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Drmic IE, MacKinnon Modi B, McConnell B, Jilderda S, Hoang N, Noor A, Bassett AS, Speevak M, Stavropoulos DJ, Carter MT. Neurodevelopmental functioning in probands and non-proband carriers of 22q11.2 microduplication. Am J Med Genet A 2022; 188:2999-3008. [PMID: 35899837 DOI: 10.1002/ajmg.a.62916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/01/2022] [Accepted: 07/07/2022] [Indexed: 01/31/2023]
Abstract
Microduplication of the LCR22-A to LCR22-D region on chromosome 22q11.2 is a recurrent copy number variant found in clinical populations undergoing chromosomal microarray, and at lower frequency in controls. Often inherited, there is limited data on intellectual (IQ) and psychological functioning, particularly in those individuals ascertained through a family member rather than because of neurodevelopmental disorders. To investigate the range of cognitive-behavioral phenotypes associated with 22q11.2 duplication, we studied both probands and their non-proband carrier relatives. Twenty-two individuals with 22q11.2 duplication (10 probands, 12 non-proband carriers) were prospectively assessed with a battery of neuropsychological tests, physical examination, and medical record review. Assessment measures with standardized norms included IQ, academic, adaptive, psychiatric, behavioral, and social functioning. IQ and academic skills were within the average range, with a trend toward lower scores in probands versus non-probands. Adaptive skills were within age expectations. Prevalence of attention deficits (probands only) and anxiety (both groups) was high compared with norms. The prevalence of autism spectrum disorder was relatively low (5% of total sample). Assessment of both probands and non-probands with 22q11.2 duplication suggests that the phenotypic spectrum with respect to neurodevelopment overlaps significantly with the general population. IQ and academic abilities are in the average range for most of the individuals with 22q11.2 duplication in our study, regardless of ascertainment as a proband or non-proband relative. Symptoms of attention deficit and anxiety were identified, which require further study. Results of this study further clarify the phenotype of individuals with 22q11.2 duplication, and provides important information for genetic counseling regarding this recurrent copy number variant.
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Affiliation(s)
- Irene E Drmic
- McMaster Children's Hospital Autism Program, Ron Joyce Children's Health Centre, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | | | - Beth McConnell
- Autism Research Unit, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sanne Jilderda
- Autism Research Centre, Glenrose Rehabilitation Hospital, Edmonton, Alberta, Canada
| | - Ny Hoang
- Autism Research Unit, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Abdul Noor
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Marsha Speevak
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Credit Valley Site, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Pathology and Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Melissa T Carter
- Regional Genetics Program, The Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
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Selvarajah S, Plante S, Speevak M, Vaags A, Hamelinck D, Butcher M, McCready E, Grafodatskaya D, Blais N, Tran-Thanh D, Weng X, Nassabein R, Greer W, Walton RN, Lo B, Demetrick D, Santos S, Sadikovic B, Zhang X, Zhang T, Spence T, Stockley T, Feilotter H, Joubert P. A Pan-Canadian Validation Study for the Detection of EGFR T790M Mutation Using Circulating Tumor DNA From Peripheral Blood. JTO Clin Res Rep 2021; 2:100212. [PMID: 34590051 PMCID: PMC8474449 DOI: 10.1016/j.jtocrr.2021.100212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/23/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Genotyping circulating tumor DNA (ctDNA) is a promising noninvasive clinical tool to identify the EGFR T790M resistance mutation in patients with advanced NSCLC with resistance to EGFR inhibitors. To facilitate standardization and clinical adoption of ctDNA testing across Canada, we developed a 2-phase multicenter study to standardize T790M mutation detection using plasma ctDNA testing. METHODS In phase 1, commercial reference standards were distributed to participating clinical laboratories, to use their existing platforms for mutation detection. Baseline performance characteristics were established using known and blinded engineered plasma samples spiked with predetermined concentrations of T790M, L858R, and exon 19 deletion variants. In phase II, peripheral blood collected from local patients with known EGFR activating mutations and progressing on treatment were assayed for the presence of EGFR variants and concordance with a clinically validated test at the reference laboratory. RESULTS All laboratories in phase 1 detected the variants at 0.5 % and 5.0 % allele frequencies, with no false positives. In phase 2, the concordance with the reference laboratory for detection of both the primary and resistance mutation was high, with next-generation sequencing and droplet digital polymerase chain reaction exhibiting the best overall concordance. Data also suggested that the ability to detect mutations at clinically relevant limits of detection is generally not platform-specific, but rather impacted by laboratory-specific practices. CONCLUSIONS Discrepancies among sending laboratories using the same assay suggest that laboratory-specific practices may impact performance. In addition, a negative or inconclusive ctDNA test should be followed by tumor testing when possible.
