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Nematollahi S, Dieterich K, Filges I, De Vries JIP, Van Bosse H, Natera de Benito D, Hall JG, Sawatzky B, Bedard T, Sanchez VC, Navalon-Martinez C, Pan T, Hilton C, Dahan-Oliel N. Éléments de données communs pour l'arthrogrypose multiple congénitale: Un cadre international. Dev Med Child Neurol 2024. [PMID: 38590274 DOI: 10.1111/dmcn.15915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
RésuméObjectifAfin de faciliter les études multisites et la recherche clinique d'envergure internationale, cette étude a pour but d'identifier des éléments de données communs (EDCs) normalisés et fondés sur un consensus pour l'arthrogrypose multiple congénitale (AMC).MéthodeUne étude à méthodes mixtes comprenant plusieurs groupes de discussion et trois séries d'enquêtes Delphi modifiées pour parvenir à un consensus ont été menées.RésultatsDans l'ensemble, 45 experts cliniques ainsi qu'adultes ayant une expérience vécue (dont 12 membres d'un consortium d'AMC) ont participé à cette étude à travers 11 pays en Amérique du Nord, Europe et Australie. Les EDCs comprennent 321 éléments de données et 19 mesures standardisées dans divers domaines, du développement du fœtus à l'âge adulte. Les éléments de données relatifs aux traits phénotypiques de l'AMC ont été cartographiés conformément à l'ontologie du phénotype humain (HPO). Une structure de gouvernance universelle, des protocoles de fonctionnement et des plans de développement durable ont été identifiés comme les principaux facilitateurs considérant que la capacité limitée de partage des données et la nécessité d'une infrastructure informatique fédérée étaient les principaux obstacles.InterprétationUne collecte de données systématiques sur l'AMC à l'aide d'EDCs permettra d'étudier sur les voies étiologiques, décrire le profil épidémiologique, et établir des corrélations génotype‐phénotype de manière standardisée. Les EDCs proposés faciliteront les collaborations internationales multidisciplinaires en améliorant à grande échelle les études multicentriques, les possibilités de partage des données, ainsi que le transfert et la diffusion des connaissances.
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Affiliation(s)
- Shahrzad Nematollahi
- École de physiothérapie et d'ergothérapie, Université de McGill, Montréal, QC, Canada
- Département de recherche clinique, Hôpitaux Shriners pour enfants du Canada, Montréal, Canada
| | - Klaus Dieterich
- Inserm U1209, Institut des Biosciences Avancées, CHU Grenoble Alpes, Centre de référence de l'arthrogrypose et des maladies neuromusculaires, Université Grenoble Alpes, Grenoble, France
| | - Isabel Filges
- Génétique médicale, Institut de génétique médicale et de pathologie et Département de recherche clinique, Hôpital universitaire de Bâle et Université de Bâle, Bâle, Suisse
| | - Johanna I P De Vries
- Obstétrique et gynécologie, Amsterdam Movement Sciences, Amsterdam Centre médical universitaire, Centre médical de la Vrije Universiteit, Amsterdam, Pays-Bas
| | - Harold Van Bosse
- Département de chirurgie orthopédique, Hôpital pour enfants Cardinal Glennon/SSM Santé, Université de St. Louis University, St. Louis, MO, États-Unis
| | - Daniel Natera de Benito
- Unité neuromusculaire, Hôpital Sant Joan de Déu, Barcelone, Espagne
- Recherche appliquée en maladies neuromusculaires, Institut de Recerca Sant Joan de Déu, Barcelone, Espagne
| | - Judith G Hall
- Département de génétique médicale et de pédiatrie, Université de la Colombie-Britannique et BC hôpital pour enfants, Vancouver, Canada
| | - Bonita Sawatzky
- Département d'orthopédie, Université de la Colombie-Britannique, Vancouver, Canada
| | - Tanya Bedard
- Génétique clinique, Système de surveillance des anomalies congénitales de l'Alberta, Calgary, Alberta, Canada
| | | | | | - Tony Pan
- Département d'informatique biomédicale, Université Emory, Atlanta, GA, États-Unis
- Département d'ingénierie et de la science des données, Institut de technologie de Géorgie, Atlanta, GA, États-Unis
| | - Coleman Hilton
- Département d'Ingénierie et d'analyse des données, Shriners Children's, Siège social, Tampa, FL, États-Unis
| | - Noémi Dahan-Oliel
- École de physiothérapie et d'ergothérapie, Université de McGill, Montréal, QC, Canada
- Département de recherche clinique, Hôpitaux Shriners pour enfants du Canada, Montréal, Canada
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Nematollahi S, Dieterich K, Filges I, De Vries JIP, Van Bosse H, Natera de Benito D, Hall JG, Sawatzky B, Bedard T, Sanchez VC, Navalon-Martinez C, Pan T, Hilton C, Dahan-Oliel N. Elementos de datos comunes para la artrogriposis múltiple congénita: Un marco internacional. Dev Med Child Neurol 2024. [PMID: 38581247 DOI: 10.1111/dmcn.15914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Abstract
ResumenObjetivoPara facilitar los estudios multicéntricos y la investigación clínica internacional, este estudio pretende identificar de forma consensuada los elementos de datos estandarizados para la artrogriposis múltiple congénita (AMC).MétodoEstudio de métodos mixtos de grupos de discusión y tres rondas de encuestas Delphi modificadas para llegar a un consenso utilizando dos escalas de clasificación por niveles.ResultadosEn total, 45 expertos clínicos y adultos con experiencia vivida (incluidos 12 miembros de un consorcio de AMC) participaron en este estudio procedentes de 11 países: Norteamérica, Europa y Australia. Los CDEs incluyen 321 elementos de datos y 19 medidas estandarizadas en varios dominios desde el desarrollo fetal hasta la edad adulta. Los elementos de datos relativos a los rasgos fenotípicos del CDEs se mapearon de acuerdo con la Ontología de Fenotipos Humanos. Se identificaron como principales facilitadores la estructura de gobernanza universal, protocolos operados de forma local y los planes de sostenibilidad, mientras que los principales obstáculos observados son la capacidad limitada para compartir datos y la necesidad de una infraestructura informática federada.InterpretaciónLa recopilación de datos sistemáticos sobre la AMC mediante CDEs permitirá investigar las vías etiológicas, describir el perfil epidemiológico y establecer correlaciones genotipo‐fenotipo de forma estandarizada. Los CDEs propuestos facilitarán las colaboraciones multidisciplinares internacionales mejorando los estudios a gran escala y las oportunidades para compartir datos, translación de conocimiento y difusión.
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Affiliation(s)
- Shahrzad Nematollahi
- Escuela de Fisioterapia y Terapia Ocupacional, Universidad McGill, Montreal, Canadá
- Departamento de Investigación Clínica, Hospitales Shriners para Niños, Montreal, Canadá
| | - Klaus Dieterich
- Université Grenoble Alpes, Inserm U1209, Instituto de Biociencias Avanzadas, CHU Grenoble Alpes, Centro de Referencia de Artrogriposis y Neuromuscular, Grenoble, Francia
| | - Isabel Filges
- Genética Médica, Instituto de Genética Médica y Patología y Departamento de Investigación Clínica, Hospital Universitario de Basilea y Universidad de Basilea, Basilea, Suiza
| | - Johanna I P De Vries
- Obstetricia y Ginecología, Amsterdam Movement Sciences, Amsterdam, University Medical Center, Vrije Universiteit Medical Center, Amsterdam, the Países Bajos
| | - Harold Van Bosse
- Departamento de Cirugía Ortopédica, Cardinal Glennon Children's Hospital/SSM Health/St. Louis University, St. Louis, MO, EE.UU
| | - Daniel Natera de Benito
- Unidad Neuromuscular, Hospital Sant Joan de Déu, Barcelona, España
- Investigación Aplicada en Enfermedades Neuromusculares, Institut de Recerca Sant Joan de Déu, Barcelona, España
| | - Judith G Hall
- Departamento de Genética Médica y Pediatría, Universidad de Columbia Británica y BC Children's Hospital, Vancouver, Columbia Británica, Canadá
| | - Bonita Sawatzky
- Departamento de Ortopedia, Universidad de British Columbia, Vancouver, British Columbia Columbia, Canadá
| | - Tanya Bedard
- Sistema de Vigilancia de Anomalías Congénitas de Alberta, Genética Clínica, Alberta Children's Hospital, Alberta Health Services, Calgary, Alberta, Canadá
| | | | | | - Tony Pan
- Departamento de Informática Biomédica, Universidad de Emory, Atlanta, GA, EE.UU
- Instituto de Ingeniería y Ciencia de Datos, Instituto de Tecnología de Georgia, Atlanta, GA, EE.UU
| | | | - Noémi Dahan-Oliel
- Escuela de Fisioterapia y Terapia Ocupacional, Universidad McGill, Montreal, Canadá
- Departamento de Investigación Clínica, Hospitales Shriners para Niños, Montreal, Canadá
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Nematollahi S, Dieterich K, Filges I, De Vries JIP, Van Bosse H, Benito DND, Hall JG, Sawatzky B, Bedard T, Sanchez VC, Navalon-Martinez C, Pan T, Hilton C, Dahan-Oliel N. Common data elements for arthrogryposis multiplex congenita: An international framework. Dev Med Child Neurol 2024. [PMID: 38491830 DOI: 10.1111/dmcn.15898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 03/18/2024]
Abstract
AIM To facilitate multisite studies and international clinical research, this study aimed to identify consensus-based, standardized common data elements (CDEs) for arthrogryposis multiplex congenita (AMC). METHOD A mixed-methods study comprising of several focus group discussions and three rounds of modified Delphi surveys to achieve consensus using two tiered-rating scales were conducted. RESULTS Overall, 45 clinical experts and adults with lived experience (including 12 members of an AMC consortium) participated in this study from 11 countries in North America, Europe, and Australia. The CDEs include 321 data elements and 19 standardized measures across various domains from fetal development to adulthood. Data elements pertaining to AMC phenotypic traits were mapped according to the Human Phenotype Ontology. A universal governance structure, local operating protocols, and sustainability plans were identified as the main facilitators, whereas limited capacity for data sharing and the need for a federated informatics infrastructure were the main barriers. INTERPRETATION Collection of systematic data on AMC using CDEs will allow investigations on etiological pathways, describe epidemiological profile, and establish genotype-phenotype correlations in a standardized manner. The proposed CDEs will facilitate international multidisciplinary collaborations by improving large-scale studies and opportunities for data sharing, knowledge translation, and dissemination.
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Affiliation(s)
- Shahrzad Nematollahi
- School of Physical and Occupational Therapy, McGill University, Montreal, Canada
- Department of Clinical Research, Shriners Hospitals for Children, Montreal, Canada
| | - Klaus Dieterich
- Université Grenoble Alpes, Inserm U1209, Institute of Advanced Biosciences, CHU Grenoble Alpes, Arthrogryposis and Neuromuscular Reference Center, Grenoble, France
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology and Department of Clinical Research, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Johanna I P De Vries
- Obstetrics and Gynecology, Amsterdam Movement Sciences, Amsterdam University Medical Center, Vrije Universiteit Medical Center, Amsterdam, the Netherlands
| | - Harold Van Bosse
- Department of Orthopaedic Surgery, Cardinal Glennon Children's Hospital/SSM Health/St. Louis University, St. Louis, MO, USA
| | - Daniel Natera-De Benito
- Neuromuscular Unit, Hospital Sant Joan de Déu, Barcelona, Spain
- Applied Research in Neuromuscular Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Judith G Hall
- Department of Medical Genetics and Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Bonita Sawatzky
- Department of Orthopaedics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tanya Bedard
- Alberta Congenital Anomalies Surveillance System, Clinical Genetics, Alberta Children's Hospital, Alberta Health Services, Calgary, Alberta, Canada
| | | | | | - Tony Pan
- Department of Biomedical Informatics, Emory University, Atlanta, GA, USA
- Institute for Data Engineering and Science, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Noémi Dahan-Oliel
- School of Physical and Occupational Therapy, McGill University, Montreal, Canada
- Department of Clinical Research, Shriners Hospitals for Children, Montreal, Canada
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Eichinger J, Zimmermann B, Elger B, McLennan S, Filges I, Koné I. 'It's a nightmare': informed consent in paediatric genome-wide sequencing. A qualitative expert interview study from Germany and Switzerland. Eur J Hum Genet 2023; 31:1398-1406. [PMID: 37773517 PMCID: PMC10689462 DOI: 10.1038/s41431-023-01468-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/27/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
The use of genome-wide sequencing (GWS) in paediatrics has added complexity to informed consent (IC) and pretest counselling because of the vast number and interpretation of potential findings, and their implications. However, empirical data from continental Europe on these issues remains limited. This study therefore aimed to explore the experiences and views of medical geneticists working with children in Germany and Switzerland regarding the challenges of obtaining valid IC in paediatric GWS. Qualitative interviews with 20 medical geneticists were analysed employing reflexive thematic analysis. In the interviews, many medical geneticists questioned the validity of parents' IC due to the enormous amount of relevant information given and the variety and complexity of the possible test outcomes. Key barriers identified included familial implications, administrative challenges and struggles with non-directiveness. Medical geneticists' suggestions for improvement included increasing the number of genetics professionals and better information material, which is crucial as GWS becomes a diagnostic standard in the early care pathways of children. An adjustment of aspirations from still existing ideal of traditional fully IC to appropriate IC seems to be needed. Such a more realistic and ethically sound adaptation of the requirements for IC can lead to better 'informedness' and improve the validity of the consent. This might also help reduce the moral distress for the medical geneticists involved.
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Affiliation(s)
- Johanna Eichinger
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland.
| | - Bettina Zimmermann
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
- Institute of History and Ethics in Medicine, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Philosophy & Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Bernice Elger
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
- Center for Legal Medicine (CURML), University of Geneva, Geneva, Switzerland
| | - Stuart McLennan
- Institute of History and Ethics in Medicine, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Clinical Research, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Insa Koné
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
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Filges I, Jünemann S, Viehweger E, Tercanli S. Fetal arthrogryposis-what do we tell the prospective parents? Prenat Diagn 2023; 43:798-805. [PMID: 36588183 DOI: 10.1002/pd.6299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/11/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
Abstract
Arthrogryposis, also termed arthrogryposis multiplex congenita, is a descriptive term for conditions with multiple congenital contractures (MCC). The etiology is extremely heterogeneous. More than 400 specific disorders have been identified so far, which may lead to or are associated with MCC and/or fetal hypo- and akinesia as a clinical sign. With improved sensitivity of prenatal ultrasound and expanding prenatal diagnostic options, clinicians are tasked with providing early detection in order to counsel the prospective parents regarding further prenatal diagnostic as well as management options. We summarize the most important knowledge to raise awareness for early detection in pregnancy. We review essential points for counseling when MCC is detected in order to provide answers to common questions, which, however, cannot replace interdisciplinary expert opinion in the individual case.
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Affiliation(s)
- Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Stephanie Jünemann
- Pediatric Neurology and Developmental Medicine, University Children's Hospital Basel UKBB and University of Basel, Basel, Switzerland
| | - Elke Viehweger
- Pediatric Orthopedics, Neuro-Orthopedics and Movement Analysis Center, University Children's Hospital Basel UKBB and University of Basel, Basel, Switzerland
| | - Sevgi Tercanli
- Center for Prenatal Ultrasound, Basel and University of Basel, Basel, Switzerland
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Tercanli S, Filges I. Fetal hyperechogenic kidneys: the significance of family assessment. Ultraschall Med 2023; 44:8. [PMID: 36750051 DOI: 10.1055/a-1985-4319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
| | - Isabel Filges
- Medical Genetics, Institute for Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland
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Dhombres F, Morgan P, Chaudhari BP, Filges I, Sparks TN, Lapunzina P, Roscioli T, Agarwal U, Aggarwal S, Beneteau C, Cacheiro P, Carmody LC, Collardeau‐Frachon S, Dempsey EA, Dufke A, Duyzend MH, el Ghosh M, Giordano JL, Glad R, Grinfelde I, Iliescu DG, Ladewig MS, Munoz‐Torres MC, Pollazzon M, Radio FC, Rodo C, Silva RG, Smedley D, Sundaramurthi JC, Toro S, Valenzuela I, Vasilevsky NA, Wapner RJ, Zemet R, Haendel MA, Robinson PN. Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology. Am J Med Genet C Semin Med Genet 2022; 190:231-242. [PMID: 35872606 PMCID: PMC9588534 DOI: 10.1002/ajmg.c.31989] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/01/2022] [Indexed: 01/07/2023]
Abstract
Technological advances in both genome sequencing and prenatal imaging are increasing our ability to accurately recognize and diagnose Mendelian conditions prenatally. Phenotype-driven early genetic diagnosis of fetal genetic disease can help to strategize treatment options and clinical preventive measures during the perinatal period, to plan in utero therapies, and to inform parental decision-making. Fetal phenotypes of genetic diseases are often unique and at present are not well understood; more comprehensive knowledge about prenatal phenotypes and computational resources have an enormous potential to improve diagnostics and translational research. The Human Phenotype Ontology (HPO) has been widely used to support diagnostics and translational research in human genetics. To better support prenatal usage, the HPO consortium conducted a series of workshops with a group of domain experts in a variety of medical specialties, diagnostic techniques, as well as diseases and phenotypes related to prenatal medicine, including perinatal pathology, musculoskeletal anomalies, neurology, medical genetics, hydrops fetalis, craniofacial malformations, cardiology, neonatal-perinatal medicine, fetal medicine, placental pathology, prenatal imaging, and bioinformatics. We expanded the representation of prenatal phenotypes in HPO by adding 95 new phenotype terms under the Abnormality of prenatal development or birth (HP:0001197) grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort. The expansion of prenatal phenotypes in HPO will support phenotype-driven prenatal exome and genome sequencing for precision genetic diagnostics of rare diseases to support prenatal care.
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Affiliation(s)
- Ferdinand Dhombres
- Sorbonne University, GRC26, INSERM, Limics, Armand Trousseau Hospital, Fetal Medicine Department, APHPParisFrance
| | - Patricia Morgan
- American College of Medical Genetics and Genomics, Newborn Screening Translational Research NetworkBethesdaMarylandUSA
| | - Bimal P. Chaudhari
- Institute for Genomic MedicineNationwide Children's HospitalColumbusOhioUSA
| | - Isabel Filges
- University Hospital Basel and University of Basel, Medical GeneticsBaselSwitzerland
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, & Reproductive SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Pablo Lapunzina
- CIBERER and Hospital Universitario La Paz, INGEMM‐Institute of Medical and Molecular GeneticsMadridSpain
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), University of New South WalesSydneyNew South WalesAustralia
| | - Umber Agarwal
- Department of Maternal and Fetal MedicineLiverpool Women's NHS Foundation TrustLiverpoolUK
| | - Shagun Aggarwal
- Department of Medical GeneticsNizam's Institute of Medical SciencesHyderabadTelanganaIndia
| | - Claire Beneteau
- Service de Génétique Médicale, UF 9321 de Fœtopathologie et Génétique, CHU de NantesNantesFrance
| | - Pilar Cacheiro
- William Harvey Research InstituteQueen Mary University of LondonLondonUK
| | - Leigh C. Carmody
- Department of Genomic MedicineThe Jackson LaboratoryFarmingtonConnecticutUSA
| | | | - Esther A. Dempsey
- St George's University of London, Molecular and Clinical Sciences Research InstituteLondonUK
| | - Andreas Dufke
- University of Tübingen, Institute of Medical Genetics and Applied GenomicsTübingenGermany
| | | | | | - Jessica L. Giordano
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Ragnhild Glad
- Department of Obstetrics and GynecologyUniversity Hospital of North NorwayTromsøNorway
| | - Ieva Grinfelde
- Department of Medical Genetics and Prenatal diagnosisChildren's University HospitalRigaLatvia
| | - Dominic G. Iliescu
- Department of Obstetrics and GynecologyUniversity of Medicine and Pharmacy CraiovaCraiovaDoljRomania
| | - Markus S. Ladewig
- Department of OphthalmologyKlinikum SaarbrückenSaarbrückenSaarlandGermany
| | - Monica C. Munoz‐Torres
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Marzia Pollazzon
- Azienda USL‐IRCCS di Reggio EmiliaMedical Genetics UnitReggio EmiliaItaly
| | | | - Carlota Rodo
- Vall d'Hebron Hospital Campus, Maternal & Fetal MedicineBarcelonaSpain
| | - Raquel Gouveia Silva
- Hospital Santa Maria, Serviço de Genética, Departamento de PediatriaHospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de LisboaLisboaPortugal
| | - Damian Smedley
- William Harvey Research InstituteQueen Mary University of LondonLondonUK
| | | | - Sabrina Toro
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Irene Valenzuela
- Hospital Vall d'Hebron, Clinical and Molecular Genetics AreaBarcelonaSpain
| | - Nicole A. Vasilevsky
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Ronald J. Wapner
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Roni Zemet
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Melissa A Haendel
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Peter N. Robinson
- Department of Genomic MedicineThe Jackson LaboratoryFarmingtonConnecticutUSA
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Kalantari S, Filges I. Gene Ontology Enrichment Analysis of Renal Agenesis: Improving Prenatal Molecular Diagnosis. Mol Syndromol 2021; 12:362-371. [PMID: 34899145 DOI: 10.1159/000518115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/24/2020] [Accepted: 06/24/2021] [Indexed: 11/19/2022] Open
Abstract
Uni- or bilateral renal agenesis (RA) is a commonly occurring major congenital anomaly impacting fetal and neonatal outcomes. Since the etiology is highly heterogeneous, our aim was to provide a logically structured approach by highlighting the genes in which variants have been identified to be associated with RA and to define the pathways involved in this type of abnormal kidney development. We used Phenolyzer to collect a list of all the genes known as causative for RA. Using ClueGO gene enrichment analysis, we classified the relationship between these genes and the biological processes defined by gene ontology. We identified 287 genes and 69 groups of enriched biological processes. About 50% included pathways directly related to the development of urogenital organ tissues. Several ciliary, axis specification, hindgut development, and endocrine pathways were enriched, which may relate to different clinical presentations of RA. Our gene ontology enrichment analysis shows that genes representing distinct biological pathways are significantly enriched. This knowledge will lead to an improved molecular diagnosis in clinical care when applying genome-wide sequencing approaches. The findings will also allow to further study the biological pathways involved in RA and to identify novel candidate genes and pathways.
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Affiliation(s)
- Silvia Kalantari
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland.,Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel and University of Basel, Basel, Switzerland
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Abstract
New genomic laboratory technology namely microarrays and high throughput sequencing (HTS) as well as a steady progress in sonographic image capture and processing have changed the practice of prenatal diagnosis during the last decade fundamentally. Pregnancies at high risk for common trisomies are reliably identified by non-invasive prenatal testing (NIPT) and expert sonography has greatly improved the assessment of the fetal phenotype. Preconceptional comprehensive carrier screening using HTS is available for all parents, if they should wish to do so. A definite fetal diagnosis, however, will still require invasive testing for most conditions. Chromosomal microarrays (CMA) have greatly enhanced the resolution in the detection of chromosome anomalies and other causal copy number variations (CNV). Gene panel or whole exome sequencing (WES) is becoming the routine follow up of many anomalies detected by ultrasound after CNVs have been excluded. The benefits and limitations of the various screening as well as diagnostic options are perceived as complex by many who find it challenging to cope with the need for immediate choices. The communication of facts to ensure an informed decision making is obviously a growing challenge with the advent of the new genomic testing options. This contribution provides an overview of the current practice and policies in Switzerland.
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Affiliation(s)
- Isabel Filges
- Institut für Medizinische Genetik und Pathologie and Departement Klinische Forschung, Universitätsspital Basel, Basel, Switzerland
| | - Peter Miny
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Basel, Switzerland
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Eichinger J, Elger BS, Koné I, Filges I, Shaw D, Zimmermann B, McLennan S. The full spectrum of ethical issues in pediatric genome-wide sequencing: a systematic qualitative review. BMC Pediatr 2021; 21:387. [PMID: 34488686 PMCID: PMC8420043 DOI: 10.1186/s12887-021-02830-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background The use of genome-wide sequencing in pediatric medicine and research is growing exponentially. While this has many potential benefits, the normative and empirical literature has highlighted various ethical issues. There have not been, however, any systematic reviews of these issues. The aim of this systematic review is to determine systematically the spectrum of ethical issues that is raised for stakeholders in in pediatric genome-wide sequencing. Methods A systematic review in PubMed and Google Books (publications in English or German between 2004 and 2021) was conducted. Further references were identified via reference screening. Data were analyzed and synthesized using qualitative content analysis. Ethical issues were defined as arising when a relevant normative principle is not adequately considered or when two principles come into conflict. Results Our literature search retrieved 3175 publications of which 143 were included in the analysis. Together these mentioned 106 ethical issues in pediatric genome-wide sequencing, categorized into five themes along the pediatric genome-wide sequencing lifecycle. Most ethical issues identified in relation to genome-wide sequencing typically reflect ethical issues that arise in general genetic testing, but they are often amplified by the increased quantity of data obtained, and associated uncertainties. The most frequently discussed ethical aspects concern the issue of unsolicited findings. Conclusion Concentration of the debate on unsolicited findings risks overlooking other ethical challenges. An overarching difficulty presents the terminological confusion: both with regard to both the test procedure/ the scope of analysis, as well as with the topic of unsolicited findings. It is important that the genetics and ethics communities together with other medical professions involved work jointly on specific case related guidelines to grant the maximum benefit for the care of the children, while preventing patient harm and disproportionate overload of clinicians and the healthcare system by the wealth of available options and economic incentives to increase testing. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-021-02830-w.
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Affiliation(s)
- Johanna Eichinger
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland. .,Institute of History and Ethics in Medicine, Technical University of Munich, Munich, Germany.
| | - Bernice S Elger
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland.,Center for legal medicine (CURML), University of Geneva, Geneva, Switzerland
| | - Insa Koné
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel and University of Basel, Basel, Switzerland
| | - David Shaw
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland.,Care and Public Health Research Institute, Maastricht University, Maastricht, The Netherlands
| | - Bettina Zimmermann
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland.,Institute of History and Ethics in Medicine, Technical University of Munich, Munich, Germany
| | - Stuart McLennan
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland.,Institute of History and Ethics in Medicine, Technical University of Munich, Munich, Germany
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11
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Kalantari S, Carlston C, Alsaleh N, Abdel-Salam GMH, Alkuraya F, Kato M, Matsumoto N, Miyatake S, Yamamoto T, Fares-Taie L, Rozet JM, Chassaing N, Vincent-Delorme C, Kang-Bellin A, McWalter K, Bupp C, Palen E, Wagner MD, Niceta M, Cesario C, Milone R, Kaplan J, Wadman E, Dobyns WB, Filges I. Expanding the KIF4A-associated phenotype. Am J Med Genet A 2021; 185:3728-3739. [PMID: 34346154 PMCID: PMC9291479 DOI: 10.1002/ajmg.a.62443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 01/30/2023]
Abstract
Kinesin super family (KIF) genes encode motor kinesins, a family of evolutionary conserved proteins, involved in intracellular trafficking of various cargoes. These proteins are critical for various physiological processes including neuron function and survival, ciliary function and ciliogenesis, and cell‐cycle progression. Recent evidence suggests that alterations in motor kinesin genes can lead to a variety of human diseases, including monogenic disorders. Neuropathies, impaired higher brain functions, structural brain abnormalities and multiple congenital anomalies (i.e., renal, urogenital, and limb anomalies) can result from pathogenic variants in many KIF genes. We expand the phenotype associated with KIF4A variants from developmental delay and intellectual disability with or without epilepsy to a congenital anomaly phenotype with hydrocephalus and various brain anomalies at the more severe end of phenotypic manifestations. Additional anomalies of the kidneys and urinary tract, congenital lymphedema, eye, and dental anomalies seem to be variably associated and overlap with clinical signs observed in other kinesinopathies. Caution still applies to missense variants, but hopefully, future work will further establish genotype–phenotype correlations in a larger number of patients and functional studies may give further insights into the complex function of KIF4A.
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Affiliation(s)
- Silvia Kalantari
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Colleen Carlston
- Division of Medical Genetics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Norah Alsaleh
- Division of Medical Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ghada M H Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Fowzan Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Shinagawa-ku, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Tatsuya Yamamoto
- Department of Pediatrics, Hirosaki University School of Medicine, Hirosaki, Japan
| | - Lucas Fares-Taie
- INSERM UMR1163, Imagine - Institute of Genetic Diseases, Paris Descartes University, Paris, France
| | - Jean-Michel Rozet
- INSERM UMR1163, Imagine - Institute of Genetic Diseases, Paris Descartes University, Paris, France
| | - Nicolas Chassaing
- Department of Medical Genetics, CHU Toulouse, Purpan Hospital, Toulouse, France
| | | | | | | | - Caleb Bupp
- Spectrum Health, Grand Rapids, Michigan, USA
| | - Emily Palen
- Autism & Developmental Medicine Institute, Danville, Pennsylvania, USA
| | - Monisa D Wagner
- Autism & Developmental Medicine Institute, Danville, Pennsylvania, USA
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Claudia Cesario
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Roberta Milone
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Calambrone, Pisa, Italy
| | - Julie Kaplan
- Division of Genetics, Department of Pediatrics, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, Delaware, USA
| | - Erin Wadman
- Division of Genetics, Department of Pediatrics, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, Delaware, USA
| | - William B Dobyns
- Division of Genetics, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
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12
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Siebert R, Scholz C, Zschocke J, Filges I, Porret N, Kohlschmidt N, Schlegelberger B. Altbewährt – und dennoch (fast) ganz neu. MED GENET-BERLIN 2020. [DOI: 10.1515/medgen-2020-2014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Kalantari S, Filges I. 'Kinesinopathies': emerging role of the kinesin family member genes in birth defects. J Med Genet 2020; 57:797-807. [PMID: 32430361 PMCID: PMC7691813 DOI: 10.1136/jmedgenet-2019-106769] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/23/2020] [Accepted: 03/28/2020] [Indexed: 12/19/2022]
Abstract
Motor kinesins are a family of evolutionary conserved proteins involved in intracellular trafficking of various cargoes, first described in the context of axonal transport. They were discovered to have a key importance in cell-cycle dynamics and progression, including chromosomal condensation and alignment, spindle formation and cytokinesis, as well as ciliogenesis and cilia function. Recent evidence suggests that impairment of kinesins is associated with a variety of human diseases consistent with their functions and evolutionary conservation. Through the advent of gene identification using genome-wide sequencing approaches, their role in monogenic disorders now emerges, particularly for birth defects, in isolated as well as multiple congenital anomalies. We can observe recurrent phenotypical themes such as microcephaly, certain brain anomalies, and anomalies of the kidney and urinary tract, as well as syndromic phenotypes reminiscent of ciliopathies. Together with the molecular and functional data, we suggest understanding these ‘kinesinopathies’ as a recognisable entity with potential value for research approaches and clinical care.
