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Sabbagh Q, Haghshenas S, Piard J, Trouvé C, Amiel J, Attié-Bitach T, Balci T, Barat-Houari M, Belonis A, Boute O, Brightman DS, Bruel AL, Caraffi SG, Chatron N, Collet C, Dufour W, Edery P, Fong CT, Fusco C, Gatinois V, Gouy E, Guerrot AM, Heide S, Joshi A, Karp N, Keren B, Lesieur-Sebellin M, Levy J, Levy MA, Lozano C, Lyonnet S, Margot H, Marzin P, McConkey H, Michaud V, Nicolas G, Nizard M, Paulet A, Peluso F, Pernin V, Perrin L, Philippe C, Prasad C, Prasad M, Relator R, Rio M, Rondeau S, Ruault V, Ruiz-Pallares N, Sanchez E, Shears D, Siu VM, Sorlin A, Tedder M, Tharreau M, Mau-Them FT, van der Laan L, Van Gils J, Verloes A, Whalen S, Willems M, Yauy K, Zuntini R, Kerkhof J, Sadikovic B, Geneviève D. Clinico-biological refinement of BCL11B-related disorder and identification of an episignature: A series of 20 unreported individuals. Genet Med 2024; 26:101007. [PMID: 37860968 DOI: 10.1016/j.gim.2023.101007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
PURPOSE BCL11B-related disorder (BCL11B-RD) arises from rare genetic variants within the BCL11B gene, resulting in a distinctive clinical spectrum encompassing syndromic neurodevelopmental disorder, with or without intellectual disability, associated with facial features and impaired immune function. This study presents an in-depth clinico-biological analysis of 20 newly reported individuals with BCL11B-RD, coupled with a characterization of genome-wide DNA methylation patterns of this genetic condition. METHODS Through an international collaboration, clinical and molecular data from 20 individuals were systematically gathered, and a comparative analysis was conducted between this series and existing literature. We further scrutinized peripheral blood DNA methylation profile of individuals with BCL11B-RD, contrasting them with healthy controls and other neurodevelopmental disorders marked by established episignature. RESULTS Our findings unveil rarely documented clinical manifestations, notably including Rubinstein-Taybi-like facial features, craniosynostosis, and autoimmune disorders, all manifesting within the realm of BCL11B-RD. We refine the intricacies of T cell compartment alterations of BCL11B-RD, revealing decreased levels naive CD4+ T cells and recent thymic emigrants while concurrently observing an elevated proportion of effector-memory expressing CD45RA CD8+ T cells (TEMRA). Finally, a distinct DNA methylation episignature exclusive to BCL11B-RD is unveiled. CONCLUSION This study serves to enrich our comprehension of the clinico-biological landscape of BCL11B-RD, potentially furnishing a more precise framework for diagnosis and follow-up of individuals carrying pathogenic BCL11B variant. Moreover, the identification of a unique DNA methylation episignature offers a valuable diagnosis tool for BCL11B-RD, thereby facilitating routine clinical practice by empowering physicians to reevaluate variants of uncertain significance within the BCL11B gene.
