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Kang H, Chen Y, Wang L, Gao C, Li X, Hu Y. Pathogenic recurrent copy number variants in 7,078 pregnancies via chromosomal microarray analysis. J Perinat Med 2024; 52:171-180. [PMID: 38081620 DOI: 10.1515/jpm-2022-0580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 09/30/2023] [Indexed: 02/09/2024]
Abstract
OBJECTIVES To investigate the incidence of pathogenic recurrent CNVs in fetuses with different referral indications and review the intrauterine phenotypic features of each CNV. METHODS A total of 7,078 amniotic fluid samples were collected for chromosome microarray analysis (CMA) and cases carrying pathogenic recurrent CNVs were further studied. RESULTS The highest incidence of pathogenic recurrent CNVs was 2.25 % in fetal ultrasound anomalies (FUA) group. Moreover, regardless of other indications, pregnant women with advanced maternal age have a lower incidence compared with whom less than 35 years old (p<0.05). In total 1.17 % (83/7,078) samples carried pathogenic recurrent CNVs: 20 cases with 22q11.2 recurrent region (12 microdeletion and eight microduplication), 11 with 1q21.1 (five microdeletion and six microduplication) and 16p13.11 (four microdeletion and seven microduplication), 10 with 15q11.2 recurrent microdeletion, seven with Xp22.31 recurrent microdeletion and 16p11.2 (three microdeletion and four microduplication), four with 7q11.23 (two microdeletion and two microduplication), three with 17p11.2 (three microdeletion), 17p12 (two microdeletion and one microduplication) and 17q12 (two microdeletion and one microduplication). The rest ones were rare in this study. CONCLUSIONS Pathogenic recurrent CNVs are more likely to be identified in FUA group. Pregnant women with advanced maternal age have a lower incidence of pathogenic recurrent CNVs. The profile of pathogenic recurrent CNVs between prenatal and postnatal is different, especially in 22q11.2, 1q21.1, 15q13.3 recurrent region and 15q11.2 deletion.
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Affiliation(s)
- Han Kang
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Yifei Chen
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Lingxi Wang
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Chonglan Gao
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Xingyu Li
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Yu Hu
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
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Bassett AS, Reuter MS, Malecki S, Silversides C, Oechslin E. Clinically Relevant Genetic Considerations for Patients With Tetralogy of Fallot. CJC PEDIATRIC AND CONGENITAL HEART DISEASE 2023; 2:426-439. [PMID: 38161665 PMCID: PMC10755827 DOI: 10.1016/j.cjcpc.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/05/2023] [Indexed: 01/03/2024]
Abstract
Genetic changes affect embryogenesis, cardiac and extracardiac phenotype, development, later onset conditions, and both short- and long-term outcomes and comorbidities in the increasing population of individuals with tetralogy of Fallot (TOF). In this review, we focus on current knowledge about clinically relevant genetics for patients with TOF across the lifespan. The latest findings for TOF genetics that are pertinent to day-to-day practice and lifelong management are highlighted: morbidity/mortality, cardiac/extracardiac features, including neurodevelopmental expression, and recent changes to prenatal screening and diagnostics. Genome-wide microarray is the first-line clinical genetic test for TOF across the lifespan, detecting relevant structural changes including the most common for TOF, the 22q11.2 microdeletion. Accumulating evidence illustrates opportunities for advances in understanding and care that may arise from genetic diagnosis at any age. We also glimpse into the near future when the multigenic nature of TOF will be more fully revealed, further enhancing possibilities for preventive care. Precision medicine is nigh.
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Affiliation(s)
- Anne S. Bassett
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Toronto Adult Congenital Heart Disease Program, Division of Cardiology, Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, and Campbell Family Mental Health Research Institute, Toronto, Ontario, Canada
| | - Miriam S. Reuter
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Sarah Malecki
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Candice Silversides
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Toronto Adult Congenital Heart Disease Program, Division of Cardiology, Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Erwin Oechslin
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Toronto Adult Congenital Heart Disease Program, Division of Cardiology, Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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3
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Caseras X, Legge SE, Bracher-Smith M, Anney R, Owen MJ, Escott-Price V, Kirov G. Copy Number Variants Increasing Risk for Schizophrenia: Shared and Distinct Effects on Brain Morphometry and Cognitive Performance. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2023; 3:902-911. [PMID: 37881570 PMCID: PMC10593876 DOI: 10.1016/j.bpsgos.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Background Copy number variations (CNVs) conferring risk for mental disorders are associated with brain changes and cognitive deficits. However, whether these effects are shared or distinct across CNVs remains untested. Here we compared the effects on brain morphometry and cognitive performance across CNVs with shared psychiatric liability. Methods Unaffected and unrelated participants of White British and Irish ancestry were drawn from the UK Biobank. After quality control, we retained 31,941 participants not carrying any damaging CNVs and 202 participants carrying one CNV increasing risk for schizophrenia. Using regression analyses, we tested the association between brain morphometry and cognitive performance with CNV carrying status and compared these effect sizes across CNVs using z test for the equality of regression coefficients. Equation modeling was used to examine the mediation of brain phenotypes on the association between CNVs and cognitive performance. Results We detected different patterns of association between CNVs and brain morphometry and cognitive abilities. Comparing across CNVs, 1q21.1 deletion showed the strongest association with surface area in frontal lobe (β = -1.03, p = 4 × 10-8; β = -0.81, p = .00001) and performance in digit memory (β = -1.58, p = .00003), while 1q21.1 duplication showed the strongest association with volume of the putamen (β = -0.70, p = .0004) and reaction time (β = -1.14, p = .000002). We also showed that even when 2 CNVs were associated with performance in the same cognitive ability, these associations were mediated by different brain changes. Conclusions Despite sharing similar psychiatric liability, the CNVs under study appeared to have different effects on brain morphometry and on performance in cognitive abilities, suggesting the existence of distinctive neurobiological pathways into the same clinical phenotypes.
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Affiliation(s)
- Xavier Caseras
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Sophie E. Legge
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Matthew Bracher-Smith
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Richard Anney
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Michael J. Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Valentina Escott-Price
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - George Kirov
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
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Zarrei M, Burton CL, Engchuan W, Higginbotham EJ, Wei J, Shaikh S, Roslin NM, MacDonald JR, Pellecchia G, Nalpathamkalam T, Lamoureux S, Manshaei R, Howe J, Trost B, Thiruvahindrapuram B, Marshall CR, Yuen RKC, Wintle RF, Strug LJ, Stavropoulos DJ, Vorstman JAS, Arnold P, Merico D, Woodbury-Smith M, Crosbie J, Schachar RJ, Scherer SW. Gene copy number variation and pediatric mental health/neurodevelopment in a general population. Hum Mol Genet 2023; 32:2411-2421. [PMID: 37154571 PMCID: PMC10360394 DOI: 10.1093/hmg/ddad074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health and cognition in a community sample of 7100 unrelated children and youth of European or East Asian ancestry (Spit for Science). Clinically significant or susceptibility CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of attention-deficit/hyperactivity disorder (ADHD) traits (P = 5.0 × 10-3), longer response inhibition (a cognitive deficit found in several mental health and neurodevelopmental disorders; P = 1.0 × 10-2) and increased prevalence of mental health diagnoses (P = 1.9 × 10-6, odds ratio: 3.09), specifically ADHD, autism spectrum disorder anxiety and learning problems/learning disorder (P's < 0.01). There was an increased burden of rare deletions in gene-sets related to brain function or expression in brain associated with more ADHD traits. With the current mental health crisis, our data established a baseline for delineating genetic contributors in pediatric-onset conditions.