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Affiliation(s)
- Shamini Selvarajah
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sophie Plante
- Institut Universitaire de Cardiologie et de Pneumologie de Québec-Université Laval, Québec, Quebec, Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Vaags
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Darren Hamelinck
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Martin Butcher
- Department of Oncology, McMaster University, Hamilton, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Daria Grafodatskaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Normand Blais
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Danh Tran-Thanh
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Xiaoduan Weng
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Rami Nassabein
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Wenda Greer
- Queen Elizabeth II Health Sciences Center, Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Bryan Lo
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Doug Demetrick
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - Stephanie Santos
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Xiao Zhang
- Laboratory Genetics, Kingston Health Sciences Center, Kingston, Ontario, Canada
| | - Tong Zhang
- Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada
| | - Tara Spence
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Tracy Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada
| | - Harriet Feilotter
- Laboratory Genetics, Kingston Health Sciences Center, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec-Université Laval, Québec, Quebec, Canada
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Andersen EF, Herriges J, Coe B, Conlin L, Goodenberger M, Hilton B, Jobanputra V, Levy B, Paulraj P, Riggs ER, Runke C, Schleede J, Speevak M, Zhang S, Thorland E, Martin CL. 3. Standardizing recurrent copy number variant classification – From benign to reduced and high penetrance regions. Cancer Genet 2021. [DOI: 10.1016/j.cancergen.2021.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Selvarajah S, Plante S, Speevak M, Vaags A, Mccready E, Grafodatskaya D, Blais N, Tran-Thanh D, Greer W, Lo B, Demetrick D, Sadikovic B, Walton R, Stockley T, Feilotter H, Joubert P. FP07.08 A Pan-Canadian Validation Study for the Detection of EGFR-T790M Mutations Using Circulating Tumour DNA (ctDNA) from Blood. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chen S, DeMarco ML, Estey MP, Kyle B, Parker ML, Agbor TA, Kawada P, Speevak M, Nelson TN, Mattman A. Null Canada: A novel α 1-antitrypsin allele with in cis variants Glu366Lys and Ile100Asn. Clin Biochem 2020; 79:23-27. [PMID: 32087139 DOI: 10.1016/j.clinbiochem.2020.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/23/2020] [Accepted: 02/18/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND α1-Antitrypsin (A1AT) deficiency predisposes patients to pulmonary disease due to inadequate protection against human neutrophil elastase released during inflammatory responses. A1AT deficiency is caused by homozygosity or compound heterozygosity for A1AT variants; individuals with A1AT deficiency most commonly have at least one Z variant allele (c.1096G > A (Glu366Lys)). Null variants that result in complete absence of A1AT in the plasma are much rarer. With one recent exception, all reported A1AT variants are characterized by a single pathogenic variant. CASE An 8 years old patient from Edmonton, Alberta, Canada, was investigated for A1AT deficiency. His A1AT phenotype was determined to be M (wild type)/Null by isoelectric focusing (IEF) but M/Z by targeted genotyping. Gene sequencing revealed two heterozygous variants: Z and Ile100Asn (c.299 T > A). The Ile100Asn substitution is predicted to disrupt the secondary structure of an α-helix in which it resides and the neighbouring tertiary structure, resulting in intracellular degradation of A1AT prior to hepatocyte secretion. METHODS Family testing was conducted to verify potential inheritance of an A1AT allele carrying the two mutations in cis, as this arrangement of the mutations would explain "Z" detection by genotyping but not by IEF. Molecular modeling was used to assess the effect of the variants on A1AT structure and stability. DISCUSSION Carrier status for a novel variant NullCanada with in cis mutations (c.[299 T > A;1096G > A], p.[(Ileu100Asn;Glu366Lys)]) was confirmed. A sibling was identified as having A1AT deficiency on the basis of compound heterozygosity for two alleles: NullCanada and the common Z allele. A separate pedigree from the Maritimes was subsequently recognized as carrying NullCanada. CONCLUSION In cis mutations such as NullCanada may be more common than previously described due to failure to detect such mutations using historical testing methods. Combined approaches that include gene sequencing and segregation studies allow recognition of rare A1AT variants, including in cis mutations.
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Affiliation(s)
- Sharon Chen
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, BC, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, BC, Canada; Centre for Heart Lung Innovation, University of British Columbia, BC, Canada
| | - Mathew P Estey
- DynaLIFE Medical Labs, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, AB, Canada
| | - Barry Kyle
- DynaLIFE Medical Labs, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, AB, Canada
| | - Michelle L Parker
- DynaLIFE Medical Labs, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, AB, Canada
| | - Terence A Agbor
- DynaLIFE Medical Labs, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, AB, Canada
| | - Patricia Kawada
- Division of Pediatric Gastroenterology & Nutrition, Department of Pediatrics, University of Alberta, AB, Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, ON, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, University of British Columbia, BC, Canada; Department of Pathology and Laboratory Medicine, BC Children's & BC Women's Hospitals, BC, Canada
| | - Andre Mattman
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, BC, Canada.
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Zarrei M, Burton CL, Engchuan W, Young EJ, Higginbotham EJ, MacDonald JR, Trost B, Chan AJS, Walker S, Lamoureux S, Heung T, Mojarad BA, Kellam B, Paton T, Faheem M, Miron K, Lu C, Wang T, Samler K, Wang X, Costain G, Hoang N, Pellecchia G, Wei J, Patel RV, Thiruvahindrapuram B, Roifman M, Merico D, Goodale T, Drmic I, Speevak M, Howe JL, Yuen RKC, Buchanan JA, Vorstman JAS, Marshall CR, Wintle RF, Rosenberg DR, Hanna GL, Woodbury-Smith M, Cytrynbaum C, Zwaigenbaum L, Elsabbagh M, Flanagan J, Fernandez BA, Carter MT, Szatmari P, Roberts W, Lerch J, Liu X, Nicolson R, Georgiades S, Weksberg R, Arnold PD, Bassett AS, Crosbie J, Schachar R, Stavropoulos DJ, Anagnostou E, Scherer SW. A large data resource of genomic copy number variation across neurodevelopmental disorders. NPJ Genom Med 2019; 4:26. [PMID: 31602316 PMCID: PMC6779875 DOI: 10.1038/s41525-019-0098-3] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/05/2019] [Indexed: 12/29/2022] Open
Abstract
Copy number variations (CNVs) are implicated across many neurodevelopmental disorders (NDDs) and contribute to their shared genetic etiology. Multiple studies have attempted to identify shared etiology among NDDs, but this is the first genome-wide CNV analysis across autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), schizophrenia (SCZ), and obsessive-compulsive disorder (OCD) at once. Using microarray (Affymetrix CytoScan HD), we genotyped 2,691 subjects diagnosed with an NDD (204 SCZ, 1,838 ASD, 427 ADHD and 222 OCD) and 1,769 family members, mainly parents. We identified rare CNVs, defined as those found in <0.1% of 10,851 population control samples. We found clinically relevant CNVs (broadly defined) in 284 (10.5%) of total subjects, including 22 (10.8%) among subjects with SCZ, 209 (11.4%) with ASD, 40 (9.4%) with ADHD, and 13 (5.6%) with OCD. Among all NDD subjects, we identified 17 (0.63%) with aneuploidies and 115 (4.3%) with known genomic disorder variants. We searched further for genes impacted by different CNVs in multiple disorders. Examples of NDD-associated genes linked across more than one disorder (listed in order of occurrence frequency) are NRXN1, SEH1L, LDLRAD4, GNAL, GNG13, MKRN1, DCTN2, KNDC1, PCMTD2, KIF5A, SYNM, and long non-coding RNAs: AK127244 and PTCHD1-AS. We demonstrated that CNVs impacting the same genes could potentially contribute to the etiology of multiple NDDs. The CNVs identified will serve as a useful resource for both research and diagnostic laboratories for prioritization of variants.