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Affiliation(s)
- Quentin Sabbagh
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Juliette Piard
- University Hospital of Besançon, Department of Clinical Genetics, Besançon, France
| | - Chloé Trouvé
- University Hospital of Besançon, Department of Clinical Genetics, Besançon, France
| | - Jeanne Amiel
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Tania Attié-Bitach
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Tugce Balci
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Mouna Barat-Houari
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Alyce Belonis
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, OH; University of Cincinnati College of Medicine, Department of Pediatrics, Cincinnati, OH
| | - Odile Boute
- University Hospital of Lille, Department of Clinical Genetics, Lille, France
| | - Diana S Brightman
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, OH
| | - Ange-Line Bruel
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France
| | | | - Nicolas Chatron
- University Hospital of Lyon, Laboratory of Medical Genetics, AURAGEN Platform, Lyon, France
| | - Corinne Collet
- Robert Debré University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - William Dufour
- University Hospital of Lille, Department of Clinical Genetics, Lille, France
| | - Patrick Edery
- University Hospital of Lyon, Department of Clinical Genetics, Lyon, France
| | - Chin-To Fong
- University of Rochester, Department of Genetics, Rochester, NY
| | - Carlo Fusco
- Azienda USL-IRCCS di Reggio Emilia, Child Neurology and Psychiatry Unit, 42123 Reggio Emilia, Italy
| | - Vincent Gatinois
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Evan Gouy
- University Hospital of Lyon, Department of Clinical Genetics, Lyon, France
| | - Anne-Marie Guerrot
- Rouen-Normandie University, University Hospital of Rouen, Department of Genetics, Reference Center for Developmental Disorders, Inserm UMR1245, F-76000 Rouen, France
| | - Solveig Heide
- Pitié-Salpêtrière University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Aakash Joshi
- Churchill Hospital, Department of Clinical Genetics, ERN-ITHACA, Oxford, United Kingdom
| | - Natalya Karp
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Boris Keren
- Pitié-Salpêtrière University Hospital, Laboratory of Molecular Genetics and Cytogenetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marion Lesieur-Sebellin
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jonathan Levy
- Robert Debré University Hospital, Laboratory of Cytogenetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Claire Lozano
- University Hospital of Montpellier, Department of Immunology, Montpellier, France
| | - Stanislas Lyonnet
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Henri Margot
- University of Bordeaux, University Hospital of Bordeaux, Department of Medical Genetics, MRGM Inserm UMR1211, F-33000 Bordeaux, France
| | - Pauline Marzin
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Vincent Michaud
- University of Bordeaux, University Hospital of Bordeaux, Department of Medical Genetics, MRGM Inserm UMR1211, F-33000 Bordeaux, France
| | - Gaël Nicolas
- Rouen-Normandie University, University Hospital of Rouen, Department of Genetics, Reference Center for Developmental Disorders, Inserm UMR1245, F-76000 Rouen, France
| | - Mevyn Nizard
- Necker-Enfants Malades University Hospital, Department of Pediatric Endocrinology, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Alix Paulet
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Francesca Peluso
- Azienda USL-IRCCS di Reggio Emilia, Medical Genetics Unit, 42123 Reggio Emilia, Italy
| | - Vincent Pernin
- University of Montpellier, Department of Nephrology, Montpellier, France
| | - Laurence Perrin
- Robert Debré University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Christophe Philippe
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France; Hospital of Metz-Thionville, Mercy Hospital, Laboratory of Genetics, Metz, France
| | - Chitra Prasad
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Madhavi Prasad
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Marlène Rio
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Sophie Rondeau
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Valentin Ruault
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Nathalie Ruiz-Pallares
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Elodie Sanchez
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Debbie Shears
- Churchill Hospital, Department of Clinical Genetics, ERN-ITHACA, Oxford, United Kingdom
| | - Victoria Mok Siu
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Arthur Sorlin
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France
| | | | - Mylène Tharreau
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Frédéric Tran Mau-Them
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France
| | - Liselot van der Laan
- University of Amsterdam, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, AUMC Department of Human Genetics, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Julien Van Gils
- University of Bordeaux, University Hospital of Bordeaux, Department of Medical Genetics, MRGM Inserm UMR1211, F-33000 Bordeaux, France
| | - Alain Verloes
- Robert Debré University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Sandra Whalen
- Pitié-Salpêtrière University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marjolaine Willems
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Kévin Yauy
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Roberta Zuntini
- Azienda USL-IRCCS di Reggio Emilia, Medical Genetics Unit, 42123 Reggio Emilia, Italy
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - David Geneviève
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France.
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Wells CF, Boursier G, Yauy K, Ruiz-Pallares N, Mechin D, Ruault V, Tharreau M, Blanchet P, Pinson L, Coubes C, Fila M, Baleine J, Pidoux O, Badr M, Milesi C, Cambonie G, Mesnage R, Dereure M, Ardouin O, Guignard T, Geneviève D, Barat-Houari M, Willems M. Rapid exome sequencing in critically ill infants: implementation in routine care from French regional hospital's perspective. Eur J Hum Genet 2022; 30:1076-1082. [PMID: 35729264 PMCID: PMC9436918 DOI: 10.1038/s41431-022-01133-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/18/2022] [Accepted: 06/09/2022] [Indexed: 01/15/2023] Open
Abstract
This monocentric study included fifteen children under a year old in intensive care with suspected monogenic conditions for rapid trio exome sequencing (rES) between April 2019 and April 2021. The primary outcome was the time from blood sampling to rapid exome sequencing report to parents. All results were available within 16 days and were reported to parents in or under 16 days in 13 of the 15 individuals (86%). Six individuals (40%) received a diagnosis with rES, two had a genetic condition not diagnosed by rES. Eight individuals had their care impacted by their rES results, four were discharged or died before the results. This small-scale study shows that rES can be implemented in a regional University hospital with rapid impactful diagnosis to improve care in critically ill infants.
