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Alhazmi S, Alharthi M, Alzahrani M, Alrofaidi A, Basingab F, Almuhammadi A, Alkhatabi H, Ashi A, Chaudhary A, Elaimi A. Copy number variations in autistic children. Biomed Rep 2024; 21:107. [PMID: 38868529 PMCID: PMC11168027 DOI: 10.3892/br.2024.1795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/30/2024] [Indexed: 06/14/2024] Open
Abstract
Autism spectrum disorder (ASD) manifests as a neurodevelopmental condition marked by challenges in social communication, interaction and the performing of repetitive behaviors. The prevalence of autism increases markedly on an annual basis; however, the etiology remains incompletely understood. Cytogenetically visible chromosomal abnormalities, including copy number variations (CNVs), have been shown to contribute to the pathogenesis of ASD. More than 1% of ASD conditions can be explained based on a known genetic locus, whereas CNVs account for 5-10% of cases. However, there are no studies on the Saudi Arabian population for the detection of CNVs linked to ASD, to the best of our knowledge. Therefore, the aim of the present study was to explore the prevalence of CNVs in autistic Saudi Arabian children. Genomic DNA was extracted from the peripheral blood of 14 autistic children along with four healthy control children and then array-based comparative genomic hybridization (aCGH) was used to detect CNVs. Bioinformatics analysis of the aCGH results showed the presence of recurrent and non-recurrent deletion/duplication CNVs in several regions of the genome of autistic children. The most frequent CNVs were 1q21.2, 3p26.3, 4q13.2, 6p25.3, 6q24.2, 7p21.1, 7q34, 7q11.1, 8p23.2, 13q32.3, 14q11.1-q11.2 and 15q11.1-q11.2. In the present study, CNVs in autistic Saudi Arabian children were identified to improve the understanding of the etiology of autism and facilitate its diagnosis. Additionally, the present study identified certain possible pathogenic genes in the CNV region associated with several developmental and neurogenetic diseases.
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Affiliation(s)
- Safiah Alhazmi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Neuroscience and Geroscience Research Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Central Laboratory of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Maram Alharthi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Maryam Alzahrani
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Aisha Alrofaidi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Asma Almuhammadi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Heba Alkhatabi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Hematology Research Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Abrar Ashi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Adeel Chaudhary
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Aisha Elaimi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
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Bamford RA, Zuko A, Eve M, Sprengers JJ, Post H, Taggenbrock RLRE, Fäβler D, Mehr A, Jones OJR, Kudzinskas A, Gandawijaya J, Müller UC, Kas MJH, Burbach JPH, Oguro-Ando A. CNTN4 modulates neural elongation through interplay with APP. Open Biol 2024; 14:240018. [PMID: 38745463 DOI: 10.1098/rsob.240018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 05/16/2024] Open
Abstract
The neuronal cell adhesion molecule contactin-4 (CNTN4) is genetically associated with autism spectrum disorder (ASD) and other psychiatric disorders. Cntn4-deficient mouse models have previously shown that CNTN4 plays important roles in axon guidance and synaptic plasticity in the hippocampus. However, the pathogenesis and functional role of CNTN4 in the cortex has not yet been investigated. Our study found a reduction in cortical thickness in the motor cortex of Cntn4 -/- mice, but cortical cell migration and differentiation were unaffected. Significant morphological changes were observed in neurons in the M1 region of the motor cortex, indicating that CNTN4 is also involved in the morphology and spine density of neurons in the motor cortex. Furthermore, mass spectrometry analysis identified an interaction partner for CNTN4, confirming an interaction between CNTN4 and amyloid-precursor protein (APP). Knockout human cells for CNTN4 and/or APP revealed a relationship between CNTN4 and APP. This study demonstrates that CNTN4 contributes to cortical development and that binding and interplay with APP controls neural elongation. This is an important finding for understanding the physiological function of APP, a key protein for Alzheimer's disease. The binding between CNTN4 and APP, which is involved in neurodevelopment, is essential for healthy nerve outgrowth.
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Affiliation(s)
- Rosemary A Bamford
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
| | - Amila Zuko
- Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University , Nijmegen, The Netherlands
| | - Madeline Eve
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
| | - Jan J Sprengers
- Department of Translational Neuroscience, UMC Utrecht Brain Center, UMC Utrecht , Utrecht 3508 AB, The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht, Institute for Pharmaceutical Sciences, Utrecht University , Utrecht, The Netherlands
- Netherlands Proteomics Centre , Utrecht, The Netherlands
| | - Renske L R E Taggenbrock
- Department of Translational Neuroscience, UMC Utrecht Brain Center, UMC Utrecht , Utrecht 3508 AB, The Netherlands
| | - Dominique Fäβler
- Institute for Pharmacy and Molecular Biotechnology (IPMB), Functional Genomics, University of Heidelberg , Heidelberg 69120, Germany
| | - Annika Mehr
- Institute for Pharmacy and Molecular Biotechnology (IPMB), Functional Genomics, University of Heidelberg , Heidelberg 69120, Germany
| | - Owen J R Jones
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
| | - Aurimas Kudzinskas
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
| | - Josan Gandawijaya
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
| | - Ulrike C Müller
- Institute for Pharmacy and Molecular Biotechnology (IPMB), Functional Genomics, University of Heidelberg , Heidelberg 69120, Germany
| | - Martien J H Kas
- Department of Translational Neuroscience, UMC Utrecht Brain Center, UMC Utrecht , Utrecht 3508 AB, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen , Groningen, The Netherlands
| | - J Peter H Burbach
- Department of Translational Neuroscience, UMC Utrecht Brain Center, UMC Utrecht , Utrecht 3508 AB, The Netherlands
| | - Asami Oguro-Ando
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, Tokyo University of Science , Noda, Chiba, Japan
- Research Institute for Science and Technology, Tokyo University of Science , Tokyo, Japan
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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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Cavirani B, Spagnoli C, Caraffi SG, Cavalli A, Cesaroni CA, Cutillo G, De Giorgis V, Frattini D, Marchetti GB, Masnada S, Peron A, Rizzi S, Varesio C, Spaccini L, Vignoli A, Canevini MP, Veggiotti P, Garavelli L, Fusco C. Genetic Epilepsies and Developmental Epileptic Encephalopathies with Early Onset: A Multicenter Study. Int J Mol Sci 2024; 25:1248. [PMID: 38279250 PMCID: PMC10816990 DOI: 10.3390/ijms25021248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
The genetic causes of epilepsies and developmental and epileptic encephalopathies (DEE) with onset in early childhood are increasingly recognized. Their outcomes vary from benign to severe disability. In this paper, we wished to retrospectively review the clinical, genetic, EEG, neuroimaging, and outcome data of patients experiencing the onset of epilepsy in the first three years of life, diagnosed and followed up in four Italian epilepsy centres (Epilepsy Centre of San Paolo University Hospital in Milan, Child Neurology and Psychiatry Unit of AUSL-IRCCS di Reggio Emilia, Pediatric Neurology Unit of Vittore Buzzi Children's Hospital, Milan, and Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, Pavia). We included 168 patients (104 with monogenic conditions, 45 with copy number variations (CNVs) or chromosomal abnormalities, and 19 with variants of unknown significance), who had been followed up for a mean of 14.75 years. We found a high occurrence of generalized seizures at onset, drug resistance, abnormal neurological examination, global developmental delay and intellectual disability, and behavioural and psychiatric comorbidities. We also documented differing presentations between monogenic issues versus CNVs and chromosomal conditions, as well as atypical/rare phenotypes. Genetic early-childhood-onset epilepsies and DEE show a very wide phenotypic and genotypic spectrum, with a high risk of complex neurological and neuropsychiatric phenotypes.
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Affiliation(s)
- Benedetta Cavirani
- Child Neuropsychiatry Unit, Azienda USL di Parma, 43121 Parma, Italy;
- Child Neurology and Psychiatry Unit, Department of Pediatrics, Presidio Ospedaliero Santa Maria Nuova, AUSL-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (A.C.); (C.A.C.); (D.F.); (S.R.); (C.F.)
| | - Carlotta Spagnoli
- Child Neurology and Psychiatry Unit, Department of Pediatrics, Presidio Ospedaliero Santa Maria Nuova, AUSL-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (A.C.); (C.A.C.); (D.F.); (S.R.); (C.F.)
| | - Stefano Giuseppe Caraffi
- Medical Genetics Unit, Presidio Ospedaliero Santa Maria Nuova, AUSL-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy (L.G.)
| | - Anna Cavalli
- Child Neurology and Psychiatry Unit, Department of Pediatrics, Presidio Ospedaliero Santa Maria Nuova, AUSL-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (A.C.); (C.A.C.); (D.F.); (S.R.); (C.F.)
| | - Carlo Alberto Cesaroni
- Child Neurology and Psychiatry Unit, Department of Pediatrics, Presidio Ospedaliero Santa Maria Nuova, AUSL-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (A.C.); (C.A.C.); (D.F.); (S.R.); (C.F.)
| | - Gianni Cutillo
- Pediatric Neurology Unit, Department of Pediatric Neurology, Buzzi Children’s Hospital, 20154 Milan, Italy; (G.C.); (S.M.); (P.V.)
| | - Valentina De Giorgis
- Department of Brain and Behavioural Sciences, University of Pavia, 27100 Pavia, Italy; (V.D.G.); (C.V.)
- Department of Child Neurology and Psychiatriy, IRCCS Mondino Foundation, ERN-Epicare, 27100 Pavia, Italy
| | - Daniele Frattini
- Child Neurology and Psychiatry Unit, Department of Pediatrics, Presidio Ospedaliero Santa Maria Nuova, AUSL-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (A.C.); (C.A.C.); (D.F.); (S.R.); (C.F.)
| | - Giulia Bruna Marchetti
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Silvia Masnada
- Pediatric Neurology Unit, Department of Pediatric Neurology, Buzzi Children’s Hospital, 20154 Milan, Italy; (G.C.); (S.M.); (P.V.)
| | - Angela Peron
- Medical Genetics, Meyer Children’s Hospital IRCCS, 50139 Florence, Italy;
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, Università degli Studi di Firenze, 50121 Florence, Italy
- Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, 20142 Milan, Italy
| | - Susanna Rizzi
- Child Neurology and Psychiatry Unit, Department of Pediatrics, Presidio Ospedaliero Santa Maria Nuova, AUSL-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (A.C.); (C.A.C.); (D.F.); (S.R.); (C.F.)
| | - Costanza Varesio
- Department of Brain and Behavioural Sciences, University of Pavia, 27100 Pavia, Italy; (V.D.G.); (C.V.)
- Department of Child Neurology and Psychiatriy, IRCCS Mondino Foundation, ERN-Epicare, 27100 Pavia, Italy
| | - Luigina Spaccini
- Clinical Genetics Unit, Department of Obstetrics and Gynecology, V. Buzzi Children’s Hospital, University of Milan, 20157 Milan, Italy;
| | - Aglaia Vignoli
- Child Neuropsychiatry Unit-Epilepsy Center, ASST Santi Paolo e Carlo, San Paolo Hospital, 20142 Milan, Italy; (A.V.); (M.P.C.)
- Department of Health Sciences, University of Milan, 20157 Milan, Italy
| | - Maria Paola Canevini
- Child Neuropsychiatry Unit-Epilepsy Center, ASST Santi Paolo e Carlo, San Paolo Hospital, 20142 Milan, Italy; (A.V.); (M.P.C.)
- Department of Health Sciences, University of Milan, 20157 Milan, Italy
| | - Pierangelo Veggiotti
- Pediatric Neurology Unit, Department of Pediatric Neurology, Buzzi Children’s Hospital, 20154 Milan, Italy; (G.C.); (S.M.); (P.V.)