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Affiliation(s)
- Mehdi Zarrei
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Christie L Burton
- 3Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Worrawat Engchuan
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Edwin J Young
- 4Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON Canada
| | - Edward J Higginbotham
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada.,5Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Jeffrey R MacDonald
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Brett Trost
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Ada J S Chan
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada.,5Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Susan Walker
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Sylvia Lamoureux
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Tracy Heung
- 6Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON Canada
| | - Bahareh A Mojarad
- 2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Barbara Kellam
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Tara Paton
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Muhammad Faheem
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Karin Miron
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Chao Lu
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Ting Wang
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Kozue Samler
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Xiaolin Wang
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Gregory Costain
- 7Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON Canada.,8Medical Genetics Residency Training Program, University of Toronto, Toronto, ON Canada
| | - Ny Hoang
- 2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada.,5Department of Molecular Genetics, University of Toronto, Toronto, ON Canada.,9Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON Canada
| | - Giovanna Pellecchia
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - John Wei
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Rohan V Patel
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | | | - Maian Roifman
- 7Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON Canada.,10The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON Canada.,11Department of Paediatrics, University of Toronto, Toronto, ON Canada
| | - Daniele Merico
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,Deep Genomics Inc., Toronto, ON Canada
| | - Tara Goodale
- 3Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Irene Drmic
- Hamilton Health Sciences, Ron Joyce Children's Health Centre, Hamilton, On Canada
| | - Marsha Speevak
- 14Trillium Health Partners Credit Valley Site, Mississauga, Ontario Canada
| | - Jennifer L Howe
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Ryan K C Yuen
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Janet A Buchanan
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Jacob A S Vorstman
- 15Department of Psychiatry, University of Toronto, Toronto, ON Canada.,16Autism Research Unit, The Hospital for Sick Children, Toronto, ON Canada
| | - Christian R Marshall
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,4Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON Canada.,17Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Richard F Wintle
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - David R Rosenberg
- 18Department of Psychiatry and Behavioral Neurosciences, Wayne State University, Detroit, MI USA.,19The Children's Hospital of Michigan, Detroit, MI United States
| | - Gregory L Hanna
- 20Department of Psychiatry, University of Michigan, Ann Arbor, MI USA
| | - Marc Woodbury-Smith
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,21Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Cheryl Cytrynbaum
- 2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada.,5Department of Molecular Genetics, University of Toronto, Toronto, ON Canada.,7Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON Canada.,22Dalla Lana School of Public Health and the Department of Family and Community Medicine, University of Toronto, Toronto, ON Canada
| | | | - Mayada Elsabbagh
- 24Montreal Neurological Institute, McGill University, Montreal, QC Canada
| | - Janine Flanagan
- 11Department of Paediatrics, University of Toronto, Toronto, ON Canada
| | - Bridget A Fernandez
- 25Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL Canada
| | - Melissa T Carter
- 26Regional Genetics Program, The Children's Hospital of Eastern Ontario, Ottawa, ON Canada
| | - Peter Szatmari
- 15Department of Psychiatry, University of Toronto, Toronto, ON Canada.,27Centre for Addiction and Mental Health, Toronto, ON Canada.,28Department of Psychiatry, The Hospital for Sick Children, Toronto, ON Canada
| | - Wendy Roberts
- 16Autism Research Unit, The Hospital for Sick Children, Toronto, ON Canada
| | - Jason Lerch
- 29Mouse Imaging Centre, Hospital for Sick Children, Toronto, ON Canada.,30Department of Medical Biophysics, The University of Toronto, Toronto, ON Canada
| | - Xudong Liu
- 31Department of Psychiatry, Queen's University, Kinston, ON Canada
| | - Rob Nicolson
- 32Children's Health Research Institute, London, ON Canada.,33Western University, London, ON Canada
| | - Stelios Georgiades
- 34Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON Canada
| | - Rosanna Weksberg
- 2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada.,7Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON Canada.,5Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Paul D Arnold
- 2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada.,35Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB Canada.,36Departments of Psychiatry and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Anne S Bassett
- 6Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON Canada.,15Department of Psychiatry, University of Toronto, Toronto, ON Canada.,37The Dalglish Family 22q Clinic, Toronto General Hospital, Toronto, ON Canada
| | - Jennifer Crosbie
- 3Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON Canada.,15Department of Psychiatry, University of Toronto, Toronto, ON Canada
| | - Russell Schachar
- 3Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON Canada.,15Department of Psychiatry, University of Toronto, Toronto, ON Canada.,38Institute of Medical Science, University of Toronto, Toronto, ON Canada
| | - Dimitri J Stavropoulos
- 4Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON Canada
| | - Evdokia Anagnostou
- 39Holland Bloorview Kids Rehabilitation Hospital, University of Toronto, Toronto, ON Canada
| | - Stephen W Scherer
- 1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada.,2Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada.,5Department of Molecular Genetics, University of Toronto, Toronto, ON Canada.,40Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON Canada
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Hume S, Nelson TN, Speevak M, McCready E, Agatep R, Feilotter H, Parboosingh J, Stavropoulos DJ, Taylor S, Stockley TL. CCMG practice guideline: laboratory guidelines for next-generation sequencing. J Med Genet 2019; 56:792-800. [PMID: 31300550 PMCID: PMC6929709 DOI: 10.1136/jmedgenet-2019-106152] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022]
Abstract
PurposeThe purpose of this document is to provide guidance for the use of next-generation sequencing (NGS, also known as massively parallel sequencing or MPS) in Canadian clinical genetic laboratories for detection of genetic variants in genomic DNA and mitochondrial DNA for inherited disorders, as well as somatic variants in tumour DNA for acquired cancers. They are intended for Canadian clinical laboratories engaged in developing, validating and using NGS methods. METHODS OF STATEMENT DEVELOPMENT: The document was drafted by the Canadian College of Medical Geneticists (CCMG) Ad Hoc Working Group on NGS Guidelines to make recommendations relevant to NGS. The statement was circulated for comment to the CCMG Laboratory Practice and Clinical Practice committees, and to the CCMG membership. Following incorporation of feedback, the document was approved by the CCMG Board of Directors. DISCLAIMER: The CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada. The current CCMG Practice Guidelines were developed as a resource for clinical laboratories in Canada and should not be considered to be inclusive of all information laboratories should consider in the validation and use of NGS for a clinical laboratory service.