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Affiliation(s)
- Constance F Wells
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Guilaine Boursier
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Kevin Yauy
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
- Institute of Advanced Biosciences, Centre de recherche UGA, Inserm U 1209, CNRS UMR 5309, Grenoble, France
- SeqOne Genomics, Montpellier, France
| | - Nathalie Ruiz-Pallares
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Déborah Mechin
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Valentin Ruault
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Mylène Tharreau
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Patricia Blanchet
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Lucile Pinson
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Christine Coubes
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Marc Fila
- Pediatric Nephrology department, Montpellier university hospital, Univ, Montpellier, France
| | - Julien Baleine
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Odile Pidoux
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Maliha Badr
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Christophe Milesi
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Gilles Cambonie
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Renaud Mesnage
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Maëlle Dereure
- Clinical research and epidemiology department, Montpellier university hospital, Univ, Montpellier, France
| | - Olivier Ardouin
- Molecular medicine and genomics platform, Montpellier university hospital, Montpellier, France
| | - Thomas Guignard
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Montpellier university hospital, Univ, Montpellier, France
| | - David Geneviève
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Mouna Barat-Houari
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Marjolaine Willems
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France.
- Inserm U1298, INM, CHU Montpellier, Univ. Montpellier, Montpellier, France.
- Reference Centre AD SOOR, AnDDI-RARE, Competence Centre for Rare Skeletal Disorders, OSCAR Network, Montpellier, France.
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Rouxel F, Relator R, Kerkhof J, McConkey H, Levy M, Dias P, Barat-Houari M, Bednarek N, Boute O, Chatron N, Cherik F, Delahaye-Duriez A, Doco-Fenzy M, Faivre L, Gauthier LW, Heron D, Hildebrand MS, Lesca G, Lespinasse J, Mazel B, Menke LA, Morgan AT, Pinson L, Quelin C, Rossi M, Ruiz-Pallares N, Tran-Mau-Them F, Van Kessel IN, Vincent M, Weber M, Willems M, Leguyader G, Sadikovic B, Genevieve D. CDK13-related disorder: Report of a series of 18 previously unpublished individuals and description of an epigenetic signature. Genet Med 2022; 24:1096-1107. [PMID: 35063350 DOI: 10.1016/j.gim.2021.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 01/02/2023] Open
Abstract
PURPOSE Rare genetic variants in CDK13 are responsible for CDK13-related disorder (CDK13-RD), with main clinical features being developmental delay or intellectual disability, facial features, behavioral problems, congenital heart defect, and seizures. In this paper, we report 18 novel individuals with CDK13-RD and provide characterization of genome-wide DNA methylation. METHODS We obtained clinical phenotype and neuropsychological data for 18 and 10 individuals, respectively, and compared this series with the literature. We also compared peripheral blood DNA methylation profiles in individuals with CDK13-RD, controls, and other neurodevelopmental disorders episignatures. Finally, we developed a support vector machine-based classifier distinguishing CDK13-RD and non-CDK13-RD samples. RESULTS We reported health and developmental parameters, clinical data, and neuropsychological profile of individuals with CDK13-RD. Genome-wide differential methylation analysis revealed a global hypomethylated profile in individuals with CDK13-RD in a highly sensitive and specific model that could aid in reclassifying variants of uncertain significance. CONCLUSION We describe the novel features such as anxiety disorder, cryptorchidism, and disrupted sleep in CDK13-RD. We define a CDK13-RD DNA methylation episignature as a diagnostic tool and a defining functional feature of the evolving clinical presentation of this disorder. We also show overlap of the CDK13 DNA methylation profile in an individual with a functionally and clinically related CCNK-related disorder.
