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Carter MT, Srour M, Au PYB, Buhas D, Dyack S, Eaton A, Inbar-Feigenberg M, Howley H, Kawamura A, Lewis SME, McCready E, Nelson TN, Vallance H. Genetic and metabolic investigations for neurodevelopmental disorders: position statement of the Canadian College of Medical Geneticists (CCMG). J Med Genet 2023; 60:523-532. [PMID: 36822643 DOI: 10.1136/jmg-2022-108962] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023]
Abstract
PURPOSE AND SCOPE The aim of this position statement is to provide recommendations for clinicians regarding the use of genetic and metabolic investigations for patients with neurodevelopmental disorders (NDDs), specifically, patients with global developmental delay (GDD), intellectual disability (ID) and/or autism spectrum disorder (ASD). This document also provides guidance for primary care and non-genetics specialists caring for these patients while awaiting consultation with a clinical geneticist or metabolic specialist. METHODS OF STATEMENT DEVELOPMENT A multidisciplinary group reviewed existing literature and guidelines on the use of genetic and metabolic investigations for the diagnosis of NDDs and synthesised the evidence to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and to the Canadian Pediatric Society (Mental Health and Developmental Disabilities Committee); following incorporation of feedback, it was approved by the CCMG Board of Directors on 1 September 2022. RESULTS AND CONCLUSIONS Chromosomal microarray is recommended as a first-tier test for patients with GDD, ID or ASD. Fragile X testing should also be done as a first-tier test when there are suggestive clinical features or family history. Metabolic investigations should be done if there are clinical features suggestive of an inherited metabolic disease, while the patient awaits consultation with a metabolic physician. Exome sequencing or a comprehensive gene panel is recommended as a second-tier test for patients with GDD or ID. Genetic testing is not recommended for patients with NDDs in the absence of GDD, ID or ASD, unless accompanied by clinical features suggestive of a syndromic aetiology or inherited metabolic disease.
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Affiliation(s)
| | - Myriam Srour
- Division of Neurology, McGill University Health Centre, Montreal, Québec, Canada
- Department of Pediatrics, McGill University, Montréal, QC, Canada
| | - Ping-Yee Billie Au
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sarah Dyack
- Division of Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Alison Eaton
- Department of Medical Genetics, Stollery Children's Hospital, Edmonton, Alberta, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michal Inbar-Feigenberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Heather Howley
- Office of Research Services, CHEO Research Institute, Ottawa, Ontario, Canada
| | - Anne Kawamura
- Division of Developmental Pediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Mental Health and Developmental Disability Committee, Canadian Pediatric Society, Ottawa, ON, Canada
- Canadian Paediatric Society, Toronto, Ontario, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's and Women's Hospital, Vancouver, British Columbia, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, McMaster University, Hamilton, ON, Canada, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hilary Vallance
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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Loureiro LO, Howe JL, Reuter MS, Iaboni A, Calli K, Roshandel D, Pritišanac I, Moses A, Forman-Kay JD, Trost B, Zarrei M, Rennie O, Lau LYS, Marshall CR, Srivastava S, Godlewski B, Buttermore ED, Sahin M, Hartley D, Frazier T, Vorstman J, Georgiades S, Lewis SME, Szatmari P, Bradley CAL, Tabet AC, Willems M, Lumbroso S, Piton A, Lespinasse J, Delorme R, Bourgeron T, Anagnostou E, Scherer SW. A recurrent SHANK3 frameshift variant in Autism Spectrum Disorder. NPJ Genom Med 2021; 6:91. [PMID: 34737294 PMCID: PMC8568906 DOI: 10.1038/s41525-021-00254-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/23/2021] [Indexed: 01/22/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is genetically complex with ~100 copy number variants and genes involved. To try to establish more definitive genotype and phenotype correlations in ASD, we searched genome sequence data, and the literature, for recurrent predicted damaging sequence-level variants affecting single genes. We identified 18 individuals from 16 unrelated families carrying a heterozygous guanine duplication (c.3679dup; p.Ala1227Glyfs*69) occurring within a string of 8 guanines (genomic location [hg38]g.50,721,512dup) affecting SHANK3, a prototypical ASD gene (0.08% of ASD-affected individuals carried the predicted p.Ala1227Glyfs*69 frameshift variant). Most probands carried de novo mutations, but five individuals in three families inherited it through somatic mosaicism. We scrutinized the phenotype of p.Ala1227Glyfs*69 carriers, and while everyone (17/17) formally tested for ASD carried a diagnosis, there was the variable expression of core ASD features both within and between families. Defining such recurrent mutational mechanisms underlying an ASD outcome is important for genetic counseling and early intervention.