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Affiliation(s)
- Stacey Hume
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Ron Agatep
- Department of Biochemistry and Molecular Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Genomics Laboratory, Shared Health Diagnostic Services, Winnipeg, Manitoba, Canada
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Jillian Parboosingh
- Department of Medical Genetics, University of Calgary Cumming School of Medicine, Calgary, Alberta, Canada.,Research Institute, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Dimitri J Stavropoulos
- Department of Paediatric Laboratory Medicine, Genome Diagnostics, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sherryl Taylor
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Tracy L Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada .,Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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8
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Andersen E, Burnside R, Coe B, Conlin L, Herriges J, Higginbotham T, Hilton B, Jobanputra V, Kearney H, Ouyang K, Paulraj P, Riggs ER, Rowsey R, Speevak M, Thorland E, Zhang L, Martin CL. 28. Dosage sensitivity curation of recurrent copy number variant regions. Cancer Genet 2018. [DOI: 10.1016/j.cancergen.2018.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Uddin M, Unda BK, Kwan V, Holzapfel NT, White SH, Chalil L, Woodbury-Smith M, Ho KS, Harward E, Murtaza N, Dave B, Pellecchia G, D’Abate L, Nalpathamkalam T, Lamoureux S, Wei J, Speevak M, Stavropoulos J, Hope KJ, Doble BW, Nielsen J, Wassman ER, Scherer SW, Singh KK. OTUD7A Regulates Neurodevelopmental Phenotypes in the 15q13.3 Microdeletion Syndrome. Am J Hum Genet 2018; 102:278-295. [PMID: 29395074 PMCID: PMC5985537 DOI: 10.1016/j.ajhg.2018.01.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/10/2018] [Indexed: 12/28/2022] Open
Abstract
Copy-number variations (CNVs) are strong risk factors for neurodevelopmental and psychiatric disorders. The 15q13.3 microdeletion syndrome region contains up to ten genes and is associated with numerous conditions, including autism spectrum disorder (ASD), epilepsy, schizophrenia, and intellectual disability; however, the mechanisms underlying the pathogenesis of 15q13.3 microdeletion syndrome remain unknown. We combined whole-genome sequencing, human brain gene expression (proteome and transcriptome), and a mouse model with a syntenic heterozygous deletion (Df(h15q13)/+ mice) and determined that the microdeletion results in abnormal development of cortical dendritic spines and dendrite outgrowth. Analysis of large-scale genomic, transcriptomic, and proteomic data identified OTUD7A as a critical gene for brain function. OTUD7A was found to localize to dendritic and spine compartments in cortical neurons, and its reduced levels in Df(h15q13)/+ cortical neurons contributed to the dendritic spine and dendrite outgrowth deficits. Our results reveal OTUD7A as a major regulatory gene for 15q13.3 microdeletion syndrome phenotypes that contribute to the disease mechanism through abnormal cortical neuron morphological development.