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Affiliation(s)
- Flavien Rouxel
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France
| | - Raissa Relator
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Haley McConkey
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Michael Levy
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Patricia Dias
- Genetics Department, Hospital Center of Lisbon North, ERN ITHACA, Lisbon, Portugal
| | - Mouna Barat-Houari
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique des Maladies Rares et Auto-Inflammatoires, CHU Montpellier, Université de Montpellier, Montpellier, France
| | - Nathalie Bednarek
- Genetics Department, CHU Reims, Medical school IFR53, EA3801, Reims, France
| | - Odile Boute
- Genetics Department, Guy Fontaine Medical Center, CLAD Nord de France, Jeanne de Flandre Hospital, CHRU Lille, Lille, France
| | - Nicolas Chatron
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France
| | - Florian Cherik
- Genetics Department, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Andrée Delahaye-Duriez
- Department of Histology Embryology and Cytogenetics, Jean Verdier Hospital; Paris 13 University, Sorbonne Paris Cité, UFR SMBH Bobigny; PROTECT, INSERM, Paris Diderot University, Paris, France
| | - Martine Doco-Fenzy
- Genetics Department, CHU Reims, Medical school IFR53, EA3801, Reims, France
| | - Laurence Faivre
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France; Genetics of Developmental Disorders, INSERM - Bourgogne Franche-Comté University, UMR 1231 GAD Team, Dijon, France
| | - Lucas W Gauthier
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France
| | - Delphine Heron
- Genetics Department, University Hospital Pitié-Salpétrière, Paris, France
| | - Michael S Hildebrand
- Epilepsy Research Center, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia; Murdoch Children's Research Institute, Department of Audiology and Speech Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gaëtan Lesca
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France
| | | | - Benoit Mazel
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, ERN ITHACA, Amsterdam, Netherlands
| | - Angela T Morgan
- Department of Audiology and Speech Pathology, Melbourne School of Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Lucile Pinson
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France
| | - Chloe Quelin
- Department of Clinical Genetics, CLAD Ouest, CHU de Rennes, Hôpital Sud, Rennes, France
| | - Massimiliano Rossi
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France; Genetics Department, Referral Centre for Developmental Abnormalities, Lyon University Hospital Lyon, France; INSERM U1028, CNRS UMR5292, Lyon Neuroscience Research Centre, GENDEV Team, Claude Bernard Lyon 1 University, Lyon, France
| | - Nathalie Ruiz-Pallares
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique des Maladies Rares et Auto-Inflammatoires, CHU Montpellier, Université de Montpellier, Montpellier, France
| | - Frederic Tran-Mau-Them
- Genetics of Developmental Disorders, INSERM - Bourgogne Franche-Comté University, UMR 1231 GAD Team, Dijon, France; Functional Unit 6254 Innovation in Genomic Diagnosis of Rare Diseases, CHU Dijon Bourgogne, Dijon, France
| | - Imke N Van Kessel
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, ERN ITHACA, Amsterdam, Netherlands
| | | | - Mathys Weber
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Marjolaine Willems
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France
| | - Gwenael Leguyader
- Genetics Department, CHU de Poitiers, Poitiers University Hospital, Poitiers, France
| | - Bekim Sadikovic
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
| | - David Genevieve
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France.