- Department of Biomedical and Clinical Sciences, University of Milan, 20157 Milan, Italy
| | - Livia Garavelli
- Medical Genetics Unit, Presidio Ospedaliero Santa Maria Nuova, AUSL-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy (L.G.)
| | - Carlo Fusco
- Child Neurology and Psychiatry Unit, Department of Pediatrics, Presidio Ospedaliero Santa Maria Nuova, AUSL-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (A.C.); (C.A.C.); (D.F.); (S.R.); (C.F.)
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Whitford V, Byers N, O'Driscoll GA, Titone D. Eye movements and the perceptual span in disordered reading: A comparison of schizophrenia and dyslexia. Schizophr Res Cogn 2023; 34:100289. [PMID: 37435364 PMCID: PMC10331593 DOI: 10.1016/j.scog.2023.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/13/2023]
Abstract
Increasing evidence of a common neurodevelopmental etiology between schizophrenia and developmental dyslexia suggests that neurocognitive functions, such as reading, may be similarly disrupted. However, direct comparisons of reading performance in these disorders have yet to be conducted. To address this gap in the literature, we employed a gaze-contingent moving window paradigm to examine sentence-level reading fluency and perceptual span (breadth of parafoveal processing) in adults with schizophrenia (dataset from Whitford et al., 2013) and psychiatrically healthy adults with dyslexia (newly collected dataset). We found that the schizophrenia and dyslexia groups exhibited similar reductions in sentence-level reading fluency (e.g., slower reading rates, more regressions) compared to matched controls. Similar reductions were also found for standardized language/reading and executive functioning measures. However, despite these reductions, the dyslexia group exhibited a larger perceptual span (greater parafoveal processing) than the schizophrenia group, potentially reflecting a disruption in normal foveal-parafoveal processing dynamics. Taken together, our findings suggest that reading and reading-related functions are largely similarly disrupted in schizophrenia and dyslexia, providing additional support for a common neurodevelopmental etiology.
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Affiliation(s)
- Veronica Whitford
- Department of Psychology, University of New Brunswick, 38 Dineen Drive, Fredericton, New Brunswick, E3B 5A3, Canada
| | - Narissa Byers
- Department of Psychology, University of New Brunswick, 38 Dineen Drive, Fredericton, New Brunswick, E3B 5A3, Canada
| | - Gillian A. O'Driscoll
- Department of Psychology, McGill University, 2001 Avenue McGill College, Montréal, Québec, H3A 1G1, Canada
- Department of Psychiatry, McGill University, 1003 Avenue des Pins Ouest, Montréal, Québec, H3A 1A1, Canada
- Douglas Mental Health University Institute, 6875 Boulevard LaSalle, Verdun, Québec, H4H 1R3, Canada
- Montreal Neurological Institute and Hospital, 3801 Rue University, Montréal, Québec, H3A 2B4, Canada
- Department of Neurology & Neurosurgery, McGill University, 1003 Avenue des Pins Ouest, Montréal, Québec, H3A 1A1, Canada
| | - Debra Titone
- Department of Psychology, McGill University, 2001 Avenue McGill College, Montréal, Québec, H3A 1G1, Canada
- Centre for Research on Brain, Language and Music, 3640 Rue de la Montagne, Montréal, Québec, H3G 2A8, Canada
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Farrell M, Dietterich TE, Harner MK, Bruno LM, Filmyer DM, Shaughnessy RA, Lichtenstein ML, Britt AM, Biondi TF, Crowley JJ, Lázaro-Muñoz G, Forsingdal AE, Nielsen J, Didriksen M, Berg JS, Wen J, Szatkiewicz J, Mary Xavier R, Sullivan PF, Josiassen RC. Increased Prevalence of Rare Copy Number Variants in Treatment-Resistant Psychosis. Schizophr Bull 2023; 49:881-892. [PMID: 36454006 PMCID: PMC10318882 DOI: 10.1093/schbul/sbac175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
BACKGROUND It remains unknown why ~30% of patients with psychotic disorders fail to respond to treatment. Previous genomic investigations of treatment-resistant psychosis have been inconclusive, but some evidence suggests a possible link between rare disease-associated copy number variants (CNVs) and worse clinical outcomes in schizophrenia. Here, we identified schizophrenia-associated CNVs in patients with treatment-resistant psychotic symptoms and then compared the prevalence of these CNVs to previously published schizophrenia cases not selected for treatment resistance. METHODS CNVs were identified using chromosomal microarray (CMA) and whole exome sequencing (WES) in 509 patients with treatment-resistant psychosis (a lack of clinical response to ≥3 adequate antipsychotic medication trials over at least 5 years of psychiatric hospitalization). Prevalence of schizophrenia-associated CNVs in this sample was compared to that in a previously published large schizophrenia cohort study. RESULTS Integrating CMA and WES data, we identified 47 cases (9.2%) with at least one CNV of known or possible neuropsychiatric risk. 4.7% (n = 24) carried a known neurodevelopmental risk CNV. The prevalence of well-replicated schizophrenia-associated CNVs was 4.1%, with duplications of the 16p11.2 and 15q11.2-q13.1 regions, and deletions of the 22q11.2 chromosomal region as the most frequent CNVs. Pairwise loci-based analysis identified duplications of 15q11.2-q13.1 to be independently associated with treatment resistance. CONCLUSIONS These findings suggest that CNVs may uniquely impact clinical phenotypes beyond increasing risk for schizophrenia and may potentially serve as biological entry points for studying treatment resistance. Further investigation will be necessary to elucidate the spectrum of phenotypic characteristics observed in adult psychiatric patients with disease-associated CNVs.
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Affiliation(s)
- Martilias Farrell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Lisa M Bruno
- Translational Neuroscience, LLC, Conshohocken, PA, USA
| | | | | | | | - Allison M Britt
- School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tamara F Biondi
- Office of the Vice Chancellor for Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - James J Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel Lázaro-Muñoz
- Center for Bioethics, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | | | - Jacob Nielsen
- Division of Neuroscience, H. Lundbeck A/S, Valby, Denmark
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rose Mary Xavier
- School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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7
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Martin Lorenzo S, Muniz Moreno MDM, Atas H, Pellen M, Nalesso V, Raffelsberger W, Prevost G, Lindner L, Birling MC, Menoret S, Tesson L, Negroni L, Concordet JP, Anegon I, Herault Y. Changes in social behavior with MAPK2 and KCTD13/CUL3 pathways alterations in two new outbred rat models for the 16p11.2 syndromes with autism spectrum disorders. Front Neurosci 2023; 17:1148683. [PMID: 37465586 PMCID: PMC10350633 DOI: 10.3389/fnins.2023.1148683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/02/2023] [Indexed: 07/20/2023] Open
Abstract
Copy number variations (CNVs) of the human 16p11.2 locus are associated with several developmental/neurocognitive syndromes. Particularly, deletion and duplication of this genetic interval are found in patients with autism spectrum disorders, intellectual disability and other psychiatric traits. The high gene density associated with the region and the strong phenotypic variability of incomplete penetrance, make the study of the 16p11.2 syndromes extremely complex. To systematically study the effect of 16p11.2 CNVs and identify candidate genes and molecular mechanisms involved in the pathophysiology, mouse models were generated previously and showed learning and memory, and to some extent social deficits. To go further in understanding the social deficits caused by 16p11.2 syndromes, we engineered deletion and duplication of the homologous region to the human 16p11.2 genetic interval in two rat outbred strains, Sprague Dawley (SD) and Long Evans (LE). The 16p11.2 rat models displayed convergent defects in social behavior and in the novel object test in male carriers from both genetic backgrounds. Interestingly major pathways affecting MAPK1 and CUL3 were found altered in the rat 16p11.2 models with additional changes in males compared to females. Altogether, the consequences of the 16p11.2 genetic region dosage on social behavior are now found in three different species: humans, mice and rats. In addition, the rat models pointed to sexual dimorphism with lower severity of phenotypes in rat females compared to male mutants. This phenomenon is also observed in humans. We are convinced that the two rat models will be key to further investigating social behavior and understanding the brain mechanisms and specific brain regions that are key to controlling social behavior.
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Affiliation(s)
- Sandra Martin Lorenzo
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Maria Del Mar Muniz Moreno
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Helin Atas
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Marion Pellen
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Valérie Nalesso
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Wolfgang Raffelsberger
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Geraldine Prevost
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA-PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Loic Lindner
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA-PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Marie-Christine Birling
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA-PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Séverine Menoret
- Nantes Université, CHU Nantes, INSERM, CNRS, SFR Santé, Inserm UMS 016 CNRS UMS 3556, Nantes, France
- INSERM, Centre de Recherche en Transplantation et Immunologie UMR1064, Nantes Université, Nantes, France
| | - Laurent Tesson
- INSERM, Centre de Recherche en Transplantation et Immunologie UMR1064, Nantes Université, Nantes, France
| | - Luc Negroni
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | | | - Ignacio Anegon
- INSERM, Centre de Recherche en Transplantation et Immunologie UMR1064, Nantes Université, Nantes, France
| | - Yann Herault
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA-PHENOMIN, Institut Clinique de la Souris, Illkirch, France
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8
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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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9
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Liu N, Li H, Li M, Gao Y, Yan H. Prenatally diagnosed 16p11.2 copy number variations by SNP Array: A retrospective case series. Clin Chim Acta 2023; 538:15-21. [PMID: 36374846 DOI: 10.1016/j.cca.2022.10.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVE The 16p11.2 copy number variations (CNVs) are increasingly recognized as one of the most frequent genomic disorders, with a broad spectrum of phenotypes. The fetal phenotype associated with 16p11.2 CNVs is poorly described. The current study presents prenatal series of 16p11.2 CNVs and provides a better understanding of this submicroscopic imbalance in prenatal diagnosis. METHOD Retrospective case series were extracted from a single tertiary referral center performing prenatal single nucleotide polymorphism (SNP) array from April 2017 to December 2021. The maternal demographics, indication for amniocentesis, ultrasound findings, SNP array results, inheritance of the CNVs, and pregnancy outcomes were studied. RESULTS We indentified 30 fetuses carrying 16p11.2 CNVs, representing 0.35% (30/8578) of prenatal SNP array results. The series included 17 fetuses with a proximal deletion, 7 with a distal deletion, 4 with a proximal duplication, and 2 with a distal duplication. Prenatal ultrasound anomalies were reported in 80% of these cases. The most common presentation was vertebralanomalies (9/30). Other features noted in more than one fetus were increased nuchal translucency/nuchal fold (NT/NF) (5/30), absent/hypoplastic nasal bone (3/30), polyhydramnios (3/30), ventricular septal defect (VSD) (2/30), unilateral mild ventriculomegaly (2/30), fetal growth restriction (FGR) (2/30), right aortic arch (2/30). All the 9 vertebralanomalies were present in fetuses harboring proximal deletion (9/17). Familial transmission was confirmed in 44% of cases (11/25) and termination of pregnancy was requested in 62.1% (18/29) of cases. CONCLUSION The 16p11.2 CNVs can have variable prenatal phenotypes and these CNVs are frequently inherited from parents with a milder or normal phenotype. Our results underline that vertebral deformities were frequent in cases of 16p11.2 proximal deletion, and further demonstrate the incomplete penetrance of the CNVs.