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Affiliation(s)
- Livia O Loureiro
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer L Howe
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Miriam S Reuter
- Canada's Genomics Enterprise (CGEn), The Hospital for Sick Children, Toronto, ON, Canada
| | - Alana Iaboni
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
| | - Kristina Calli
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Delnaz Roshandel
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Iva Pritišanac
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Alan Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Brett Trost
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mehdi Zarrei
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Olivia Rennie
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lynette Y S Lau
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brianna Godlewski
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth D Buttermore
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mustafa Sahin
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Thomas Frazier
- Autism Speaks and Department of Psychology, John Carroll University, Cleveland, OH, USA
| | - Jacob Vorstman
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Peter Szatmari
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Clarrisa A Lisa Bradley
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anne-Claude Tabet
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, F-75015, Paris, France
- Genetics Department, Cytogenetic Unit, Robert Debré Hospital, APHP, F-75019, Paris, France
| | | | - Serge Lumbroso
- Biochimie et Biologie Moléculaire, CHU Nimes, Univ. Montpellier, Nimes, France
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
- Unité de Génétique Moléculaire, IGMA, Hôpitaux Universitaire de Strasbourg, Strasbourg, France
- Institut Universitaire de France, Paris, France
| | | | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, F-75015, Paris, France
- Child and Adolescent Psychiatry Department, Robert Debré Hospital, APHP, F-75019, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, F-75015, Paris, France
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics and the McLaughlin Centre, University of Toronto, Toronto, ON, Canada.
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Qiao Y, Mondal K, Trapani V, Wen J, Carpenter G, Wildin R, Price EM, Gibbons RJ, Eichmeyer J, Jiang R, DuPont B, Martell S, Lewis SME, Robinson WP, O'Driscoll M, Wolf FI, Zwick ME, Rajcan-Separovic E. Variant ATRX syndrome with dysfunction of ATRX and MAGT1 genes. Hum Mutat 2014; 35:58-62. [PMID: 24130152 DOI: 10.1002/humu.22465] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/24/2013] [Accepted: 10/02/2013] [Indexed: 01/10/2023]
Abstract
A 0.8 kb intronic duplication in MAGT1 and a single base pair deletion in the last exon of ATRX were identified using a chromosome X-specific microarray and exome sequencing in a family with five males demonstrating intellectual disability (ID) and unusual skin findings (e.g., generalized pruritus). MAGT1 is an Mg²⁺ transporter previously associated with primary immunodeficiency and ID, whereas mutations in ATRX cause ATRX-ID syndrome. In patient cells, the function of ATRX was demonstrated to be abnormal based on altered RNA/protein expression, hypomethylation of rDNA, and abnormal cytokinesis. Dysfunction of MAGT1 was reflected in reduced RNA/protein expression and Mg²⁺ influx. The mutation in ATRX most likely explains the ID, whereas MAGT1 disruption could be linked to abnormal skin findings, as normal magnesium homeostasis is necessary for skin health. This work supports observations that multiple mutations collectively contribute to the phenotypic variability of syndromic ID, and emphasizes the importance of correlating clinical phenotype with genomic and cell function analyses.
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hettinger JA, Liu X, Hudson ML, Lee A, Cohen IL, Michaelis RC, Schwartz CE, Lewis SME, Holden JJA. DRD2 and PPP1R1B (DARPP-32) polymorphisms independently confer increased risk for autism spectrum disorders and additively predict affected status in male-only affected sib-pair families. Behav Brain Funct 2012; 8:19. [PMID: 22559203 PMCID: PMC3479424 DOI: 10.1186/1744-9081-8-19] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 05/04/2012] [Indexed: 11/21/2022] Open
Abstract
Background The neurotransmitter dopamine (DA) modulates executive functions, learning, and emotional processing, all of which are impaired in individuals with autism spectrum disorders (ASDs). Our previous findings suggest a role for dopamine-related genes in families with only affected males. Methods We examined two additional genes which affect DA function, the DRD2 and PPP1R1B (DARPP-32) genes, in a cohort of 112 male-only affected sib-pair families. Selected polymorphisms spanning these genes were genotyped and both family-based and population-based tests were carried out for association analysis. General discriminant analysis was used to examine the gene-gene interactions in predicting autism susceptibility. Results There was a significantly increased frequency of the DRD2 rs1800498TT genotype (P = 0.007) in affected males compared to the comparison group, apparently due to over-transmission of the T allele (P = 0.0003). The frequency of the PPP1R1B rs1495099CC genotype in affected males was also higher than that in the comparison group (P = 0.002) due to preferential transmission of the C allele from parents to affected children (P = 0.0009). Alleles rs1800498T and rs1495099C were associated with more severe problems in social interaction (P = 0.0002 and P = 0.0016, respectively) and communication (P = 0.0004 and P = 0.0046), and increased stereotypic behaviours (P = 0.0021 and P = 0.00072). General discriminant analysis found that the DRD2 and PPP1R1B genes additively predicted ASDs (P = 0.00011; Canonical R = 0.26) and explain ~7% of the variance in our families. All findings remained significant following corrections for multiple testing. Conclusion Our findings support a role for the DRD2 and PPP1R1B genes in conferring risk for autism in families with only affected males and show an additive effect of these genes towards prediction of affected status in our families.
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Affiliation(s)
- Joe A Hettinger
- Department of Physiology, Queen's University, Kingston, ON, Canada
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9
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Qiao Y, Tyson C, Hrynchak M, Lopez-Rangel E, Hildebrand J, Martell S, Fawcett C, Kasmara L, Calli K, Harvard C, Liu X, Holden JJA, Lewis SME, Rajcan-Separovic E. Clinical application of 2.7M Cytogenetics array for CNV detection in subjects with idiopathic autism and/or intellectual disability. Clin Genet 2012; 83:145-54. [PMID: 22369279 DOI: 10.1111/j.1399-0004.2012.01860.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Higher resolution whole-genome arrays facilitate the identification of smaller copy number variations (CNVs) and their integral genes contributing to autism and/or intellectual disability (ASD/ID). Our study describes the use of one of the highest resolution arrays, the Affymetrix(®) Cytogenetics 2.7M array, coupled with quantitative multiplex polymerase chain reaction (PCR) of short fluorescent fragments (QMPSF) for detection and validation of small CNVs. We studied 82 subjects with ASD and ID in total (30 in the validation and 52 in the application cohort) and detected putatively pathogenic CNVs in 6/52 cases from the application cohort. This included a 130-kb maternal duplication spanning exons 64-79 of the DMD gene which was found in a 3-year-old boy manifesting autism and mild neuromotor delays. Other pathogenic CNVs involved 4p14, 12q24.31, 14q32.31, 15q13.2-13.3, and 17p13.3. We established the optimal experimental conditions which, when applied to select small CNVs for QMPSF confirmation, reduced the false positive rate from 60% to 25%. Our work suggests that selection of small CNVs based on the function of integral genes, followed by review of array experimental parameters resulting in highest confirmation rate using multiplex PCR, may enhance the usefulness of higher resolution platforms for ASD and ID gene discovery.
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Affiliation(s)
- Y Qiao
- BC Child and Family Research Institute, Vancouver, BC, Canada
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10
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Harvard C, Strong E, Mercier E, Colnaghi R, Alcantara D, Chow E, Martell S, Tyson C, Hrynchak M, McGillivray B, Hamilton S, Marles S, Mhanni A, Dawson AJ, Pavlidis P, Qiao Y, Holden JJ, Lewis SME, O'Driscoll M, Rajcan-Separovic E. Understanding the impact of 1q21.1 copy number variant. Orphanet J Rare Dis 2011; 6:54. [PMID: 21824431 PMCID: PMC3180300 DOI: 10.1186/1750-1172-6-54] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Accepted: 08/08/2011] [Indexed: 01/10/2023] Open
Abstract
Background 1q21.1 Copy Number Variant (CNV) is associated with a highly variable phenotype ranging from congenital anomalies, learning deficits/intellectual disability (ID), to a normal phenotype. Hence, the clinical significance of this CNV can be difficult to evaluate. Here we described the consequences of the 1q21.1 CNV on genome-wide gene expression and function of selected candidate genes within 1q21.1 using cell lines from clinically well described subjects. Methods and Results Eight subjects from 3 families were included in the study: six with a 1q21.1 deletion and two with a 1q21.1 duplication. High resolution Affymetrix 2.7M array was used to refine the 1q21.1 CNV breakpoints and exclude the presence of secondary CNVs of pathogenic relevance. Whole genome expression profiling, studied in lymphoblast cell lines (LBCs) from 5 subjects, showed enrichment of genes from 1q21.1 in the top 100 genes ranked based on correlation of expression with 1q21.1 copy number. The function of two top genes from 1q21.1, CHD1L/ALC1 and PRKAB2, was studied in detail in LBCs from a deletion and a duplication carrier. CHD1L/ALC1 is an enzyme with a role in chromatin modification and DNA damage response while PRKAB2 is a member of the AMP kinase complex, which senses and maintains systemic and cellular energy balance. The protein levels for CHD1L/ALC1 and PRKAB2 were changed in concordance with their copy number in both LBCs. A defect in chromatin remodeling was documented based on impaired decatenation (chromatid untangling) checkpoint (DCC) in both LBCs. This defect, reproduced by CHD1L/ALC1 siRNA, identifies a new role of CHD1L/ALC1 in DCC. Both LBCs also showed elevated levels of micronuclei following treatment with a Topoisomerase II inhibitor suggesting increased DNA breaks. AMP kinase function, specifically in the deletion containing LBCs, was attenuated. Conclusion Our studies are unique as they show for the first time that the 1q21.1 CNV not only causes changes in the expression of its key integral genes, associated with changes at the protein level, but also results in changes in their known function, in the case of AMPK, and newly identified function such as DCC activation in the case of CHD1L/ALC1. Our results support the use of patient lymphoblasts for dissecting the functional sequelae of genes integral to CNVs in carrier cell lines, ultimately enhancing understanding of biological processes which may contribute to the clinical phenotype.
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Affiliation(s)
- Chansonette Harvard
- Child and Family Research Institute, Molecular Cytogenetics and Array Laboratory, 950 West 28th Avenue, Vancouver, BC, Canada
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11
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Noor A, Whibley A, Marshall CR, Gianakopoulos PJ, Piton A, Carson AR, Orlic-Milacic M, Lionel AC, Sato D, Pinto D, Drmic I, Noakes C, Senman L, Zhang X, Mo R, Gauthier J, Crosbie J, Pagnamenta AT, Munson J, Estes AM, Fiebig A, Franke A, Schreiber S, Stewart AFR, Roberts R, McPherson R, Guter SJ, Cook EH, Dawson G, Schellenberg GD, Battaglia A, Maestrini E, Jeng L, Hutchison T, Rajcan-Separovic E, Chudley AE, Lewis SME, Liu X, Holden JJ, Fernandez B, Zwaigenbaum L, Bryson SE, Roberts W, Szatmari P, Gallagher L, Stratton MR, Gecz J, Brady AF, Schwartz CE, Schachar RJ, Monaco AP, Rouleau GA, Hui CC, Lucy Raymond F, Scherer SW, Vincent JB. Disruption at the PTCHD1 Locus on Xp22.11 in Autism spectrum disorder and intellectual disability. Sci Transl Med 2010; 2:49ra68. [PMID: 20844286 DOI: 10.1126/scitranslmed.3001267] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Autism is a common neurodevelopmental disorder with a complex mode of inheritance. It is one of the most highly heritable of the complex disorders, although the underlying genetic factors remain largely unknown. Here, we report mutations in the X-chromosome PTCHD1 (patched-related) gene in seven families with autism spectrum disorder (ASD) and in three families with intellectual disability. A 167-kilobase microdeletion spanning exon 1 was found in two brothers, one with ASD and the other with a learning disability and ASD features; a 90-kilobase microdeletion spanning the entire gene was found in three males with intellectual disability in a second family. In 900 probands with ASD and 208 male probands with intellectual disability, we identified seven different missense changes (in eight male probands) that were inherited from unaffected mothers and not found in controls. Two of the ASD individuals with missense changes also carried a de novo deletion at another ASD susceptibility locus (DPYD and DPP6), suggesting complex genetic contributions. In additional males with ASD, we identified deletions in the 5' flanking region of PTCHD1 that disrupted a complex noncoding RNA and potential regulatory elements; equivalent changes were not found in male control individuals. Thus, our systematic screen of PTCHD1 and its 5' flanking regions suggests that this locus is involved in ~1% of individuals with ASD and intellectual disability.
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Affiliation(s)
- Abdul Noor
- Neurogenetics Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
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12
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Ross CJD, Liu G, Kuivenhoven JA, Twisk J, Rip J, van Dop W, Excoffon KJDA, Lewis SME, Kastelein JJ, Hayden MR. Complete Rescue of Lipoprotein Lipase–Deficient Mice by Somatic Gene Transfer of the Naturally Occurring LPL
S447X
Beneficial Mutation. Arterioscler Thromb Vasc Biol 2005; 25:2143-50. [PMID: 16002740 DOI: 10.1161/01.atv.0000176971.27302.b0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The naturally occurring human lipoprotein lipase S447X variant (LPL
S447X
) exemplifies a gain-of function mutation with significant benefits including decreased plasma triglycerides (TG), increased high-density lipoprotein (HDL) cholesterol, and reduced risk of coronary artery disease. The S447X variant may be associated with higher LPL catalytic activity; however, in vitro data supporting this hypothesis are contradictory. We wanted to investigate the in vivo mechanism by which the LPL
S447X
variant improves the lipid profile of S447X carriers. We conducted a functional assessment of human LPL
S447X
compared with LPL
WT
in mice. LPL variants were compared in the absence of endogenous mouse LPL in newborn LPL
−/−
mice by adenoviral-mediated gene transfer. LPL
−/−
mice normally exhibit severe hypertriglyceridemia and die within 48 hours of birth. LPL
WT
gene transfer prolonged the survival of mice up to 21 days. In contrast, LPL
S447X
completely rescued 95% of the mice to adulthood and increased LPL catalytic activity in postheparin plasma 2.1-fold compared with LPL
WT
at day 3 (
P
=0.003). LPL
S447X
also reduced plasma TG 99% from baseline (
P
<0.001), 2-fold more than LPL
WT
, (
P
<0.01) and increased plasma HDL cholesterol 2.9-fold higher than LPL
WT
(
P
<0.01). These data provide in vivo evidence that the increased catalytic activity of LPL
S447X
improves plasma TG clearance and increases the HDL cholesterol pool compared with LPL
WT
.
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Affiliation(s)
- Colin J D Ross
- Department of Medical Genetics, University of British Columbia, Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
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13
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Strømme P, Mangelsdorf ME, Shaw MA, Lower KM, Lewis SME, Bruyere H, Lütcherath V, Gedeon AK, Wallace RH, Scheffer IE, Turner G, Partington M, Frints SGM, Fryns JP, Sutherland GR, Mulley JC, Gécz J. Mutations in the human ortholog of Aristaless cause X-linked mental retardation and epilepsy. Nat Genet 2002; 30:441-5. [PMID: 11889467 DOI: 10.1038/ng862] [Citation(s) in RCA: 334] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mental retardation and epilepsy often occur together. They are both heterogeneous conditions with acquired and genetic causes. Where causes are primarily genetic, major advances have been made in unraveling their molecular basis. The human X chromosome alone is estimated to harbor more than 100 genes that, when mutated, cause mental retardation. At least eight autosomal genes involved in idiopathic epilepsy have been identified, and many more have been implicated in conditions where epilepsy is a feature. We have identified mutations in an X chromosome-linked, Aristaless-related, homeobox gene (ARX), in nine families with mental retardation (syndromic and nonspecific), various forms of epilepsy, including infantile spasms and myoclonic seizures, and dystonia. Two recurrent mutations, present in seven families, result in expansion of polyalanine tracts of the ARX protein. These probably cause protein aggregation, similar to other polyalanine and polyglutamine disorders. In addition, we have identified a missense mutation within the ARX homeodomain and a truncation mutation. Thus, it would seem that mutation of ARX is a major contributor to X-linked mental retardation and epilepsy.
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Affiliation(s)
- Petter Strømme
- Department of Cytogenetics and Molecular Genetics, Women's and Children's Hospital, North Adelaide, South Australia 5006, Australia
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