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Aref-Eshghi E, Kerkhof J, Pedro VP, France GDI, Barat-Houari M, Ruiz-Pallares N, Andrau JC, Lacombe D, Van-Gils J, Fergelot P, Dubourg C, Cormier-Daire V, Rondeau S, Lecoquierre F, Saugier-Veber P, Nicolas G, Lesca G, Chatron N, Sanlaville D, Vitobello A, Faivre L, Thauvin-Robinet C, Laumonnier F, Raynaud M, Alders M, Mannens M, Henneman P, Hennekam RC, Velasco G, Francastel C, Ulveling D, Ciolfi A, Pizzi S, Tartaglia M, Heide S, Héron D, Mignot C, Keren B, Whalen S, Afenjar A, Bienvenu T, Campeau PM, Rousseau J, Levy MA, Brick L, Kozenko M, Balci TB, Siu VM, Stuart A, Kadour M, Masters J, Takano K, Kleefstra T, de Leeuw N, Field M, Shaw M, Gecz J, Ainsworth PJ, Lin H, Rodenhiser DI, Friez MJ, Tedder M, Lee JA, DuPont BR, Stevenson RE, Skinner SA, Schwartz CE, Genevieve D, Sadikovic B. Evaluation of DNA Methylation Episignatures for Diagnosis and Phenotype Correlations in 42 Mendelian Neurodevelopmental Disorders. Am J Hum Genet 2021; 108:1161-1163. [PMID: 34087165 DOI: 10.1016/j.ajhg.2021.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Aref-Eshghi E, Kerkhof J, Pedro VP, Barat-Houari M, Ruiz-Pallares N, Andrau JC, Lacombe D, Van-Gils J, Fergelot P, Dubourg C, Cormier-Daire V, Rondeau S, Lecoquierre F, Saugier-Veber P, Nicolas G, Lesca G, Chatron N, Sanlaville D, Vitobello A, Faivre L, Thauvin-Robinet C, Laumonnier F, Raynaud M, Alders M, Mannens M, Henneman P, Hennekam RC, Velasco G, Francastel C, Ulveling D, Ciolfi A, Pizzi S, Tartaglia M, Heide S, Héron D, Mignot C, Keren B, Whalen S, Afenjar A, Bienvenu T, Campeau PM, Rousseau J, Levy MA, Brick L, Kozenko M, Balci TB, Siu VM, Stuart A, Kadour M, Masters J, Takano K, Kleefstra T, de Leeuw N, Field M, Shaw M, Gecz J, Ainsworth PJ, Lin H, Rodenhiser DI, Friez MJ, Tedder M, Lee JA, DuPont BR, Stevenson RE, Skinner SA, Schwartz CE, Genevieve D, Sadikovic B, Sadikovic B. Evaluation of DNA Methylation Episignatures for Diagnosis and Phenotype Correlations in 42 Mendelian Neurodevelopmental Disorders. Am J Hum Genet 2020; 106:356-370. [PMID: 32109418 DOI: 10.1016/j.ajhg.2020.01.019] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/27/2020] [Indexed: 01/24/2023] Open
Abstract
Genetic syndromes frequently present with overlapping clinical features and inconclusive or ambiguous genetic findings which can confound accurate diagnosis and clinical management. An expanding number of genetic syndromes have been shown to have unique genomic DNA methylation patterns (called "episignatures"). Peripheral blood episignatures can be used for diagnostic testing as well as for the interpretation of ambiguous genetic test results. We present here an approach to episignature mapping in 42 genetic syndromes, which has allowed the identification of 34 robust disease-specific episignatures. We examine emerging patterns of overlap, as well as similarities and hierarchical relationships across these episignatures, to highlight their key features as they are related to genetic heterogeneity, dosage effect, unaffected carrier status, and incomplete penetrance. We demonstrate the necessity of multiclass modeling for accurate genetic variant classification and show how disease classification using a single episignature at a time can sometimes lead to classification errors in closely related episignatures. We demonstrate the utility of this tool in resolving ambiguous clinical cases and identification of previously undiagnosed cases through mass screening of a large cohort of subjects with developmental delays and congenital anomalies. This study more than doubles the number of published syndromes with DNA methylation episignatures and, most significantly, opens new avenues for accurate diagnosis and clinical assessment in individuals affected by these disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada.
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Faivre L, Van Kien PK, Callier P, Ruiz-Pallares N, Baudoin C, Plancke A, Wolf JE, Thauvin-Robinet C, Durand E, Minot D, Dulieu V, Metaizeau JD, Leheup B, Coron F, Bidot S, Huet F, Jondeau G, Boileau C, Claustres M, Mugneret F. De novo 15q21.1q21.2 deletion identified through FBN1 MLPA and refined by 244K array-CGH in a female teenager with incomplete Marfan syndrome. Eur J Med Genet 2010; 53:208-12. [DOI: 10.1016/j.ejmg.2010.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 05/04/2010] [Indexed: 10/19/2022]
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