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Affiliation(s)
- Nian Liu
- Department of Health Toxicology, MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Prenatal Diagnostic Center, Genetic Lab, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Li
- Prenatal Diagnostic Center, Genetic Lab, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Manman Li
- Prenatal Diagnostic Center, Genetic Lab, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanduo Gao
- Department of Ultrasound, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Yan
- Department of Health Toxicology, MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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10
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Kang H, Wang L, Li X, Gao C, Xie Y, Hu Y. Application of chromosome microarray analysis and karyotyping in diagnostic assessment of abnormal Down syndrome screening results. BMC Pregnancy Childbirth 2022; 22:813. [PMID: 36333674 PMCID: PMC9635180 DOI: 10.1186/s12884-022-05139-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Background Down syndrome (DS) is the most common congenital cause of intellectual disability and also leads to numerous metabolic and structural problems. This study aims to explore the application value of chromosomal microarray analysis (CMA) and karyotyping in prenatal diagnosis for pregnant women with abnormal DS screening results. Methods The study recruited 1452 pregnant women with abnormal DS screening results including 493 with an enlarged nuchal translucency thickness (NT ≥ 2.5 mm) and 959 with an abnormal second-trimester maternal serum biomarker screening results. They underwent amniocentesis to obtain amniotic fluid for CMA and karyotyping. Results CMA identified 74/1452 abnormal results, which was more efficient than karyotyping (51/1452, P < 0.05.) CMA is equivalent to traditional karyotyping for identifying aneuploidies. Compared to karyotyping CMA identified 1.90% more copy number variants (CNVs) ranging from 159Kb to 6496Kb. However, 34.4% of them were recurrent pathogenic CNVs associated with risk of neurodevelopmental disorders. CMA identified 13 variants of uncertain significance (VUS) results and 1 maternal uniparental disomy (UPD) of chromosome 7. Karyotyping identified 3 mosaic sex chromosome aneuploidy and 4 balanced translocation which could not be identified by CMA. In enlarged NT group, karyotyping identified 80.9% abnormal results while in serum screening group karyotyping identified 35.7%. However, the incidence of pathogenic/likely pathogenic (P/LP) CNVs was nearly the same in both groups. That was because aneuploidies and gross duplication/deletion were previously screened out by NT scan. Conclusions CMA and karyotyping have both advantages and disadvantages in prenatal diagnosis of pregnant women with abnormal DS screening results. However, there was not enough evidence to support routine CMA in pregnant women with abnormal DS screening results.
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Mapping the genetic architecture of cortical morphology through neuroimaging: progress and perspectives. Transl Psychiatry 2022; 12:447. [PMID: 36241627 PMCID: PMC9568576 DOI: 10.1038/s41398-022-02193-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/06/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
Cortical morphology is a key determinant of cognitive ability and mental health. Its development is a highly intricate process spanning decades, involving the coordinated, localized expression of thousands of genes. We are now beginning to unravel the genetic architecture of cortical morphology, thanks to the recent availability of large-scale neuroimaging and genomic data and the development of powerful biostatistical tools. Here, we review the progress made in this field, providing an overview of the lessons learned from genetic studies of cortical volume, thickness, surface area, and folding as captured by neuroimaging. It is now clear that morphology is shaped by thousands of genetic variants, with effects that are region- and time-dependent, thereby challenging conventional study approaches. The most recent genome-wide association studies have started discovering common genetic variants influencing cortical thickness and surface area, yet together these explain only a fraction of the high heritability of these measures. Further, the impact of rare variants and non-additive effects remains elusive. There are indications that the quickly increasing availability of data from whole-genome sequencing and large, deeply phenotyped population cohorts across the lifespan will enable us to uncover much of the missing heritability in the upcoming years. Novel approaches leveraging shared information across measures will accelerate this process by providing substantial increases in statistical power, together with more accurate mapping of genetic relationships. Important challenges remain, including better representation of understudied demographic groups, integration of other 'omics data, and mapping of effects from gene to brain to behavior across the lifespan.
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12
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Drackley A, Brew C, Wlodaver A, Spencer S, Leuer K, Rathbun P, Charrow J, Wieneke X, Lee Yap K, Ing A. Utility and Outcomes of the 2019 American College of Medical Genetics and Genomics-Clinical Genome Resource Guidelines for Interpretation of Copy Number Variants with Borderline Classifications at an Academic Clinical Diagnostic Laboratory. J Mol Diagn 2022; 24:1100-1111. [PMID: 35868509 DOI: 10.1016/j.jmoldx.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/06/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022] Open
Abstract
In 2019, American College of Medical Genetics and Genomics and the Clinical Genome Resource published updated technical standards for the interpretation and reporting of copy number variants (CNVs), introducing a semiquantitative classification system that aims to foster greater standardization and consistency between laboratories. Evaluation of these guidelines' performance will inform laboratories about the impact of their implementation into clinical practice. A total of 145 difficult-to-classify CNVs, originally assessed by an academic molecular diagnostic laboratory, were re-interpreted/classified according to the American College of Medical Genetics and Genomics-Clinical Genome Resource guidelines. Classifications between interpretation systems were then compared. The concordance rate was 60.7%, and significantly more variants of uncertain significance were obtained when using the guidelines (n = 98) versus the laboratory's classification system (n = 49; P < 0.001). The concordance rate was presumably impacted by the intentionally unclear nature of the selected variants. The difference in variant of uncertain significance rate was largely due to laboratory-specific practices for variant interpretation and reporting, as well as differences in utilization of general population data. Laboratory-specific policies and practices may need to be addressed for true standardization to be achieved. Challenges to consistent guideline utilization are centered around the general lack of high-quality curated data available for CNV interpretations and the inherent subjectivity in the selection of evidence criteria and application of evidence points. Multiple aspects of the guidelines were highlighted as potential opportunities for subsequent refinements to further improve classification standardization.
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Affiliation(s)
- Andy Drackley
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Casey Brew
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alissa Wlodaver
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Sara Spencer
- Department of Obstetrics and Gynecology, Northwestern Medicine, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Katrin Leuer
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Pamela Rathbun
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Joel Charrow
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Xuwen Wieneke
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Kai Lee Yap
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Alexander Ing
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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13
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Wen X, Xing H, Qi K, Wang H, Li X, Zhu J, Chen W, Cui L, Zhang J, Qi H. Analysis of 17 Prenatal Cases with the Chromosomal 1q21.1 Copy Number Variation. DISEASE MARKERS 2022; 2022:5487452. [PMID: 37284664 PMCID: PMC10241571 DOI: 10.1155/2022/5487452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/12/2022] [Indexed: 10/10/2023]
Abstract
Copy number variations (CNVs) at the chromosomal 1q21.1 region represent a group of hot-spot recurrent rearrangements in human genome, which have been detected in hundreds of patients with variable clinical manifestations. Yet, report of such CNVs in prenatal scenario was relatively scattered. In this study, 17 prenatal cases involving the 1q21.1 microdeletion or duplication were recruited. The clinical survey and imaging examination were performed; and genetic detection with karyotyping and CNV analysis using chromosomal microarray (CMA) or CNVseq were subsequently carried out. These cases were all positive with 1q21.1 CNV, yet presented with exceedingly various clinical and utrasonographic indications. Among them, 12 pregnancies carried 1q21.1 deletions, while the other 5 carried 1q21.1 duplications, all of which were within the previously defined breaking point (BP) regions. According to the verification results, 9 CNVs were de novo, 7 were familial, and the other 1 was not certain. We summarized the clinical information of these cases, and the size and distribution of CNVs, and attempted to analyze the association between these two aspects. The findings in our study may provide important basis for the prenatal diagnosis and genetic counseling on such conditions in the future.
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Affiliation(s)
- Xiaohui Wen
- Prenatal Diagnosis Center, Haidian Maternal and Child Health Care Hospital, Beijing, China
| | - Huanxia Xing
- Prenatal Diagnosis Center, Langfang Maternal and Child Health Care Hospital, Langfang, Hebei, China
| | - Keyan Qi
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Hao Wang
- Prenatal Diagnosis Center, Hangzhou Women's Hospital, Hangzhou, Zhejiang, China
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaojun Li
- Prenatal Diagnosis Center, Haidian Maternal and Child Health Care Hospital, Beijing, China
| | - Jianjiang Zhu
- Prenatal Diagnosis Center, Haidian Maternal and Child Health Care Hospital, Beijing, China
| | - Wenqi Chen
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, Hebei, China
| | - Limin Cui
- Prenatal Diagnosis Center, Langfang Maternal and Child Health Care Hospital, Langfang, Hebei, China
| | - Jing Zhang
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, Hebei, China
| | - Hong Qi
- Prenatal Diagnosis Center, Haidian Maternal and Child Health Care Hospital, Beijing, China
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14
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Cunningham AC, Hall J, Einfeld S, Owen MJ, van den Bree MBM. Assessment of emotions and behaviour by the Developmental Behaviour Checklist in young people with neurodevelopmental CNVs. Psychol Med 2022; 52:574-586. [PMID: 32643597 PMCID: PMC7794095 DOI: 10.1017/s0033291720002330] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/19/2020] [Accepted: 06/08/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND A number of genomic conditions caused by copy number variants (CNVs) are associated with a high risk of neurodevelopmental and psychiatric disorders (ND-CNVs). Although these patients also tend to have cognitive impairments, few studies have investigated the range of emotion and behaviour problems in young people with ND-CNVs using measures that are suitable for those with learning difficulties. METHODS A total of 322 young people with 13 ND-CNVs across eight loci (mean age: 9.79 years, range: 6.02-17.91, 66.5% male) took part in the study. Primary carers completed the Developmental Behaviour Checklist (DBC). RESULTS Of the total, 69% of individuals with an ND-CNV screened positive for clinically significant difficulties. Young people from families with higher incomes (OR = 0.71, CI = 0.55-0.91, p = .008) were less likely to screen positive. The rate of difficulties differed depending on ND-CNV genotype (χ2 = 39.99, p < 0.001), with the lowest rate in young people with 22q11.2 deletion (45.7%) and the highest in those with 1q21.1 deletion (93.8%). Specific patterns of strengths and weaknesses were found for different ND-CNV genotypes. However, ND-CNV genotype explained no more than 9-16% of the variance, depending on DBC subdomain. CONCLUSIONS Emotion and behaviour problems are common in young people with ND-CNVs. The ND-CNV specific patterns we find can provide a basis for more tailored support. More research is needed to better understand the variation in emotion and behaviour problems not accounted for by genotype.
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Affiliation(s)
- Adam C. Cunningham
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, UK
| | - Jeremy Hall
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, UK
| | - Stewart Einfeld
- Faculty of Health Sciences, University of Sydney, Sydney, Australia
| | - Michael J. Owen
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, UK
| | | | - Marianne B. M. van den Bree
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, UK
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15
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Using induced pluripotent stem cells to investigate human neuronal phenotypes in 1q21.1 deletion and duplication syndrome. Mol Psychiatry 2022; 27:819-830. [PMID: 34112971 PMCID: PMC9054650 DOI: 10.1038/s41380-021-01182-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/17/2021] [Accepted: 05/27/2021] [Indexed: 01/08/2023]
Abstract
Copy Number Variation (CNV) at the 1q21.1 locus is associated with a range of neurodevelopmental and psychiatric disorders in humans, including abnormalities in head size and motor deficits. Yet, the functional consequences of these CNVs (both deletion and duplication) on neuronal development remain unknown. To determine the impact of CNV at the 1q21.1 locus on neuronal development, we generated induced pluripotent stem cells from individuals harbouring 1q21.1 deletion or duplication and differentiated them into functional cortical neurons. We show that neurons with 1q21.1 deletion or duplication display reciprocal phenotype with respect to proliferation, differentiation potential, neuronal maturation, synaptic density and functional activity. Deletion of the 1q21.1 locus was also associated with an increased expression of lower cortical layer markers. This difference was conserved in the mouse model of 1q21.1 deletion, which displayed altered corticogenesis. Importantly, we show that neurons with 1q21.1 deletion and duplication are associated with differential expression of calcium channels and demonstrate that physiological deficits in neurons with 1q21.1 deletion or duplication can be pharmacologically modulated by targeting Ca2+ channel activity. These findings provide biological insight into the neuropathological mechanism underlying 1q21.1 associated brain disorder and indicate a potential target for therapeutic interventions.