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10
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Lowther C, Merico D, Costain G, Waserman J, Boyd K, Noor A, Speevak M, Stavropoulos DJ, Wei J, Lionel AC, Marshall CR, Scherer SW, Bassett AS. Impact of IQ on the diagnostic yield of chromosomal microarray in a community sample of adults with schizophrenia. Genome Med 2017; 9:105. [PMID: 29187259 PMCID: PMC5708103 DOI: 10.1186/s13073-017-0488-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022] Open
Abstract
Background Schizophrenia is a severe psychiatric disorder associated with IQ deficits. Rare copy number variations (CNVs) have been established to play an important role in the etiology of schizophrenia. Several of the large rare CNVs associated with schizophrenia have been shown to negatively affect IQ in population-based controls where no major neuropsychiatric disorder is reported. The aim of this study was to examine the diagnostic yield of microarray testing and the functional impact of genome-wide rare CNVs in a community ascertained cohort of adults with schizophrenia and low (< 85) or average (≥ 85) IQ. Methods We recruited 546 adults of European ancestry with schizophrenia from six community psychiatric clinics in Canada. Each individual was assigned to the low or average IQ group based on standardized tests and/or educational attainment. We used rigorous methods to detect genome-wide rare CNVs from high-resolution microarray data. We compared the burden of rare CNVs classified as pathogenic or as a variant of unknown significance (VUS) between each of the IQ groups and the genome-wide burden and functional impact of rare CNVs after excluding individuals with a pathogenic CNV. Results There were 39/546 (7.1%; 95% confidence interval [CI] = 5.2–9.7%) schizophrenia participants with at least one pathogenic CNV detected, significantly more of whom were from the low IQ group (odds ratio [OR] = 5.01 [2.28–11.03], p = 0.0001). Secondary analyses revealed that individuals with schizophrenia and average IQ had the lowest yield of pathogenic CNVs (n = 9/325; 2.8%), followed by those with borderline intellectual functioning (n = 9/130; 6.9%), non-verbal learning disability (n = 6/29; 20.7%), and co-morbid intellectual disability (n = 15/62; 24.2%). There was no significant difference in the burden of rare CNVs classified as a VUS between any of the IQ subgroups. There was a significantly (p=0.002) increased burden of rare genic duplications in individuals with schizophrenia and low IQ that persisted after excluding individuals with a pathogenic CNV. Conclusions Using high-resolution microarrays we were able to demonstrate for the first time that the burden of pathogenic CNVs in schizophrenia differs significantly between IQ subgroups. The results of this study have implications for clinical practice and may help inform future rare variant studies of schizophrenia using next-generation sequencing technologies. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0488-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chelsea Lowther
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, Canada, M5S 2S1.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Daniele Merico
- Deep Genomics Inc, Toronto, ON, Canada.,The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gregory Costain
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, Canada, M5S 2S1.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Kerry Boyd
- Department of Psychiatry & Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Abdul Noor
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Marsha Speevak
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - John Wei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anath C Lionel
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, Canada, M5S 2S1. .,Institute of Medical Science, University of Toronto, Toronto, ON, Canada. .,Toronto General Research Institute, University Health Network, Toronto, ON, Canada. .,Cambell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada. .,Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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11
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Uddin M, Pellecchia G, Thiruvahindrapuram B, D'Abate L, Merico D, Chan A, Zarrei M, Tammimies K, Walker S, Gazzellone MJ, Nalpathamkalam T, Yuen RKC, Devriendt K, Mathonnet G, Lemyre E, Nizard S, Shago M, Joseph-George AM, Noor A, Carter MT, Yoon G, Kannu P, Tihy F, Thorland EC, Marshall CR, Buchanan JA, Speevak M, Stavropoulos DJ, Scherer SW. Indexing Effects of Copy Number Variation on Genes Involved in Developmental Delay. Sci Rep 2016; 6:28663. [PMID: 27363808 PMCID: PMC4929460 DOI: 10.1038/srep28663] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 01/12/2016] [Accepted: 06/06/2016] [Indexed: 01/03/2023] Open
Abstract
A challenge in clinical genomics is to predict whether copy number variation (CNV) affecting a gene or multiple genes will manifest as disease. Increasing recognition of gene dosage effects in neurodevelopmental disorders prompted us to develop a computational approach based on critical-exon (highly expressed in brain, highly conserved) examination for potential etiologic effects. Using a large CNV dataset, our updated analyses revealed significant (P < 1.64 × 10−15) enrichment of critical-exons within rare CNVs in cases compared to controls. Separately, we used a weighted gene co-expression network analysis (WGCNA) to construct an unbiased protein module from prenatal and adult tissues and found it significantly enriched for critical exons in prenatal (P < 1.15 × 10−50, OR = 2.11) and adult (P < 6.03 × 10−18, OR = 1.55) tissues. WGCNA yielded 1,206 proteins for which we prioritized the corresponding genes as likely to have a role in neurodevelopmental disorders. We compared the gene lists obtained from critical-exon and WGCNA analysis and found 438 candidate genes associated with CNVs annotated as pathogenic, or as variants of uncertain significance (VOUS), from among 10,619 developmental delay cases. We identified genes containing CNVs previously considered to be VOUS to be new candidate genes for neurodevelopmental disorders (GIT1, MVB12B and PPP1R9A) demonstrating the utility of this strategy to index the clinical effects of CNVs.
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Affiliation(s)
- Mohammed Uddin
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lia D'Abate
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ada Chan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Neuropsychiatric Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Susan Walker
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthew J Gazzellone
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Emmanuelle Lemyre
- CHU Sainte-Justine, University de Montreal, Montreal, Quebec, Canada
| | - Sonia Nizard
- CHU Sainte-Justine, University de Montreal, Montreal, Quebec, Canada
| | - Mary Shago
- Genome Diagnostics, Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ann M Joseph-George
- Genome Diagnostics, Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Abdul Noor
- Department of Pathology and Laboratory Medicine, Division of Diagnostic Medical Genetics, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Melissa T Carter
- Department of Genetics, The Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Grace Yoon
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario M5G 2L3, Canada
| | - Peter Kannu
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario M5G 2L3, Canada
| | - Frédérique Tihy
- CHU Sainte-Justine, University de Montreal, Montreal, Quebec, Canada
| | - Erik C Thorland
- Cytogenetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Genome Diagnostics, Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Janet A Buchanan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Paediatric 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.,Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
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12
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Lowther C, Speevak M, Armour CM, Goh ES, Graham GE, Li C, Zeesman S, Nowaczyk MJM, Schultz LA, Morra A, Nicolson R, Bikangaga P, Samdup D, Zaazou M, Boyd K, Jung JH, Siu V, Rajguru M, Goobie S, Tarnopolsky MA, Prasad C, Dick PT, Hussain AS, Walinga M, Reijenga RG, Gazzellone M, Lionel AC, Marshall CR, Scherer SW, Stavropoulos DJ, McCready E, Bassett AS. Molecular characterization of NRXN1 deletions from 19,263 clinical microarray cases identifies exons important for neurodevelopmental disease expression. Genet Med 2016; 19:53-61. [PMID: 27195815 PMCID: PMC4980119 DOI: 10.1038/gim.2016.54] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/16/2016] [Indexed: 01/31/2023] Open
Abstract
Purpose The purpose of the current study was to assess the penetrance of NRXN1 deletions. Methods We compared the prevalence and genomic extent of NRXN1 deletions identified among 19,263 clinically referred cases to that of 15,264 controls. The burden of additional clinically relevant CNVs was used as a proxy to estimate the relative penetrance of NRXN1 deletions. Results We identified 41 (0.21%) previously unreported exonic NRXN1 deletions ascertained for developmental delay/intellectual disability, significantly greater than in controls [OR=8.14 (95% CI 2.91–22.72), p< 0.0001)]. Ten (22.7%) of these had a second clinically relevant CNV. Subjects with a deletion near the 3′ end of NRXN1 were significantly more likely to have a second rare CNV than subjects with a 5′ NRXN1 deletion [OR=7.47 (95% CI 2.36–23.61), p=0.0006]. The prevalence of intronic NRXN1 deletions was not statistically different between cases and controls (p=0.618). The majority (63.2%) of intronic NRXN1 deletion cases had a second rare CNV, a two-fold greater prevalence than for exonic NRXN1 deletion cases (p=0.0035). Conclusions The results support the importance of exons near the 5′ end of NRXN1 in the expression of neurodevelopmental disorders. Intronic NRXN1 deletions do not appear to substantially increase the risk for clinical phenotypes.
