University, Montreal, Canada
| | - Myriam Srour
- Division of Pediatric Neurology, Departments of Pediatrics and Neurology & Neurosurgery, McGill University, Montreal, Canada.
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23
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Selvan N, George S, Serajee FJ, Shaw M, Hobson L, Kalscheuer V, Prasad N, Levy SE, Taylor J, Aftimos S, Schwartz CE, Huq AM, Gecz J, Wells L. O-GlcNAc transferase missense mutations linked to X-linked intellectual disability deregulate genes involved in cell fate determination and signaling. J Biol Chem 2018; 293:10810-10824. [PMID: 29769320 DOI: 10.1074/jbc.ra118.002583] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/27/2018] [Indexed: 01/17/2023] Open
Abstract
It is estimated that ∼1% of the world's population has intellectual disability, with males affected more often than females. OGT is an X-linked gene encoding for the enzyme O-GlcNAc transferase (OGT), which carries out the reversible addition of N-acetylglucosamine (GlcNAc) to Ser/Thr residues of its intracellular substrates. Three missense mutations in the tetratricopeptide (TPR) repeats of OGT have recently been reported to cause X-linked intellectual disability (XLID). Here, we report the discovery of two additional novel missense mutations (c.775 G>A, p.A259T, and c.1016 A>G, p.E339G) in the TPR domain of OGT that segregate with XLID in affected families. Characterization of all five of these XLID missense variants of OGT demonstrates modest declines in thermodynamic stability and/or activities of the variants. We engineered each of the mutations into a male human embryonic stem cell line using CRISPR/Cas9. Investigation of the global O-GlcNAc profile as well as OGT and O-GlcNAc hydrolase levels by Western blotting showed no gross changes in steady-state levels in the engineered lines. However, analyses of the differential transcriptomes of the OGT variant-expressing stem cells revealed shared deregulation of genes involved in cell fate determination and liver X receptor/retinoid X receptor signaling, which has been implicated in neuronal development. Thus, here we reveal two additional mutations encoding residues in the TPR regions of OGT that appear causal for XLID and provide evidence that the relatively stable and active TPR variants may share a common, unelucidated mechanism of altering gene expression profiles in human embryonic stem cells.
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Affiliation(s)
- Nithya Selvan
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Stephan George
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Fatema J Serajee
- the Departments of Pediatrics and of Neurology, Wayne State University, Detroit, Michigan 48201
| | - Marie Shaw
- the Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide South Australia 5006, Australia
| | - Lynne Hobson
- the Women's and Children's Hospital, North Adelaide, South Australia 5006, Australia
| | - Vera Kalscheuer
- the Research Group Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Nripesh Prasad
- the Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Shawn E Levy
- the Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Juliet Taylor
- the Genetic Health Services New Zealand-Northern Hub, Auckland City Hospital, Auckland 1142, New Zealand
| | - Salim Aftimos
- the Genetic Health Services New Zealand-Northern Hub, Auckland City Hospital, Auckland 1142, New Zealand
| | | | - Ahm M Huq
- the Departments of Pediatrics and of Neurology, Wayne State University, Detroit, Michigan 48201
| | - Jozef Gecz
- the Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide South Australia 5006, Australia.,the South Australian Health and Medical Research Institute, Adelaide, South Australia 5006, Australia
| | - Lance Wells
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602,
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