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Affiliation(s)
- Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Christie L Burton
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sabah Shaikh
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nicole M Roslin
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Roozbeh Manshaei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | | | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lisa J Strug
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Departments of Statistical Sciences, Computer Science and Biostatistics, University of Toronto, Toronto, ON M5G 1Z5, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jacob A S Vorstman
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Paul Arnold
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB T2N 1N4, Canada
- Departments of Psychiatry & Medical Genetics, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Deep Genomics Inc., Toronto, ON M5G 1M1, Canada
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jennifer Crosbie
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Russell J Schachar
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
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5
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Molloy CJ, Quigley C, McNicholas Á, Lisanti L, Gallagher L. A review of the cognitive impact of neurodevelopmental and neuropsychiatric associated copy number variants. Transl Psychiatry 2023; 13:116. [PMID: 37031194 PMCID: PMC10082763 DOI: 10.1038/s41398-023-02421-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
The heritability of intelligence or general cognitive ability is estimated at 41% and 66% in children and adults respectively. Many rare copy number variants are associated with neurodevelopmental and neuropsychiatric conditions (ND-CNV), including schizophrenia and autism spectrum disorders, and may contribute to the observed variability in cognitive ability. Here, we reviewed studies of intelligence quotient or cognitive function in ND-CNV carriers, from both general population and clinical cohorts, to understand the cognitive impact of ND-CNV in both contexts and identify potential genotype-specific cognitive phenotypes. We reviewed aggregate studies of sets ND-CNV broadly linked to neurodevelopmental and neuropsychiatric conditions, and genotype-first studies of a subset of 12 ND-CNV robustly associated with schizophrenia and autism. Cognitive impacts were observed across ND-CNV in both general population and clinical cohorts, with reports of phenotypic heterogeneity. Evidence for ND-CNV-specific impacts were limited by a small number of studies and samples sizes. A comprehensive understanding of the cognitive impact of ND-CNVs would be clinically informative and could identify potential educational needs for ND-CNV carriers. This could improve genetic counselling for families impacted by ND-CNV, and clinical outcomes for those with complex needs.
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Affiliation(s)
- Ciara J Molloy
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland.
- Trinity Centre for Health Sciences, St. James's Hospital, Dublin, Ireland.
| | - Ciara Quigley
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
- Trinity Centre for Health Sciences, St. James's Hospital, Dublin, Ireland
| | - Áine McNicholas
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
- Trinity Centre for Health Sciences, St. James's Hospital, Dublin, Ireland
| | - Linda Lisanti
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
- Trinity Centre for Health Sciences, St. James's Hospital, Dublin, Ireland
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
- Trinity Centre for Health Sciences, St. James's Hospital, Dublin, Ireland
- The Hospital for SickKids, Toronto, ON, Canada
- The Peter Gilgan Centre for Research and Learning, SickKids Research Institute, SickKids Research Institute, Toronto, ON, Canada
- The Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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6
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Mollon J, Almasy L, Jacquemont S, Glahn DC. The contribution of copy number variants to psychiatric symptoms and cognitive ability. Mol Psychiatry 2023; 28:1480-1493. [PMID: 36737482 PMCID: PMC10213133 DOI: 10.1038/s41380-023-01978-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
Copy number variants (CNVs) are deletions and duplications of DNA sequence. The most frequently studied CNVs, which are described in this review, are recurrent CNVs that occur in the same locations on the genome. These CNVs have been strongly implicated in neurodevelopmental disorders, namely autism spectrum disorder (ASD), intellectual disability (ID), and developmental delay (DD), but also in schizophrenia. More recent work has also shown that CNVs increase risk for other psychiatric disorders, namely, depression, bipolar disorder, and post-traumatic stress disorder. Many of the same CNVs are implicated across all of these disorders, and these neuropsychiatric CNVs are also associated with cognitive ability in the general population, as well as with structural and functional brain alterations. Neuropsychiatric CNVs also show incomplete penetrance, such that carriers do not always develop any psychiatric disorder, and may show only mild symptoms, if any. Variable expressivity, whereby the same CNVs are associated with many different phenotypes of varied severity, also points to highly complex mechanisms underlying disease risk in CNV carriers. Comprehensive and longitudinal phenotyping studies of individual CNVs have provided initial insights into these mechanisms. However, more work is needed to estimate and predict the effect of non-recurrent, ultra-rare CNVs, which also contribute to psychiatric and cognitive outcomes. Moreover, delineating the broader phenotypic landscape of neuropsychiatric CNVs in both clinical and general population cohorts may also offer important mechanistic insights.
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Affiliation(s)
- Josephine Mollon
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Laura Almasy
- Department of Genetics, Perelman School of Medicine, Penn-CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Sebastien Jacquemont
- Department of Pediatrics, Université de Montréal, Montreal, QC, Canada
- Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC, Canada
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT, USA
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Erady C, Amin K, Onilogbo TOAE, Tomasik J, Jukes-Jones R, Umrania Y, Bahn S, Prabakaran S. Novel open reading frames in human accelerated regions and transposable elements reveal new leads to understand schizophrenia and bipolar disorder. Mol Psychiatry 2022; 27:1455-1468. [PMID: 34937870 PMCID: PMC9095477 DOI: 10.1038/s41380-021-01405-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/16/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022]
Abstract
Schizophrenia (SCZ) and bipolar disorder are debilitating neuropsychiatric disorders arising from a combination of environmental and genetic factors. Novel open reading frames (nORFs) are genomic loci that give rise to previously uncharacterized transcripts and protein products. In our previous work, we have shown that nORFs can be biologically regulated and that they may play a role in cancer and rare diseases. More importantly, we have shown that nORFs may emerge in accelerated regions of the genome giving rise to species-specific functions. We hypothesize that nORFs represent a potentially important group of biological factors that may contribute to SCZ and bipolar disorder pathophysiology. Human accelerated regions (HARs) are genomic features showing human-lineage-specific rapid evolution that may be involved in biological regulation and have additionally been found to associate with SCZ genes. Transposable elements (TEs) are another set of genomic features that have been shown to regulate gene expression. As with HARs, their relevance to SCZ has also been suggested. Here, nORFs are investigated in the context of HARs and TEs. This work shows that nORFs whose expression is disrupted in SCZ and bipolar disorder are in close proximity to HARs and TEs and that some of them are significantly associated with SCZ and bipolar disorder genomic hotspots. We also show that nORF encoded proteins can form structures and potentially constitute novel drug targets.
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Affiliation(s)
- Chaitanya Erady
- grid.5335.00000000121885934Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Krishna Amin
- grid.5335.00000000121885934Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Temiloluwa O. A. E. Onilogbo
- grid.5335.00000000121885934Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK ,grid.5335.00000000121885934Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Jakub Tomasik
- grid.5335.00000000121885934Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Rebekah Jukes-Jones
- grid.9918.90000 0004 1936 8411Leicester Cancer Research Centre, RKCSB, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - Yagnesh Umrania
- grid.5335.00000000121885934Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR UK
| | - Sabine Bahn
- grid.5335.00000000121885934Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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8
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Dalvie S, Chatzinakos C, Al Zoubi O, Georgiadis F, Lancashire L, Daskalakis NP. From genetics to systems biology of stress-related mental disorders. Neurobiol Stress 2021; 15:100393. [PMID: 34584908 PMCID: PMC8456113 DOI: 10.1016/j.ynstr.2021.100393] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 01/20/2023] Open
Abstract
Many individuals will be exposed to some form of traumatic stress in their lifetime which, in turn, increases the likelihood of developing stress-related disorders such as post-traumatic stress disorder (PTSD), major depressive disorder (MDD) and anxiety disorders (ANX). The development of these disorders is also influenced by genetics and have heritability estimates ranging between ∼30 and 70%. In this review, we provide an overview of the findings of genome-wide association studies for PTSD, depression and ANX, and we observe a clear genetic overlap between these three diagnostic categories. We go on to highlight the results from transcriptomic and epigenomic studies, and, given the multifactorial nature of stress-related disorders, we provide an overview of the gene-environment studies that have been conducted to date. Finally, we discuss systems biology approaches that are now seeing wider utility in determining a more holistic view of these complex disorders.