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Affiliation(s)
- Chelsea Lowther
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Marsha Speevak
- Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada
| | - Christine M Armour
- Regional Genetics Program, Children's Hospital of Eastern Ontario, Toronto, ON, Canada
| | - Elaine S Goh
- Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada
| | - Gail E Graham
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Chumei Li
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada.,McMaster Children's Hospital, Department of Pediatrics and Clinical Genetics Program, Hamilton, Ontario, Canada
| | - Susan Zeesman
- McMaster Children's Hospital, Department of Pediatrics and Clinical Genetics Program, Hamilton, Ontario, Canada
| | - Malgorzata J M Nowaczyk
- McMaster Children's Hospital, Department of Pediatrics and Clinical Genetics Program, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Lee-Anne Schultz
- McMaster Children's Hospital, Department of Pediatrics and Clinical Genetics Program, Hamilton, Ontario, Canada
| | - Antonella Morra
- Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada
| | - Rob Nicolson
- Department of Psychiatry, Western University, London, Ontario, Canada
| | | | - Dawa Samdup
- Hotel Dieu Hospital, Child Development Centre, Kingston, Ontario, Canada
| | - Mostafa Zaazou
- Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada
| | - Kerry Boyd
- Department of Psychiatry, McMaster University, Hamilton, Ontario, Canada
| | - Jack H Jung
- London Health Sciences Centre, Children's Hospital of Western Ontario, London, Ontario, Canada
| | - Victoria Siu
- Department of Pediatrics, Schulich School of Medicine and Dentistry, London, Ontario, Canada
| | | | - Sharan Goobie
- Department of Pediatrics, Schulich School of Medicine and Dentistry, London, Ontario, Canada
| | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Chitra Prasad
- Department of Pediatrics, Schulich School of Medicine and Dentistry, London, Ontario, Canada
| | - Paul T Dick
- Grey Bruce Health Services, Owen Sound, Ontario, Canada
| | - Asmaa S Hussain
- London Health Sciences Centre, Children's Hospital of Western Ontario, London, Ontario, Canada
| | | | | | - Matthew Gazzellone
- The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anath C Lionel
- The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- Cytogenetics Laboratory, Department of Pediatric Laboratory Medicine, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Anne S Bassett
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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13
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Lowther C, Speevak M, Armour C, Goh E, Graham G, Li C, Zeesman S, Nowaczyk MJM, Schultz LA, Morra A, Nicolson R, Rajguru M, Goobie S, Tarnopolsky MA, Prasad C, Dick PT, Hussain AS, Gazzellone M, Lionel AC, Marshall CR, Scherer SW, Stavropoulos DJ, McCready E, Bassett AS. MG-123 Exonic and intronic NRXN1 deletions: Novel genotype-phenotype correlations. J Med Genet 2015. [DOI: 10.1136/jmedgenet-2015-103578.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Hashemi B, Bassett A, Chitayat D, Chong K, Feldman M, Flanagan J, Goobie S, Kawamura A, Lowther C, Prasad C, Siu V, So J, Tung S, Speevak M, Stavropoulos DJ, Carter MT. Deletion of 15q11.2(BP1-BP2) region: Further evidence for lack of phenotypic specificity in a pediatric population. Am J Med Genet A 2015; 167A:2098-102. [DOI: 10.1002/ajmg.a.37134] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/13/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Bita Hashemi
- Division of Clinical and Metabolics Genetics, Department of Pediatrics; The Hospital for Sick Children, University of Toronto; Toronto Ontario Canada
| | - Anne Bassett
- Clinical Genetics Research Program; Center for Addiction and Mental Health; Toronto Ontario Canada
| | - David Chitayat
- Division of Clinical and Metabolics Genetics, Department of Pediatrics; The Hospital for Sick Children, University of Toronto; Toronto Ontario Canada
- The Prenatal Diagnosis and Medical Genetics Program; Mount Sinai Hospital; Toronto Ontario Canada
| | - Karen Chong
- The Prenatal Diagnosis and Medical Genetics Program; Mount Sinai Hospital; Toronto Ontario Canada
| | - Mark Feldman
- Divison of Pediatric Medicine, Department of Pediatrics; The Hospital for Sick Children, University of Toronto; Toronto Ontario Canada
| | | | - Sharan Goobie
- Department of Pediatrics; Western University Children's Hospital Research Institute; London Ontario Canada
| | - Anne Kawamura
- Division of Developmental Pediatrics; Holland Bloorview Kids Rehabilitation Hospital; Toronto Ontario Canada
| | - Chelsea Lowther
- Clinical Genetics Research Program; Center for Addiction and Mental Health; Toronto Ontario Canada
| | - Chitra Prasad
- Department of Pediatrics; Western University Children's Hospital Research Institute; London Ontario Canada
| | - Victoria Siu
- Department of Pediatrics; Western University Children's Hospital Research Institute; London Ontario Canada
| | - Joyce So
- The Fred A. Litwin Family Center in Genetic Medicine; University Health Network and Mount Sinai Hospital; Toronto Canada
- Neurogenetics Lab, Neuroscience Research Department; Center for Addiction and Mental Health; Toronto Ontario Canada
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children; Laboratory Medicine and Pathobiology, University of Toronto; Toronto Ontario Canada
| | - Sharon Tung