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16
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Milone R, Tancredi R, Cosenza A, Ferrari AR, Scalise R, Cioni G, Battini R. 17q12 Recurrent Deletions and Duplications: Description of a Case Series with Neuropsychiatric Phenotype. Genes (Basel) 2021; 12:genes12111660. [PMID: 34828266 PMCID: PMC8620923 DOI: 10.3390/genes12111660] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/22/2022] Open
Abstract
Syndromic neurodevelopmental disorders are usually investigated through genetics technologies, within which array comparative genomic hybridization (Array-CGH) is still considered the first-tier clinical diagnostic test. Among recurrent syndromic imbalances, 17q12 deletions and duplications are characterized by neurodevelopmental disorders associated with visceral developmental disorders, although expressive variability is common. Here we describe a case series of 12 patients with 17q12 chromosomal imbalances, in order to expand the phenotypic characterization of these recurrent syndromes whose diagnosis is often underestimated, especially if only mild traits are present. Gene content and genotype-phenotype correlations have been discussed, with special regard to neuropsychiatric features, whose impact often requires etiologic analysis.
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Affiliation(s)
- Roberta Milone
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy; (R.M.); (R.T.); (A.C.); (A.R.F.); (R.S.); (G.C.)
| | - Raffaella Tancredi
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy; (R.M.); (R.T.); (A.C.); (A.R.F.); (R.S.); (G.C.)
| | - Angela Cosenza
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy; (R.M.); (R.T.); (A.C.); (A.R.F.); (R.S.); (G.C.)
| | - Anna Rita Ferrari
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy; (R.M.); (R.T.); (A.C.); (A.R.F.); (R.S.); (G.C.)
| | - Roberta Scalise
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy; (R.M.); (R.T.); (A.C.); (A.R.F.); (R.S.); (G.C.)
- Tuscan PhD Program of Neuroscience, University of Florence, Pisa and Siena, 50139 Florence, Italy
| | - Giovanni Cioni
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy; (R.M.); (R.T.); (A.C.); (A.R.F.); (R.S.); (G.C.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy; (R.M.); (R.T.); (A.C.); (A.R.F.); (R.S.); (G.C.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
- Correspondence:
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17
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Arnett AB, Wang T, Eichler EE, Bernier RA. Reflections on the genetics-first approach to advancements in molecular genetic and neurobiological research on neurodevelopmental disorders. J Neurodev Disord 2021; 13:24. [PMID: 34148555 PMCID: PMC8215789 DOI: 10.1186/s11689-021-09371-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and intellectual disability (ID), are common diagnoses with highly heterogeneous phenotypes and etiology. The genetics-first approach to research on NDDs has led to the identification of hundreds of genes conferring risk for ASD, ID, and related symptoms. MAIN BODY Although relatively few individuals with NDDs share likely gene-disruptive (LGD) mutations in the same gene, characterization of overlapping functions, protein networks, and temporospatial expression patterns among these genes has led to increased understanding of the neurobiological etiology of NDDs. This shift in focus away from single genes and toward broader gene-brain-behavior pathways has been accelerated by the development of publicly available transcriptomic databases, cell type-specific research methods, and sequencing of non-coding genomic regions. CONCLUSIONS The genetics-first approach to research on NDDs has advanced the identification of critical protein function pathways and temporospatial expression patterns, expanding the impact of this research beyond individuals with single-gene mutations to the broader population of patients with NDDs.
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Affiliation(s)
- Anne B Arnett
- Department of Psychiatry and Behavioral Sciences, University of Washington, CHDD, Box 357920, Seattle, WA, 98195, USA.
- Department of Psychiatry and Behavioral Medicine, Seattle Children's Hospital, Seattle, WA, USA.
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, CHDD, Box 357920, Seattle, WA, 98195, USA
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Mulle JG, Sullivan PF, Hjerling-Leffler J. Editorial overview: Rare CNV disorders and neuropsychiatric phenotypes: opportunities, challenges, solutions. Curr Opin Genet Dev 2021; 68:iii-ix. [PMID: 34059379 PMCID: PMC8722467 DOI: 10.1016/j.gde.2021.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Jennifer Gladys Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta GA 30322, United States.
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, United States; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Jens Hjerling-Leffler
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.
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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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The "missing heritability"-Problem in psychiatry: Is the interaction of genetics, epigenetics and transposable elements a potential solution? Neurosci Biobehav Rev 2021; 126:23-42. [PMID: 33757815 DOI: 10.1016/j.neubiorev.2021.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023]
Abstract
Psychiatric disorders exhibit an enormous burden on the health care systems worldwide accounting for around one-third of years lost due to disability among adults. Their etiology is largely unknown and diagnostic classification is based on symptomatology and course of illness and not on objective biomarkers. Most psychiatric disorders are moderately to highly heritable. However, it is still unknown what mechanisms may explain the discrepancy between heritability estimates and the present data from genetic analysis. In addition to genetic differences also epigenetic modifications are considered as potentially relevant in the transfer of susceptibility to psychiatric diseases. Though, whether or not epigenetic alterations can be inherited for many generations is highly controversial. In the present article, we will critically summarize both the genetic findings and the results from epigenetic analyses, including also those of noncoding RNAs. We will argue that one possible solution to the "missing heritability" problem in psychiatry is a potential role of retrotransposons, the exploration of which is presently only in its beginnings.
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21
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Cunningham AC, Hall J, Owen MJ, van den Bree MBM. Coordination difficulties, IQ and psychopathology in children with high-risk copy number variants. Psychol Med 2021; 51:290-299. [PMID: 31739810 PMCID: PMC7234895 DOI: 10.1017/s0033291719003210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND The prevalence and impact of motor coordination difficulties in children with copy number variants associated with neurodevelopmental disorders (ND-CNVs) remains unknown. This study aims to advance understanding of motor coordination difficulties in children with ND-CNVs and establish relationships between intelligence quotient (IQ) and psychopathology. METHODS 169 children with an ND-CNV (67% male, median age = 8.88 years, range 6.02-14.81) and 72 closest-in-age unaffected siblings (controls; 55% male, median age = 10.41 years, s.d. = 3.04, range 5.89-14.75) were assessed with the Developmental Coordination Disorder Questionnaire, alongside psychiatric interviews and standardised assessments of IQ. RESULTS The children with ND-CNVs had poorer coordination ability (b = 28.98, p < 0.001) and 91% of children with an ND-CNV screened positive for suspected developmental coordination disorder, compared to 19% of controls (OR = 42.53, p < 0.001). There was no difference in coordination ability between ND-CNV genotypes (F = 1.47, p = 0.184). Poorer coordination in children with ND-CNV was associated with more attention deficit hyperactivity disorder (ADHD) (β = -0.18, p = 0.021) and autism spectrum disorder trait (β = -0.46, p < 0.001) symptoms, along with lower full-scale (ß = 0.21, p = 0.011), performance (β = -0.20, p = 0.015) and verbal IQ (β = 0.17, p = 0.036). Mediation analysis indicated that coordination ability was a full mediator of anxiety symptoms (69% mediated, p = 0.012), and a partial mediator of ADHD (51%, p = 0.001) and autism spectrum disorder trait symptoms (66%, p < 0.001) as well as full scale IQ (40%, p = 0.002), performance IQ (40%, p = 0.005) and verbal IQ (38%, p = 0.006) scores. CONCLUSIONS The findings indicate that poor motor coordination is highly prevalent and closely linked to risk of mental health disorder and lower intellectual function in children with ND-CNVs. Future research should explore whether early interventions for poor coordination ability could ameliorate neurodevelopmental risk.
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Affiliation(s)
- Adam C. Cunningham
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Jeremy Hall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Michael J. Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Marianne B. M. van den Bree
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
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22
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Brain-Enriched Coding and Long Non-coding RNA Genes Are Overrepresented in Recurrent Neurodevelopmental Disorder CNVs. Cell Rep 2020; 33:108307. [PMID: 33113368 DOI: 10.1016/j.celrep.2020.108307] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/15/2020] [Accepted: 10/02/2020] [Indexed: 11/20/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition with substantial phenotypic and etiological heterogeneity. Although 10%-20% of ASD cases are attributable to copy number variation (CNV), causative genomic loci and constituent genes remain unclarified. We have developed SNATCNV, a tool that outperforms existing tools, to identify 47 recurrent ASD CNV regions from 19,663 cases and 6,479 controls documented in the AutDB database. Analysis of ASD CNV gene content using FANTOM5 shows that constituent coding genes and long non-coding RNAs have brain-enriched patterns of expression. Notably, such enrichment is not observed for regions identified by using other tools. We also find evidence of sexual dimorphism, one locus uniquely comprising a single lncRNA gene, and correlation of CNVs to distinct clinical and behavioral traits. Finally, we analyze a large dataset for schizophrenia to further demonstrate that SNATCNV is an effective, publicly available tool to define genomic loci and causative genes for multiple CNV-associated conditions.
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23
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Yokoyama E, Villarroel CE, Diaz S, Del Castillo V, Pérez-Vera P, Salas C, Gómez S, Barreda R, Molina B, Frias S. Non-classical 1p36 deletion in a patient with Duane retraction syndrome: case report and literature review. Mol Cytogenet 2020; 13:42. [PMID: 32939224 PMCID: PMC7487539 DOI: 10.1186/s13039-020-00510-5] [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: 05/30/2020] [Accepted: 08/19/2020] [Indexed: 11/13/2022] Open
Abstract
Background Monosomy of 1p36 is considered the most common terminal microdeletion syndrome. It is characterized by intellectual disability, growth retardation, seizures, congenital anomalies, and distinctive facial features that are absent when the deletion is proximal, beyond the 1p36.32 region. In patients with proximal deletions, little is known about the associated phenotype, since only a few cases have been reported in the literature. Ocular manifestations in patients with classical 1p36 monosomy are frequent and include strabismus, myopia, hypermetropia, and nystagmus. However, as of today only one patient with 1p36 deletion and Duane retraction syndrome (DRS) has been reported. Case presentation We describe a patient with intellectual disability, facial dysmorphism, and bilateral Duane retraction syndrome (DRS) type 1. Array CGH showed a 7.2 Mb de novo deletion from 1p36.31 to 1p36.21. Discussion Our patient displayed DRS, which is not part of the classical phenotype and is not a common clinical feature in 1p36 deletion syndrome; we hypothesized that this could be associated with the overlapping deletion between the distal and proximal 1p36 regions. DRS is one of the Congenital Cranial Dysinnervation Disorders, and a genetic basis for the syndrome has been extensively reported. The HES3 gene is located at 1p36.31 and could be associated with oculomotor alterations, including DRS, since this gene is involved in the development of the 3rd cranial nerve and the 6th cranial nerve’s nucleus. We propose that oculomotor anomalies, including DRS, could be related to proximal 1p36 deletion, warranting a detailed ophthalmologic evaluation of these patients.
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Affiliation(s)
- Emiy Yokoyama
- Departamento de Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Camilo E Villarroel
- Departamento de Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Sinhué Diaz
- Enlace Científico, Shire Pharmaceuticals México, Mexico City, Mexico
| | - Victoria Del Castillo
- Departamento de Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Patricia Pérez-Vera
- Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Consuelo Salas
- Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | | | - Reneé Barreda
- Departamento de Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Bertha Molina
- Laboratorio de Citogenética, Departamento de Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Sara Frias
- Laboratorio de Citogenética, Departamento de Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida IMAN No. 1, Torre de Investigación, Insurgentes Cuicuilco, Coyoacán, 04530 Mexico City, Mexico
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24
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Milone R, Cesario C, Goldoni M, Pasquariello R, Fusilli C, Giovannetti A, Giglio S, Novelli A, Caputo V, Cioni G, Mazza T, Battaglia A, Bernardini L, Battini R. Correlating Neuroimaging and CNVs Data: 7 Years of Cytogenomic Microarray Analysis on Patients Affected by Neurodevelopmental Disorders. J Pediatr Genet 2020; 10:292-299. [PMID: 34849274 DOI: 10.1055/s-0040-1716398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/27/2020] [Indexed: 11/08/2022]
Abstract
The aim of this study was to evaluate the relationship between neurodevelopmental disorders, brain anomalies, and copy number variations (CNVs) and to estimate the diagnostic potential of cytogenomical microarray analysis (CMA) in individuals neuroradiologically characterized with intellectual developmental disorders (IDDs) isolated or associated with autism spectrum disorders (ASDs) and epilepsy (EPI), all of which were identified as a "synaptopathies." We selected patients who received CMA and brain magnetic resonance imaging (MRI) over a 7-year period. We divided them into four subgroups: IDD, IDD + ASD, IDD + EPI, and IDD + ASD + EPI. The diagnostic threshold of CMA was 16%. The lowest detection rate for both CMA and brain anomalies was found in IDD + ASD, while MRI was significantly higher in IDD and IDD + EPI subgroups. CMA detection rate was significantly higher in patients with brain anomalies, so CMA may be even more appropriate in patients with pathological MRI, increasing the diagnostic value of the test. Conversely, positive CMA in IDD patients should require an MRI assessment, which is more often associated with brain anomalies. Posterior fossa anomalies, both isolated and associated with other brain anomalies, showed a significantly higher rate of CMA positive results and of pathogenic CNVs. In the next-generation sequencing era, our study confirms once again the relevant diagnostic output of CMA in patients with IDD, either isolated or associated with other comorbidities. Since more than half of the patients presented brain anomalies in this study, we propose that neuroimaging should be performed in such cases, particularly in the presence of genomic imbalances.
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Affiliation(s)
- Roberta Milone
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Claudia Cesario
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marina Goldoni
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Rosa Pasquariello
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Caterina Fusilli
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Agnese Giovannetti
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Sabrina Giglio
- Medical Genetics Unit, Meyer Children's University Hospital, Florence, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Giovanni Cioni
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Agatino Battaglia
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Laura Bernardini
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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25
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Leu C, Bautista JF, Sudarsanam M, Niestroj LM, Stefanski A, Ferguson L, Daly MJ, Jehi L, Najm IM, Busch RM, Lal D. Neurological disorder-associated genetic variants in individuals with psychogenic nonepileptic seizures. Sci Rep 2020; 10:15205. [PMID: 32938993 PMCID: PMC7495430 DOI: 10.1038/s41598-020-72101-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/24/2020] [Indexed: 12/19/2022] Open
Abstract
Psychogenic nonepileptic seizures (PNES) are diagnosed in approximately 30% of patients referred to tertiary care epilepsy centers. Little is known about the molecular pathology of PNES, much less about possible underlying genetic factors. We generated whole-exome sequencing and whole-genome genotyping data to identify rare, pathogenic (P) or likely pathogenic (LP) variants in 102 individuals with PNES and 448 individuals with focal (FE) or generalized (GE) epilepsy. Variants were classified for all individuals based on the ACMG-AMP 2015 guidelines. For research purposes only, we considered genes associated with neurological or psychiatric disorders as candidate genes for PNES. We observe in this first genetic investigation of PNES that six (5.88%) individuals with PNES without coexistent epilepsy carry P/LP variants (deletions at 10q11.22-q11.23, 10q23.1-q23.2, distal 16p11.2, and 17p13.3, and nonsynonymous variants in NSD1 and GABRA5). Notably, the burden of P/LP variants among the individuals with PNES was similar and not significantly different to the burden observed in the individuals with FE (3.05%) or GE (1.82%) (PNES vs. FE vs. GE (3 × 2 χ2), P = 0.30; PNES vs. epilepsy (2 × 2 χ2), P = 0.14). The presence of variants in genes associated with monogenic forms of neurological and psychiatric disorders in individuals with PNES shows that genetic factors are likely to play a role in PNES or its comorbidities in a subset of individuals. Future large-scale genetic research studies are needed to further corroborate these interesting findings in PNES.
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Affiliation(s)
- Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, 02142, USA.
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK.
| | - Jocelyn F Bautista
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Monica Sudarsanam
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Lisa-Marie Niestroj
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, DE, 50931, USA
| | - Arthur Stefanski
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Lisa Ferguson
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Psychiatry & Psychology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, 02142, USA
- Institute of Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Lara Jehi
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Imad M Najm
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Robyn M Busch
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Psychiatry & Psychology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, 02142, USA.
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, DE, 50931, USA.
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26
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Muys J, Jacquemyn Y, Blaumeiser B, Bourlard L, Brison N, Bulk S, Chiarappa P, De Leener A, De Rademaeker M, Désir J, Destrée A, Devriendt K, Dheedene A, Duquenne A, Fieuw A, Fransen E, Gatot J, Jamar M, Janssens S, Kerstjens J, Keymolen K, Lederer D, Menten B, Pichon B, Rombout S, Sznajer Y, Van Den Bogaert A, Van Den Bogaert K, Vermeesch J, Janssens K. Prenatally detected copy number variants in a national cohort: A postnatal follow‐up study. Prenat Diagn 2020; 40:1272-1283. [DOI: 10.1002/pd.5751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/13/2020] [Accepted: 05/16/2020] [Indexed: 01/17/2023]
Affiliation(s)
- Joke Muys
- Department of Gynaecology University Hospital Antwerp Edegem Belgium
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
| | - Yves Jacquemyn
- Department of Gynaecology University Hospital Antwerp Edegem Belgium
- ASTARC and Global Health Institute Universiteit Antwerpen Antwerpen Belgium
| | - Bettina Blaumeiser
- Department of Gynaecology University Hospital Antwerp Edegem Belgium
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
| | - Laura Bourlard
- Center for Medical Genetics Université Libre de Bruxelles Bruxelles Belgium
| | - Nathalie Brison
- Center for Medical Genetics Katholieke Universiteit Leuven Leuven Belgium
| | - Saskia Bulk
- Center for Medical Genetics Centre Hospitalier Universitaire de Liège Liege Belgium
| | - Patrizia Chiarappa
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | - Anne De Leener
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | | | - Julie Désir
- Center for Medical Genetics Université Libre de Bruxelles Bruxelles Belgium
| | - Anne Destrée
- Center for Medical Genetics Institut de Pathologie et de Génétique Gosselies Gosselies Belgium
| | - Koenraad Devriendt
- Center for Medical Genetics Katholieke Universiteit Leuven Leuven Belgium
| | | | - Armelle Duquenne
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | - Annelies Fieuw
- Center for Medical Genetics Vrije Universiteit Brussel Brussel Belgium
| | - Erik Fransen
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
| | - Jean‐Stéphane Gatot
- Center for Medical Genetics Centre Hospitalier Universitaire de Liège Liege Belgium
| | - Mauricette Jamar
- Center for Medical Genetics Centre Hospitalier Universitaire de Liège Liege Belgium
| | | | - Jorien Kerstjens
- Faculty for Medical Sciences Rijksuniversteit Groningen Groningen The Netherlands
| | | | - Damien Lederer
- Center for Medical Genetics Institut de Pathologie et de Génétique Gosselies Gosselies Belgium
| | - Björn Menten
- Center for Medical Genetics Universiteit Gent Gent Belgium
| | - Bruno Pichon
- Center for Medical Genetics Université Libre de Bruxelles Bruxelles Belgium
| | - Sonia Rombout
- Center for Medical Genetics Institut de Pathologie et de Génétique Gosselies Gosselies Belgium
| | - Yves Sznajer
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | | | | | - Joris Vermeesch
- Center for Medical Genetics Katholieke Universiteit Leuven Leuven Belgium
| | - Katrien Janssens
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
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27
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Expression alteration of microRNAs in Nucleus Accumbens is associated with chronic stress and antidepressant treatment in rats. BMC Med Inform Decis Mak 2019; 19:271. [PMID: 31856805 PMCID: PMC6921443 DOI: 10.1186/s12911-019-0964-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Nucleus Accumbens (NAc) is a vital brain region for the process of reward and stress, whereas microRNA plays a crucial role in depression pathology. However, the abnormality of NAc miRNA expression during the stress-induced depression and antidepressant treatment, as well as its biological significance, are still unknown. METHODS We performed the small RNA-sequencing in NAc of rats from three groups: control, chronic unpredictable mild stress (CUMS), and CUMS with an antidepressant, Escitalopram. We applied an integrative pipeline for analyzing the miRNA expression alternation in different model groups, including differential expression analysis, co-expression analysis, as well as a subsequent pathway/network analysis to discover both miRNA alteration pattern and its biological significance. RESULT A total of 423 miRNAs were included in analysis.18/8 differential expressing (DE) miRNA (adjusted p < 0.05, |log2FC| > 1) were observed in controls Vs. depression/depression Vs. treatment, 2 of which are overlapping. 78% (14/18) of these miRNAs showed opposite trends of alteration in stress and treatment. Two micro RNA, miR-10b-5p and miR-214-3p, appeared to be hubs in the regulation networks and also among the top findings in both differential analyses. Using co-expression analysis, we found a functional module that strongly correlated with stress (R = 0.96, P = 0.003), and another functional module with a moderate correlation with anhedonia (R = 0.89, P = 0.02). We also found that predicted targets of these miRNAs were significantly enriched in the Ras signaling pathway, which is associated with both depression, anhedonia, and antidepressant treatment. CONCLUSION Escitalopram treatment can significantly reverse NAc miRNA abnormality induced by chronic stress. However, the novel miRNA alteration that is absent in stress pathology also emerges, which means that antidepressant treatment is unlikely to bring miRNA expression back to the same level as the controls. Also, the Ras-signaling pathway may be involved in explaining the depression disease etiology, the clinical symptom, and treatment response of stress-induced depression.
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Lamont RE, Xi Y, Popko C, Lazier J, Bernier FP, Lauzon JL, Innes AM, Parboosingh JS, Thomas MA. Next-Generation Sequencing Using a Cardiac Gene Panel in Prenatally Diagnosed Cardiac Anomalies. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2019; 40:1417-1423. [PMID: 30473118 DOI: 10.1016/j.jogc.2018.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 02/01/2018] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Most prenatally identified congenital heart defects (CHDs) are the sole structural anomaly detected; however, there is a subgroup of cases where the specific genetic cause will impact prognosis, including chromosome abnormalities and single-gene causes. Next-generation sequencing of all the protein coding regions in the genome or targeted to genes involved in cardiac development is currently possible in the prenatal period, but there are minimal data on the clinical utility of such an approach. This study assessed the outcome of a CHD gene panel that included single-gene causes of syndromic and non-syndromic CHDs. METHOD Sixteen cases with a fetal CHD identified on prenatal ultrasound were studied using a 108 CHD gene panel. DNA was extracted from cultured amniocytes. RESULTS There was no diagnostic pathogenic variant identified in these cases. There was an average of 2.9 reportable variants identified per case and the majority of them were variants of uncertain significance. CONCLUSION Next-generation sequencing has the potential for increased genetic diagnosis for fetal anomalies. However, the large number of variants and the absence of an examinable patient make the interpretation of these variants challenging.
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Affiliation(s)
- Ryan E Lamont
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB; Alberta Children's Hospital Research Institute, Calgary, AB
| | - Yanwei Xi
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB
| | - Claire Popko
- Bachelor of Health Sciences Program, University of Calgary, Calgary, AB
| | - Joanna Lazier
- Department of Medical Genetics, University of Alberta, Edmonton, AB
| | - Francois P Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB; Alberta Children's Hospital Research Institute, Calgary, AB
| | - Julie L Lauzon
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB; Alberta Children's Hospital Research Institute, Calgary, AB
| | - Jillian S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB; Alberta Children's Hospital Research Institute, Calgary, AB
| | - Mary Ann Thomas
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB; Alberta Children's Hospital Research Institute, Calgary, AB.
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Malt EA, Juhasz K, Frengen A, Wangensteen T, Emilsen NM, Hansen B, Agafonov O, Nilsen HL. Neuropsychiatric phenotype in relation to gene variants in the hemizygous allele in 3q29 deletion carriers: A case series. Mol Genet Genomic Med 2019; 7:e889. [PMID: 31347308 PMCID: PMC6732294 DOI: 10.1002/mgg3.889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/19/2022] Open
Abstract
Background Genetic risk variants in the hemizygous allele may influence neuropsychiatric manifestations and clinical course in 3q29 deletion carriers. Methods In‐depth phenotypic assessment in two deletion carriers included medical records, medical, genetic, psychiatric and neuropsychological evaluations, brain MRI scan and EEG. Blood samples were analyzed for copy number variations, and deep sequencing of the affected 3q29 region was performed in patients and seven first‐degree relatives. Risk variants were identified through bioinformatic analysis. Results One deletion carrier was diagnosed with learning difficulties and childhood autism, the other with mild intellectual disability and schizophrenia. EEG abnormalities in childhood normalized in adulthood in both. Cognitive abilities improved during adolescence in one deletion carrier. Both had microcytic, hypochromic erythrocytes and suffered from chronic pain and fatigue. Molecular and bioinformatic analyses identified risk variants in the hemizygous allele that were not present in the homozygous state in relatives in genes involved in cilia function and insulin action in the autistic individual and in synaptic function and neurosteroid transport in the subject with schizophrenia. Conclusion 3q29 deletion carriers may undergo developmental phenotypic transition and need regular medical follow‐up. Identified risk variants in the remaining hemizygous allele should be explored further in autism and schizophrenia research.
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Affiliation(s)
- Eva Albertsen Malt
- Department of Adult Habilitation, Akershus University Hospital, Lorenskog, Norway.,Campus Ahus, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Katalin Juhasz
- Department of Adult Habilitation, Akershus University Hospital, Lorenskog, Norway
| | - Anna Frengen
- Campus Ahus, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Section for Clinical Molecular Biology, Akershus University Hospital, Lorenskog, Norway
| | | | - Nina Merete Emilsen
- Department of Adult Habilitation, Akershus University Hospital, Lorenskog, Norway
| | - Borre Hansen
- Department of Adult Habilitation, Akershus University Hospital, Lorenskog, Norway
| | - Oleg Agafonov
- Bioinformatics Core Facility, Department of Core Facilities, Institute of Cancer Research, Radium Hospital, Part of Oslo University Hospital, Oslo, Norway
| | - Hilde Loge Nilsen
- Campus Ahus, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Section for Clinical Molecular Biology, Akershus University Hospital, Lorenskog, Norway
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Martorell L, Sanfeliu A, Blázquez A, Lojo E, Cortés MJ, de Pablo J, Vilella E. Genetics and genetic counseling in psychiatry: Results from an opinion survey of professionals and users. Mol Genet Genomic Med 2019; 7:e830. [PMID: 31254460 PMCID: PMC6687663 DOI: 10.1002/mgg3.830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/08/2019] [Accepted: 05/17/2019] [Indexed: 12/16/2022] Open
Abstract
Background The heritability of several psychiatric disorders is high, and specific at‐risk variants have been identified. Therefore, genetic counseling and genetic testing can be prescribed to some psychiatric patients, but these services are not standardized for most of the population. The aims of the study were to gather opinions from mental health professionals and users regarding (a) the genetics of psychiatric disorders and (b) the usefulness of a genetic counseling unit in psychiatry. Methods The survey was conducted in the province of Tarragona (Spain), and we analyzed 152 valid questionnaires from professionals and 959 from users. Results Sixty‐one percent of professionals strongly believed that psychiatric disorders have a genetic basis, and 59% rated a genetic counseling unit in psychiatry as very or extremely useful. However, only a few professionals reported that patients asked them about the genetics of their diseases (12%) or the possibility of transmitting the disease to offspring (19%). Forty‐seven percent of users strongly believed that psychiatric disorders have a genetic basis, 30% responded that they talked with their families about the genetics of their diseases, and 43% were worried about transmitting the disease to offspring; however, only 14% reported that their psychiatrist had talked to them about this topic. Remarkably, 80% of users would consider a genetic counseling unit very or extremely useful. Conclusions The present study showed that mental health professionals were more aware of the genetic basis of psychiatric disorders than users, and both considered the implementation of a genetic counseling service very useful.
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Affiliation(s)
- Lourdes Martorell
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Reus, Spain.,Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Madrid, Spain
| | - Annabel Sanfeliu
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Ana Blázquez
- Department of Child and Adolescent Psychiatry and Psychology, Clinic Institute of Neurosciences, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Elia Lojo
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Maria José Cortés
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Reus, Spain.,Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Madrid, Spain
| | - Joan de Pablo
- Germans Trias i Pujol Hospital. UAB, Badalona, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Reus, Spain.,Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Madrid, Spain
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Gao C, Wang X, Mei S, Li D, Duan J, Zhang P, Chen B, Han L, Gao Y, Yang Z, Li B, Yang XA. Diagnostic Yields of Trio-WES Accompanied by CNVseq for Rare Neurodevelopmental Disorders. Front Genet 2019; 10:485. [PMID: 31178897 PMCID: PMC6542989 DOI: 10.3389/fgene.2019.00485] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 05/06/2019] [Indexed: 01/20/2023] Open
Abstract
Objective This study is to investigate the diagnostic yield of the combination of trio whole exome sequencing (Trio-WES) and copy number variation sequencing (CNVseq) for rare neurodevelopmental disorders (NDDs). Methods Clinical data from consecutive pediatric patients who were diagnosed with rare NDDs that were suspected to be monogenic disorders, who were admitted to our hospital from April 2017 to March 2019, and who underwent next generation sequencing (NGS) were extracted from the medical records. Patients for whom Trio-WES and CNVseq data were available were enrolled in this study. Sanger sequencing was applied for the validation of the variants identified by Trio-WES. Sequence alignment and structural modeling were conducted for analyzing the possibility of the variants in the onset of the NDDs. Results In total, 54 patients were enrolled in this study, with the median age of 15 (8–26) months. A total of 242 phenotypic abnormalities belonging to 20 different systems were identified in the cohort. Twenty-four patients were diagnosed by Trio-WES, eight patients were diagnosed by CNVseq, and one case was identified by both WES and CNVseq. Compared with Trio-WES, the diagnosis rate of Trio-WES accompanied by CNVseq was significantly higher (P = 0.016). Trio-WES identified 36 variants in 26 different genes, among which 27 variants were novel. CNVseq detected four duplications and eight deletions, ranging from 310 kb to 23.27 Mb. Our case examples demonstrated the high heterogeneity of NDDs and showed the challenges of rare NDDs for physicians. Conclusion The significantly higher diagnosis rate of Trio-WES accompanied by CNVseq makes this strategy a potential alternative to the most widely used approaches for pediatric children with rare and undiagnosed NDDs.
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Affiliation(s)
- Chao Gao
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China.,Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Xiaona Wang
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Shiyue Mei
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Dongxiao Li
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Jiali Duan
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Pei Zhang
- Department of Pediatric Neurology and Rehabilitation, First People's Hospital of Shangqiu, Shangqiu, China
| | - Baiyun Chen
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Liang Han
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Yang Gao
- Graduate School of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Yang
- Third People's Hospital of Qingdao West Coast New District, Qingdao, China
| | - Bing Li
- Central Laboratory, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Xiu-An Yang
- School of Basic Medical Science, Chengde Medical University, Chengde, China
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Cheng SSW, Chan KYK, Leung KKP, Au PKC, Tam WK, Li SKM, Luk HM, Kan ASY, Chung BHY, Lo IFM, Tang MHY. Experience of chromosomal microarray applied in prenatal and postnatal settings in Hong Kong. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:196-207. [PMID: 30903683 DOI: 10.1002/ajmg.c.31697] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/14/2022]
Abstract
Chromosomal microarray (CMA) is recommended as a first tier investigation for patients with developmental delay (DD), intellectual disability (ID), autistic spectrum disorder (ASD), and multiple congenital anomalies (MCA). It is widely used in the prenatal and postnatal settings for detection of chromosomal aberrations. This is a retrospective review of all array comparative genomic hybridization (aCGH/ array CGH) findings ascertained in two major prenatal and postnatal genetic diagnostic centers in Hong Kong from June 2012 to December 2017. Medical records were reviewed for cases with pathogenic and variants of uncertain clinical significance (VUS). Classification of copy number variants (CNVs) was based on current knowledge and experience by August 2018. The aims of this review are to study the diagnostic yield of array CGH application in prenatal and postnatal settings in Hong Kong and to describe the spectrum of abnormalities found. Prenatal indications included abnormal ultrasound findings, positive Down syndrome screening, abnormal noninvasive prenatal test results, advanced maternal age and family history of chromosomal or genetic abnormalities. Postnatal indications included unexplained DD, ID, ASD, and MCA. A total of 1,261 prenatal subjects and 3,096 postnatal patients were reviewed. The prenatal diagnostic yield of pathogenic CNV and VUS (excluding those detectable by karyotype) was 3.5%. The postnatal diagnostic yield of pathogenic CNV was 15.2%. The detection rates for well-defined microdeletion and microduplication syndromes were 4.6% in prenatal and 6.1% (1 in 16 index patients) in postnatal cases, respectively. Chromosomes 15, 16, and 22 accounted for over 21 and 25% of pathogenic CNVs detected in prenatal and postnatal cohorts, respectively. This review provides the first large scale overview of genomic imbalance of mostly Chinese patients in prenatal and postnatal settings.
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Affiliation(s)
| | - Kelvin Y K Chan
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | | | - Patrick K C Au
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Wai-Keung Tam
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Samuel K M Li
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong
| | - Ho-Ming Luk
- Department of Health, Clinical Genetic Service, Hong Kong
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong
| | - Brian H Y Chung
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, HKSAR.,Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, HKSAR
| | - Ivan F M Lo
- Department of Health, Clinical Genetic Service, Hong Kong
| | - Mary H Y Tang
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, HKSAR
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Refining the Phenotype of Recurrent Rearrangements of Chromosome 16. Int J Mol Sci 2019; 20:ijms20051095. [PMID: 30836598 PMCID: PMC6429492 DOI: 10.3390/ijms20051095] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 01/08/2023] Open
Abstract
Chromosome 16 is one of the most gene-rich chromosomes of our genome, and 10% of its sequence consists of segmental duplications, which give instability and predisposition to rearrangement by the recurrent mechanism of non-allelic homologous recombination. Microarray technologies have allowed for the analysis of copy number variations (CNVs) that can contribute to the risk of developing complex diseases. By array comparative genomic hybridization (CGH) screening of 1476 patients, we detected 27 cases with CNVs on chromosome 16. We identified four smallest regions of overlapping (SROs): one at 16p13.11 was found in seven patients; one at 16p12.2 was found in four patients; two close SROs at 16p11.2 were found in twelve patients; finally, six patients were found with atypical rearrangements. Although phenotypic variability was observed, we identified a male bias for Childhood Apraxia of Speech associated to 16p11.2 microdeletions. We also reported an elevated frequency of second-site genomic alterations, supporting the model of the second hit to explain the clinical variability associated with CNV syndromes. Our goal was to contribute to the building of a chromosome 16 disease-map based on disease susceptibility regions. The role of the CNVs of chromosome 16 was increasingly made clear in the determination of developmental delay. We also found that in some cases a second-site CNV could explain the phenotypic heterogeneity by a simple additive effect or a pejorative synergistic effect.
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Zhang X, Zhang Y, Zhu X, Purmann C, Haney MS, Ward T, Khechaduri A, Yao J, Weissman SM, Urban AE. Local and global chromatin interactions are altered by large genomic deletions associated with human brain development. Nat Commun 2018; 9:5356. [PMID: 30559385 PMCID: PMC6297223 DOI: 10.1038/s41467-018-07766-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/09/2018] [Indexed: 01/18/2023] Open
Abstract
Large copy number variants (CNVs) in the human genome are strongly associated with common neurodevelopmental, neuropsychiatric disorders such as schizophrenia and autism. Here we report on the epigenomic effects of the prominent large deletion CNVs on chromosome 22q11.2 and on chromosome 1q21.1. We use Hi-C analysis of long-range chromosome interactions, including haplotype-specific Hi-C analysis, ChIP-Seq analysis of regulatory histone marks, and RNA-Seq analysis of gene expression patterns. We observe changes on all the levels of analysis, within the deletion boundaries, in the deletion flanking regions, along chromosome 22q, and genome wide. We detect gene expression changes as well as pronounced and multilayered effects on chromatin states, chromosome folding and on the topological domains of the chromatin, that emanate from the large CNV locus. These findings suggest basic principles of how such large genomic deletions can alter nuclear organization and affect genomic molecular activity. Copy number variants in the human genome (CNVs) are associated with neurodevelopmental and psychiatric disorders such as schizophrenia and autism. Here the authors investigate how the large deletion CNV on chromosome 22q11.2 alters chromatin organization.
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Affiliation(s)
- Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA
| | - Ying Zhang
- Department of Genetics, Yale University, New Haven, 06520, CT, USA.,Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai & Sema4 NYC Laboratory, New York, 10029, NY, USA
| | - Xiaowei Zhu
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA
| | - Carolin Purmann
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA
| | - Michael S Haney
- Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA
| | - Thomas Ward
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA
| | - Arineh Khechaduri
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | - Jie Yao
- Department of Cell Biology, Yale University School of Medicine, New Haven, 06520, CT, USA.,Sun Yat-sen University, Guangzhou, 510080, Guangdong, China
| | | | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA.
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Wang L, Zhao H, Xu Y, Li J, Deng C, Deng Y, Bai J, Li X, Xiao Y, Zhang Y. Systematic identification of lincRNA-based prognostic biomarkers by integrating lincRNA expression and copy number variation in lung adenocarcinoma. Int J Cancer 2018; 144:1723-1734. [PMID: 30226269 DOI: 10.1002/ijc.31865] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/30/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022]
Abstract
Copy number alterations (CNAs) of lincRNAs act as one of important mechanisms in disrupting lincRNA expression which may play critical roles during tumorigenesis in lung adenocarcinoma (LUAD). The copy number alterations of lincRNAs can mark the spectrum of cancer progression and may serve as biomarkers for prognosis in LUAD, however it is rarely studied. We analyzed RNASeq data for 488 LUAD patients from TCGA portal and 58 healthy subjects to identify prognostic lincRNAs predictive of patient survival. Computational analysis entailing integration of expression and copy number alteration data revealed five prognostic lincRNAs: RBPMS-AS1, TDRKH-AS1, LINC00578, RP11-470 M17.2 and LINC00941. The copy number alterations in the LINC00578 and RP11-470 M17.2 genes were positively associated with the longer overall survival of LUAD patients. The CNA in LINC00941 was negatively associated with the longer overall survival. Copy number amplification significantly correlated with increased expression of TDRKH-AS1, which regulates telomere organization and EZH2-mediated epigenetic silencing of CDKN1A, CDKN1B and IL24. Decreased survival of LUAD patients was associated with high LINC00941 expression. The LINC00941 regulates the PI3K-AKT signaling pathway, focal adhesion by influencing potential targets, such as KRAS proto-oncogene GTPase and VEGFC. These lincRNA-based prognostic biomarkers may destroy important cancer-related biological processes contributing to LUAD prognosis. In summary, we demonstrate the prognostic potential of four differentially expressed lincRNAs with copy number alterations (RBPMS-AS1, TDRKH-AS1, LINC00578 and RP11-470 M17.2) that are positively associated with longer overall survival of LUAD patients. One differentially expressed lincRNA LINC00941 with copy number alterations was negatively associated with longer overall survival of LUAD patients.
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Affiliation(s)
- Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yingqi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Li
- Department of Ultrasonic medicine, The 1st Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Chunyu Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yulan Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Juan-Perez C, Farrand S, Velakoulis D. Schizophrenia and epilepsy as a result of maternally inherited CNTN6 copy number variant. Schizophr Res 2018; 202:111-112. [PMID: 29983269 DOI: 10.1016/j.schres.2018.06.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 06/29/2018] [Accepted: 06/30/2018] [Indexed: 01/28/2023]
Abstract
BACKGROUND Copy number variants have made important contributions to understanding neuropsychiatric disorders, including schizophrenia. Deletions in genes encoding neuronal cell adhesion molecules have identified widely varied neurodevelopmental phenotypes. CASE SUMMARY A 27-year old woman presented with schizophrenia, borderline intellectual functioning and shortened metacarpal bones. Subsequent electroencephalogram confirmed genetic generalised epilepsy and microarray analysis found a 0.2 megabase deletion of chromosome 3p26.3. CONCLUSIONS We report the first case of schizophrenia in a proband with a CNTN6 deletion. Schizophrenia has been reported in relatives of probands with this deletion but not in probands themselves. This finding further contributes to the evolving literature regarding schizophrenia pathogenesis.
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Affiliation(s)
- Cecilia Juan-Perez
- Department of Psychiatry, Ramon y Cajal University Hospital, Ctra. De Colmenar Viejo, km. 9,100, 28034 Madrid, Spain
| | - Sarah Farrand
- Neuropsychiatry Unit, Royal Melbourne Hospital, Grattan St, Parkville, VIC 3050, Australia.
| | - Dennis Velakoulis
- Neuropsychiatry Unit, Royal Melbourne Hospital, Grattan St, Parkville, VIC 3050, Australia; Melbourne Neuropsychiatry Centre, University of Melbourne, Parkville, VIC 3052, Australia.
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Mechanisms Underlying Aggressive Behavior Induced by Antiepileptic Drugs: Focus on Topiramate, Levetiracetam, and Perampanel. Behav Neurol 2018; 2018:2064027. [PMID: 30581496 PMCID: PMC6276511 DOI: 10.1155/2018/2064027] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/30/2018] [Indexed: 12/28/2022] Open
Abstract
Antiepileptic drugs (AEDs) are effective against seizures, but their use is often limited by adverse effects, among them psychiatric and behavioral ones including aggressive behavior (AB). Knowledge of the incidence, risk factors, and the underlying mechanisms of AB induced by AEDs may help to facilitate management and reduce the risk of such side effects. The exact incidence of AB as an adverse effect of AEDs is difficult to estimate, but frequencies up to 16% have been reported. Primarily, levetiracetam (LEV), perampanel (PER), and topiramate (TPM), which have diverse mechanisms of action, have been associated with AB. Currently, there is no evidence for a specific pharmacological mechanism solely explaining the increased incidence of AB with LEV, PER, and TPM. Serotonin (5-HT) and GABA, and particularly glutamate (via the AMPA receptor), seem to play key roles. Other mechanisms involve hormones, epigenetics, and “alternative psychosis” and related phenomena. Increased individual susceptibility due to an underlying neurological and/or a mental health disorder may further explain why people with epilepsy are at an increased risk of AB when using AEDs. Remarkably, AB may occur with a delay of weeks or months after start of treatment. Information to patients, relatives, and caregivers, as well as sufficient clinical follow-up, is crucial, and there is a need for further research to understand the complex relationship between AED mechanisms of action and the induction/worsening of AB.
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Muys J, Blaumeiser B, Jacquemyn Y, Bandelier C, Brison N, Bulk S, Chiarappa P, Courtens W, De Leener A, De Rademaeker M, Désir J, Destrée A, Devriendt K, Dheedene A, Fieuw A, Fransen E, Gatot JS, Holmgren P, Jamar M, Janssens S, Keymolen K, Lederer D, Menten B, Meuwissen M, Parmentier B, Pichon B, Rombout S, Sznajer Y, Van Den Bogaert A, Van Den Bogaert K, Vanakker O, Vermeesch J, Janssens K. The Belgian MicroArray Prenatal (BEMAPRE) database: A systematic nationwide repository of fetal genomic aberrations. Prenat Diagn 2018; 38:1120-1128. [PMID: 30334587 DOI: 10.1002/pd.5373] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 10/01/2018] [Accepted: 10/04/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVE With the replacement of karyotyping by chromosomal microarray (CMA) in invasive prenatal diagnosis, new challenges have arisen. By building a national database, we standardize the classification and reporting of prenatally detected copy number variants (CNVs) across Belgian genetic centers. This database, which will link genetic and ultrasound findings with postnatal development, forms a unique resource to investigate the pathogenicity of variants of uncertain significance and to refine the phenotypic spectrum of pathogenic and susceptibility CNVs. METHODS The Belgian MicroArray Prenatal (BEMAPRE) consortium is a collaboration of all genetic centers in Belgium. We collected data from all invasive prenatal procedures performed between May 2013 and July 2016. RESULTS In this three-year period, 13 266 prenatal CMAs were performed. By national agreement, a limited number of susceptibility CNVs and no variants of uncertain significance were reported. Added values for using CMA versus conventional karyotyping were 1.8% in the general invasive population and 2.7% in cases with an ultrasound anomaly. Of the reported CNVs, 31.5% would have remained undetected with non-invasive prenatal test as the first-tier test. CONCLUSION The establishment of a national database for prenatal CNV data allows for a uniform reporting policy and the investigation of the prenatal and postnatal genotype-phenotype correlation.
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Affiliation(s)
- Joke Muys
- Department of Obstetrics and Gynaecology, University Hospital Antwerp, Edegem, Belgium.,Center for Medical Genetics, Universiteit Antwerpen, Antwerp, Belgium
| | - Bettina Blaumeiser
- Center for Medical Genetics, Universiteit Antwerpen, Antwerp, Belgium.,Department of Medical Genetics, University Hospital Antwerp, Edegem, Belgium
| | - Yves Jacquemyn
- Department of Obstetrics and Gynaecology, University Hospital Antwerp, Edegem, Belgium
| | - Claude Bandelier
- Center for Medical Genetics, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Nathalie Brison
- Center for Medical Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Saskia Bulk
- Center for Medical Genetics, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Patrizia Chiarappa
- Center for Medical Genetics, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Winnie Courtens
- Center for Medical Genetics, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Anne De Leener
- Center for Medical Genetics, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Marjan De Rademaeker
- Department of Medical Genetics, University Hospital Antwerp, Edegem, Belgium.,Center for Medical Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Julie Désir
- Center for Medical Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Anne Destrée
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Koenraad Devriendt
- Center for Medical Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Annelies Fieuw
- Center for Medical Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Erik Fransen
- Center for Medical Genetics, Universiteit Antwerpen, Antwerp, Belgium
| | - Jean-Stéphane Gatot
- Center for Medical Genetics, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Philip Holmgren
- Center for Medical Genetics, Universiteit Antwerpen, Antwerp, Belgium
| | - Mauricette Jamar
- Center for Medical Genetics, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Universiteit Gent, Ghent, Belgium
| | - Kathelijn Keymolen
- Center for Medical Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Damien Lederer
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Björn Menten
- Center for Medical Genetics, Universiteit Gent, Ghent, Belgium
| | - Marije Meuwissen
- Center for Medical Genetics, Universiteit Antwerpen, Antwerp, Belgium
| | - Benoit Parmentier
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Bruno Pichon
- Center for Medical Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Sonia Rombout
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Yves Sznajer
- Center for Medical Genetics, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | | | | - Joris Vermeesch
- Center for Medical Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Katrien Janssens
- Center for Medical Genetics, Universiteit Antwerpen, Antwerp, Belgium
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Homma TK, Krepischi ACV, Furuya TK, Honjo RS, Malaquias AC, Bertola DR, Costa SS, Canton AP, Roela RA, Freire BL, Kim CA, Rosenberg C, Jorge AAL. Recurrent Copy Number Variants Associated with Syndromic Short Stature of Unknown Cause. Horm Res Paediatr 2018; 89:13-21. [PMID: 29130988 DOI: 10.1159/000481777] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND/AIMS Genetic imbalances are responsible for many cases of short stature of unknown etiology. This study aims to identify recurrent pathogenic copy number variants (CNVs) in patients with syndromic short stature of unknown cause. METHODS We selected 229 children with short stature and dysmorphic features, developmental delay, and/or intellectual disability, but without a recognized syndrome. All patients were evaluated by chromosomal microarray (array-based comparative genomic hybridization/single nucleotide polymorphism array). Additionally, we searched databases and previous studies to recover recurrent pathogenic CNVs associated with short stature. RESULTS We identified 32 pathogenic/probably pathogenic CNVs in 229 patients. By reviewing the literature, we selected 4 previous studies which evaluated CNVs in cohorts of patients with short stature. Taken together, there were 671 patients with short stature of unknown cause evaluated by chromosomal microarray. Pathogenic/probably pathogenic CNVs were identified in 87 patients (13%). Seven recurrent CNVs, 22q11.21, 15q26, 1p36.33, Xp22.33, 17p13.3, 1q21.1, 2q24.2, were observed. They are responsible for about 40% of all pathogenic/probably pathogenic genomic imbalances found in short stature patients of unknown cause. CONCLUSION CNVs seem to play a significant role in patients with short stature. Chromosomal microarray should be used as a diagnostic tool for evaluation of growth disorders, especially for syndromic short stature of unknown cause.
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Affiliation(s)
- Thais K Homma
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM42, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Ana C V Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (IB-USP), Sao Paulo, Brazil
| | - Tatiane K Furuya
- Laboratorio de Oncologia Experimental LIM24, Departamento de Radiologia e Oncologia, Centro de Investigação Translacional em Oncologia do Instituto do Cancer do Estado de Sao Paulo (CTO/ICESP), Faculdade de Medicina da Universidade de São Paulo (FMUSP), Sao Paulo, Brazil
| | - Rachel S Honjo
- Unidade de Genetica do Instituto da Criança, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Alexsandra C Malaquias
- Unidade de Endocrinologia Pediatrica, Departamento de Pediatria, Irmandade da Santa Casa de Misericórdia de São Paulo, Faculdade de Ciências Médicas da Santa Casa de São Paulo, Sao Paulo, Brazil
| | - Debora R Bertola
- Unidade de Genetica do Instituto da Criança, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Silvia S Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (IB-USP), Sao Paulo, Brazil
| | - Ana P Canton
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Rosimeire A Roela
- Laboratorio de Oncologia Experimental LIM24, Departamento de Radiologia e Oncologia, Centro de Investigação Translacional em Oncologia do Instituto do Cancer do Estado de Sao Paulo (CTO/ICESP), Faculdade de Medicina da Universidade de São Paulo (FMUSP), Sao Paulo, Brazil
| | - Bruna L Freire
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM42, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Chong A Kim
- Unidade de Genetica do Instituto da Criança, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (IB-USP), Sao Paulo, Brazil
| | - Alexander A L Jorge
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM42, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
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The Cytoscan HD Array in the Diagnosis of Neurodevelopmental Disorders. High Throughput 2018; 7:ht7030028. [PMID: 30223503 PMCID: PMC6164295 DOI: 10.3390/ht7030028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Submicroscopic chromosomal copy number variations (CNVs), such as deletions and duplications, account for about 15–20% of patients affected with developmental delay, intellectual disability, multiple congenital anomalies, and autism spectrum disorder. Most of CNVs are de novo or inherited rearrangements with clinical relevance, but there are also rare inherited imbalances with unknown significance that make difficult the clinical management and genetic counselling. Chromosomal microarrays analysis (CMA) are recognized as the first-line test for CNV detection and are now routinely used in the clinical diagnostic laboratory. The recent use of CMA platforms that combine classic copy number analysis with single-nucleotide polymorphism (SNP) genotyping has increased the diagnostic yields. Here we discuss the application of the Cytoscan high-density (HD) SNP-array for the detection of CNVs. We provide an overview of molecular analyses involved in identifying pathogenic CNVs and highlight important guidelines to establish pathogenicity of CNV.
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Hammond CL, Willoughby JM, Parker MJ. Genomics for paediatricians: promises and pitfalls. Arch Dis Child 2018; 103:895-900. [PMID: 29574410 DOI: 10.1136/archdischild-2017-314558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/05/2018] [Accepted: 03/07/2018] [Indexed: 12/22/2022]
Abstract
In recent years, there have been significant advances in genetic technologies, evolving the field of genomics from genetics. This has huge diagnostic potential, as genomic testing increasingly becomes part of mainstream medicine. However, there are numerous potential pitfalls in the interpretation of genomic data. It is therefore essential that we educate clinicians more widely about the appropriate interpretation and utilisation of genomic testing.
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Affiliation(s)
- Carrie Louise Hammond
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Josh Matthew Willoughby
- Sheffield Diagnostic Genetic Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Michael James Parker
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
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Peycheva V, Kamenarova K, Ivanova N, Stamatov D, Avdjieva-Tzavella D, Alexandrova I, Zhelyazkova S, Pacheva I, Dimova P, Ivanov I, Litvinenko I, Bozhinova V, Tournev I, Simeonov E, Mitev V, Jordanova A, Kaneva R. Chromosomal microarray analysis of Bulgarian patients with epilepsy and intellectual disability. Gene 2018; 667:45-55. [DOI: 10.1016/j.gene.2018.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/13/2018] [Accepted: 05/03/2018] [Indexed: 12/08/2022]
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LaBianca S, Pagsberg AK, Jakobsen KD, Demur AB, Bartalan M, LaBianca J, Werge T. Brief Report: Clusters and Trajectories Across the Autism and/or ADHD Spectrum. J Autism Dev Disord 2018; 48:3629-3636. [DOI: 10.1007/s10803-018-3618-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Deshpande A, Weiss LA. Recurrent reciprocal copy number variants: Roles and rules in neurodevelopmental disorders. Dev Neurobiol 2018; 78:519-530. [PMID: 29575775 DOI: 10.1002/dneu.22587] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/08/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022]
Abstract
Deletions and duplications, called reciprocal CNVs when they occur at the same locus, are implicated in neurodevelopmental phenotypes ranging from morphological to behavioral. In this article, we propose three models of how differences in gene expression in deletion and duplication genotypes may result in deleterious phenotypes. To explore these models, we use examples of the similarities and differences in clinical phenotypes of five reciprocal CNVs known to cause neurodevelopmental disorders: 1q21.1, 7q11.23, 15q13.3, 16p11.2, and 22q11.2. These models and examples may inform some insights into better understanding of gene-phenotype relationships. © 2018 Wiley Periodicals, Inc. Develop Neurobiol 78: 519-530, 2018.
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Affiliation(s)
- Aditi Deshpande
- Department of Psychiatry, University of California, San Francisco, San Francisco, California, 94143.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California, 94143.,Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, 94143
| | - Lauren A Weiss
- Department of Psychiatry, University of California, San Francisco, San Francisco, California, 94143.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California, 94143.,Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, 94143
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Maini I, Ivanovski I, Djuric O, Caraffi SG, Errichiello E, Marinelli M, Franchi F, Bizzarri V, Rosato S, Pollazzon M, Gelmini C, Malacarne M, Fusco C, Gargano G, Bernasconi S, Zuffardi O, Garavelli L. Prematurity, ventricular septal defect and dysmorphisms are independent predictors of pathogenic copy number variants: a retrospective study on array-CGH results and phenotypical features of 293 children with neurodevelopmental disorders and/or multiple congenital anomalies. Ital J Pediatr 2018; 44:34. [PMID: 29523172 PMCID: PMC5845186 DOI: 10.1186/s13052-018-0467-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/21/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Since 2010, array-CGH (aCGH) has been the first-tier test in the diagnostic approach of children with neurodevelopmental disorders (NDD) or multiple congenital anomalies (MCA) of unknown origin. Its broad application led to the detection of numerous variants of uncertain clinical significance (VOUS). How to appropriately interpret aCGH results represents a challenge for the clinician. METHOD We present a retrospective study on 293 patients with age range 1 month - 29 years (median 7 years) with NDD and/or MCA and/or dysmorphisms, investigated through aCGH between 2005 and 2016. The aim of the study was to analyze clinical and molecular cytogenetic data in order to identify what elements could be useful to interpret unknown or poorly described aberrations. Comparison of phenotype and cytogenetic characteristics through univariate analysis and multivariate logistic regression was performed. RESULTS Copy number variations (CNVs) with a frequency < 1% were detected in 225 patients of the total sample, while 68 patients presented only variants with higher frequency (heterozygous deletions or amplification) and were considered to have negative aCGH. Proved pathogenic CNVs were detected in 70 patients (20.6%). Delayed psychomotor development, intellectual disability, intrauterine growth retardation (IUGR), prematurity, congenital heart disease, cerebral malformations and dysmorphisms correlated to reported pathogenic CNVs. Prematurity, ventricular septal defect and dysmorphisms remained significant predictors of pathogenic CNVs in the multivariate logistic model whereas abnormal EEG and limb dysmorphisms were mainly detected in the group with likely pathogenic VOUS. A flow-chart regarding the care for patients with NDD and/or MCA and/or dysmorphisms and the interpretation of aCGH has been made on the basis of the data inferred from this study and literature. CONCLUSION Our work contributes to make the investigative process of CNVs more informative and suggests possible directions in aCGH interpretation and phenotype correlation.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Adolescent
- Adult
- Child
- Child, Preschool
- Comparative Genomic Hybridization/methods
- DNA Copy Number Variations
- Facies
- Female
- Genetic Testing
- Heart Septal Defects, Ventricular/diagnosis
- Heart Septal Defects, Ventricular/genetics
- Humans
- Infant
- Infant, Newborn
- Infant, Premature, Diseases/diagnosis
- Infant, Premature, Diseases/genetics
- Male
- Muscular Atrophy/diagnosis
- Muscular Atrophy/genetics
- Neurodevelopmental Disorders/diagnosis
- Neurodevelopmental Disorders/genetics
- Phenotype
- Retrospective Studies
- Young Adult
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Affiliation(s)
- I. Maini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - I. Ivanovski
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - O. Djuric
- Institute of Epidemiology, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - S. G. Caraffi
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - E. Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - M. Marinelli
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - F. