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Ding L, Wei LW, Li TS, Chen J. Mental retardation, seizures and language delay caused by new SETD1B mutations: Three case reports. World J Clin Cases 2024; 12:383-391. [PMID: 38313655 PMCID: PMC10835677 DOI: 10.12998/wjcc.v12.i2.383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND The SETD1B gene is instrumental in human intelligence and nerve development. Mutations in the SETD1B gene have been linked in recent studies to neurodevelopmental disorders, seizures, and language delay. CASE SUMMARY This study aimed to analyze the clinical manifestations and treatment of three patients suffering from mental retardation, epilepsy, and language delay resulting from a new mutation in the SETD1B gene. Three individuals with these symptoms were selected, and their clinical symptoms, gene test results, and treatment were analyzed. This article discusses the impact of the SETD1B gene mutation on patients and outlines the treatment approach. Among the three patients (two females and one male, aged 8, 4, and 1, respectively), all exhibited psychomotor retardation, attention deficit, and hyperactivity disorder, and two had epilepsy. Antiepileptic treatment with sodium tripolyvalproate halted the seizures in the affected child, although mental development remained somewhat delayed. Whole exome sequencing revealed new mutations in the SETD1B gene for all patients, specifically with c.5473C>T (p.Arg1825trp), c.4120C>T (p.Gln1374*, 593), c.14_15insC (p.His5Hisfs*33). CONCLUSION Possessing the SETD1B gene mutation may cause mental retardation accompanied by seizures and language delay. Although the exact mechanism is not fully understood, interventions such as drug therapy, rehabilitation training, and family support can assist patients in managing their symptoms and enhancing their quality of life. Furthermore, genetic testing supplies healthcare providers with more precise diagnostic and therapeutic guidance, informs families about genetic disease risks, and contributes to understanding disease pathogenesis and drug research and development.
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Affiliation(s)
- Le Ding
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Li-Wan Wei
- Chigene (Beijing) Translational Medical Research Center, Co. Ltd., Beijing 101111, China
| | - Tai-Song Li
- Chigene (Beijing) Translational Medical Research Center, Co. Ltd., Beijing 101111, China
| | - Jing Chen
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
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2
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Zhou R, Jiao J, Wang Y, Meng L, Li Y, Xu Y, Hu P, Xu Z. Systematic analysis of copy number variants of uncertain significance partially overlapping with the haploinsufficient or triplosensitive genes in clinical testing. Ann Med 2023; 55:2276824. [PMID: 37917952 PMCID: PMC10623895 DOI: 10.1080/07853890.2023.2276824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023] Open
Abstract
Background: Copy number variants of uncertain significance (VUS) has brought much distress for patients and great counselling challenges for clinicians. Of these, a special type of VUS (HT-VUS), harbouring one or both breakpoints within the established haploinsufficient or triplosensitive genes, were considered to be more likely to cause clinical effects compared with other types of VUS.Methods: We retrospectively evaluated the properties and clinical significance of those HT-VUS samples in clinical testing for chromosome microarray analysis (CMA).Results: A total of 7150 samples were selected for HT-VUS screening, and 75 (1.05%) subjects with 75 HT-VUS were found. The majority of these HT-VUS were heterozygous duplications and chromosome X had the most HT-VUS. The prevalence of HT-VUS was 0.90% (28/3116) for prenatal low-risk samples, 1.18% (26/2196) for prenatal high-risk samples, 1.37% (10/728) for postnatal samples and 0.99% (11/1110) for early pregnancy loss samples. However, the incidence of HT-VUS was not statistically different between different groups.Conclusions: HT-VUS (deletions or duplications) involving introns and HT-VUS (duplications) including terminal coding exons (either the first or last exons) might be clinically neutral. Our study will be helpful for both interpretation and genetic counselling in the future.
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Affiliation(s)
- Ran Zhou
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jiao Jiao
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Lulu Meng
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yiming Li
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yiyun Xu
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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Ambrosetti I, Bernardini L, Pollazzon M, Giuffrida MG, Guida V, Peluso F, Baroni MC, Polizzi V, Napoli M, Rosato S, Trimarchi G, Gelmini C, Caraffi SG, Wischmeijer A, Frattini D, Novelli A, Garavelli L. Split Hand-Foot and Deafness in a Patient with 7q21.13-q21.3 Deletion Not Including the DLX5/6 Genes. Genes (Basel) 2023; 14:1526. [PMID: 37628577 PMCID: PMC10454356 DOI: 10.3390/genes14081526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Split Hand-Foot Malformation (SHFM) is a congenital limb defect characterized by a median cleft of the hands and/or feet due to the absence/hypoplasia of the central rays. It may occur as part of a syndromic condition or as an isolated malformation. The most common of the six genetic loci identified for this condition is correlated to SHFM1 and maps in the 7q21q22 region. SHFM1 is characterized by autosomal dominant transmission, incomplete penetrance and variable expressivity. Associated features often include hearing loss, intellectual disability/developmental delay and craniofacial abnormalities. Disruption of the DLX5/DLX6 genes, mapping within the SHFM1 locus, is now known to be responsible for the phenotype. Through SNP array, we analyzed a patient affected by SHFM1 associated with deafness and an abnormality of the inner ear (incomplete partition type I); we identified a deletion in 7q21, not involving the DLX5/6 genes, but including exons 15 and 17 of DYNC1I1, known to act as exonic enhancers (eExons) of the DLX5/6 genes. We further demonstrated the role of DYNC1I1 eExons in regulating DLX5/6 expression by means of showing a reduced expression of the DLX5/6 genes through RT-PCR in a patient-derived lymphoblastoid cell line. Furthermore, our data and a review of published cases do not support the hypothesis that DLX5/6 are imprinted in humans. This work is an example of how the disruption of regulatory elements can be responsible for congenital malformations.
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Affiliation(s)
- Irene Ambrosetti
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (I.A.)
- Clinical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Laura Bernardini
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Marzia Pollazzon
- Clinical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Maria Grazia Giuffrida
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Valentina Guida
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Francesca Peluso
- Clinical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Maria Chiara Baroni
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (I.A.)
- Clinical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Valeria Polizzi
- Department of Audiology, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Manuela Napoli
- Neuroradiology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Simonetta Rosato
- Clinical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Gabriele Trimarchi
- Clinical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Chiara Gelmini
- Clinical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | | | - Anita Wischmeijer
- Clinical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
- Clinical Genetics Service and Coordination Center for Rare Diseases, Department of Pediatrics, Regional Hospital of Bolzano, 39100 Bolzano, Italy
| | - Daniele Frattini
- Child Neurology and Psychiatry Unit, Azienda AUSL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital IRCCS, 00165 Rome, Italy
| | - Livia Garavelli
- Clinical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
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4
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Yüksel Ülker A, Uludağ Alkaya D, Çağlayan AO, Usluer E, Aykut A, Aslanger A, Vural M, Tüysüz B. An investigation of the etiology and follow-up findings in 35 children with overgrowth syndromes, including biallelic SUZ12 variant. Am J Med Genet A 2023; 191:1530-1545. [PMID: 36919607 DOI: 10.1002/ajmg.a.63180] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/01/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023]
Abstract
Overgrowth-intellectual disability (OGID) syndromes are clinically and genetically heterogeneous group of disorders. The aim of this study was to examine the molecular etiology and long-term follow-up findings of Turkish OGID cohort. Thirty-five children with OGID were included in the study. Single gene sequencing, clinical exome analysis, chromosomal microarray analysis and whole exome sequencing were performed. Five pathogenic copy number variants were detected in the patients; three of them located on chromosome 5q35.2 (encompassing NSD1), others on 9q22.3 and 22q13.31. In 19 of 35 patients; we identified pathogenic variants in OGID genes associated with epigenetic regulation, NSD1 (n = 15), HIST1H1E (n = 1), SETD1B (n = 1), and SUZ12 (n = 2). The pathogenic variants in PIK3CA (n = 2), ABCC9 (n = 1), GPC4 (n = 2), FIBP (n = 1), and TMEM94 (n = 1) which had a role in other growth pathways were detected in seven patients. The diagnostic yield was 31/35(88%). Twelve pathogenic variants were novel. The common facial feature of the patients was prominent forehead. The patients with Sotos syndrome were observed to have milder intellectual disability than patients with other OGID syndromes. In conclusion, this study showed, for the first time, that biallelic variants of SUZ12 caused Imagawa-Matsumoto syndrome, monoallelic variants in SETDIB resulted in OGID. Besides expanded the phenotypes of very rare OGID syndromes caused by FIBP and TMEM94.
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Affiliation(s)
- Aylin Yüksel Ülker
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Dilek Uludağ Alkaya
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ahmet Okay Çağlayan
- Departments of Neurosurgery, Neurobiology and Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Esra Usluer
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ayça Aykut
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ayça Aslanger
- Department of Medical Genetics, Bezmialem University, Istanbul, Turkey
| | - Mehmet Vural
- Department of Neonatology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
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5
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van Jaarsveld RH, Reilly J, Cornips MC, Hadders MA, Agolini E, Ahimaz P, Anyane-Yeboa K, Bellanger SA, van Binsbergen E, van den Boogaard MJ, Brischoux-Boucher E, Caylor RC, Ciolfi A, van Essen TAJ, Fontana P, Hopman S, Iascone M, Javier MM, Kamsteeg EJ, Kerkhof J, Kido J, Kim HG, Kleefstra T, Lonardo F, Lai A, Lev D, Levy MA, Lewis MES, Lichty A, Mannens MMAM, Matsumoto N, Maya I, McConkey H, Megarbane A, Michaud V, Miele E, Niceta M, Novelli A, Onesimo R, Pfundt R, Popp B, Prijoles E, Relator R, Redon S, Rots D, Rouault K, Saida K, Schieving J, Tartaglia M, Tenconi R, Uguen K, Verbeek N, Walsh CA, Yosovich K, Yuskaitis CJ, Zampino G, Sadikovic B, Alders M, Oegema R. Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature. Genet Med 2023; 25:49-62. [PMID: 36322151 PMCID: PMC9825659 DOI: 10.1016/j.gim.2022.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022] Open
Abstract
PURPOSE Pathogenic variants in genes involved in the epigenetic machinery are an emerging cause of neurodevelopment disorders (NDDs). Lysine-demethylase 2B (KDM2B) encodes an epigenetic regulator and mouse models suggest an important role during development. We set out to determine whether KDM2B variants are associated with NDD. METHODS Through international collaborations, we collected data on individuals with heterozygous KDM2B variants. We applied methylation arrays on peripheral blood DNA samples to determine a KDM2B associated epigenetic signature. RESULTS We recruited a total of 27 individuals with heterozygous variants in KDM2B. We present evidence, including a shared epigenetic signature, to support a pathogenic classification of 15 KDM2B variants and identify the CxxC domain as a mutational hotspot. Both loss-of-function and CxxC-domain missense variants present with a specific subepisignature. Moreover, the KDM2B episignature was identified in the context of a dual molecular diagnosis in multiple individuals. Our efforts resulted in a cohort of 21 individuals with heterozygous (likely) pathogenic variants. Individuals in this cohort present with developmental delay and/or intellectual disability; autism; attention deficit disorder/attention deficit hyperactivity disorder; congenital organ anomalies mainly of the heart, eyes, and urogenital system; and subtle facial dysmorphism. CONCLUSION Pathogenic heterozygous variants in KDM2B are associated with NDD and a specific epigenetic signature detectable in peripheral blood.
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Affiliation(s)
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Marie-Claire Cornips
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Michael A Hadders
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00165 Rome, Italy
| | - Priyanka Ahimaz
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Severine Audebert Bellanger
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Ton A J van Essen
- Department of Medical Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Paolo Fontana
- Medical Genetics Unit, A.O.R.N. San Pio, Benevento, Italy
| | - Saskia Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maria Iascone
- Laboratorio di Genetica Medica - ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Margaret M Javier
- Department of Medical Genetics, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Jun Kido
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Abbe Lai
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program and Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dorit Lev
- The Rina Mor Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach-Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Andre Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon; Institut Jérôme Lejeune, Paris, France
| | - Vincent Michaud
- Department of Medical Genetics, CHU Bordeaux, Bordeaux, France
| | - Evelina Miele
- Department of Pediatric Hematology and Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00165 Rome, Italy
| | - Roberta Onesimo
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany; Center of Functional Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Sylvia Redon
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France; Université de Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Dmitrijs Rots
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Karen Rouault
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France; Université de Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Jolanda Schieving
- Department of Pediatric Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Romano Tenconi
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, Padova, Italy
| | - Kevin Uguen
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France
| | - Nienke Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA
| | - Keren Yosovich
- Molecular Genetic Laboratory, Edith Wolfson Medical Center, Holon, Israel
| | - Christopher J Yuskaitis
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Giuseppe Zampino
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Faculty of Medicine and Surgery, Catholic University of Sacred Heart, Rome, Italy
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada.
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.
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Impaired KDM2B-mediated PRC1 recruitment to chromatin causes defective neural stem cell self-renewal and ASD/ID-like behaviors. iScience 2022; 25:103742. [PMID: 35128353 PMCID: PMC8800019 DOI: 10.1016/j.isci.2022.103742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/01/2021] [Accepted: 01/05/2022] [Indexed: 01/19/2023] Open
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7
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Iafusco F, De Sanctis P, Pirozzi D, Capone S, Lombardo B, Gambale A, Confetto S, Zanfardino A, Iolascon A, Pastore L, Iafusco D, Tinto N. Molecular diagnosis of MODY3 permitted to reveal a de novo 12q24.31 deletion and to explain a complex phenotype in a young diabetic patient. Clin Chem Lab Med 2020; 57:e306-e310. [PMID: 31188748 DOI: 10.1515/cclm-2019-0137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/15/2019] [Indexed: 02/07/2023]
Affiliation(s)
- Fernanda Iafusco
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | - Paola De Sanctis
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | - Daniele Pirozzi
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | - Silvana Capone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Barbara Lombardo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Antonella Gambale
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Santino Confetto
- Dipartimento di Pediatria, Università della Campania Luigi Vanvitelli, Naples, Italy
| | - Angela Zanfardino
- Dipartimento di Pediatria, Università della Campania Luigi Vanvitelli, Naples, Italy
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Lucio Pastore
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Dario Iafusco
- Dipartimento di Pediatria, Università della Campania Luigi Vanvitelli, Naples, Italy
| | - Nadia Tinto
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
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8
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Roston A, Evans D, Gill H, McKinnon M, Isidor B, Cogné B, Mwenifumbo J, van Karnebeek C, An J, Jones SJM, Farrer M, Demos M, Connolly M, Gibson WT. SETD1B-associated neurodevelopmental disorder. J Med Genet 2020; 58:196-204. [PMID: 32546566 DOI: 10.1136/jmedgenet-2019-106756] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/11/2020] [Accepted: 04/14/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Dysfunction of histone methyltransferases and chromatin modifiers has been implicated in complex neurodevelopmental syndromes and cancers. SETD1B encodes a lysine-specific methyltransferase that assists in transcriptional activation of genes by depositing H3K4 methyl marks. Previous reports of patients with rare variants in SETD1B describe a distinctive phenotype that includes seizures, global developmental delay and intellectual disability. METHODS Two of the patients described herein were identified via genome-wide and exome-wide testing, with microarray and research-based exome, through the CAUSES (Clinical Assessment of the Utility of Sequencing and Evaluation as a Service) Research Clinic at the University of British Columbia. The third Vancouver patient had clinical trio exome sequencing through Blueprint Genetics. The fourth patient underwent singleton exome sequencing in Nantes, with subsequent recruitment to this cohort through GeneMatcher. RESULTS Here we present clinical reports of four patients with rare coding variants in SETD1B that demonstrate a shared phenotype, including intellectual disability, language delay, conserved musculoskeletal findings and seizures that may be treatment-refractory. We include supporting evidence from next-generation sequencing among a cohort of paediatric patients with epilepsy. CONCLUSION Rare coding variants in SETD1B can cause a diagnosable syndrome and could contribute as a risk factor for epilepsy, autism and other neurodevelopmental phenotypes. In the long term, some patients may also be at increased risk for cancers and other complex diseases. Thus, longitudinal studies are required to further elucidate the precise role of SETD1B in neurodevelopmental disorders and other systemic disease.
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Affiliation(s)
- Alexandra Roston
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Dan Evans
- Centre for Applied Neurogenetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Harinder Gill
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,Provincial Medical Genetics Program, BC Women's Hospital and Health Centre, Vancouver, British Columbia, Canada
| | - Margaret McKinnon
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Bertrand Isidor
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, Pays de la Loire, France
| | - Benjamin Cogné
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, Pays de la Loire, France.,INSERM, CNRS, UNIV Nantes, l'institut du thorax, Nantes, Frances
| | - Jill Mwenifumbo
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Emma Children's Hospital, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, Netherlands.,Department of Pediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Jianghong An
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Matthew Farrer
- Centre for Applied Neurogenetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Demos
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mary Connolly
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - William T Gibson
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
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9
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Lin J, Souza-Lin GRD, Antunes FC, Wessler LB, Streck EL, Gonçalves CL. Autism associated with 12q (12q24.31-q24.33) deletion: further report of an exceedingly rare disorder. EINSTEIN-SAO PAULO 2020; 18:eRC5335. [PMID: 32578677 PMCID: PMC7279891 DOI: 10.31744/einstein_journal/2020rc5335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/29/2019] [Indexed: 11/15/2022] Open
Abstract
Chromosomal abnormalities are responsible for several congenital malformations in the world, some of these are associated to telomeric/subtelomeric deletions. The abnormalities involving the telomere of chromosome 12 are rare, with few reports of deletions involving 12q24.31 region in the literature, and, to our knowledge, only four of them in the 12q24.31-q24.33 region. We report a further case of interstitial deletion of bands 12q24.31-q24.33 associated with autism spectrum disorder. A 2-year-old boy with global developmental delay associated with multiple congenital anomalies. The Human Genome CGH Microarray 60K confirmed the diagnosis of 12q deletion syndrome. This study made a review of the current literature comparing our patient with previously reported cases. These detailed analyses contribute to the development of genotype/phenotype correlations for 12q deletions that will aid in better diagnosis and prognosis of this deletion.
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Affiliation(s)
- Jaime Lin
- Universidade do Sul de Santa Catarina, Tubarão, SC, Brazil.,Universidade do Extremo Sul Catarinense, Criciúma, SC, Brazil
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10
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Krzyzewska IM, Maas SM, Henneman P, Lip KVD, Venema A, Baranano K, Chassevent A, Aref-Eshghi E, van Essen AJ, Fukuda T, Ikeda H, Jacquemont M, Kim HG, Labalme A, Lewis SME, Lesca G, Madrigal I, Mahida S, Matsumoto N, Rabionet R, Rajcan-Separovic E, Qiao Y, Sadikovic B, Saitsu H, Sweetser DA, Alders M, Mannens MMAM. A genome-wide DNA methylation signature for SETD1B-related syndrome. Clin Epigenetics 2019; 11:156. [PMID: 31685013 PMCID: PMC6830011 DOI: 10.1186/s13148-019-0749-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/22/2019] [Indexed: 01/02/2023] Open
Abstract
SETD1B is a component of a histone methyltransferase complex that specifically methylates Lys-4 of histone H3 (H3K4) and is responsible for the epigenetic control of chromatin structure and gene expression. De novo microdeletions encompassing this gene as well as de novo missense mutations were previously linked to syndromic intellectual disability (ID). Here, we identify a specific hypermethylation signature associated with loss of function mutations in the SETD1B gene which may be used as an epigenetic marker supporting the diagnosis of syndromic SETD1B-related diseases. We demonstrate the clinical utility of this unique epi-signature by reclassifying previously identified SETD1B VUS (variant of uncertain significance) in two patients.
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Affiliation(s)
- I M Krzyzewska
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - S M Maas
- Amsterdam UMC, Department of Pediatrics, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - P Henneman
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - K V D Lip
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - A Venema
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - K Baranano
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - A Chassevent
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - E Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner's Road E, London, ON, N6A 5W9, Canada
| | - A J van Essen
- University Medical Centre Groningen, University of Groningen, Department of Medical Genetics, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - T Fukuda
- Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - H Ikeda
- National Epilepsy Centre, NHO, Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - M Jacquemont
- Department of medical genetics, CHU La Reunion-Groupe Hospitalier Sud Reunion, La Reunion, France
| | - H-G Kim
- Neurological Disorder Center Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - A Labalme
- Department of medical genetics, Hospices Civils de Lyon, Bron, France
| | - S M E Lewis
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - G Lesca
- Department of medical genetics, Hospices Civils de Lyon, Bron, France
| | - I Madrigal
- Biochemistry and Molecular Genetics Service, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Center for Biomedical Network Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - S Mahida
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - N Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - R Rabionet
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, av diagonal 643, 08028, Barcelona, Spain
| | - E Rajcan-Separovic
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - Y Qiao
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - B Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner's Road E, London, ON, N6A 5W9, Canada
| | - H Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - D A Sweetser
- MassGeneral Hospital, Division of Medical Genetics and Metabolism, 175 Cambridge St, Suite 500, Boston, Massachusetts, 02114, USA
| | - M Alders
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
| | - M M A M Mannens
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
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11
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Adapting ACMG/AMP sequence variant classification guidelines for single-gene copy number variants. Genet Med 2019; 22:336-344. [PMID: 31534211 DOI: 10.1038/s41436-019-0655-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022] Open
Abstract
PURPOSE The ability of a single technology, next-generation sequencing, to provide both sequence and copy number variant (CNV) results has driven the merger of clinical cytogenetics and molecular genetics. Consequently, the distinction between the definition of a sequence variant and a CNV is blurry. As the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) standards and guidelines for interpretation of sequence variants address CNV classification only sparingly, this study focused on adapting ACMG/AMP criteria for single-gene CNV interpretation. METHODS CNV-specific modifications of the 2015 ACMG/AMP criteria were developed and their utility was independently tested by three diagnostic laboratories. Each laboratory team interpreted the same 12 single-gene CNVs using three systems: (1) without ACMG/AMP guidance, (2) with ACMG/AMP criteria, and (3) with new modifications. A replication study of 12 different CNVs validated the modified criteria. RESULTS The adapted criteria system presented here showed improved concordance and usability for single-gene CNVs compared with using the ACMG/AMP interpretation guidelines focused on sequence variants. CONCLUSION These single-gene CNV criteria modifications could be used as a supplement to the ACMG/AMP guidelines for sequence variants, allowing for a streamlined workflow and a step toward a uniform classification system for both sequence and copy number alterations.
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12
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Callaghan DB, Rogic S, Tan PPC, Calli K, Qiao Y, Baldwin R, Jacobson M, Belmadani M, Holmes N, Yu C, Li Y, Li Y, Kurtzke F, Kuzeljevic B, Yu AY, Hudson M, Mcaughton AJ, Xu Y, Dionne‐Laporte A, Girard S, Liang P, Separovic ER, Liu X, Rouleau G, Pavlidis P, Lewis MS. Whole genome sequencing and variant discovery in the ASPIRE autism spectrum disorder cohort. Clin Genet 2019; 96:199-206. [DOI: 10.1111/cge.13556] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Daniel Benjamin Callaghan
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Sanja Rogic
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Powell Patrick Cheng Tan
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Kristina Calli
- Department of Medical GeneticsBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
| | - Ying Qiao
- Department of Medical GeneticsBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
| | - Robert Baldwin
- Department of Biological SciencesBrock University St. Catharines Canada
| | - Matthew Jacobson
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Manuel Belmadani
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Nathan Holmes
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Chang Yu
- Medical Division, BGI‐Shenzhen Shenzhen China
| | - Yanchen Li
- Medical Division, BGI‐Shenzhen Shenzhen China
| | - Yingrui Li
- Medical Division, BGI‐Shenzhen Shenzhen China
| | - Franz‐Edward Kurtzke
- Department of Medical GeneticsBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
| | - Boris Kuzeljevic
- Clinical Research Support UnitBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
| | - An Yi Yu
- Department of Medical GeneticsBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
| | - Melissa Hudson
- Queen's Genomics Lab at OngwanadaOngwanada Resource Center Kingston Canada
- Department of PsychiatryQueen's University Kingston Canada
| | - Amy J.M. Mcaughton
- Queen's Genomics Lab at OngwanadaOngwanada Resource Center Kingston Canada
- Department of PsychiatryQueen's University Kingston Canada
| | - Yuchen Xu
- Department of Biological SciencesBrock University St. Catharines Canada
| | - Alexandre Dionne‐Laporte
- Montreal Neurological Institute Quebec Canada
- Department of Neurology and NeurosurgeryMcGill University Quebec Canada
| | - Simon Girard
- Département des sciences fondamentales, Université du Québec à Chicoutimi Chicoutimi Canada
| | - Ping Liang
- Department of Biological SciencesBrock University St. Catharines Canada
| | - Evica Rajcan Separovic
- Department of Pathology and Laboratory MedicineUniversity of British Columbia Vancouver Canada
| | - Xudong Liu
- Queen's Genomics Lab at OngwanadaOngwanada Resource Center Kingston Canada
- Department of PsychiatryQueen's University Kingston Canada
| | - Guy Rouleau
- Montreal Neurological Institute Quebec Canada
- Department of Neurology and NeurosurgeryMcGill University Quebec Canada
| | - Paul Pavlidis
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - M.E. Suzanne Lewis
- Department of Medical GeneticsBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
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13
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A novel de novo frameshift variant in SETD1B causes epilepsy. J Hum Genet 2019; 64:821-827. [DOI: 10.1038/s10038-019-0617-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 01/03/2023]
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14
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Chromosome 12q24.31 microdeletion and congenital heart disease: a case report and review of the literature. Clin Dysmorphol 2018; 28:53-56. [PMID: 30507726 DOI: 10.1097/mcd.0000000000000245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Qiao Y, Bagheri H, Tang F, Badduke C, Martell S, Lewis SME, Robinson W, Connolly MB, Arbour L, Rajcan-Separovic E. Exome sequencing identified a de novo mutation of PURA gene in a patient with familial Xp22.31 microduplication. Eur J Med Genet 2018; 62:103-108. [PMID: 29908350 DOI: 10.1016/j.ejmg.2018.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 06/08/2018] [Accepted: 06/10/2018] [Indexed: 11/28/2022]
Abstract
The clinical significance of Xp22.31 microduplication is controversial as it is reported in subjects with developmental delay (DD), their unaffected relatives and unrelated controls. We performed multifaceted studies in a family of a boy with hypotonia, dysmorphic features and DD who carried a 600 Kb Xp22.31 microduplication (7515787-8123310bp, hg19) containing two genes, VCX and PNPLA4. The duplication was transmitted from his cognitively normal maternal grandfather. We found no evidence of the duplication causing the proband's DD and congenital anomalies based on unaltered expression of PNPLA4 in the proband and his mother in comparison to controls and preferential activation of the paternal chromosome X with Xp22.31 duplication in proband's mother. However, a de novo, previously reported deleterious, missense mutation in Pur-alpha gene (PURA) (5q31.2), with a role in neuronal differentiation was detected in the proband by exome sequencing. We propose that the variability in the phenotype in carriers of Xp22.31 microduplication can be due to a second and more deleterious genetic mutation in more severely affected carriers. Widespread use of whole genome next generation sequencing in families with Xp22.31 CNV could help identify such cases.
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Affiliation(s)
- Ying Qiao
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Hani Bagheri
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | - Flamingo Tang
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | | | - Sally Martell
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | - Suzanne M E Lewis
- BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medical Genetics, UBC, Vancouver, BC, Canada
| | - Wendy Robinson
- Department of Medical Genetics, UBC, Vancouver, BC, Canada
| | - Mary B Connolly
- Division of Pediatric Neurology, Department of Pediatrics, UBC and BC Children's Hospital, Vancouver, BC, Canada
| | - Laura Arbour
- Department of Medical Genetics, University of Victoria, Victoria, BC, Canada.
| | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada.
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16
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Hiraide T, Nakashima M, Yamoto K, Fukuda T, Kato M, Ikeda H, Sugie Y, Aoto K, Kaname T, Nakabayashi K, Ogata T, Matsumoto N, Saitsu H. De novo variants in SETD1B are associated with intellectual disability, epilepsy and autism. Hum Genet 2018; 137:95-104. [DOI: 10.1007/s00439-017-1863-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/26/2017] [Indexed: 01/10/2023]
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17
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El Naqa I, Kerns SL, Coates J, Luo Y, Speers C, West CML, Rosenstein BS, Ten Haken RK. Radiogenomics and radiotherapy response modeling. Phys Med Biol 2017; 62:R179-R206. [PMID: 28657906 PMCID: PMC5557376 DOI: 10.1088/1361-6560/aa7c55] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Advances in patient-specific information and biotechnology have contributed to a new era of computational medicine. Radiogenomics has emerged as a new field that investigates the role of genetics in treatment response to radiation therapy. Radiation oncology is currently attempting to embrace these recent advances and add to its rich history by maintaining its prominent role as a quantitative leader in oncologic response modeling. Here, we provide an overview of radiogenomics starting with genotyping, data aggregation, and application of different modeling approaches based on modifying traditional radiobiological methods or application of advanced machine learning techniques. We highlight the current status and potential for this new field to reshape the landscape of outcome modeling in radiotherapy and drive future advances in computational oncology.
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Affiliation(s)
- Issam El Naqa
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States of America
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18
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Qiao Y, Badduke C, Tang F, Cowieson D, Martell S, Lewis SME, Peñaherrera MS, Robinson WP, Volchuk A, Rajcan-Separovic E. Whole exome sequencing of families with 1q21.1 microdeletion or microduplication. Am J Med Genet A 2017; 173:1782-1791. [DOI: 10.1002/ajmg.a.38247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/16/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Ying Qiao
- Department of Pathology; University of British Columbia (UBC); Vancouver British Columbia Canada
- BC Children's Hospital Research Institute; Vancouver British Columbia Canada
| | - Chansonette Badduke
- Department of Pathology; University of British Columbia (UBC); Vancouver British Columbia Canada
| | - Flamingo Tang
- Department of Pathology; University of British Columbia (UBC); Vancouver British Columbia Canada
| | - David Cowieson
- Division of Advanced Diagnostics-Metabolism Toronto General Research Institute; University Health Network; Toronto Ontario Canada
| | - Sally Martell
- Department of Pathology; University of British Columbia (UBC); Vancouver British Columbia Canada
- BC Children's Hospital Research Institute; Vancouver British Columbia Canada
| | | | - Maria S. Peñaherrera
- BC Children's Hospital Research Institute; Vancouver British Columbia Canada
- Department of Medical Genetics; UBC; Vancouver British Columbia Canada
| | - Wendy P. Robinson
- BC Children's Hospital Research Institute; Vancouver British Columbia Canada
- Department of Medical Genetics; UBC; Vancouver British Columbia Canada
| | - Allen Volchuk
- Keenan Research Centre for Biomedical Science; St. Michael's Hospital; Toronto Ontario Canada
| | - Evica Rajcan-Separovic
- Department of Pathology; University of British Columbia (UBC); Vancouver British Columbia Canada
- BC Children's Hospital Research Institute; Vancouver British Columbia Canada
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19
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Labonne JDJ, Lee KH, Iwase S, Kong IK, Diamond MP, Layman LC, Kim CH, Kim HG. An atypical 12q24.31 microdeletion implicates six genes including a histone demethylase KDM2B and a histone methyltransferase SETD1B in syndromic intellectual disability. Hum Genet 2016; 135:757-71. [PMID: 27106595 DOI: 10.1007/s00439-016-1668-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/31/2016] [Indexed: 12/22/2022]
Abstract
Microdeletion syndromes are frequent causes of neuropsychiatric disorders leading to intellectual disability as well as autistic features accompanied by epilepsy and craniofacial anomalies. From comparative deletion mapping of the smallest microdeletion to date at 12q24.31, found in a patient with overlapping clinical features of 12q24.31 microdeletion syndrome, we narrowed the putative critical region to 445 kb containing seven genes, one microRNA, and one non-coding RNA. Zebrafish in situ hybridization and comprehensive transcript analysis of annotated genes in the panels of human organ and brain suggest that these are all candidates for neurological phenotypes excluding the gene HPD. This is also corroborated by synteny analysis revealing the conservation of the order of these six candidate genes between humans and zebrafish. Among them, we propose histone demethylase KDM2B and histone methyltransferase SETD1B as the two most plausible candidate genes involved in intellectual disability, autism, epilepsy, and craniofacial anomalies. These two chromatin modifiers located approximately 224 kb apart were both commonly deleted in six patients, while two additional patients had either KDM2B or SETD1B deleted. The four additional candidate genes (ORAI1, MORN3, TMEM120B, RHOF), a microRNA MIR548AQ, and a non-coding RNA LINC01089 are localized between KDM2B and SETD1B. The 12q24.31 microdeletion syndrome with syndromic intellectual disability extends the growing list of microdeletion syndromes and underscores the causative roles of chromatin modifiers in cognitive and craniofacial development.
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Affiliation(s)
- Jonathan D J Labonne
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, 30912, USA
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA
| | - Kang-Han Lee
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Il-Keun Kong
- Division of Applied Life Science (BK21plus), Department of Animal Science, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Gyeongsangnam-do, Korea
| | - Michael P Diamond
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, 30912, USA
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, 30912, USA
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA
- Neuroscience Program, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Hyung-Goo Kim
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, 30912, USA.
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA.
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Amarillo IE, Nievera I, Hagan A, Huchthagowder V, Heeley J, Hollander A, Koenig J, Austin P, Wang T. Integrated small copy number variations and epigenome maps of disorders of sex development. Hum Genome Var 2016; 3:16012. [PMID: 27340555 PMCID: PMC4899613 DOI: 10.1038/hgv.2016.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/24/2016] [Accepted: 03/26/2016] [Indexed: 02/03/2023] Open
Abstract
Small copy number variations (CNVs) have typically not been analyzed or reported in clinical settings and hence have remained underrepresented in databases and the literature. Here, we focused our investigations on these small CNVs using chromosome microarray analysis (CMA) data previously obtained from patients with atypical characteristics or disorders of sex development (DSD). Using our customized CMA track targeting 334 genes involved in the development of urogenital and reproductive structures and a less stringent analysis filter, we uncovered small genes with recurrent and overlapping CNVs as small as 1 kb, and small regions of homozygosity (ROHs), imprinting and position effects. Detailed analysis of these high-resolution data revealed CNVs and ROHs involving structural and functional domains, repeat elements, active transcription sites and regulatory regions. Integration of these genomic data with DNA methylation, histone modification and predicted RNA expression profiles in normal testes and ovaries suggested spatiotemporal and tissue-specific gene regulation. This study emphasized a DSD-specific and gene-targeted CMA approach that uncovered previously unanalyzed or unreported small genes and CNVs, contributing to the growing resources on small CNVs and facilitating the narrowing of the genomic gap for identifying candidate genes or regions. This high-resolution analysis tool could improve the diagnostic utility of CMA, not only in patients with DSD but also in other clinical populations. These integrated data provided a better genomic-epigenomic landscape of DSD and greater opportunities for downstream research.
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Affiliation(s)
- Ina E Amarillo
- Cytogenomics and Molecular Pathology Laboratory, Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA; Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA
| | - Isabelle Nievera
- Washington University in St Louis School of Medicine DSD Team , St Louis, MO, USA
| | - Andrew Hagan
- Division of Biology and Biomedical Sciences, Washington University in St Louis , St Louis, MO, USA
| | - Vishwa Huchthagowder
- Cytogenomics and Molecular Pathology Laboratory, Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St Louis School of Medicine , St Louis, MO, USA
| | - Jennifer Heeley
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Abby Hollander
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Joel Koenig
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Surgery, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Paul Austin
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Surgery, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University in St Louis School of Medicine , St Louis, MO, USA
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21
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Bagheri H, Badduke C, Qiao Y, Colnaghi R, Abramowicz I, Alcantara D, Dunham C, Wen J, Wildin RS, Nowaczyk MJ, Eichmeyer J, Lehman A, Maranda B, Martell S, Shan X, Lewis SM, O’Driscoll M, Gregory-Evans CY, Rajcan-Separovic E. Identifying candidate genes for 2p15p16.1 microdeletion syndrome using clinical, genomic, and functional analysis. JCI Insight 2016; 1:e85461. [PMID: 27699255 PMCID: PMC5033885 DOI: 10.1172/jci.insight.85461] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/09/2016] [Indexed: 01/14/2023] Open
Abstract
The 2p15p16.1 microdeletion syndrome has a core phenotype consisting of intellectual disability, microcephaly, hypotonia, delayed growth, common craniofacial features, and digital anomalies. So far, more than 20 cases of 2p15p16.1 microdeletion syndrome have been reported in the literature; however, the size of the deletions and their breakpoints vary, making it difficult to identify the candidate genes. Recent reports pointed to 4 genes (XPO1, USP34, BCL11A, and REL) that were included, alone or in combination, in the smallest deletions causing the syndrome. Here, we describe 8 new patients with the 2p15p16.1 deletion and review all published cases to date. We demonstrate functional deficits for the above 4 candidate genes using patients' lymphoblast cell lines (LCLs) and knockdown of their orthologs in zebrafish. All genes were dosage sensitive on the basis of reduced protein expression in LCLs. In addition, deletion of XPO1, a nuclear exporter, cosegregated with nuclear accumulation of one of its cargo molecules (rpS5) in patients' LCLs. Other pathways associated with these genes (e.g., NF-κB and Wnt signaling as well as the DNA damage response) were not impaired in patients' LCLs. Knockdown of xpo1a, rel, bcl11aa, and bcl11ab resulted in abnormal zebrafish embryonic development including microcephaly, dysmorphic body, hindered growth, and small fins as well as structural brain abnormalities. Our multifaceted analysis strongly implicates XPO1, REL, and BCL11A as candidate genes for 2p15p16.1 microdeletion syndrome.
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Affiliation(s)
- Hani Bagheri
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Chansonette Badduke
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Ying Qiao
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Rita Colnaghi
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Iga Abramowicz
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Diana Alcantara
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Christopher Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Jiadi Wen
- University of Texas at Dallas, Dallas, Texas, USA
| | | | - Malgorzata J.M. Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University Medical Centre, Hamilton, Ontario, Canada
| | | | - Anna Lehman
- Department of Medical Genetics, UBC, Vancouver, British Columbia, Canada
| | - Bruno Maranda
- Medical Genetics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sally Martell
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Xianghong Shan
- Department of Ophthalmology, UBC, Vancouver, British Columbia, Canada
| | - Suzanne M.E. Lewis
- Department of Medical Genetics, UBC, Vancouver, British Columbia, Canada
| | - Mark O’Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | | | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
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22
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Merikangas AK, Segurado R, Heron EA, Anney RJL, Paterson AD, Cook EH, Pinto D, Scherer SW, Szatmari P, Gill M, Corvin AP, Gallagher L. The phenotypic manifestations of rare genic CNVs in autism spectrum disorder. Mol Psychiatry 2015; 20:1366-72. [PMID: 25421404 PMCID: PMC4759095 DOI: 10.1038/mp.2014.150] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 08/10/2014] [Accepted: 09/19/2014] [Indexed: 12/28/2022]
Abstract
Significant evidence exists for the association between copy number variants (CNVs) and Autism Spectrum Disorder (ASD); however, most of this work has focused solely on the diagnosis of ASD. There is limited understanding of the impact of CNVs on the 'sub-phenotypes' of ASD. The objective of this paper is to evaluate associations between CNVs in differentially brain expressed (DBE) genes or genes previously implicated in ASD/intellectual disability (ASD/ID) and specific sub-phenotypes of ASD. The sample consisted of 1590 cases of European ancestry from the Autism Genome Project (AGP) with a diagnosis of an ASD and at least one rare CNV impacting any gene and a core set of phenotypic measures, including symptom severity, language impairments, seizures, gait disturbances, intelligence quotient (IQ) and adaptive function, as well as paternal and maternal age. Classification analyses using a non-parametric recursive partitioning method (random forests) were employed to define sets of phenotypic characteristics that best classify the CNV-defined groups. There was substantial variation in the classification accuracy of the two sets of genes. The best variables for classification were verbal IQ for the ASD/ID genes, paternal age at birth for the DBE genes and adaptive function for de novo CNVs. CNVs in the ASD/ID list were primarily associated with communication and language domains, whereas CNVs in DBE genes were related to broader manifestations of adaptive function. To our knowledge, this is the first study to examine the associations between sub-phenotypes and CNVs genome-wide in ASD. This work highlights the importance of examining the diverse sub-phenotypic manifestations of CNVs in ASD, including the specific features, comorbid conditions and clinical correlates of ASD that comprise underlying characteristics of the disorder.
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Affiliation(s)
- A K Merikangas
- Department of Psychiatry, Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 8, Ireland,Department of Psychiatry, Neuropsychiatric Genetics Research Group, Trinity College Dublin, Institute of Molecular Medicine, St. James's Hospital, James's Street, Dublin, Dublin 8, Ireland. E-mail:
| | - R Segurado
- Centre for Support and Training in Analysis and Research, University College Dublin, Dublin 4, Ireland
| | - E A Heron
- Department of Psychiatry, Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - R J L Anney
- Department of Psychiatry, Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - A D Paterson
- Program in Genetics and Genome Biology, Hospital for Sick Children, Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - E H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - D Pinto
- Departments of Psychiatry, and Genetics and Genomic Sciences, Seaver Autism Center, The Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S W Scherer
- Department of Molecular Genetics, The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - P Szatmari
- The Division of Child and Adolescent Psychiatry, Centre for Addiction and Mental Health, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - M Gill
- Department of Psychiatry, Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - A P Corvin
- Department of Psychiatry, Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - L Gallagher
- Department of Psychiatry, Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 8, Ireland
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23
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Miranda R, Nagapin F, Bozon B, Laroche S, Aubin T, Vaillend C. Altered social behavior and ultrasonic communication in the dystrophin-deficient mdx mouse model of Duchenne muscular dystrophy. Mol Autism 2015; 6:60. [PMID: 26527530 PMCID: PMC4627616 DOI: 10.1186/s13229-015-0053-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 10/22/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The Duchenne and Becker muscular dystrophies (DMD, BMD) show significant comorbid diagnosis for autism, and the genomic sequences encoding the proteins responsible for these diseases, the dystrophin and associated proteins, have been proposed as new candidate risk loci for autism. Dystrophin is expressed not only in muscles but also in central inhibitory synapses in the cerebellum, hippocampus, amygdala, and cerebral cortex, where it contributes to the organization of autism-associated trans-synaptic neurexin-neuroligin complexes and to the clustering of synaptic gamma-aminobutyric acid (GABA)A receptors. While brain defects due to dystrophin loss are associated with deficits in cognitive and executive functions, communication skills and social behavior, only a subpopulation of DMD patients meet the criteria for autism, suggesting that mutations in the dystrophin gene may confer a vulnerability to autism. The loss of dystrophin in the mdx mouse model of DMD has been associated with cognitive and emotional alterations, but social behavior and communication abilities have never been studied in this model. METHODS Here, we carried out the first in-depth analysis of social behavior and ultrasonic communication in dystrophin-deficient mdx mice, using a range of socially relevant paradigms involving various degrees of executive and cognitive demands, from simple presentation of sexual olfactory stimuli to social choice situations and direct encounters with female and male mice of various genotypes. RESULTS We identified context-specific alterations in social behavior and ultrasonic vocal communication in mdx mice during direct encounters in novel environments. Social behavior disturbances depended on intruders' genotype and behavior, suggesting alterations in executive functions and adaptive behaviors, and were associated with selective alterations of the development, rate, acoustic properties, and use of the ultrasonic vocal repertoire. CONCLUSIONS This first evidence that a mutation impeding expression of brain dystrophin affects social behavior and communication sheds new light on critical cognitive, emotional, and conative factors contributing to the development of autistic-like traits in this disease model.
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Affiliation(s)
- Rubén Miranda
- CNRS, Neuroscience Paris Saclay Institute, UMR 9197, Orsay, 91405 France ; Univ Paris-Sud, UMR 9197, Orsay, 91405 France ; Present address: Department of Psychobiology, Universidad Complutense de Madrid, Ciudad Universitaria, 28040 Madrid, Spain
| | - Flora Nagapin
- CNRS, Neuroscience Paris Saclay Institute, UMR 9197, Orsay, 91405 France ; Univ Paris-Sud, UMR 9197, Orsay, 91405 France
| | - Bruno Bozon
- CNRS, Neuroscience Paris Saclay Institute, UMR 9197, Orsay, 91405 France ; Univ Paris-Sud, UMR 9197, Orsay, 91405 France
| | - Serge Laroche
- CNRS, Neuroscience Paris Saclay Institute, UMR 9197, Orsay, 91405 France ; Univ Paris-Sud, UMR 9197, Orsay, 91405 France
| | - Thierry Aubin
- CNRS, Neuroscience Paris Saclay Institute, UMR 9197, Orsay, 91405 France ; Univ Paris-Sud, UMR 9197, Orsay, 91405 France
| | - Cyrille Vaillend
- CNRS, Neuroscience Paris Saclay Institute, UMR 9197, Orsay, 91405 France ; Univ Paris-Sud, UMR 9197, Orsay, 91405 France
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24
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Contribution of copy number variants (CNVs) to congenital, unexplained intellectual and developmental disabilities in Lebanese patients. Mol Cytogenet 2015; 8:26. [PMID: 25922617 PMCID: PMC4411788 DOI: 10.1186/s13039-015-0130-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Chromosomal microarray analysis (CMA) is currently the most widely adopted clinical test for patients with unexplained intellectual disability (ID), developmental delay (DD), and congenital anomalies. Its use has revealed the capacity to detect copy number variants (CNVs), as well as regions of homozygosity, that, based on their distribution on chromosomes, indicate uniparental disomy or parental consanguinity that is suggestive of an increased probability of recessive disease. Results We screened 149 Lebanese probands with ID/DD and 99 healthy controls using the Affymetrix Cyto 2.7 M and SNP6.0 arrays. We report all identified CNVs, which we divided into groups. Pathogenic CNVs were identified in 12.1% of the patients. We review the genotype/phenotype correlation in a patient with a 1q44 microdeletion and refine the minimal critical regions responsible for the 10q26 and 16q monosomy syndromes. Several likely causative CNVs were also detected, including new homozygous microdeletions (9p23p24.1, 10q25.2, and 8p23.1) in 3 patients born to consanguineous parents, involving potential candidate genes. However, the clinical interpretation of several other CNVs remains uncertain, including a microdeletion affecting ATRNL1. This CNV of unknown significance was inherited from the patient’s unaffected-mother; therefore, additional ethnically matched controls must be screened to obtain enough evidence for classification of this CNV. Conclusion This study has provided supporting evidence that whole-genome analysis is a powerful method for uncovering chromosomal imbalances, regardless of consanguinity in the parents of patients and despite the challenge presented by analyzing some CNVs. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0130-y) contains supplementary material, which is available to authorized users.
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25
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D'Amours G, Langlois M, Mathonnet G, Fetni R, Nizard S, Srour M, Tihy F, Phillips MS, Michaud JL, Lemyre E. SNP arrays: comparing diagnostic yields for four platforms in children with developmental delay. BMC Med Genomics 2014; 7:70. [PMID: 25539807 PMCID: PMC4299176 DOI: 10.1186/s12920-014-0070-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 12/11/2014] [Indexed: 11/28/2022] Open
Abstract
Background Molecular karyotyping is now the first-tier genetic test for patients affected with unexplained intellectual disability (ID) and/or multiple congenital anomalies (MCA), since it identifies a pathogenic copy number variation (CNV) in 10-14% of them. High-resolution microarrays combining molecular karyotyping and single nucleotide polymorphism (SNP) genotyping were recently introduced to the market. In addition to identifying CNVs, these platforms detect loss of heterozygosity (LOH), which can indicate the presence of a homozygous mutation or uniparental disomy. Since these abnormalities can be associated with ID and/or MCA, their detection is of particular interest for patients whose phenotype remains unexplained. However, the diagnostic yield obtained with these platforms is not confirmed, and the real clinical value of LOH detection has not been established. Methods We selected 21 children affected with ID, with or without congenital malformations, for whom standard genetic analyses failed to provide a diagnosis. We performed high-resolution SNP array analysis with four platforms (Affymetrix Genome-Wide Human SNP Array 6.0, Affymetrix Cytogenetics Whole-Genome 2.7 M array, Illumina HumanOmni1-Quad BeadChip, and Illumina HumanCytoSNP-12 DNA Analysis BeadChip) on whole-blood samples obtained from children and their parents to detect pathogenic CNVs and LOHs, and compared the results with those obtained on a moderate resolution array-based comparative genomic hybridization platform (NimbleGen CGX-12 Cytogenetics Array), already used in the clinical setting. Results We identified a total of four pathogenic CNVs in three patients, and all arrays successfully detected them. With the SNP arrays, we also identified a LOH containing a gene associated with a recessive disorder consistent with the patient’s phenotype (i.e., an informative LOH) in four children (including two siblings). A homozygous mutation within the informative LOH was found in three of these patients. Therefore, we were able to increase the diagnostic yield from 14.3% to 28.6% as a result of the information provided by LOHs. Conclusions This study shows the clinical usefulness of SNP arrays in children with ID, since they successfully detect pathogenic CNVs, identify informative LOHs that can lead to the diagnosis of a recessive disorder. It also highlights some challenges associated with the use of SNP arrays in a clinical laboratory. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0070-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guylaine D'Amours
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
| | - Mathieu Langlois
- Centre de pharmacogénomique, Institut de cardiologie de Montréal, Montréal, QC, Canada.
| | | | - Raouf Fetni
- Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Département de pathologie, CHU Sainte-Justine, Montréal, QC, Canada. .,Pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada.
| | - Sonia Nizard
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
| | - Myriam Srour
- Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada.
| | - Frédérique Tihy
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada.
| | - Michael S Phillips
- Centre de pharmacogénomique, Institut de cardiologie de Montréal, Montréal, QC, Canada.
| | - Jacques L Michaud
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
| | - Emmanuelle Lemyre
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
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26
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Uddin M, Thiruvahindrapuram B, Walker S, Wang Z, Hu P, Lamoureux S, Wei J, MacDonald JR, Pellecchia G, Lu C, Lionel AC, Gazzellone MJ, McLaughlin JR, Brown C, Andrulis IL, Knight JA, Herbrick JA, Wintle RF, Ray P, Stavropoulos DJ, Marshall CR, Scherer SW. A high-resolution copy-number variation resource for clinical and population genetics. Genet Med 2014; 17:747-52. [PMID: 25503493 DOI: 10.1038/gim.2014.178] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/07/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Chromosomal microarray analysis to assess copy-number variation has become a first-tier genetic diagnostic test for individuals with unexplained neurodevelopmental disorders or multiple congenital anomalies. More than 100 cytogenetic laboratories worldwide use the new ultra-high resolution Affymetrix CytoScan-HD array to genotype hundreds of thousands of samples per year. Our aim was to develop a copy-number variation resource from a new population sample that would enable more accurate interpretation of clinical genetics data on this microarray platform and others. METHODS Genotyping of 1,000 adult volunteers who are broadly representative of the Ontario population (as obtained from the Ontario Population Genomics Platform) was performed with the CytoScan-HD microarray system, which has 2.7 million probes. Four independent algorithms were applied to detect copy-number variations. Reproducibility and validation metrics were quantified using sample replicates and quantitative-polymerase chain reaction, respectively. RESULTS DNA from 873 individuals passed quality control and we identified 71,178 copy-number variations (81 copy-number variations/individual); 9.8% (6,984) of these copy-number variations were previously unreported. After applying three layers of filtering criteria, from our highest confidence copy-number variation data set we obtained >95% reproducibility and >90% validation rates (73% of these copy-number variations overlapped at least one gene). CONCLUSION The genotype data and annotated copy-number variations for this largely Caucasian population will represent a valuable public resource enabling clinical genetics research and diagnostics.
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Affiliation(s)
- Mohammed Uddin
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Susan Walker
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Zhuozhi Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pingzhao Hu
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chao Lu
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anath C Lionel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthew J Gazzellone
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - John R McLaughlin
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Public Health Ontario, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Catherine Brown
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julia A Knight
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jo-Anne Herbrick
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Ray
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Molecular Genetics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- Division of Molecular Genetics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Molecular Genetics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Zanolli MT, Capasso J, Khetan V, Aristimuño B, Levin AV. Unusual retinal abnormalities in sisters with tetralogy of Fallot. J AAPOS 2014; 18:601-4. [PMID: 25448148 DOI: 10.1016/j.jaapos.2014.07.163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/01/2014] [Accepted: 07/05/2014] [Indexed: 11/19/2022]
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease and can occur in the setting of chromosomal aberrations or multisystem malformation syndromes. We report unusual focal bilateral retinal defects in sisters with TOF.
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Affiliation(s)
- Mario T Zanolli
- Ocular Genetics, Wills Eye Hospital, Philadelphia, Pennsylvania
| | - Jenina Capasso
- Ocular Genetics, Wills Eye Hospital, Philadelphia, Pennsylvania
| | - Vikas Khetan
- Ocular Genetics, Wills Eye Hospital, Philadelphia, Pennsylvania
| | | | - Alex V Levin
- Ocular Genetics, Wills Eye Hospital, Philadelphia, Pennsylvania; Thomas Jefferson University, Philadelphia.
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Palumbo O, Palumbo P, Delvecchio M, Palladino T, Stallone R, Crisetti M, Zelante L, Carella M. Microdeletion of 12q24.31: report of a girl with intellectual disability, stereotypies, seizures and facial dysmorphisms. Am J Med Genet A 2014; 167A:438-44. [PMID: 25428890 DOI: 10.1002/ajmg.a.36872] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 10/04/2014] [Indexed: 12/17/2022]
Abstract
We provide a detailed clinical and molecular characterization of an 11-year-old female patient presenting with neurodevelopmental delay (NDD), intellectual disability (ID), seizures, stereotypies and dysmorphic features. Chromosomal microarrays analysis (CMA) detected a small, rare de novo deletion on chromosome 12q24.31 encompassing 31 protein-coding RefSeq genes and a microRNA. Phenotypic comparison with molecularly well-defined cases previously reported in the literature harboring an overlapping 12q24.31 microdeletion indicate that these patients shared common clinical features including neurodevelopmental delay, intellectual disability and behavioral problems. Also, seizures and dysmorphic features are frequent and a consistent pattern was recognized. Since there are remarkable resemblance between the patient described here and at least another one previously reported, our report is provides supportive evidence for the existence of an emerging syndrome caused by a microdeletion in 12q24.31. We propose a minimal region shared among patients contributing to the etiology of the common clinical features observed suggesting as candidate, for the first time, the gene SETD1B which is a component of a histone methyltransferase complex. In addition, we speculate on the possible contributive role of the MIR4304 to some clinical features observed in our patient. Evaluation of more patients with well-characterized deletions within 12q24.31, as well as careful clinical assessment of them, is needed to corroborate our hypothesis, to perform a more detailed genotype-phenotype correlation and, finally, to fully delineate this emerging microdeletion syndrome.
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Affiliation(s)
- Orazio Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
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Verhoeven WM, Egger JI, van den Bergh JP, van Beek R, Kleefstra T, de Leeuw N. A 12q24.31 interstitial deletion in an adult male with MODY3: Neuropsychiatric and neuropsychological characteristics. Am J Med Genet A 2014; 167A:169-73. [DOI: 10.1002/ajmg.a.36730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/17/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Willem M.A. Verhoeven
- Vincent van Gogh Institute for Psychiatry; Centre of Excellence for Neuropsychiatry; Venray The Netherlands
- Erasmus University Medical Centre; Department of Psychiatry; Rotterdam The Netherlands
| | - Jos I.M. Egger
- Vincent van Gogh Institute for Psychiatry; Centre of Excellence for Neuropsychiatry; Venray The Netherlands
- Donders Institute for Brain; Cognition and Behaviour; Behavioural Science Institute; Radboud University Nijmegen; Nijmegen The Netherlands
| | - Joop P.W. van den Bergh
- VieCuri Medical Centre; Department of Internal Medicine; Venlo The Netherlands
- Maastricht University Medical Centre; Department of Internal Medicine; Maastricht The Netherlands
| | - Ronald van Beek
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen The Netherlands
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Moreira DP, Griesi-Oliveira K, Bossolani-Martins AL, Lourenço NCV, Takahashi VNO, da Rocha KM, Moreira ES, Vadasz E, Meira JGC, Bertola D, Halloran EO, Magalhães TR, Fett-Conte AC, Passos-Bueno MR. Investigation of 15q11-q13, 16p11.2 and 22q13 CNVs in autism spectrum disorder Brazilian individuals with and without epilepsy. PLoS One 2014; 9:e107705. [PMID: 25255310 PMCID: PMC4177849 DOI: 10.1371/journal.pone.0107705] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 08/21/2014] [Indexed: 11/18/2022] Open
Abstract
Copy number variations (CNVs) are an important cause of ASD and those located at 15q11-q13, 16p11.2 and 22q13 have been reported as the most frequent. These CNVs exhibit variable clinical expressivity and those at 15q11-q13 and 16p11.2 also show incomplete penetrance. In the present work, through multiplex ligation-dependent probe amplification (MLPA) analysis of 531 ethnically admixed ASD-affected Brazilian individuals, we found that the combined prevalence of the 15q11-q13, 16p11.2 and 22q13 CNVs is 2.1% (11/531). Parental origin could be determined in 8 of the affected individuals, and revealed that 4 of the CNVs represent de novo events. Based on CNV prediction analysis from genome-wide SNP arrays, the size of those CNVs ranged from 206 kb to 2.27 Mb and those at 15q11-q13 were limited to the 15q13.3 region. In addition, this analysis also revealed 6 additional CNVs in 5 out of 11 affected individuals. Finally, we observed that the combined prevalence of CNVs at 15q13.3 and 22q13 in ASD-affected individuals with epilepsy (6.4%) was higher than that in ASD-affected individuals without epilepsy (1.3%; p<0.014). Therefore, our data show that the prevalence of CNVs at 15q13.3, 16p11.2 and 22q13 in Brazilian ASD-affected individuals is comparable to that estimated for ASD-affected individuals of pure or predominant European ancestry. Also, it suggests that the likelihood of a greater number of positive MLPA results might be found for the 15q13.3 and 22q13 regions by prioritizing ASD-affected individuals with epilepsy.
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MESH Headings
- Adolescent
- Base Sequence
- Brazil
- Child
- Child Development Disorders, Pervasive/complications
- Child Development Disorders, Pervasive/genetics
- Chromosomes, Human/genetics
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 16/genetics
- Chromosomes, Human, Pair 22/genetics
- DNA Copy Number Variations
- Epilepsy/complications
- Female
- Genomics
- Humans
- Male
- Pedigree
- Polymorphism, Single Nucleotide
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Affiliation(s)
- Danielle P. Moreira
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Karina Griesi-Oliveira
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Ana L. Bossolani-Martins
- Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brasil
| | - Naila C. V. Lourenço
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Vanessa N. O. Takahashi
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Kátia M. da Rocha
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Eloisa S. Moreira
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Estevão Vadasz
- Instituto de Psiquiatria do Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brasil
| | - Joanna Goes Castro Meira
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Debora Bertola
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
- Instituto da Criança da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brasil
| | - Eoghan O’ Halloran
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Tiago R. Magalhães
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital, Dublin, Ireland
| | - Agnes C. Fett-Conte
- Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brasil
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
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Qiao Y, Mercier E, Dastan J, Hurlburt J, McGillivray B, Chudley AE, Farrell S, Bernier FP, Lewis MS, Pavlidis P, Rajcan-Separovic E. Copy number variants (CNVs) analysis in a deeply phenotyped cohort of individuals with intellectual disability (ID). BMC MEDICAL GENETICS 2014; 15:82. [PMID: 25030379 PMCID: PMC4107469 DOI: 10.1186/1471-2350-15-82] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 07/03/2014] [Indexed: 01/13/2023]
Abstract
Background DNA copy number variants (CNVs) are found in 15% of subjects with ID but their association with phenotypic abnormalities has been predominantly studied in smaller cohorts of subjects with detailed yet non-systematically categorized phenotypes, or larger cohorts (thousands of cases) with smaller number of generalized phenotypes. Methods We evaluated the association of de novo, familial and common CNVs detected in 78 ID subjects with phenotypic abnormalities classified using the Winter-Baraitser Dysmorphology Database (WBDD) (formerly the London Dysmorphology Database). Terminology for 34 primary (coarse) and 169 secondary (fine) phenotype features were used to categorize the abnormal phenotypes and determine the prevalence of each phenotype in patients grouped by the type of CNV they had. Results In our cohort more than 50% of cases had abnormalities in primary categories related to head (cranium, forehead, ears, eye globes, eye associated structures, nose) as well as hands and feet. The median number of primary and secondary abnormalities was 12 and 18 per subject, respectively, indicating that the cohort consisted of subjects with a high number of phenotypic abnormalities (median De Vries score for the cohort was 5). The prevalence of each phenotypic abnormality was comparable in patients with de novo or familial CNVs in comparison to those with only common CNVs, although a trend for increased frequency of cranial and forehead abnormalities was noted in subjects with rare de novo and familial CNVs. Two clusters of subjects were identified based on the prevalence of each fine phenotypic feature, with an average of 28.3 and 13.5 abnormal phenotypes/subject in the two clusters respectively (P < 0.05). Conclusions Our study is a rare example of using standardized, deep morphologic phenotype clustering with phenotype/CNV correlation in a cohort of subjects with ID. The composition of the cohort inevitably influences the phenotype/genotype association, and our studies show that the influence of the de novo CNVs on the phenotype is less obvious in cohorts consisting of subjects with a high number of phenotypic abnormalities. The outcome of phenotype/genotype analysis also depends on the choice of phenotypes assessed and standardized phenotyping is required to minimize variability.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Me Suzanne Lewis
- Department of Pathology (Cytogenetics), BC Child and Family Research Institute, University of British Columbia (UBC), 950 West 28th, Room 3060, Vancouver, BC V5Z 4H4, Canada.
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Bartlett CW, Hou L, Flax JF, Hare A, Cheong SY, Fermano Z, Zimmerman-Bier B, Cartwright C, Azaro MA, Buyske S, Brzustowicz LM. A genome scan for loci shared by autism spectrum disorder and language impairment. Am J Psychiatry 2014; 171:72-81. [PMID: 24170272 PMCID: PMC4431698 DOI: 10.1176/appi.ajp.2013.12081103] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The authors conducted a genetic linkage study of families that have both autism spectrum disorder (ASD) and language-impaired probands to find common communication impairment loci. The hypothesis was that these families have a high genetic loading for impairments in language ability, thus influencing the language and communication deficits of the family members with ASD. Comprehensive behavioral phenotyping of the families also enabled linkage analysis of quantitative measures, including normal, subclinical, and disordered variation in all family members for the three general autism symptom domains: social, communication, and compulsive behaviors. METHOD The primary linkage analysis coded persons with either ASD or specific language impairment as "affected." The secondary linkage analysis consisted of quantitative metrics of autism-associated behaviors capturing normal to clinically severe variation, measured in all family members. RESULTS Linkage to language phenotypes was established at two novel chromosomal loci, 15q23-26 and 16p12. The secondary analysis of normal and disordered quantitative variation in social and compulsive behaviors established linkage to two loci for social behaviors (at 14q and 15q) and one locus for repetitive behaviors (at 13q). CONCLUSION These data indicate shared etiology of ASD and specific language impairment at two novel loci. Additionally, nonlanguage phenotypes based on social aloofness and rigid personality traits showed compelling evidence for linkage in this study group. Further genetic mapping is warranted at these loci.
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Affiliation(s)
- Christopher W. Bartlett
- The Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Liping Hou
- The Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Judy F. Flax
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ
| | - Abby Hare
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ
| | - Soo Yeon Cheong
- The Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Zena Fermano
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ
| | - Barbie Zimmerman-Bier
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ,Department of Pediatrics, Saint Peter's University Hospital, New Brunswick, NJ
| | - Charles Cartwright
- Department of Psychiatry, University of Medicine and Dentistry of New Jersey – New Jersey Medical School, Newark, NJ
| | - Marco A. Azaro
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ
| | - Steven Buyske
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ,Department of Statistics and Biostatistics, Rutgers University, Rutgers University, Piscataway, NJ
| | - Linda M. Brzustowicz
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ,Corresponding Author:
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Chouery E, Guissart C, Mégarbané H, Aral B, Nassif C, Thauvin-Robinet C, Faivre L, Mégarbané A. Craniosynostosis, anal anomalies, and porokeratosis (CDAGS syndrome): Case report and literature review. Eur J Med Genet 2013; 56:674-7. [DOI: 10.1016/j.ejmg.2013.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 09/23/2013] [Indexed: 11/25/2022]
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34
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Qiao Y, Badduke C, Mercier E, Lewis SME, Pavlidis P, Rajcan-Separovic E. miRNA and miRNA target genes in copy number variations occurring in individuals with intellectual disability. BMC Genomics 2013; 14:544. [PMID: 23937676 PMCID: PMC3750877 DOI: 10.1186/1471-2164-14-544] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 08/06/2013] [Indexed: 12/20/2022] Open
Abstract
Background MicroRNAs (miRNAs) are a family of short, non-coding RNAs modulating expression of human protein coding genes (miRNA target genes). Their dysfunction is associated with many human diseases, including neurodevelopmental disorders. It has been recently shown that genomic copy number variations (CNVs) can cause aberrant expression of integral miRNAs and their target genes, and contribute to intellectual disability (ID). Results To better understand the CNV-miRNA relationship in ID, we investigated the prevalence and function of miRNAs and miRNA target genes in five groups of CNVs. Three groups of CNVs were from 213 probands with ID (24 de novo CNVs, 46 familial and 216 common CNVs), one group of CNVs was from a cohort of 32 cognitively normal subjects (67 CNVs) and one group of CNVs represented 40 ID related syndromic regions listed in DECIPHER (30 CNVs) which served as positive controls for CNVs causing or predisposing to ID. Our results show that 1). The number of miRNAs is significantly higher in de novo or DECIPHER CNVs than in familial or common CNV subgroups (P < 0.01). 2). miRNAs with brain related functions are more prevalent in de novo CNV groups compared to common CNV groups. 3). More miRNA target genes are found in de novo, familial and DECIPHER CNVs than in the common CNV subgroup (P < 0.05). 4). The MAPK signaling cascade is found to be enriched among the miRNA target genes from de novo and DECIPHER CNV subgroups. Conclusions Our findings reveal an increase in miRNA and miRNA target gene content in de novo versus common CNVs in subjects with ID. Their expression profile and participation in pathways support a possible role of miRNA copy number change in cognition and/or CNV-mediated developmental delay. Systematic analysis of expression/function of miRNAs in addition to coding genes integral to CNVs could uncover new causes of ID.
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Affiliation(s)
- Ying Qiao
- Department of Pathology and Lab Medicine, BC Child and Family Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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Chouery E, Choucair N, Abou Ghoch J, El Sabbagh S, Corbani S, Mégarbané A. Report on a patient with a 12q24.31 microdeletion inherited from an insulin-dependent diabetes mellitus father. Mol Syndromol 2013; 4:136-42. [PMID: 23653585 DOI: 10.1159/000346473] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2012] [Indexed: 12/22/2022] Open
Abstract
We report a 2.3-year-old female patient with global developmental delay, infantile spasms, hypotonia, microcephaly, flat face, full cheeks, macroglossia, highly arched palate, retro-gnathia, narrow ear orifices, and café-au-lait spots. Molecular karyotyping revealed approximately a 1-Mb interstitial deletion of the long arm of one chromosome 12, del(12)(q24.31). The same deletion was identified in her father who presents insulin-dependent diabetes mellitus (IDDM) diagnosed at 14 years. Only one other patient with a similar de novo deletion has been reported previously [Mol Syndromol 2010;1:42-45]. A phenotype-genotype correlation is discussed, and the description of a novel rare microdeletion entity is raised.
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Affiliation(s)
- E Chouery
- Unité de Génétique Médicale et Laboratoire Associé INSERM à l'Unité UMR_S 910, Pôle Technologie Santé, Université Saint-Joseph, Beirut, Lebanon
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