- Genetics Program; North Bay Parry Sound District Health Unit; North Bay Ontario Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Pathobiology; University of Toronto; Toronto Ontario Canada
| | - Dimitri J. Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children; Laboratory Medicine and Pathobiology, University of Toronto; Toronto Ontario Canada
| | - Melissa T. Carter
- Division of Clinical and Metabolics Genetics, Department of Pediatrics; The Hospital for Sick Children, University of Toronto; Toronto Ontario Canada
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15
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Ganjavi H, Siu VM, Speevak M, MacDonald PA. A fourth case of Feingold syndrome type 2: psychiatric presentation and management. BMJ Case Rep 2014; 2014:bcr-2014-207501. [PMID: 25391829 DOI: 10.1136/bcr-2014-207501] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Feingold syndrome (FGLDS1) is an autosomal dominant disorder caused by mutations in the MYCN oncogene on the short arm of chromosome 2 (2p24.1). It is characterised by microcephaly, digital abnormalities, oesophageal and duodenal atresias, and often learning disability or mental retardation. In 2011, individuals sharing the skeletal abnormalities of FGLDS1 but lacking mutations in MYCN, were found to harbour hemizygous deletions of the MIR17HG gene on chromosome 13q31.3. These individuals share many of the characteristics of FGLDS1 except for gastrointestinal atresia. The condition was termed Feingold syndrome type 2 (FGLDS2). We describe the presentation and management of a fourth known case of FGLDS2 in an 18-year-old girl with microcephaly, short stature, mildly dysmorphic features, digital malformations and significant cognitive and psychiatric symptoms. Comparative genomic hybridisation array testing confirmed a 7.4 Mb microdeletion in chromosome region 13q31.1q.31.3 corresponding to the MIR17HG gene.
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Affiliation(s)
- Hooman Ganjavi
- Department of Psychiatry, University of Western Ontario, London, Ontario, Canada
| | - Victoria Mok Siu
- Department of Paediatrics, University of Western Ontario, London, Ontario, Canada Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Penny Anne MacDonald
- Brain and Mind Institute, University of Western Ontario, London, Ontario, Canada Department of Clinical Neurological Sciences, University of Western Ontario, London, Ontario, Canada
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16
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Lionel AC, Tammimies K, Vaags AK, Rosenfeld JA, Ahn JW, Merico D, Noor A, Runke CK, Pillalamarri VK, Carter MT, Gazzellone MJ, Thiruvahindrapuram B, Fagerberg C, Laulund LW, Pellecchia G, Lamoureux S, Deshpande C, Clayton-Smith J, White AC, Leather S, Trounce J, Melanie Bedford H, Hatchwell E, Eis PS, Yuen RKC, Walker S, Uddin M, Geraghty MT, Nikkel SM, Tomiak EM, Fernandez BA, Soreni N, Crosbie J, Arnold PD, Schachar RJ, Roberts W, Paterson AD, So J, Szatmari P, Chrysler C, Woodbury-Smith M, Brian Lowry R, Zwaigenbaum L, Mandyam D, Wei J, Macdonald JR, Howe JL, Nalpathamkalam T, Wang Z, Tolson D, Cobb DS, Wilks TM, Sorensen MJ, Bader PI, An Y, Wu BL, Musumeci SA, Romano C, Postorivo D, Nardone AM, Monica MD, Scarano G, Zoccante L, Novara F, Zuffardi O, Ciccone R, Antona V, Carella M, Zelante L, Cavalli P, Poggiani C, Cavallari U, Argiropoulos B, Chernos J, Brasch-Andersen C, Speevak M, Fichera M, Ogilvie CM, Shen Y, Hodge JC, Talkowski ME, Stavropoulos DJ, Marshall CR, Scherer SW. Disruption of the ASTN2/TRIM32 locus at 9q33.1 is a risk factor in males for autism spectrum disorders, ADHD and other neurodevelopmental phenotypes. Hum Mol Genet 2013; 23:2752-68. [PMID: 24381304 DOI: 10.1093/hmg/ddt669] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Rare copy number variants (CNVs) disrupting ASTN2 or both ASTN2 and TRIM32 have been reported at 9q33.1 by genome-wide studies in a few individuals with neurodevelopmental disorders (NDDs). The vertebrate-specific astrotactins, ASTN2 and its paralog ASTN1, have key roles in glial-guided neuronal migration during brain development. To determine the prevalence of astrotactin mutations and delineate their associated phenotypic spectrum, we screened ASTN2/TRIM32 and ASTN1 (1q25.2) for exonic CNVs in clinical microarray data from 89 985 individuals across 10 sites, including 64 114 NDD subjects. In this clinical dataset, we identified 46 deletions and 12 duplications affecting ASTN2. Deletions of ASTN1 were much rarer. Deletions near the 3' terminus of ASTN2, which would disrupt all transcript isoforms (a subset of these deletions also included TRIM32), were significantly enriched in the NDD subjects (P = 0.002) compared with 44 085 population-based controls. Frequent phenotypes observed in individuals with such deletions include autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), speech delay, anxiety and obsessive compulsive disorder (OCD). The 3'-terminal ASTN2 deletions were significantly enriched compared with controls in males with NDDs, but not in females. Upon quantifying ASTN2 human brain RNA, we observed shorter isoforms expressed from an alternative transcription start site of recent evolutionary origin near the 3' end. Spatiotemporal expression profiling in the human brain revealed consistently high ASTN1 expression while ASTN2 expression peaked in the early embryonic neocortex and postnatal cerebellar cortex. Our findings shed new light on the role of the astrotactins in psychopathology and their interplay in human neurodevelopment.
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Costain G, Lionel AC, Merico D, Forsythe P, Russell K, Lowther C, Yuen T, Husted J, Stavropoulos DJ, Speevak M, Chow EWC, Marshall CR, Scherer SW, Bassett AS. Pathogenic rare copy number variants in community-based schizophrenia suggest a potential role for clinical microarrays. Hum Mol Genet 2013; 22:4485-501. [PMID: 23813976 DOI: 10.1093/hmg/ddt297] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Individually rare, large copy number variants (CNVs) contribute to genetic vulnerability for schizophrenia. Unresolved questions remain, however, regarding the anticipated yield of clinical microarray testing in schizophrenia. Using high-resolution genome-wide microarrays and rigorous methods, we investigated rare CNVs in a prospectively recruited community-based cohort of 459 unrelated adults with schizophrenia and estimated the minimum prevalence of clinically significant CNVs that would be detectable on a clinical microarray. A blinded review by two independent clinical cytogenetic laboratory directors of all large (>500 kb) rare CNVs in cases and well-matched controls showed that those deemed to be clinically significant were highly enriched in schizophrenia (16.4-fold increase, P < 0.0001). In a single community catchment area, the prevalence of individuals with these CNVs was 8.1%. Rare 1.7 Mb CNVs at 2q13 were found to be significantly associated with schizophrenia for the first time, compared with the prevalence in 23 838 population-based controls (42.9-fold increase, P = 0.0002). Additional novel findings that will facilitate the future clinical interpretation of smaller CNVs in schizophrenia include: (i) a greater proportion of individuals with two or more rare exonic CNVs >10 kb in size (1.5-fold increase, P = 0.0109) in schizophrenia; (ii) the systematic discovery of new candidate genes for schizophrenia; and, (iii) functional gene enrichment mapping highlighting a differential impact in schizophrenia of rare exonic deletions involving diverse functions, including neurodevelopmental and synaptic processes (4.7-fold increase, P = 0.0060). These findings suggest consideration of a potential role for clinical microarray testing in schizophrenia, as is now the suggested standard of care for related developmental disorders like autism.
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Affiliation(s)
- Gregory Costain
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada M5S 2S1
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Fan YS, Zhang Y, Speevak M, Farrell S, Jung JH, Siu VM. Detection of submicroscopic aberrations in patients with unexplained mental retardation by fluorescence in situ hybridization using multiple subtelomeric probes. Genet Med 2001; 3:416-21. [PMID: 11715006 DOI: 10.1097/00125817-200111000-00007] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [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: 12/08/2022] Open
Abstract
PURPOSE To further assess the frequency of subtelomeric aberrations in a selected population and to examine the feasibility of a clinical testing. METHODS Patients were selected based on the following criteria: (1) mental retardation (IQ < 70) or developmental delay with dysmorphic features; (2) a normal karyotype at the level of resolution of 450 to 500 bands; and (3) exclusion of other possible etiologies by a full genetic assessment and relevant tests. Fluorescence in situ hybridization (FISH) was performed using multiple subtelomeric probes. Abnormal findings were confirmed by 24-color spectral karyotyping or FISH with a specific subtelomeric probe, and family studies were carried out to determine inheritance. RESULTS Clinically significant aberrations were detected in 6 of 150 proband patients (4%), while deletion of the 2q subtelomeric region appeared to be a common variant (6%). CONCLUSIONS FISH with multiple subtelomeric probes is a valuable clinical test for establishing a definitive diagnosis for patients with unexplained mental retardation/developmental disorders.
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Affiliation(s)
- Y S Fan
- London Health Sciences Centre and the University of Western Ontario, London, Canada
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Speevak M, Farrell SA, Chadwick D. Molecular and cytogenetic characterization of a prenatally ascertained de novo (X;Y) translocation. Am J Med Genet 2001; 98:107-8. [PMID: 11426448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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Abstract
Greater use of genetic amniocentesis in the Eastern Ontario region occurred once the results from the various national trials were published. Acceptance also paralleled an increase in the number of low parity older women having children and the centralisation and greater publicity given to our programme in the late 1970s. A centralised approach has had the positive effects of preventing unnecessary procedures, assuring appropriate patient counselling, follow up, and review, and of increasing obstetric and laboratory expertise. Advanced maternal age has been largely responsible for the increased demand for the service and accounted for an increasing proportion of tests performed, while the absolute number for several other diagnostic categories remained unchanged. We found no evidence that women with a history of previous miscarriage had a higher rate of pregnancy loss following the procedure, and comparison with a group of women who declined amniocentesis did not show that the test increased the risk of miscarriage.
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Abstract
G banded chromosomal analysis of cells from a routine amniocentesis revealed a Y to X translocation in the fetus. The same unbalanced translocation was found in the mother who was disproportionately short. H-Y antigen titers in the mother were intermediate and steroid sulfatase activity was in the normal female range. At birth the baby exhibited few dysmorphic features but appeared to have short limbs.
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