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Affiliation(s)
- Shareefa Dalvie
- South African Medical Research Council (SAMRC), Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC), Unit on Child & Adolescent Health, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Chris Chatzinakos
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Obada Al Zoubi
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Foivos Georgiadis
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Lee Lancashire
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Data Science, Cohen Veterans Bioscience, New York, USA
| | - Nikolaos P. Daskalakis
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
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9
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Abstract
Tourette syndrome (TS) is a severe neuropsychiatric disorder characterized by recurrent, involuntary physical and verbal tics. With a prevalence as high as 1% in children, a deeper understanding of the etiology of the disorder and contributions to risk is critical. Here, we cover the current body of knowledge in scientific literature regarding the genetics of TS. We first review the history and diagnostic criteria for TS cases. We then cover the prevalence, and begin to address the etiology of the disorder. We highlight long-standing evidence for a genetic contribution to TS risk from epidemiology studies focused on twins, families, and population-scale data. Finally, we summarize current large-scale genetic studies of TS along specific classes of genetic variation, including common variation, rare copy number variation, and de novo variation that impact protein-coding sequence. Although these variants do not account for the entirety of TS genetic risk, current evidence is clear that each class of variation is a factor in the overall risk architecture across TS cases.
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Affiliation(s)
- Laura Domènech
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Carolina Cappi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Matt Halvorsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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10
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Brikell I, Burton C, Mota NR, Martin J. Insights into attention-deficit/hyperactivity disorder from recent genetic studies. Psychol Med 2021; 51:2274-2286. [PMID: 33814023 DOI: 10.1017/s0033291721000982] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a common and highly heritable neurodevelopmental disorder (NDD). In this narrative review, we summarize recent advances in quantitative and molecular genetic research from the past 5-10 years. Combined with large-scale international collaboration, these advances have resulted in fast-paced progress in understanding the etiology of ADHD and how genetic risk factors map on to clinical heterogeneity. Studies are converging on a number of key insights. First, ADHD is a highly polygenic NDD with a complex genetic architecture encompassing risk variants across the spectrum of allelic frequencies, which are implicated in neurobiological processes. Second, genetic studies strongly suggest that ADHD diagnosis shares a large proportion of genetic risks with continuously distributed traits of ADHD in the population, with shared genetic risks also seen across development and sex. Third, ADHD genetic risks are shared with those implicated in many other neurodevelopmental, psychiatric and somatic phenotypes. As sample sizes and the diversity of genetic studies continue to increase through international collaborative efforts, we anticipate further success with gene discovery, characterization of how the ADHD phenotype relates to other human traits and growing potential to use genomic risk factors for understanding clinical trajectories and for precision medicine approaches.
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Affiliation(s)
- Isabell Brikell
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
| | - Christie Burton
- Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Canada
| | - Nina Roth Mota
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Joanna Martin
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
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11
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Wu X, Huai C, Shen L, Li M, Yang C, Zhang J, Chen L, Zhu W, Fan L, Zhou W, Xing Q, He L, Wan C, Qin S. Genome-wide study of copy number variation implicates multiple novel loci for schizophrenia risk in Han Chinese family trios. iScience 2021; 24:102894. [PMID: 34401673 PMCID: PMC8358640 DOI: 10.1016/j.isci.2021.102894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/17/2021] [Accepted: 07/19/2021] [Indexed: 01/22/2023] Open
Abstract
Schizophrenia (SCZ) is a severe neuropsychiatric disorder that affects 1% of the global population. Copy number variations (CNVs) have been shown to play a critical role in its pathophysiology; however, only case-control studies on SCZ susceptibility CNVs have been conducted in Han Chinese. Here, we performed an array comparative genomic hybridization-based genome-wide CNV analysis in 100 Chinese family trios with SCZ. Burden test suggested that the SCZ probands carried more duplications than their healthy parents and unrelated healthy controls. Besides, five CNV loci were firstly reported to be associated with SCZ here, including both unbalanced transmitted CNVs and enriched de novo CNVs. Moreover, two genes (CTDSPL and MGAM) in these CNVs showed significant SCZ relevance in the expression level. Our findings support the crucial role of CNVs in the etiology of SCZ and provide new insights into the underlying mechanism of SCZ pathogenesis.
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Affiliation(s)
- Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Mo Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Chao Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Juan Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Luan Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wenli Zhu
- The Fourth People's Hospital of Wuhu, Wuhu, Anhui, 241000, China
| | - Lingzi Fan
- Zhumadian Psychiatric Hospital, Zhumadian, Henan, 463000, China
| | - Wei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qinghe Xing
- Children's Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Corresponding author
| | - Chunling Wan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Corresponding author
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Corresponding author
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12
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Yoon J, Mao Y. Dissecting Molecular Genetic Mechanisms of 1q21.1 CNV in Neuropsychiatric Disorders. Int J Mol Sci 2021; 22:5811. [PMID: 34071723 PMCID: PMC8197994 DOI: 10.3390/ijms22115811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Pathogenic copy number variations (CNVs) contribute to the etiology of neurodevelopmental/neuropsychiatric disorders (NDs). Increased CNV burden has been found to be critically involved in NDs compared with controls in clinical studies. The 1q21.1 CNVs, rare and large chromosomal microduplications and microdeletions, are detected in many patients with NDs. Phenotypes of duplication and deletion appear at the two ends of the spectrum. Microdeletions are predominant in individuals with schizophrenia (SCZ) and microcephaly, whereas microduplications are predominant in individuals with autism spectrum disorder (ASD) and macrocephaly. However, its complexity hinders the discovery of molecular pathways and phenotypic networks. In this review, we summarize the recent genome-wide association studies (GWASs) that have identified candidate genes positively correlated with 1q21.1 CNVs, which are likely to contribute to abnormal phenotypes in carriers. We discuss the clinical data implicated in the 1q21.1 genetic structure that is strongly associated with neurodevelopmental dysfunctions like cognitive impairment and reduced synaptic plasticity. We further present variations reported in the phenotypic severity, genomic penetrance and inheritance.
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Affiliation(s)
| | - Yingwei Mao
- Department of Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA;
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13
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Vorstman J, Scherer SW. What a finding of gene copy number variation can add to the diagnosis of developmental neuropsychiatric disorders. Curr Opin Genet Dev 2021; 68:18-25. [PMID: 33454514 DOI: 10.1016/j.gde.2020.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 11/26/2022]
Abstract
Among medical disciplines, diagnosis in psychiatry depends highly upon descriptive signs and symptoms, rather than biomarkers. Clear descriptions of specific genetic etiologies have been lacking; genomic technologies, however, are rapidly changing that landscape. Notably, chromosomal microarrays-which detect gene copy number variants (CNVs)-are a recommended standard of care for neurodevelopmental disorders. As a result, an increasing number of patients now receive a clinical diagnosis based on the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) and an identified genetic etiological variant. However, psychiatric and genetic diagnoses are frequently communicated and managed as two disconnected diagnostic parameters. Here, we advocate for a transition model, allowing the integration of genetic etiological information-starting with diagnostically proven CNVs-within the DSM-5 classification framework.
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Affiliation(s)
- Jacob Vorstman
- Department of Psychiatry, Hospital for Sick Children University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Canada
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, Hospital for Sick Children, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Canada; McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Canada.
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14
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Thygesen JH, Presman A, Harju-Seppänen J, Irizar H, Jones R, Kuchenbaecker K, Lin K, Alizadeh BZ, Austin-Zimmerman I, Bartels-Velthuis A, Bhat A, Bruggeman R, Cahn W, Calafato S, Crespo-Facorro B, de Haan L, de Zwarte SMC, Di Forti M, Díez-Revuelta Á, Hall J, Hall MH, Iyegbe C, Jablensky A, Kahn R, Kalaydjieva L, Kravariti E, Lawrie S, Luykx JJ, Mata I, McDonald C, McIntosh AM, McQuillin A, Muir R, Ophoff R, Picchioni M, Prata DP, Ranlund S, Rujescu D, Rutten BPF, Schulze K, Shaikh M, Schirmbeck F, Simons CJP, Toulopoulou T, van Amelsvoort T, van Haren N, van Os J, van Winkel R, Vassos E, Walshe M, Weisbrod M, Zartaloudi E, Bell V, Powell J, Lewis CM, Murray RM, Bramon E. Genetic copy number variants, cognition and psychosis: a meta-analysis and a family study. Mol Psychiatry 2021; 26:5307-5319. [PMID: 32719466 PMCID: PMC8589646 DOI: 10.1038/s41380-020-0820-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023]
Abstract
The burden of large and rare copy number genetic variants (CNVs) as well as certain specific CNVs increase the risk of developing schizophrenia. Several cognitive measures are purported schizophrenia endophenotypes and may represent an intermediate point between genetics and the illness. This paper investigates the influence of CNVs on cognition. We conducted a systematic review and meta-analysis of the literature exploring the effect of CNV burden on general intelligence. We included ten primary studies with a total of 18,847 participants and found no evidence of association. In a new psychosis family study, we investigated the effects of CNVs on specific cognitive abilities. We examined the burden of large and rare CNVs (>200 kb, <1% MAF) as well as known schizophrenia-associated CNVs in patients with psychotic disorders, their unaffected relatives and controls (N = 3428) from the Psychosis Endophenotypes International Consortium (PEIC). The carriers of specific schizophrenia-associated CNVs showed poorer performance than non-carriers in immediate (P = 0.0036) and delayed (P = 0.0115) verbal recall. We found suggestive evidence that carriers of schizophrenia-associated CNVs had poorer block design performance (P = 0.0307). We do not find any association between CNV burden and cognition. Our findings show that the known high-risk CNVs are not only associated with schizophrenia and other neurodevelopmental disorders, but are also a contributing factor to impairment in cognitive domains such as memory and perceptual reasoning, and act as intermediate biomarkers of disease risk.
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Affiliation(s)
- Johan H. Thygesen
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Amelia Presman
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Jasmine Harju-Seppänen
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Haritz Irizar
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Rebecca Jones
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Karoline Kuchenbaecker
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK ,grid.83440.3b0000000121901201UCL Genetics Institute, University College London, London, UK
| | - Kuang Lin
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK ,grid.4991.50000 0004 1936 8948Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Behrooz Z. Alizadeh
- grid.4494.d0000 0000 9558 4598University of Groningen, University Medical Center Groningen, University Center for Psychiatry, Rob Giel Research Center, Groningen, The Netherlands ,grid.4494.d0000 0000 9558 4598Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Agna Bartels-Velthuis
- grid.4494.d0000 0000 9558 4598University of Groningen, University Medical Center Groningen, University Center for Psychiatry, Rob Giel Research Center, Groningen, The Netherlands
| | - Anjali Bhat
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Richard Bruggeman
- grid.4494.d0000 0000 9558 4598University of Groningen, University Medical Center Groningen, University Center for Psychiatry, Rob Giel Research Center, Groningen, The Netherlands ,grid.4830.f0000 0004 0407 1981Department of Clinical and Developmental Neuropsychology, University of Groningen, Groningen, The Netherlands
| | - Wiepke Cahn
- grid.5477.10000000120346234University Medical Center Utrecht, Department of Psychiatry, Brain Centre Rudolf Magnus, Utrecht University, Utrecht, The Netherlands ,grid.413664.2Altrecht, General Mental Health Care, Utrecht, The Netherlands
| | - Stella Calafato
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Benedicto Crespo-Facorro
- grid.469673.90000 0004 5901 7501CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Sevilla, Spain ,grid.7821.c0000 0004 1770 272XUniversity Hospital Marqués de Valdecilla, University of Cantabria–IDIVAL, Santander, Spain ,grid.9224.d0000 0001 2168 1229Hospital Universitario Virgen del Rocío, IBiS, Department of Psychiatry, School of Medicine, University of Sevilla, Sevilla, Spain
| | - Liewe de Haan
- grid.7177.60000000084992262Amsterdam UMC, Department of Psychiatry, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands ,grid.491093.60000 0004 0378 2028Arkin, Institute for Mental Health, Amsterdam, The Netherlands
| | - Sonja M. C. de Zwarte
- grid.5477.10000000120346234University Medical Center Utrecht, Department of Psychiatry, Brain Centre Rudolf Magnus, Utrecht University, Utrecht, The Netherlands
| | - Marta Di Forti
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK
| | - Álvaro Díez-Revuelta
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK ,grid.5690.a0000 0001 2151 2978Laboratory of Cognitive and Computational Neuroscience—Centre for Biomedical Technology (CTB), Complutense University and Technical University of Madrid, Madrid, Spain
| | - Jeremy Hall
- grid.5600.30000 0001 0807 5670School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, UK
| | - Mei-Hua Hall
- grid.38142.3c000000041936754XPsychosis Neurobiology Laboratory, Harvard Medical School, McLean Hospital, Belmont, MA USA
| | - Conrad Iyegbe
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK
| | - Assen Jablensky
- grid.1012.20000 0004 1936 7910Centre for Clinical Research in Neuropsychiatry, The University of Western Australia, Perth, WA Australia
| | - Rene Kahn
- grid.5477.10000000120346234University Medical Center Utrecht, Department of Psychiatry, Brain Centre Rudolf Magnus, Utrecht University, Utrecht, The Netherlands ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Luba Kalaydjieva
- grid.1012.20000 0004 1936 7910Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Perth, WA Australia
| | - Eugenia Kravariti
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK
| | - Stephen Lawrie
- grid.4305.20000 0004 1936 7988Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, Scotland UK
| | - Jurjen J. Luykx
- grid.5477.10000000120346234University Medical Center Utrecht, Department of Psychiatry, Brain Centre Rudolf Magnus, Utrecht University, Utrecht, The Netherlands ,grid.7692.a0000000090126352Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands ,grid.491146.f0000 0004 0478 3153Second opinion outpatient clinic, GGNet Mental Health, Warsnveld, The Netherlands
| | - Igancio Mata
- grid.469673.90000 0004 5901 7501CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Sevilla, Spain ,Fundación Argibide, Pamplona, Spain
| | - Colm McDonald
- grid.6142.10000 0004 0488 0789The Centre for Neuroimaging & Cognitive Genomics (NICOG) and NCBES Galway Neuroscience Centre, National University of Ireland Galway, Galway, Ireland
| | - Andrew M. McIntosh
- grid.4305.20000 0004 1936 7988Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, Scotland UK ,grid.4305.20000 0004 1936 7988Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Andrew McQuillin
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Rebecca Muir
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Roel Ophoff
- grid.19006.3e0000 0000 9632 6718Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA ,grid.5645.2000000040459992XDepartment of Psychiatry, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marco Picchioni
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK
| | - Diana P. Prata
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK ,grid.9983.b0000 0001 2181 4263Instituto de Biofísica e Engenharia Biomédica, Faculdade de Ciencias da Universidade de Lisboa, Lisboa, Portugal ,grid.45349.3f0000 0001 2220 8863Centre for Psychological Research and Social Intervention, ISCTE-IUL, Lisboa, Portugal
| | - Siri Ranlund
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK ,grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK
| | - Dan Rujescu
- grid.5252.00000 0004 1936 973XDepartment of Psychiatry, Ludwig-Maximilians University of Munich, Munich, Germany ,grid.9018.00000 0001 0679 2801Department of Psychiatry, Psychotherapy and Psychosomatics, University of Halle Wittenberg, Halle, Germany
| | - Bart P. F. Rutten
- grid.412966.e0000 0004 0480 1382Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands ,grid.412966.e0000 0004 0480 1382The Brain+Nerve Centre, Maastricht University Medical Centre+ (MUMC+), Maastricht, The Netherlands
| | - Katja Schulze
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK ,grid.37640.360000 0000 9439 0839South London and Maudsley NHS Foundation Trust, London, UK
| | - Madiha Shaikh
- grid.451079.e0000 0004 0428 0265North East London Foundation Trust, London, UK ,grid.83440.3b0000000121901201Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - Frederike Schirmbeck
- grid.7177.60000000084992262Amsterdam UMC, Department of Psychiatry, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands ,grid.491093.60000 0004 0378 2028Arkin, Institute for Mental Health, Amsterdam, The Netherlands
| | - Claudia J. P. Simons
- grid.412966.e0000 0004 0480 1382Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands ,grid.491104.9GGzE Institute for Mental Health Care, Eindhoven, The Netherlands
| | - Timothea Toulopoulou
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK ,grid.18376.3b0000 0001 0723 2427Department of Psychology, Bilkent University, Main Campus, Bilkent, Ankara Turkey
| | - Therese van Amelsvoort
- grid.412966.e0000 0004 0480 1382Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Neeltje van Haren
- grid.5477.10000000120346234University Medical Center Utrecht, Department of Psychiatry, Brain Centre Rudolf Magnus, Utrecht University, Utrecht, The Netherlands ,grid.5645.2000000040459992XDepartment of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Sophia’s Children Hospital, Rotterdam, The Netherlands
| | - Jim van Os
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK ,grid.412966.e0000 0004 0480 1382Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands ,grid.7692.a0000000090126352Department of Psychiatry, UMC Utrecht Brain Center, Utrecht, The Netherlands
| | - Ruud van Winkel
- grid.5596.f0000 0001 0668 7884KU Leuven, Department of Neuroscience, Research Group Psychiatry, Leuven, Belgium
| | - Evangelos Vassos
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK
| | - Muriel Walshe
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Matthias Weisbrod
- grid.7700.00000 0001 2190 4373Department of General Psychiatry, Center of Psychosocial Medicine, University of Heidelberg, Heidelberg, Germany ,grid.490718.30000000406368535SRH Klinikum, Karlsbad-Langensteinbach, Germany
| | - Eirini Zartaloudi
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - Vaughan Bell
- grid.83440.3b0000000121901201Division of Psychiatry, University College London, London, UK
| | - John Powell
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK
| | - Cathryn M. Lewis
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK
| | - Robin M. Murray
- grid.13097.3c0000 0001 2322 6764Institute of Psychiatry, Psychology & Neuroscience at King’s College London, London, UK ,grid.37640.360000 0000 9439 0839South London and Maudsley NHS Foundation Trust, London, UK
| | - Elvira Bramon
- Division of Psychiatry, University College London, London, UK. .,Institute of Psychiatry, Psychology & Neuroscience at King's College London, London, UK. .,Institute of Cognitive Neuroscience, University College London, London, UK.
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15
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Jiang L, Huguet G, Schramm C, Ciampi A, Main A, Passo C, Jean‐Louis M, Auger M, Schumann G, Porteous D, Jacquemont S, Greenwood CMT. Estimating the effects of copy‐number variants on intelligence using hierarchical Bayesian models. Genet Epidemiol 2020; 44:825-840. [DOI: 10.1002/gepi.22344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/24/2020] [Accepted: 07/21/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Lai Jiang
- Lady Davis Institute Jewish General Hospital Montreal Canada
- Department of Epidemiology, Biostatistics and Occupational Health McGill University Montreal Canada
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
| | - Guillaume Huguet
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Catherine Schramm
- Lady Davis Institute Jewish General Hospital Montreal Canada
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Antonio Ciampi
- Department of Epidemiology, Biostatistics and Occupational Health McGill University Montreal Canada
| | - Antoine Main
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
- Department of Decision Sciences Hautes etudes commerciales de Montreal (HEC) Montreal Canada
| | - Claudine Passo
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Martineau Jean‐Louis
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Maude Auger
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Gunter Schumann
- Institute of Psychiatry, Psychology, and Neuroscience King's College London London UK
| | - David Porteous
- Department of Psychology, Lothian Birth Cohorts Group, School of Philosophy, Psychology and Language Sciences The University of Edinburgh Edinburgh UK
- Medical Genetics Section, Centre for Genomic Experimental Medicine, MRC Institute of Genetics Molecular Medicine, Western General Hospital The University of Edinburgh Edinburgh UK
- Generation Scotland, Centre for Genomic and Experimental Medicine University of Edinburgh Edinburgh UK
| | - Sébastien Jacquemont
- Centre Hospitalier Universitaire (CHU) Sainte‐Justine Montreal Canada
- Universite de Montreal Montreal Canada
| | - Celia M. T. Greenwood
- Lady Davis Institute Jewish General Hospital Montreal Canada
- Department of Epidemiology, Biostatistics and Occupational Health McGill University Montreal Canada
- Gerald Bronfman Department of Oncology McGill University Montreal Canada
- Department of Human Genetics McGill University Montreal Canada
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16
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Population prevalence and inheritance pattern of recurrent CNVs associated with neurodevelopmental disorders in 12,252 newborns and their parents. Eur J Hum Genet 2020; 29:205-215. [PMID: 32778765 PMCID: PMC7852900 DOI: 10.1038/s41431-020-00707-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/19/2020] [Accepted: 07/21/2020] [Indexed: 12/30/2022] Open
Abstract
Recurrent copy number variations (CNVs) are common causes of neurodevelopmental disorders (NDDs) and associated with a range of psychiatric traits. These CNVs occur at defined genomic regions that are particularly prone to recurrent deletions and duplications and often exhibit variable expressivity and incomplete penetrance. Robust estimates of the population prevalence and inheritance pattern of recurrent CNVs associated with neurodevelopmental disorders (NDD CNVs) are lacking. Here we perform array-based CNV calling in 12,252 mother–father–child trios from the Norwegian Mother, Father, and Child Cohort Study (MoBa) and analyse the inheritance pattern of 26 recurrent NDD CNVs in 13 genomic regions. We estimate the total prevalence of recurrent NDD CNVs (duplications and deletions) in live-born children to 0.48% (95% C.I.: 0.37–0.62%), i.e., ~1 in 200 newborns has either a deletion or duplication in these NDDs associated regions. Approximately a third of the newborn recurrent NDD CNVs (34%, N = 20/59) are de novo variants. We provide prevalence estimates and inheritance information for each of the 26 NDD CNVs and find higher prevalence than previously reported for 1q21.1 deletions (~1:2000), 15q11.2 duplications (~1:4000), 15q13.3 microdeletions (~1:2500), 16p11.2 proximal microdeletions (~1:2000) and 17q12 deletions (~1:4000) and lower than previously reported prevalence for the 22q11.2 deletion (~1:12,000). In conclusion, our analysis of an unselected and representative population of newborns and their parents provides a clearer picture of the rate of recurrent microdeletions/duplications implicated in neurodevelopmental delay. These results will provide an important resource for genetic diagnostics and counseling.
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17
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Myers L, Blyth M, Moradkhani K, Hranilović D, Polesie S, Isaksson J, Nordgren A, Bucan M, Vincent M, Bölte S, Anderlid BM, Tammimies K. Variable neurodevelopmental and morphological phenotypes of carriers with 12q12 duplications. Mol Genet Genomic Med 2019; 8:e1013. [PMID: 31730283 PMCID: PMC6978403 DOI: 10.1002/mgg3.1013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Variable size deletions affecting 12q12 have been found in individuals with neurodevelopmental disorders (NDDs) and distinct facial and physical features. For many genetic loci affected by deletions in individuals with NDDs, reciprocal duplications have been described. However, for the 12q12 region, there are no detailed descriptions of duplication cases in the literature. METHODS We report a phenotypic description of a family with monozygotic twins diagnosed with NDDs, carrying a 9 Mb duplication at 12q12, and five other individuals with overlapping duplications ranging from 4.54 Mb up to 15.16 Mb. RESULTS The duplication carriers had language delays, cognitive delays, and were diagnosed with autism spectrum disorder. Additionally, distinct facial features (e.g., high foreheads, deeply set eyes, short palpebral fissures, small ears, high nasal bridges, abnormalities of the nose tip, thin lips), large feet, and abnormalities in the digits were noted. We also describe incomplete penetrance of the NDD phenotypes among the individuals with 12q12 duplication. CONCLUSION This case series expands our knowledge on this rare genetic aberration and suggests that large 12q12 duplications may increase the risk for developing NDDs.
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Affiliation(s)
- Lynnea Myers
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet & Child and Adolescent Psychiatry, Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Moira Blyth
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds, UK
| | | | - Dubravka Hranilović
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Sam Polesie
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Dermatology and Venereology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Johan Isaksson
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet & Child and Adolescent Psychiatry, Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden.,Department of Neuroscience, Child and Adolescent Psychiatry and Psychiatry Unit, Uppsala University, Uppsala, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Bucan
- Department of Genetics and Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marie Vincent
- Centre Hospitalier, University of Nantes, Nantes, France
| | - Sven Bölte
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet & Child and Adolescent Psychiatry, Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden.,Curtin Autism Research Group, School of Occupational Therapy, Social Work and Speech Pathology, Curtin University, Perth, Western Australia, Australia
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet & Child and Adolescent Psychiatry, Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
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18
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Pfeiffer D, Chen B, Schlicht K, Ginsbach P, Abboud S, Bersano A, Bevan S, Brandt T, Caso V, Debette S, Erhart P, Freitag-Wolf S, Giacalone G, Grau AJ, Hayani E, Jern C, Jiménez-Conde J, Kloss M, Krawczak M, Lee JM, Lemmens R, Leys D, Lichy C, Maguire JM, Martin JJ, Metso AJ, Metso TM, Mitchell BD, Pezzini A, Rosand J, Rost NS, Stenman M, Tatlisumak T, Thijs V, Touzé E, Traenka C, Werner I, Woo D, Del Zotto E, Engelter ST, Kittner SJ, Cole JW, Grond-Ginsbach C, Lyrer PA, Lindgren A. Genetic Imbalance Is Associated With Functional Outcome After Ischemic Stroke. Stroke 2019; 50:298-304. [PMID: 30661490 DOI: 10.1161/strokeaha.118.021856] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background and Purpose- We sought to explore the effect of genetic imbalance on functional outcome after ischemic stroke (IS). Methods- Copy number variation was identified in high-density single-nucleotide polymorphism microarray data of IS patients from the CADISP (Cervical Artery Dissection and Ischemic Stroke Patients) and SiGN (Stroke Genetics Network)/GISCOME (Genetics of Ischaemic Stroke Functional Outcome) networks. Genetic imbalance, defined as total number of protein-coding genes affected by copy number variations in an individual, was compared between patients with favorable (modified Rankin Scale score of 0-2) and unfavorable (modified Rankin Scale score of ≥3) outcome after 3 months. Subgroup analyses were confined to patients with imbalance affecting ohnologs-a class of dose-sensitive genes, or to those with imbalance not affecting ohnologs. The association of imbalance with outcome was analyzed by logistic regression analysis, adjusted for age, sex, stroke subtype, stroke severity, and ancestry. Results- The study sample comprised 816 CADISP patients (age 44.2±10.3 years) and 2498 SiGN/GISCOME patients (age 67.7±14.2 years). Outcome was unfavorable in 122 CADISP and 889 SiGN/GISCOME patients. Multivariate logistic regression analysis revealed that increased genetic imbalance was associated with less favorable outcome in both samples (CADISP: P=0.0007; odds ratio=0.89; 95% CI, 0.82-0.95 and SiGN/GISCOME: P=0.0036; odds ratio=0.94; 95% CI, 0.91-0.98). The association was independent of age, sex, stroke severity on admission, stroke subtype, and ancestry. On subgroup analysis, imbalance affecting ohnologs was associated with outcome (CADISP: odds ratio=0.88; 95% CI, 0.80-0.95 and SiGN/GISCOME: odds ratio=0.93; 95% CI, 0.89-0.98) whereas imbalance without ohnologs lacked such an association. Conclusions- Increased genetic imbalance was associated with poorer functional outcome after IS in both study populations. Subgroup analysis revealed that this association was driven by presence of ohnologs in the respective copy number variations, suggesting a causal role of the deleterious effects of genetic imbalance.
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Affiliation(s)
- Dorothea Pfeiffer
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Bowang Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China (B.C.)
| | - Kristina Schlicht
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, Germany (K.S., S.F.-W., M. Krawczak)
| | - Philip Ginsbach
- School of Informatics, University of Edinburgh, United Kingdom (P.G.)
| | - Sherine Abboud
- Laboratory of Experimental Neurology, Université Libre de Bruxelles, Brussels, Belgium (S.A.)
| | - Anna Bersano
- Cerebrovascular Unit IRCCS Foundation C. Besta Neurological Institute, Milan, Italy (A.B.)
| | - Steve Bevan
- School of Life Science, University of Lincoln, United Kingdom (S.B.)
| | - Tobias Brandt
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.).,Suva/Swiss National Accident Insurance Fund, Lucerne, Switzerland (T.B.)
| | - Valeria Caso
- Stroke Unit, Perugia University Hospital, Italy (V.C.)
| | - Stéphanie Debette
- Inserm, Bordeaux Population Health Research Center, UMR 1219, University of Bordeaux, France (S.D.).,Department of Neurology, Bordeaux University Hospital, France (S.D.)
| | - Philipp Erhart
- Department of Vascular and Endovascular Surgery, University Hospital Heidelberg, Germany (P.E.)
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, Germany (K.S., S.F.-W., M. Krawczak)
| | - Giacomo Giacalone
- Department of Neurology, San Raffaele University Hospital, Milan, Italy (G.G.)
| | - Armin J Grau
- Department of Neurology, Klinikum Ludwigshafen, Germany (A.J.G.)
| | - Eyad Hayani
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Christina Jern
- The Sahlgrenska Academy, University of Gothenburg, Sweden (C.J.).,Sahlgrenska University Hospital, Sweden (C.J.)
| | | | - Manja Kloss
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, Germany (K.S., S.F.-W., M. Krawczak)
| | - Jin-Moo Lee
- Department of Neurology, Washington University School of Medicine, St Louis, MO (J.-M.L.)
| | - Robin Lemmens
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute, KU Leuven, University of Leuven, Belgium (R.L.).,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium (R.L.).,Department of Neurology, University Hospitals Leuven, Belgium (R.L.)
| | - Didier Leys
- Department of Neurology, University of Lille, France (D.L.)
| | | | - Jane M Maguire
- Faculty of Health, University of Technology Sydney, Australia (J.M.M.).,Hunter Medical Research Institute, Priority Research Centre for Stroke and Traumatic Brain Injury, University of Newcastle, Australia (J.M.M.)
| | - Juan J Martin
- Department of Neurology, Sanatorio Allende, Cordoba, Argentina (J.J.M.)
| | - Antti J Metso
- Department of Neurology, Helsinki University Central Hospital, Finland (A.J.M., T.M.M., T.T.)
| | - Tiina M Metso
- Department of Neurology, Helsinki University Central Hospital, Finland (A.J.M., T.M.M., T.T.)
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore (B.D.M.).,Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD (B.D.M.)
| | - Alessandro Pezzini
- Department of Clinical and Experimental Sciences, Neurology Clinic, University of Brescia, Italy (A.P., E.D.Z.)
| | - Jonathan Rosand
- Center for Genomic Medicine (J.R.), Massachusetts General Hospital, Boston
| | - Natalia S Rost
- Department of Neurology (N.S.R.), Massachusetts General Hospital, Boston
| | - Martin Stenman
- Department of Clinical Sciences Lund, Neurology, Lund University, Sweden (M.S., A.L.).,Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden (M.S., A.L.)
| | - Turgut Tatlisumak
- Department of Neurology, Helsinki University Central Hospital, Finland (A.J.M., T.M.M., T.T.).,Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Sweden (T.T.).,Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden (T.T.)
| | - Vincent Thijs
- Stroke Division, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Heidelberg, Victoria, Australia (V.T.).,Department of Neurology, Austin Health, Heidelberg, Victoria, Australia (V.T.)
| | - Emmanuel Touzé
- Paris Descartes University, INSERM UMR S894, Department of Neurology, Sainte-Anne Hospital, Paris, France (E.T.).,Normandie Université, Université Caen-Normandie, Inserm U1237, CHU Côte de Nacre, Service de Neurologie, Caen, France (E.T.)
| | - Christopher Traenka
- Department of Neurology and Stroke Center, University Hospital Basel, Switzerland (C.T., S.T.E., P.A.L.)
| | - Inge Werner
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Daniel Woo
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati, OH (D.W.)
| | - Elisabetta Del Zotto
- Department of Clinical and Experimental Sciences, Neurology Clinic, University of Brescia, Italy (A.P., E.D.Z.)
| | - Stefan T Engelter
- Department of Neurology and Stroke Center, University Hospital Basel, Switzerland (C.T., S.T.E., P.A.L.).,Neurorehabilitation Unit, University of Basel, Switzerland (S.T.E.).,University Center for Medicine of Aging, Felix Platter Hospital, Basel, Switzerland (S.T.E.)
| | - Steven J Kittner
- Department of Neurology, Veterans Affairs Medical Center, Baltimore, MD (S.J.K., J.W.C.); and Department of Neurology University of Maryland School of Medicine, Baltimore (S.J.K., J.W.C.)
| | - John W Cole
- Department of Neurology, Veterans Affairs Medical Center, Baltimore, MD (S.J.K., J.W.C.); and Department of Neurology University of Maryland School of Medicine, Baltimore (S.J.K., J.W.C.)
| | - Caspar Grond-Ginsbach
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Philippe A Lyrer
- Department of Neurology and Stroke Center, University Hospital Basel, Switzerland (C.T., S.T.E., P.A.L.)
| | - Arne Lindgren
- Department of Clinical Sciences Lund, Neurology, Lund University, Sweden (M.S., A.L.).,Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden (M.S., A.L.)
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19
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Savory K, Manivannan S, Zaben M, Uzun O, Syed YA. Impact of copy number variation on human neurocognitive deficits and congenital heart defects: A systematic review. Neurosci Biobehav Rev 2019; 108:83-93. [PMID: 31682886 DOI: 10.1016/j.neubiorev.2019.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/26/2019] [Indexed: 12/16/2022]
Abstract
Copy number variant (CNV) syndromes are often associated with both neurocognitive deficits (NCDs) and congenital heart defects (CHDs). Children and adults with cardiac developmental defects likely to have NCDs leading to increased risk of hospitalisation and reduced level of independence. To date, the association between these two phenotypes have not been explored in relation to CNV syndromes. In order to address this question, we systematically reviewed the prevalence of CHDs in a range of CNV syndromes associated with NCDs. A meta-analysis showed a relationship with the size of CNV and its association with both NCDs and CHDs, and also inheritance pattern. To our knowledge, this is the first review to establish association between NCD and CHDs in CNV patients, specifically in relation to the severity of NCD. Importantly, we also found specific types of CHDs were associated with severe neurocognitive deficits. Finally, we discuss the implications of these results for patients in the clinical setting which warrants further exploration of this association in order to lead an improvement in the quality of patient's life.
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Affiliation(s)
- Katrina Savory
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK; School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK
| | - Susruta Manivannan
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK
| | - Malik Zaben
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK
| | - Orhan Uzun
- University Hospital of Wales, Heath Park, Cardiff, CF10 3AX, UK
| | - Yasir Ahmed Syed
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK; School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK.
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20
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Pös O, Budis J, Kubiritova Z, Kucharik M, Duris F, Radvanszky J, Szemes T. Identification of Structural Variation from NGS-Based Non-Invasive Prenatal Testing. Int J Mol Sci 2019; 20:E4403. [PMID: 31500242 PMCID: PMC6769840 DOI: 10.3390/ijms20184403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 01/18/2023] Open
Abstract
Copy number variants (CNVs) are an important type of human genome variation, which play a significant role in evolution contribute to population diversity and human genetic diseases. In recent years, next generation sequencing has become a valuable tool for clinical diagnostics and to provide sensitive and accurate approaches for detecting CNVs. In our previous work, we described a non-invasive prenatal test (NIPT) based on low-coverage massively parallel whole-genome sequencing of total plasma DNA for detection of CNV aberrations ≥600 kbp. We reanalyzed NIPT genomic data from 5018 patients to evaluate CNV aberrations in the Slovak population. Our analysis of autosomal chromosomes identified 225 maternal CNVs (47 deletions; 178 duplications) ranging from 600 to 7820 kbp. According to the ClinVar database, 137 CNVs (60.89%) were fully overlapping with previously annotated variants, 66 CNVs (29.33%) were in partial overlap, and 22 CNVs (9.78%) did not overlap with any previously described variant. Identified variants were further classified with the AnnotSV method. In summary, we identified 129 likely benign variants, 13 variants of uncertain significance, and 83 likely pathogenic variants. In this study, we use NIPT as a valuable source of population specific data. Our results suggest the utility of genomic data from commercial CNV analysis test as background for a population study.
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Affiliation(s)
- Ondrej Pös
- Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia.
- Geneton Ltd., 841 04 Bratislava, Slovakia.
| | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia.
- Comenius University Science Park, 841 04 Bratislava, Slovakia.
- Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia.
| | - Zuzana Kubiritova
- Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia.
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia.
| | | | - Frantisek Duris
- Geneton Ltd., 841 04 Bratislava, Slovakia.
- Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia.
| | - Jan Radvanszky
- Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia.
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia.
| | - Tomas Szemes
- Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia.
- Geneton Ltd., 841 04 Bratislava, Slovakia.
- Comenius University Science Park, 841 04 Bratislava, Slovakia.
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21
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Martin J, Tammimies K, Karlsson R, Lu Y, Larsson H, Lichtenstein P, Magnusson PKE. Copy number variation and neuropsychiatric problems in females and males in the general population. Am J Med Genet B Neuropsychiatr Genet 2019; 180:341-350. [PMID: 30307693 PMCID: PMC6767107 DOI: 10.1002/ajmg.b.32685] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/09/2018] [Accepted: 09/06/2018] [Indexed: 11/05/2022]
Abstract
Neurodevelopmental problems (NPs) are more common in males, whereas anxiety and depression are more common in females. Rare copy number variants (CNVs) have been implicated in neurodevelopmental disorders. The aim of this study was to characterize the relationship between rare CNVs with NPs, anxiety, and depression in a childhood population sample, as well as to examine sex-specific effects. We analyzed a sample of N = 12,982 children, of whom 5.3% had narrowly defined NPs (clinically diagnosed), 20.9% had broadly defined NPs (based on validated screening measures, but no diagnosis), and 3.0% had clinically diagnosed anxiety or depression. Rare (<1% frequency) CNVs were categorized by size (100-500 kb or > 500 kb), type, and putative relevance to NPs. We tested for association of CNV categories with outcomes and examined sex-specific effects. Medium deletions (OR[CI] = 1.18[1.05-1.33], p = .0053) and large duplications (OR[CI] = 1.45[1.19-1.75], p = .00017) were associated with broadly defined NPs. Large deletions (OR[CI] = 1.85[1.14-3.01], p = .013) were associated with narrowly defined NPs. There were no significant sex differences in CNV burden in individuals with NPs. Although CNVs were not associated with anxiety/depression in the whole sample, in individuals diagnosed with these disorders, females were more likely to have large CNVs (OR[CI] = 3.75[1.45-9.68], p = .0064). Rare CNVs are associated with both narrowly and broadly defined NPs in a general population sample of children. Our results also suggest that large, rare CNVs may show sex-specific phenotypic effects.
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Affiliation(s)
- Joanna Martin
- Department of Medical Epidemiology & BiostatisticsKarolinska InstitutetStockholmSweden
- MRC Centre for Neuropsychiatric Genetics and GenomicsCardiff UniversityCardiffUnited Kingdom
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND), Department of Women's and Children's HealthKarolinska Institutet and Center for Psychiatry ResearchStockholmSweden
| | - Robert Karlsson
- Department of Medical Epidemiology & BiostatisticsKarolinska InstitutetStockholmSweden
| | - Yi Lu
- Department of Medical Epidemiology & BiostatisticsKarolinska InstitutetStockholmSweden
| | - Henrik Larsson
- Department of Medical Epidemiology & BiostatisticsKarolinska InstitutetStockholmSweden
- School of Medical SciencesÖrebro UniversityÖrebroSweden
| | - Paul Lichtenstein
- Department of Medical Epidemiology & BiostatisticsKarolinska InstitutetStockholmSweden
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22
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Guyatt AL, Stergiakouli E, Martin J, Walters J, O'Donovan M, Owen M, Thapar A, Kirov G, Rodriguez S, Rai D, Zammit S, Gaunt TR. Association of copy number variation across the genome with neuropsychiatric traits in the general population. Am J Med Genet B Neuropsychiatr Genet 2018; 177:489-502. [PMID: 29687944 PMCID: PMC6099375 DOI: 10.1002/ajmg.b.32637] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 02/12/2018] [Accepted: 03/27/2018] [Indexed: 11/06/2022]
Abstract
Copy number variants (CNVs) are associated with psychiatric conditions in clinical populations. The relationship between rare CNV burden and neuropsychiatric traits in young, general populations is underexplored. A total of 6,807 children from the Avon Longitudinal Study of Parents and Children (ALSPAC) were studied. CNVs were inferred from single nucleotide polymorphism-array data using PennCNV. After excluding children with known candidate CNVs for schizophrenia (SCZ), rare (<1%) CNV burden (total number of genes affected by CNVs, total length of CNVs, and largest CNV carried) was analyzed in relation to: psychotic experiences (PEs) and anxiety/depression in adolescence; autism spectrum disorder (ASD) and attention-deficit hyperactivity disorder (ADHD), ASD and ADHD traits, and cognitive measures during childhood. Outcomes were also assessed in relation to known SCZ CNVs. The number of genes affected by rare CNVs was associated with a continuous measure of ASD: the standardized mean difference [SMD] per gene affected was increased by 0.018 [95%CI 0.011,0.025], p = 3e-07 for duplications and by 0.021 [95%CI 0.010, 0.032], p = 1e-04 for deletions. In line with our published results on educational attainment in ALSPAC, intelligence quotient (IQ) was associated with CNV burden: the SMD per gene affected was -0.017 [95%CI -0.025, -0.008] p = 1e-04 for duplications and -0.023 [95%CI -0.037, -0.009], p = .002 for deletions. Associations were also observed for measures of coherence, attention, memory, and social cognition. SCZ-associated deletions were associated with IQ (SMD: -0.617 [95%CI -0.936, -0.298], p = 2e-04), but not with PEs or other traits. We found that rare CNV burden and known SCZ candidate CNVs are associated with neuropsychiatric phenotypes in a nonclinically ascertained sample of young people.
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Affiliation(s)
- Anna L. Guyatt
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of BristolBristolUnited Kingdom
| | - Evie Stergiakouli
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of BristolBristolUnited Kingdom
- Centre for Academic Mental Health, Population Health Sciences, University of BristolBristolUnited Kingdom
| | - Joanna Martin
- MRC Centre for Neuropsychiatric Genetics and GenomicsCardiff UniversityCardiffUnited Kingdom
- Department of Medical Epidemiology & BiostatisticsKarolinska InstitutetStockholmSweden
| | - James Walters
- MRC Centre for Neuropsychiatric Genetics and GenomicsCardiff UniversityCardiffUnited Kingdom
| | - Michael O'Donovan
- MRC Centre for Neuropsychiatric Genetics and GenomicsCardiff UniversityCardiffUnited Kingdom
| | - Michael Owen
- MRC Centre for Neuropsychiatric Genetics and GenomicsCardiff UniversityCardiffUnited Kingdom
| | - Anita Thapar
- MRC Centre for Neuropsychiatric Genetics and GenomicsCardiff UniversityCardiffUnited Kingdom
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and GenomicsCardiff UniversityCardiffUnited Kingdom
| | - Santiago Rodriguez
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of BristolBristolUnited Kingdom
| | - Dheeraj Rai
- Centre for Academic Mental Health, Population Health Sciences, University of BristolBristolUnited Kingdom
| | - Stan Zammit
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of BristolBristolUnited Kingdom
- Centre for Academic Mental Health, Population Health Sciences, University of BristolBristolUnited Kingdom
- MRC Centre for Neuropsychiatric Genetics and GenomicsCardiff UniversityCardiffUnited Kingdom
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of BristolBristolUnited Kingdom
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