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Affiliation(s)
- Silvia Kalantari
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland .,Department of Clinical Research, University Hospital Basel and University of Basel, Basel, Switzerland
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14
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Filges I, Genewein A, Weber P, Meier S, Deigendesch N, Bruder E, Prüfer F, Tercanli S. Dual independent genetic etiologies in a lethal complex malformation phenotype. Ultraschall Med 2020; 41:112-114. [PMID: 32259861 DOI: 10.1055/a-1104-3625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Isabel Filges
- Medical Genetics, Institute for Medical Genetics and Pathology, University Hospital Basel and University of Basel, Switzerland
| | - Agnes Genewein
- Neonatology, University Children's Hospital Basel and University of Basel, Switzerland
| | - Peter Weber
- Pediatric Neurology and Developmental Medicine, University Children's Hospital Basel and University of Basel, Switzerland
| | - Stephanie Meier
- Medical Genetics, Institute for Medical Genetics and Pathology, University Hospital Basel and University of Basel, Switzerland
| | - Nikolaus Deigendesch
- Pathology, Institute for Medical Genetics and Pathology, University Hospital Basel and University of Basel, Switzerland
| | - Elisabeth Bruder
- Pathology, Institute for Medical Genetics and Pathology, University Hospital Basel and University of Basel, Switzerland
| | - Friederike Prüfer
- Pediatric Radiology, University Children's Hospital Basel and University of Basel, Switzerland
| | - Sevgi Tercanli
- Center for Prenatal Ultrasound, Freie Strasse, Basel and University of Basel, Switzerland
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15
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Meier N, Bruder E, Miny P, Tercanli S, Filges I. Expanding the spectrum of SMAD3-related phenotypes to agnathia-otocephaly. Mol Genet Genomic Med 2020; 8:e1178. [PMID: 32100971 PMCID: PMC7196462 DOI: 10.1002/mgg3.1178] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/12/2020] [Accepted: 01/30/2020] [Indexed: 12/20/2022] Open
Abstract
Background Agnathia‐otocephaly is a rare and lethal anomaly affecting craniofacial structures derived from the first pharyngeal arch. It is characterized by agnathia, microstomia, aglossia, and abnormally positioned auricles with or without associated anomalies. Variants affecting function of OTX2 and PRRX1, which together regulate the neural crest cells and the patterning of the first pharyngeal arch as well as skeletal and limb development, were identified to be causal for the anomaly in a few patients. Methods Family‐based exome sequencing (ES) on a fetus with severe agnathia‐otocephaly, cheilognathopalatoschisis, laryngeal hypoplasia, fused lung lobes and other organ abnormalities and mRNA expression analysis were performed. Results Exome sequencing detected a de novo SMAD3 missense variant in exon 6 (c.860G>A) associated with decreased mRNA expression. Variants in SMAD3 cause Loeys–Dietz syndrome 3 presenting with craniofacial anomalies such as mandibular hypoplasia, micro‐ or retro‐gnathia, bifid uvula and cleft palate as well as skeletal anomalies and arterial tortuosity. The SMAD3 protein acts as a transcriptional regulator in the transforming growth factor β (TGFB) and bone morphogenetic (BMP) signaling pathways, which play a key role in the development of craniofacial structures originating from the pharyngeal arches. Conclusion Agnathia‐otocephaly with or without associated anomalies may represent the severe end of a phenotypic spectrum related to variants in genes in the interacting SMAD/TGFB/BMP/SHH/FGF developmental pathways.
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Affiliation(s)
- Nicole Meier
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Elisabeth Bruder
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Peter Miny
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland
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16
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Filges I, Tercanli S, Hall JG. Fetal arthrogryposis: Challenges and perspectives for prenatal detection and management. Am J Med Genet C Semin Med Genet 2019; 181:327-336. [PMID: 31318155 DOI: 10.1002/ajmg.c.31723] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/23/2019] [Accepted: 06/27/2019] [Indexed: 12/28/2022]
Abstract
Antenatal identification of fetuses with multiple congenital contractures or arthrogryposis multiplex congenita (AMC) may be challenging. The first clinical sign is often reduced fetal movement and/or contractures, as seen on prenatal ultrasounds. This can be apparent at any point, from early to late pregnancy, may range from mild to severe involvement, with or without associated other structural anomalies. Possible etiologies and their prognosis need to be interpreted with respect to developmental timing. The etiology of AMC is highly heterogeneous and making the specific diagnosis will guide prognosis, counseling and prenatal and perinatal management. Current ultrasound practice identifies only approximately 25% of individuals with arthrogryposis prenatally before 24 weeks of pregnancy in a general obstetrics care population. There are currently no studies and guidelines that address the question of when and how to assess for fetal contractures and movements during pregnancy. The failure to identify fetuses with arthrogryposis before 24 weeks of pregnancy means that physicians and families are denied reproductive options and interventions that may improve outcome. We review current practice and recommend adjusting the current prenatal imaging and genetic diagnostic strategies to achieve early prenatal detection and etiologic diagnosis. We suggest exploring options for in utero therapy to increase fetal movement for ongoing pregnancies.
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Affiliation(s)
- Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Sevgi Tercanli
- Center for Prenatal Ultrasound, Basel and University of Basel, Basel, Switzerland
| | - Judith G Hall
- Department of Medical Genetics and Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
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17
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Reilly ML, Stokman MF, Magry V, Jeanpierre C, Alves M, Paydar M, Hellinga J, Delous M, Pouly D, Failler M, Martinovic J, Loeuillet L, Leroy B, Tantau J, Roume J, Gregory-Evans CY, Shan X, Filges I, Allingham JS, Kwok BH, Saunier S, Giles RH, Benmerah A. Loss-of-function mutations in KIF14 cause severe microcephaly and kidney development defects in humans and zebrafish. Hum Mol Genet 2019; 28:778-795. [PMID: 30388224 PMCID: PMC6381319 DOI: 10.1093/hmg/ddy381] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/28/2022] Open
Abstract
Mutations in KIF14 have previously been associated with either severe, isolated or syndromic microcephaly with renal hypodysplasia (RHD). Syndromic microcephaly-RHD was strongly reminiscent of clinical ciliopathies, relating to defects of the primary cilium, a signalling organelle present on the surface of many quiescent cells. KIF14 encodes a mitotic kinesin, which plays a key role at the midbody during cytokinesis and has not previously been shown to be involved in cilia-related functions. Here, we analysed four families with fetuses presenting with the syndromic form and harbouring biallelic variants in KIF14. Our functional analyses showed that the identified variants severely impact the activity of KIF14 and likely correspond to loss-of-function mutations. Analysis in human fetal tissues further revealed the accumulation of KIF14-positive midbody remnants in the lumen of ureteric bud tips indicating a shared function of KIF14 during brain and kidney development. Subsequently, analysis of a kif14 mutant zebrafish line showed a conserved role for this mitotic kinesin. Interestingly, ciliopathy-associated phenotypes were also present in mutant embryos, supporting a potential direct or indirect role for KIF14 at cilia. However, our in vitro and in vivo analyses did not provide evidence of a direct role for KIF14 in ciliogenesis and suggested that loss of kif14 causes ciliopathy-like phenotypes through an accumulation of mitotic cells in ciliated tissues. Altogether, our results demonstrate that KIF14 mutations result in a severe syndrome associating microcephaly and RHD through its conserved function in cytokinesis during kidney and brain development.
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Affiliation(s)
- Madeline Louise Reilly
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Imagine Institute, Paris, France
- Paris Diderot University, Department of Life Sciences, Paris, France
| | - Marijn F Stokman
- Department of Genetics, University Medical Center Utrecht, Utrecht University, JE Utrecht, Netherlands
| | - Virginie Magry
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Cecile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Marine Alves
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Mohammadjavad Paydar
- Institute for Research in Immunology and Cancer, Département de médecine, Université de Montréal, PO Box 6128, Station Centre-Ville, Montréal, QC, Canada
| | - Jacqueline Hellinga
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Marion Delous
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Daniel Pouly
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Marion Failler
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Jelena Martinovic
- Unit of Fetal Pathology, Antoine Béclère Hospital, AP-HP, Clamart, France
- INSERM U-788, Génétique/Neurogénétique, 94270 Le Kremlin-Bicêtre, France
| | - Laurence Loeuillet
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker–Enfants Malades, AP-HP, Paris, France
| | - Brigitte Leroy
- Service d'Anatomie et de Cytologie Pathologiques, Centre hospitalier intercommunal de Poissy, Saint Germain en Laye, France
| | - Julia Tantau
- Service d'Anatomie et de Cytologie Pathologiques, Centre hospitalier intercommunal de Poissy, Saint Germain en Laye, France
| | - Joelle Roume
- Service de Génétique, Centre hospitalier intercommunal de Poissy, 78100 Saint Germain en Laye, France
| | - Cheryl Y Gregory-Evans
- Department of Ophthalmology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xianghong Shan
- Department of Ophthalmology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital of Basel, University of Basel, Basel, Switzerland
- Department of Clinical Research, University Hospital of Basel, University of Basel, Basel, Switzerland
- Department of Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - John S Allingham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Benjamin H Kwok
- Institute for Research in Immunology and Cancer, Département de médecine, Université de Montréal, PO Box 6128, Station Centre-Ville, Montréal, QC, Canada
| | - Sophie Saunier
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Rachel H Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht University, 3512 JE Utrecht, Netherlands
| | - Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Imagine Institute, Paris, France
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18
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Meier N, Bruder E, Lapaire O, Hoesli I, Kang A, Hench J, Hoeller S, De Geyter J, Miny P, Heinimann K, Chaoui R, Tercanli S, Filges I. Exome sequencing of fetal anomaly syndromes: novel phenotype-genotype discoveries. Eur J Hum Genet 2019; 27:730-737. [PMID: 30679815 PMCID: PMC6461982 DOI: 10.1038/s41431-018-0324-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/02/2018] [Accepted: 12/04/2018] [Indexed: 01/05/2023] Open
Abstract
The monogenic etiology of most severe fetal anomaly syndromes is poorly understood. Our objective was to use exome sequencing (ES) to increase our knowledge on causal variants and novel candidate genes associated with specific fetal phenotypes. We employed ES in a cohort of 19 families with one or more fetuses presenting with a distinctive anomaly pattern and/or phenotype recurrence at increased risk for lethal outcomes. Candidate variants were identified in 12 families (63%); in 6 of them a definite diagnosis was achieved including known or novel variants in recognized disease genes (MKS1, OTX2, FGFR2, and RYR1) and variants in novel disease genes describing new fetal phenotypes (CENPF, KIF14). We identified variants likely causal after clinical and functional review (SMAD3, KIF4A, and PIGW) and propose novel candidate genes (PTK7, DNHD1, and TTC28) for early human developmental disease supported by functional and cross-species phenotyping evidence. We describe rare and novel fetal anomaly syndromes and highlight the diagnostic utility of ES, but also its contribution to discovery. The diagnostic yield of the future application of prenatal ES will depend on our ability to increase our knowledge on the specific phenotype–genotype correlations during fetal development.
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Affiliation(s)
- Nicole Meier
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Elisabeth Bruder
- University of Basel, Basel, Switzerland.,Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Olav Lapaire
- Department of Obstetrics and Gynecology, University Hospital Basel, Basel, Switzerland
| | - Irene Hoesli
- Department of Obstetrics and Gynecology, University Hospital Basel, Basel, Switzerland
| | - Anjeung Kang
- Centre for Prenatal Ultrasound, Freie Strasse, Basel, Switzerland
| | - Jürgen Hench
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Sylvia Hoeller
- University of Basel, Basel, Switzerland.,Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Julie De Geyter
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Peter Miny
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Karl Heinimann
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Rabih Chaoui
- Centre for Prenatal Diagnosis, Friedrichstrasse, Berlin, Germany
| | - Sevgi Tercanli
- University of Basel, Basel, Switzerland.,Centre for Prenatal Ultrasound, Freie Strasse, Basel, Switzerland
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland. .,Department of Clinical Research, University Hospital Basel, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
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19
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De Geyter J, Filges I, Tercanli S. A Diagnostic Challenge: Prenatal Ultrasound Findings in Severe Epidermolysis Bullosa. Ultraschall Med 2018; 39:600-601. [PMID: 30551226 DOI: 10.1055/a-0720-8983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Julie De Geyter
- Medical Genetics, Institute of Medical Genetics and Pathology, University-Hospital and University of Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University-Hospital and University of Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Department of Clinical Research, University-Hospital Basel, Basel, Switzerland
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20
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Meier N, Bruder E, Filges I. A novel homozygous splice‐site mutation in
RYR1
causes fetal hydrops and affects skeletal and smooth muscle development. Prenat Diagn 2017; 37:720-724. [DOI: 10.1002/pd.5073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/27/2017] [Accepted: 05/14/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Nicole Meier
- Medical Genetics University Hospital Basel Basel Switzerland
- Department of Clinical Research University Hospital Basel Basel Switzerland
- University of Basel Basel Switzerland
| | - Elisabeth Bruder
- University of Basel Basel Switzerland
- Pathology University Hospital Basel Basel Switzerland
| | - Isabel Filges
- Medical Genetics University Hospital Basel Basel Switzerland
- Department of Clinical Research University Hospital Basel Basel Switzerland
- University of Basel Basel Switzerland
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Strunk D, Weber P, Röthlisberger B, Filges I. Autism and intellectual disability in a patient with two microdeletions in 6q16: a contiguous gene deletion syndrome? Mol Cytogenet 2016; 9:88. [PMID: 27980676 PMCID: PMC5135825 DOI: 10.1186/s13039-016-0299-8] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/21/2016] [Indexed: 01/19/2023] Open
Abstract
Background Copy number variations play a significant role in the aetiology of developmental disabilities including non-syndromic intellectual disability and autism. Case presentation We describe a 19-year old patient with intellectual disability and autism for whom chromosomal microarray (CMA) analysis showed the unusual finding of two de novo microdeletions in cis position on chromosome 6q16.1q16.2 and 6q16.3. The two deletions span 10 genes, including FBXL4, POU3F2, PRDM13, CCNC, COQ3 and GRIK2. We compared phenotypes of patients with similar deletions and looked at the involvement of the genes in neuronal networks in order to determine the pathogenicity of our patient’s deletions. Conclusions We suggest that both deletions on 6q are causing his disease phenotype since they harbour several genes which are implicated in pathways of neuronal development and function. Further studies regarding the interaction between PRDM13 and GRIK2 specifically may be interesting.
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Affiliation(s)
- Daniela Strunk
- Medical Genetics, University Hospital Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland
| | - Peter Weber
- Division of Neuropediatrics and Developmental Pediatrics, University Children's Hospital, Spitalstrasse 33, CH-4056 Basel, Switzerland
| | - Benno Röthlisberger
- Medical Genetics, Department of Laboratory Medicine, Cantonal Hospital Aarau, Tellstrasse, CH-5001 Aarau, Switzerland
| | - Isabel Filges
- Medical Genetics, University Hospital Basel and University of Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland
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Filges I, Bruder E, Brandal K, Meier S, Undlien DE, Waage TR, Hoesli I, Schubach M, de Beer T, Sheng Y, Hoeller S, Schulzke S, Røsby O, Miny P, Tercanli S, Oppedal T, Meyer P, Selmer KK, Strømme P. Strømme Syndrome Is a Ciliary Disorder Caused by Mutations in CENPF. Hum Mutat 2016; 37:711. [DOI: 10.1002/humu.22997] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Isabel Filges
- Medical Genetics; University Hospital Basel; Basel Switzerland
| | | | - Kristin Brandal
- Department of Medical Genetics; Oslo University Hospital and University of Oslo; Oslo Norway
| | - Stephanie Meier
- Medical Genetics; University Hospital Basel; Basel Switzerland
| | - Dag Erik Undlien
- Department of Medical Genetics; Oslo University Hospital and University of Oslo; Oslo Norway
| | - Trine Rygvold Waage
- Section of Paediatric Neurohabilitation; Department of Clinical Neurosciences for Children; Oslo University Hospital; Ullevål, Oslo Norway
| | - Irene Hoesli
- Obstetrics and Gynecology; University Hospital Basel; Basel Switzerland
| | - Max Schubach
- Institute for Medical and Human Genetics; Charité-Universitätsmedizin Berlin; Berlin Germany
| | - Tjaart de Beer
- Biozentrum and Swiss Institute of Bioinformatics; University of Basel; Basel Switzerland
| | - Ying Sheng
- Department of Medical Genetics; Oslo University Hospital and University of Oslo; Oslo Norway
| | | | - Sven Schulzke
- Neonatology; University Children's Hospital Basel; Basel Switzerland
| | - Oddveig Røsby
- Department of Medical Genetics; Oslo University Hospital and University of Oslo; Oslo Norway
| | - Peter Miny
- Medical Genetics; University Hospital Basel; Basel Switzerland
| | | | - Truls Oppedal
- Department of Ophthalmology; Section for Pediatric Ophthalmology; Oslo University Hospital; Ullevål, Oslo Norway
| | - Peter Meyer
- Pathology; University Hospital Basel; Basel Switzerland
| | - Kaja Kristine Selmer
- Department of Medical Genetics; Oslo University Hospital and University of Oslo; Oslo Norway
| | - Petter Strømme
- Section for Clinical Neurosciences; Department of Pediatrics; Oslo University Hospital and University of Oslo; Oslo Norway
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Filges I, Bruder E, Brandal K, Meier S, Undlien DE, Waage TR, Hoesli I, Schubach M, de Beer T, Sheng Y, Hoeller S, Schulzke S, Røsby O, Miny P, Tercanli S, Oppedal T, Meyer P, Selmer KK, Strømme P. Strømme Syndrome Is a Ciliary Disorder Caused by Mutations in CENPF. Hum Mutat 2016; 37:359-63. [PMID: 26820108 DOI: 10.1002/humu.22960] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 09/21/2015] [Accepted: 01/08/2016] [Indexed: 11/10/2022]
Abstract
Strømme syndrome was first described by Strømme et al. (1993) in siblings presenting with "apple peel" type intestinal atresia, ocular anomalies and microcephaly. The etiology remains unknown to date. We describe the long-term clinical follow-up data for the original pair of siblings as well as two previously unreported siblings with a severe phenotype overlapping that of the Strømme syndrome including fetal autopsy results. Using family-based whole-exome sequencing, we identified truncating mutations in the centrosome gene CENPF in the two nonconsanguineous Caucasian sibling pairs. Compound heterozygous inheritance was confirmed in both families. Recently, mutations in this gene were shown to cause a fetal lethal phenotype, the phenotype and functional data being compatible with a human ciliopathy [Waters et al., 2015]. We show for the first time that Strømme syndrome is an autosomal-recessive disease caused by mutations in CENPF that can result in a wide phenotypic spectrum.
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Affiliation(s)
- Isabel Filges
- Medical Genetics, University Hospital Basel, Basel, Switzerland
| | | | - Kristin Brandal
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Stephanie Meier
- Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Dag Erik Undlien
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Trine Rygvold Waage
- Section of Paediatric Neurohabilitation, Department of Clinical Neurosciences for Children, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Irene Hoesli
- Obstetrics and Gynecology, University Hospital Basel, Basel, Switzerland
| | - Max Schubach
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tjaart de Beer
- Biozentrum and Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland
| | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Sylvia Hoeller
- Pathology, University Hospital Basel, Basel, Switzerland
| | - Sven Schulzke
- Neonatology, University Children's Hospital Basel, Basel, Switzerland
| | - Oddveig Røsby
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Peter Miny
- Medical Genetics, University Hospital Basel, Basel, Switzerland
| | | | - Truls Oppedal
- Department of Ophthalmology, Section for Pediatric Ophthalmology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Peter Meyer
- Pathology, University Hospital Basel, Basel, Switzerland
| | - Kaja Kristine Selmer
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Petter Strømme
- Section for Clinical Neurosciences, Department of Pediatrics, Oslo University Hospital and University of Oslo, Oslo, Norway
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Tercanli S, Filges I. An Appeal for Ultrasound and Current Guidelines. Ultraschall Med 2015; 36:424-426. [PMID: 26468769 DOI: 10.1055/s-0035-1553777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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Tercanli S, Miny P, Filges I. Increased Fetal Nuchal Translucency - Also a Risk for a Rare Submicroscopic Chromosomal Abnormalities. Ultraschall Med 2015; 36:419-420. [PMID: 26759849 DOI: 10.1055/s-0035-1552269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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Filges I, Manokhina I, Peñaherrera MS, McFadden DE, Louie K, Nosova E, Friedman JM, Robinson WP. Recurrent triploidy due to a failure to complete maternal meiosis II: whole-exome sequencing reveals candidate variants. Mol Hum Reprod 2014; 21:339-46. [PMID: 25504873 DOI: 10.1093/molehr/gau112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [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: 08/12/2014] [Accepted: 12/05/2014] [Indexed: 01/16/2023] Open
Abstract
Triploidy is a relatively common cause of miscarriage; however, recurrent triploidy has rarely been reported. A healthy 34-year-old woman was ascertained because of 18 consecutive miscarriages with triploidy found in all 5 karyotyped losses. Molecular results in a sixth loss were also consistent with triploidy. Genotyping of markers near the centromere on multiple chromosomes suggested that all six triploid conceptuses occurred as a result of failure to complete meiosis II (MII). The proband's mother had also experienced recurrent miscarriage, with a total of 18 miscarriages. Based on the hypothesis that an inherited autosomal-dominant maternal predisposition would explain the phenotype, whole-exome sequencing of the proband and her parents was undertaken to identify potential candidate variants. After filtering for quality and rarity, potentially damaging variants shared between the proband and her mother were identified in 47 genes. Variants in genes coding for proteins implicated in oocyte maturation, oocyte activation or polar body extrusion were then prioritized. Eight of the most promising candidate variants were confirmed by Sanger sequencing. These included a novel change in the PLCD4 gene, and a rare variant in the OSBPL5 gene, which have been implicated in oocyte activation upon fertilization and completion of MII. Several variants in genes coding proteins playing a role in oocyte maturation and early embryonic development were also identified. The genes identified may be candidates for the study in other women experiencing recurrent triploidy or recurrent IVF failure.
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Affiliation(s)
- I Filges
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4 Medical Genetics, Department of Biomedicine, University Hospital Basel, Basel 4031, Switzerland
| | - I Manokhina
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - M S Peñaherrera
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - D E McFadden
- Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4 Department of Pathology, University of British Columbia, Vancouver, BC, Canada V6T 2B5
| | - K Louie
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - E Nosova
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada V5Z 4H4 Centre for Applied Neurogenetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - J M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - W P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4
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Chaudhry A, Noor A, Degagne B, Baker K, Bok LA, Brady AF, Chitayat D, Chung BH, Cytrynbaum C, Dyment D, Filges I, Helm B, Hutchison HT, Jeng LJB, Laumonnier F, Marshall CR, Menzel M, Parkash S, Parker MJ, Raymond LF, Rideout AL, Roberts W, Rupps R, Schanze I, Schrander-Stumpel CTRM, Speevak MD, Stavropoulos DJ, Stevens SJC, Thomas ERA, Toutain A, Vergano S, Weksberg R, Scherer SW, Vincent JB, Carter MT. Phenotypic spectrum associated withPTCHD1deletions and truncating mutations includes intellectual disability and autism spectrum disorder. Clin Genet 2014; 88:224-33. [DOI: 10.1111/cge.12482] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 11/28/2022]
Affiliation(s)
- A. Chaudhry
- Department of Pediatrics; Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto Ontario Canada
| | - A. Noor
- Department of Pathology and Laboratory Medicine; The Hospital for Sick Children; Toronto Ontario Canada
- Molecular Neuropsychiatry and Development Lab; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health; Toronto Ontario Canada
| | - B. Degagne
- Molecular Neuropsychiatry and Development Lab; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health; Toronto Ontario Canada
| | - K. Baker
- Department of Medical Genetics; Cambridge UK
- Institute for Medical Research Wellcome Trust; University of Cambridge; Cambridge UK
| | - L. A. Bok
- Department of Clinical Genetics, Unit of Cytogenetics; Maastricht University Medical Center; Maastricht The Netherlands
| | - A. F. Brady
- North West Thames Regional Genetics Service; Northwick Park Hospital; Harrow UK
| | - D. Chitayat
- Department of Pediatrics; Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto Ontario Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital; University of Toronto; Toronto Ontario Canada
| | - B. H. Chung
- Department of Pediatrics and Adolescent Medicine, Department of Obstetrics and Gynaecology, Centre for Reproduction, Development and Growth, Centre for Genomic Sciences; The University of Hong Kong; Pok Fu Lam, Hong Kong
| | - C. Cytrynbaum
- Department of Pediatrics; Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto Ontario Canada
- Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - D. Dyment
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
| | - I. Filges
- Division of Medical Genetics, Department of Biomedicine; University Hospital Basel; Basel Switzerland
| | - B. Helm
- Division of Medical Genetics and Metabolism; Children's Hospital of The King's Daughters/Eastern Virginia Medical School; Norfolk VA USA
| | - H. T. Hutchison
- Departments of Neurology and Pediatrics; UCSF Fresno Medical Education Program; San Francisco CA USA
| | - L. J. B. Jeng
- Department of Laboratory Medicine; University of California; San Francisco CA USA
| | - F. Laumonnier
- UMR_INSERM U930 Faculté de Médecine; Université François Rabelais; Tours France
| | - C. R. Marshall
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Ontario Canada
| | | | - S. Parkash
- Maritime Medical Genetics Service; IWK Health Centre; Halifax Nova Scotia Canada
- Dalhousie University Halifax; Nova Scotia Canada
| | - M. J. Parker
- Sheffield Clinical Genetics Service; Sheffield Children's Hospital; Western Bank Sheffield UK
| | - L. F. Raymond
- Department of Medical Genetics; Cambridge UK
- Institute for Medical Research Wellcome Trust; University of Cambridge; Cambridge UK
| | - A. L. Rideout
- Maritime Medical Genetics Service; IWK Health Centre; Halifax Nova Scotia Canada
| | - W. Roberts
- Autism Research Unit; The Hospital for Sick Children; Toronto Ontario Canada
| | - R. Rupps
- Department of Medical Genetics, Children's and Women's Health Centre; University of British Columbia; Vancouver BC Canada
| | - I. Schanze
- Institute of Human Genetics; University Hospital Magedeburg; Magedeburg Germany
| | - C. T. R. M. Schrander-Stumpel
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW); Maastricht UMC+; Maastricht The Netherlands
| | - M. D. Speevak
- Credit Valley Site, Trillium Health Partners, Department of Laboratory Medicine and Pathobiology; University of Toronto; Toronto Onatario Canada
| | - D. J. Stavropoulos
- Department of Pathology and Laboratory Medicine; The Hospital for Sick Children; Toronto Ontario Canada
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Ontario Canada
| | - S. J. C. Stevens
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW); Maastricht UMC+; Maastricht The Netherlands
| | - E. R. A. Thomas
- Clinical Genetics Department; Guy's and St Thomas' NHS Foundation Trust; London UK
| | - A. Toutain
- UMR_INSERM U930 Faculté de Médecine; Université François Rabelais; Tours France
- Service de Génétique; Centre Hospitalo-Universitaire; Tours France
| | - S. Vergano
- Division of Medical Genetics and Metabolism; Children's Hospital of The King's Daughters/Eastern Virginia Medical School; Norfolk VA USA
| | - R. Weksberg
- Department of Pediatrics; Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto Ontario Canada
- Institute of Medical Science; Toronto Ontario Canada
- McLaughlin Centre and Department of Molecular Genetics; Toronto Ontario Canada
| | - S. W. Scherer
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Ontario Canada
- Institute of Medical Science; Toronto Ontario Canada
- McLaughlin Centre and Department of Molecular Genetics; Toronto Ontario Canada
| | - J. B. Vincent
- Molecular Neuropsychiatry and Development Lab; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health; Toronto Ontario Canada
- Institute of Medical Science; Toronto Ontario Canada
- Department of Psychiatry; University of Toronto; Toronto Ontario Canada
| | - M. T. Carter
- Department of Pediatrics; Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto Ontario Canada
- Autism Research Unit; The Hospital for Sick Children; Toronto Ontario Canada
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Filges I, Friedman JM. Exome sequencing for gene discovery in lethal fetal disorders--harnessing the value of extreme phenotypes. Prenat Diagn 2014; 35:1005-9. [PMID: 25046514 DOI: 10.1002/pd.4464] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/14/2014] [Accepted: 07/16/2014] [Indexed: 12/18/2022]
Abstract
Massively parallel sequencing has revolutionized our understanding of Mendelian disorders, and many novel genes have been discovered to cause disease phenotypes when mutant. At the same time, next-generation sequencing approaches have enabled non-invasive prenatal testing of free fetal DNA in maternal blood. However, little attention has been paid to using whole exome and genome sequencing strategies for gene identification in fetal disorders that are lethal in utero, because they can appear to be sporadic and Mendelian inheritance may be missed. We present challenges and advantages of applying next-generation sequencing approaches to gene discovery in fetal malformation phenotypes and review recent successful discovery approaches. We discuss the implication and significance of recessive inheritance and cross-species phenotyping in fetal lethal conditions. Whole exome sequencing can be used in individual families with undiagnosed lethal congenital anomaly syndromes to discover causal mutations, provided that prior to data analysis, the fetal phenotype can be correlated to a particular developmental pathway in embryogenesis. Cross-species phenotyping allows providing further evidence for causality of discovered variants in genes involved in those extremely rare phenotypes and will increase our knowledge about normal and abnormal human developmental processes. Ultimately, families will benefit from the option of early prenatal diagnosis.
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Affiliation(s)
- Isabel Filges
- Medical Genetics, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.,Department of Medical Genetics, Children's and Women's Hospital, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
| | - Jan M Friedman
- Department of Medical Genetics, Children's and Women's Hospital, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
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Filges I, Sparagana S, Sargent M, Selby K, Schlade-Bartusiak K, Lueder GT, Robichaux-Viehoever A, Schlaggar BL, Shimony JS, Shinawi M. Brain MRI abnormalities and spectrum of neurological and clinical findings in three patients with proximal 16p11.2 microduplication. Am J Med Genet A 2014; 164A:2003-12. [PMID: 24891046 DOI: 10.1002/ajmg.a.36605] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [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: 11/28/2013] [Accepted: 04/16/2014] [Indexed: 11/06/2022]
Abstract
The phenotype of recurrent ∼600 kb microdeletion and microduplication on proximal 16p11.2 is characterized by a spectrum of neurodevelopmental impairments including developmental delay and intellectual disability, epilepsy, autism and psychiatric disorders which are all subject to incomplete penetrance and variable expressivity. A variety of brain MRI abnormalities were reported in patients with 16p11.2 rearrangements, but no systematic correlation has been studied among patients with similar brain anomalies, their neurodevelopmental and clinical phenotypes. We present three patients with the proximal 16p11.2 microduplication exhibiting significant developmental delay, anxiety disorder and other variable clinical features. Our patients have abnormal brain MRI findings of cerebral T2 hyperintense foci (3/3) and ventriculomegaly (2/3). The neuroradiological or neurological findings in two cases prompted an extensive diagnostic work-up. One patient has exhibited neurological regression and progressive vision impairment and was diagnosed with juvenile neuronal ceroid-lipofuscinosis. We compare the clinical course and phenotype of these patients in regard to the clinical significance of the cerebral lesions and the need for MRI surveillance. We conclude that in all three patients the lesions were not progressive, did not show any sign of malignant transformation and could not be correlated to specific clinical features. We discuss potential etiologic mechanisms that may include overexpression of genes within the duplicated region involved in control of cell proliferation and complex molecular mechanisms such as the MAPK/ERK pathway. Systematic studies in larger cohorts are needed to confirm our observation and to establish the prevalence and clinical significance of these neuroanatomical abnormalities in patients with 16p11.2 duplications.
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Affiliation(s)
- Isabel Filges
- Department of Medical Genetics, BC Children's and Women's Hospital, Child and Family Research Institute, University of British Columbia, Vancouver, Canada; Division of Medical Genetics, Department of Biomedicine, University Hospitals Basel, Basel, Switzerland
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Al-Kateb H, Khanna G, Filges I, Hauser N, Grange DK, Shen J, Smyser CD, Kulkarni S, Shinawi M. Scoliosis and vertebral anomalies: additional abnormal phenotypes associated with chromosome 16p11.2 rearrangement. Am J Med Genet A 2014; 164A:1118-26. [PMID: 24458548 DOI: 10.1002/ajmg.a.36401] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [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: 09/11/2013] [Accepted: 11/24/2013] [Indexed: 01/23/2023]
Abstract
The typical chromosome 16p11.2 rearrangements are estimated to occur at a frequency of approximately 0.6% of all samples tested clinically and have been identified as a major cause of autism spectrum disorders, developmental delay, behavioral abnormalities, and seizures. Careful examination of patients with these rearrangements revealed association with abnormal head size, obesity, dysmorphism, and congenital abnormalities. In this report, we extend this list of phenotypic abnormalities to include scoliosis and vertebral anomalies. We present detailed characterization of phenotypic and radiological data of 10 new patients, nine with the 16p11.2 deletion and one with the duplication within the coordinates chr16:29,366,195 and 30,306,956 (hg19) with a minimal size of 555 kb. We discuss the phenotypical and radiological findings in our patients and review 5 previously reported patients with 16p11.2 rearrangement and similar skeletal abnormalities. Our data suggest that patients with the recurrent 16p11.2 rearrangement have increased incidence of scoliosis and vertebral anomalies. However, additional studies are required to confirm this observation and to establish the incidence of these anomalies. We discuss the potential implications of our findings on the diagnosis, surveillance and genetic counseling of patients with 16p11.2 rearrangement.
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Affiliation(s)
- Hussam Al-Kateb
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
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Filges I, Nosova E, Bruder E, Tercanli S, Townsend K, Gibson WT, Röthlisberger B, Heinimann K, Hall JG, Gregory-Evans CY, Wasserman WW, Miny P, Friedman JM. Exome sequencing identifies mutations in KIF14 as a novel cause of an autosomal recessive lethal fetal ciliopathy phenotype. Clin Genet 2013; 86:220-8. [PMID: 24128419 DOI: 10.1111/cge.12301] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [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: 08/17/2013] [Revised: 09/29/2013] [Accepted: 10/11/2013] [Indexed: 12/21/2022]
Abstract
Gene discovery using massively parallel sequencing has focused on phenotypes diagnosed postnatally such as well-characterized syndromes or intellectual disability, but is rarely reported for fetal disorders. We used family-based whole-exome sequencing in order to identify causal variants for a recurrent pattern of an undescribed lethal fetal congenital anomaly syndrome. The clinical signs included intrauterine growth restriction (IUGR), severe microcephaly, renal cystic dysplasia/agenesis and complex brain and genitourinary malformations. The phenotype was compatible with a ciliopathy, but not diagnostic of any known condition. We hypothesized biallelic disruption of a gene leading to a defect related to the primary cilium. We identified novel autosomal recessive truncating mutations in KIF14 that segregated with the phenotype. Mice with autosomal recessive mutations in the same gene have recently been shown to have a strikingly similar phenotype. Genotype-phenotype correlations indicate that the function of KIF14 in cell division and cytokinesis can be linked to a role in primary cilia, supported by previous cellular and model organism studies of proteins that interact with KIF14. We describe the first human phenotype, a novel lethal ciliary disorder, associated with biallelic inactivating mutations in KIF14. KIF14 may also be considered a candidate gene for allelic viable ciliary and/or microcephaly phenotypes.
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Affiliation(s)
- I Filges
- Department of Medical Genetics, University of British Columbia, and Child and Family Research Institute, Vancouver, Canada; Division of Medical Genetics, Department of Biomedicine, University Hospital, Basel, Switzerland
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Filges I, Hall JG. Failure to identify antenatal multiple congenital contractures and fetal akinesia - proposal of guidelines to improve diagnosis. Prenat Diagn 2013; 33:61-74. [DOI: 10.1002/pd.4011] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Isabel Filges
- Department of Medical Genetics, BC Children's and Women's Hospital, Child and Family Research Institute; University of British Columbia; Vancouver Canada
- Division of Medical Genetics, University Children's Hospital and Department of Biomedicine; University of Basel; Basel Switzerland
| | - Judith G. Hall
- Department of Medical Genetics, BC Children's and Women's Hospital, Child and Family Research Institute; University of British Columbia; Vancouver Canada
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Filges I, Kang A, Klug V, Wenzel F, Heinimann K, Tercanli S, Miny P. Array comparative genomic hybridization in prenatal diagnosis of first trimester pregnancies at high risk for chromosomal anomalies. Mol Cytogenet 2012; 5:38. [PMID: 22979998 PMCID: PMC3462716 DOI: 10.1186/1755-8166-5-38] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/30/2012] [Indexed: 01/14/2023] Open
Abstract
Objective To describe the diagnostic performance of array comparative genomic hybridization (aCGH) as a potential first line diagnostic method in first trimester high risk pregnancies. Method In a retrospective study we performed aCGH using a targeted array BAC platform (Constitutional Chip® 4.0, PerkinElmer, Turku Finland, median resolution 600 kB) and the Affymetrix Cytogenetics® Whole Genome 2.7 M array (at a resolution of 400kB) on 100 anonymized prenatal samples from first trimester high risk pregnancies with normal conventional karyotype. We studied the technical feasibility and turn-around-time as well as the detection rate of pathogenic submicroscopic chromosome anomalies and CNVs of unknown significance. Results We obtained results in 98 of 100 samples in 3 to a maximum of 5 days after DNA extraction. At the given resolution we did not identify any additional pathogenic CNVs but two CNVs of unknown significance in the chromosomal regions 1q21.1q21.2 (deletion) and 5p15.33 (duplication) (2%). Conclusion In accordance with a growing number of reports this study supports the concept that aCGH at a resolution of 400-600kB may be used as a first line prenatal diagnostic test with high diagnostic safety and rapid turn-around time in high-risk first trimester pregnancies. Detection rate of CNVs of unknown significance, considered as a major hindrance for replacing conventional karyotyping by aCGH, is 2%, but the diagnosis of additional submicroscopic anomalies in this heterogeneous group of patients seems to be rare.
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Affiliation(s)
- Isabel Filges
- Dr, med, Isabel Filges, Division of Medical Genetics, University Children's Hospital and Department of Biomedicine, University of Basel, Burgfelderstrasse 101, Building J, CH-4055, Basel, Switzerland.
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Filges I, Hall JG. We are failing to identify disorders of fetal movement - why? Prenat Diagn 2012; 32:919-20. [DOI: 10.1002/pd.3944] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 07/01/2012] [Indexed: 12/21/2022]
Affiliation(s)
- Isabel Filges
- Department of Medical Genetics, BC Children's and Women's Hospital, Child and Family Research Institute; University of British Columbia; Vancouver Canada
| | - Judith G. Hall
- Department of Medical Genetics, BC Children's and Women's Hospital, Child and Family Research Institute; University of British Columbia; Vancouver Canada
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Filges I, Suda L, Weber P, Datta AN, Fischer D, Dill P, Glanzmann R, Benzing J, Hegi L, Wenzel F, Huber AR, Mori AC, Miny P, Röthlisberger B. High resolution array in the clinical approach to chromosomal phenotypes. Gene 2012; 495:163-9. [PMID: 22240311 DOI: 10.1016/j.gene.2011.12.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 12/11/2022]
Abstract
Array genomic hybridization (AGH) has recently been implemented as a diagnostic tool for the detection of submicroscopic copy number variants (CNVs) in patients with developmental disorders. However, there is no consensus regarding the choice of the platform, the minimal resolution needed and systematic interpretation of CNVs. We report our experience in the clinical diagnostic use of high resolution AGH up to 100 kb on 131 patients with chromosomal phenotypes but previously normal karyotype. We evaluated the usefulness in our clinics and laboratories by the detection rate of causal CNVs and CNVs of unknown clinical significance and to what extent their interpretation would challenge the systematic use of high-resolution arrays in clinical application. Prioritizing phenotype-genotype correlation in our interpretation strategy to criteria previously described, we identified 33 (25.2%) potentially pathogenic aberrations. 16 aberrations were confirmed pathogenic (16.4% syndromic, 8.5% non-syndromic patients); 9 were new and individual aberrations, 3 of them were pathogenic although inherited and one is as small as approx 200 kb. 13 of 16 further CNVs of unknown significance were classified likely benign, for 3 the significance remained unclear. High resolution array allows the detection of up to 12.2% of pathogenic aberrations in a diagnostic clinical setting. Although the majority of aberrations are larger, the detection of small causal aberrations may be relevant for family counseling. The number of remaining unclear CNVs is limited. Careful phenotype-genotype correlations of the individual CNVs and clinical features are challenging but remain a hallmark for CNV interpretation.
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Filges I, Bischof-Renner A, Röthlisberger B, Potthoff C, Glanzmann R, Günthard J, Schneider J, Huber AR, Zumsteg U, Miny P, Szinnai G. Panhypopituitarism presenting as life-threatening heart failure caused by an inherited microdeletion in 1q25 including LHX4. Pediatrics 2012; 129:e529-34. [PMID: 22232309 DOI: 10.1542/peds.2010-3849] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Clinical presentation of hypopituitarism in the neonate may be variable, ranging from absent to severe nonspecific symptoms and may be life-threatening in patients with adrenocorticotropic hormone deficiency. The LIM homeobox gene 4 (LHX4) transcription factor regulates early embryonic development of the anterior pituitary gland. Autosomal dominant mutations in LHX4 cause congenital hypopituitarism with variable combined pituitary hormone deficiency (CPHD). We report on a neonate with unexplained heart failure and minor physical anomalies, suggesting a midline defect. She was diagnosed with complete CPHD. Cardiac function was rescued by replacement with hydrocortisone and thyroxine; hypoglycaemia stopped under growth hormone therapy. Magnetic resonance imaging revealed a dysgenetic pituitary gland suggesting an early developmental defect. Array comparative genomic hybridization showed a maternally inherited 1.5-megabase microdeletion in 1q25.2q25.3, including the LHX4 gene. Haploinsufficiency of LHX4 likely explains the predominant pituitary phenotype in the proposita and we suggest variable intrafamilial penetrance of the inherited microdeletion. To the best of our knowledge, we are the first to report on heart failure as a rare nonspecific symptom of treatable CPHD in the newborn. Variably penetrant pituitary insufficiency, including this severe and atypical presentation, can be correlated with LHX4 insufficiency and highlights the role of LHX4 for pituitary development.
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Affiliation(s)
- Isabel Filges
- Division of Medical Genetics, University Children's Hospital and Department of Biomedicine, Burgfelderstrasse 101, Building J, CH- 4055 Basel, Switzerland.
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Filges I, Miny P. Author's reply to Toutain's correspondence. Prenat Diagn 2011. [DOI: 10.1002/pd.2878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Isabel Filges
- Division of Medical Genetics; University Children's Hospital and Department of Biomedicine; Basel Switzerland
| | - Peter Miny
- Division of Medical Genetics; University Children's Hospital and Department of Biomedicine; Basel Switzerland
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Filges I, Kang A, Hench J, Wenzel F, Bruder E, Miny P, Tercanli S. Fetal polydactyly: a study of 24 cases ascertained by prenatal sonography. J Ultrasound Med 2011; 30:1021-1029. [PMID: 21705736 DOI: 10.7863/jum.2011.30.7.1021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Records of 24 pregnancies with fetal polydactyly were reviewed for the type of polydactyly, family history, associated sonographic findings, genetic testing, and postnatal/postmortem examination findings. The importance of fetal polydactyly can be mainly elucidated by the family history and absent or associated anomalies on a specialized malformation scan. Fetal karyotyping diagnoses frequent chromosomal anomalies in about half of cases with additional malformations, and array comparative genomic hybridization may be a future means of detecting cryptic chromosomal aberrations. Syndromic disorders of monogenic origin demand a careful interdisciplinary clinical assessment for establishing a clinical diagnosis and prognosis for the outcome of the child.
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Affiliation(s)
- Isabel Filges
- Division of Medical Genetics and Department of Biomedicine, University Children's Hospital, Burgfelderstrasse 101, Building J, 4005 Basel, Switzerland.
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Filges I, Kang A, Klug V, Wenzel F, Heinimann K, Tercanli S, Miny P. aCGH on chorionic villi mirrors the complexity of fetoplacental mosaicism in prenatal diagnosis. Prenat Diagn 2011; 31:473-8. [DOI: 10.1002/pd.2721] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 01/08/2011] [Accepted: 01/12/2011] [Indexed: 11/10/2022]
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Vogler C, Gschwind L, Röthlisberger B, Huber A, Filges I, Miny P, Auschra B, Stetak A, Demougin P, Vukojevic V, Kolassa IT, Elbert T, de Quervain DJF, Papassotiropoulos A. Microarray-based maps of copy-number variant regions in European and sub-Saharan populations. PLoS One 2010; 5:e15246. [PMID: 21179565 PMCID: PMC3002949 DOI: 10.1371/journal.pone.0015246] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 11/16/2010] [Indexed: 02/03/2023] Open
Abstract
The genetic basis of phenotypic variation can be partially explained by the presence of copy-number variations (CNVs). Currently available methods for CNV assessment include high-density single-nucleotide polymorphism (SNP) microarrays that have become an indispensable tool in genome-wide association studies (GWAS). However, insufficient concordance rates between different CNV assessment methods call for cautious interpretation of results from CNV-based genetic association studies. Here we provide a cross-population, microarray-based map of copy-number variant regions (CNVRs) to enable reliable interpretation of CNV association findings. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to scan the genomes of 1167 individuals from two ethnically distinct populations (Europe, N = 717; Rwanda, N = 450). Three different CNV-finding algorithms were tested and compared for sensitivity, specificity, and feasibility. Two algorithms were subsequently used to construct CNVR maps, which were also validated by processing subsamples with additional microarray platforms (Illumina 1M-Duo BeadChip, Nimblegen 385K aCGH array) and by comparing our data with publicly available information. Both algorithms detected a total of 42669 CNVs, 74% of which clustered in 385 CNVRs of a cross-population map. These CNVRs overlap with 862 annotated genes and account for approximately 3.3% of the haploid human genome. We created comprehensive cross-populational CNVR-maps. They represent an extendable framework that can leverage the detection of common CNVs and additionally assist in interpreting CNV-based association studies.
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Affiliation(s)
- Christian Vogler
- Department of Psychology, University of Basel, and Department of Biomedicine, University Children's Hospital, Basel, Switzerland.
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Filges I, Röthlisberger B, Blattner A, Boesch N, Demougin P, Wenzel F, Huber AR, Heinimann K, Weber P, Miny P. Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism. Clin Genet 2010; 79:79-85. [PMID: 21091464 DOI: 10.1111/j.1399-0004.2010.01590.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Submicroscopic chromosomal anomalies play an important role in the aetiology of intellectual disability (ID) and have been shown to account for up to 10% of non-syndromic forms. We present a family with two affected boys compatible with X-linked inheritance of a phenotype of severe neurodevelopmental disorder co-segregating with a deletion in Xp22.11 exclusively containing the PTCHD1 gene. Although the exact function of this gene is unknown to date, the structural overlap of its encoded patched domain-containing protein 1, the transmembrane protein involved in the sonic hedgehog pathway, and its expression in human cortex and cerebellum as well as in mice and drosophila brain suggests a causative role of its nullisomy in the developmental phenotype of our family. Our findings support the recent notions that PTCHD1 may play a role in X-linked intellectual disability (XLID) and autism disorders.
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Affiliation(s)
- I Filges
- Division of Medical Genetics, University Children's Hospital and Department of Biomedicine, Römergasse 8,Basel, Switzerland.
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Filges I, Shimojima K, Okamoto N, Röthlisberger B, Weber P, Huber AR, Nishizawa T, Datta AN, Miny P, Yamamoto T. Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel-Giedion syndrome. J Med Genet 2010; 48:117-22. [PMID: 21037274 DOI: 10.1136/jmg.2010.084582] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Mutations of the SET binding protein 1 gene (SETBP1) on 18q12.3 have recently been reported to cause Schinzel-Giedion syndrome (SGS). As rare 18q interstitial deletions affecting multiple genes including SETBP1 correlate with a milder phenotype, including minor physical anomalies and developmental and expressive speech delay, mutations in SETBP1 are thought to result in a gain-of-function or a dominant-negative effect. However, the consequence of the SETBP1 loss-of-function has not yet been well described. METHODS Microarray-based comparative genomic hybridisation (aCGH) analyses were performed to identify genetic causes for developmental and expressive speech delay in two patients. SETBP1 expression in fibroblasts obtained from one of the patients was analysed by real-time RT-PCR and western blotting. A cohort study to identify nucleotide changes in SETBP1 was performed in 142 Japanese patients with developmental delay. RESULTS aCGH analyses identified submicroscopic deletions of less than 1 Mb exclusively containing SETBP1. Both patients show global developmental, expressive language delay and minor facial anomalies. Decreased expression of SETBP1 was identified in the patient's skin fibroblasts. No pathogenic mutation of SETBP1 was identified in the cohort study. CONCLUSION SETBP1 expression was reduced in a patient with SETBP1 haploinsufficiency, indicating that the SETBP1 deletion phenotype is allele dose sensitive. In correlation with the exclusive deletion of SETBP1, this study delimits a milder phenotype distinct from SGS overlapping with the previously described phenotype of del(18)(q12.2q21.1) syndrome including global developmental, expressive language delay and distinctive facial features. These findings support the hypothesis that mutations in SETBP1 causing SGS may have a gain-of-function or a dominant-negative effect, whereas haploinsufficiency or loss-of-function mutations in SETBP1 cause a milder phenotype.
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Affiliation(s)
- Isabel Filges
- Division of Medical Genetics, University Children's Hospital and Department of Biomedicine, Basel, Switzerland
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Filges I, Röthlisberger B, Boesch N, Weber P, Wenzel F, Huber AR, Heinimann K, Miny P. Interstitial deletion 1q42 in a patient with agenesis of corpus callosum: Phenotype-genotype comparison to the 1q41q42 microdeletion suggests a contiguous 1q4 syndrome. Am J Med Genet A 2010; 152A:987-93. [PMID: 20358614 DOI: 10.1002/ajmg.a.33330] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interstitial deletions of 1q4 are rare and present with different deletion breakpoints and variable phenotype. We report on the clinical and molecular cytogenetic findings in a girl with minor anomalies, midline defects including prenatally ascertained agenesis of the corpus callosum, epilepsy and developmental delay. A de novo 5.45 Mb deletion almost exclusively located within 1q42 was found to cause this phenotype, which shows significant overlap with the microdeletion 1q41q42 syndrome reported in a few patients except for the agenesis of the corpus callosum. However, deletions in patients with the 1q41q42 syndrome mainly extend into the 1q41 region with a region of overlap including the DISP1 gene involved in the SHH pathway, which is not part of the 1q42 deletion in our patient. We suggest that an interaction of genes involved in pathways of embryonic development rather than haploinsufficiency of single genes in the so-called critical regions is causing complex malformation syndromes due to cytogenetic microaberrations in the 1q4 region.
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Affiliation(s)
- Isabel Filges
- Division of Medical Genetics, Department of Biomedicine, University Children's Hospital, Basel, Switzerland.
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Filges I, Röthlisberger B, Noppen C, Boesch N, Wenzel F, Necker J, Binkert F, Huber AR, Heinimann K, Miny P. Familial 14.5 Mb interstitial deletion 13q21.1-13q21.33: Clinical and array-CGH study of a benign phenotype in a three-generation family. Am J Med Genet A 2009; 149A:237-41. [DOI: 10.1002/ajmg.a.32622] [Citation(s) in RCA: 14] [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] [Indexed: 11/08/2022]
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Filges I, Röthlisberger B, Wenzel F, Heinimann K, Huber AR, Miny P. Mosaic ring chromosome 8: clinical and array-CGH findings in partial trisomy 8. Am J Med Genet A 2008; 146A:2837-41. [PMID: 18924172 DOI: 10.1002/ajmg.a.32520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Isabel Filges
- Division of Medical Genetics, Department of Biomedicine, University Children's Hospital, Basel, Switzerland.
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Martinet D, Filges I, Besuchet Schmutz N, Morris MA, Gaide AC, Dahoun S, Bottani A, Addor MC, Antonarakis SE, Beckmann JS, Béna F. Subtelomeric 6p deletion: clinical and array-CGH characterization in two patients. Am J Med Genet A 2008; 146A:2094-102. [PMID: 18629875 DOI: 10.1002/ajmg.a.32414] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report on two patients with de novo subtelomeric terminal deletion of chromosome 6p. Patient 1 is an 8-month-old female born with normal growth parameters, typical facial features of 6pter deletion, bilateral corectopia, and protruding tongue. She has severe developmental delay, profound bilateral neurosensory deafness, poor visual contact, and hypsarrhythmia since the age of 6 months. Patient 2 is a 5-year-old male born with normal growth parameters and unilateral hip dysplasia; he has a characteristic facial phenotype, bilateral embryotoxon, and moderate mental retardation. Further characterization of the deletion, using high-resolution array comparative genomic hybridization (array-CGH; Agilent Human Genome kit 244 K), revealed that Patient 1 has a 8.1 Mb 6pter-6p24.3 deletion associated with a contiguous 5.8 Mb 6p24.3-6p24.1 duplication and Patient 2 a 5.7 Mb 6pter-6p25.1 deletion partially overlapping with that of Patient 1. Complementary FISH and array analysis showed that the inv del dup(6) in Patient 1 originated de novo. Our results demonstrate that simple rearrangements are often more complex than defined by standard techniques. We also discuss genotype-phenotype correlations including previously reported cases of deletion 6p.
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Affiliation(s)
- Danielle Martinet
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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Filges I, Zaman K, Michielin O, Vulliémoz D, Perey L, Stupp R. [Present chemoprevention and future vision]. Rev Med Suisse 2005; 1:1343-6, 1349. [PMID: 15991626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cancer chemoprevention is defined as the use of natural or synthetic agents to reverse, suppress or prevent carcinogenic progression to invasive cancer. The success of several clinical trials within high-risk patients suggests that chemoprevention is a rational and promising strategy. This review will resume the principal molecular mechanisms of chemoprevention and discuss results and clinical outcome of selected clinical trials. The difficulties in clinical application and future directions will be highlighted.
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Affiliation(s)
- Isabel Filges
- Fondation du centre pluridisciplinaire d'oncologie, CHUV, 1011 Lausanne.
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Wang Y, Friedl W, Sengteller M, Jungck M, Filges I, Propping P, Mangold E. A modified multiplex PCR assay for detection of large deletions in MSH2 and MLH1. Hum Mutat 2002; 19:279-86. [PMID: 11857745 DOI: 10.1002/humu.10042] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A method for detection of large genomic deletions in the MSH2 and MLH1 genes based on multiplex PCR and quantitative evaluation of PCR products is presented. All 35 exons of MSH2 and MLH1 were screened simultaneously in seven PCR reactions, each of them including primers for both genes. The method is reliable for uncovering large genomic deletions in patients suspected of HNPCC. With this method, six novel deletions were identified, two in MSH2: EX1_10del and EX1_16del (representing deletion of the entire MSH2 gene); and four in MLH1: EX1_10del in two unrelated patients, EX3_5del, and EX4del. The deletions were detected in 18 unrelated patients in whom no germline mutation had been identified by SSCP and DHPLC. These results indicate that our modified multiplex PCR assay is suited for the detection of large deletions both in the MSH2 and MLH1 gene and therefore represents an additional valuable tool for mutation screening in HNPCC families.
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Affiliation(s)
- Yaping Wang
- Institute of Human Genetics, University of Bonn, Bonn, Germany
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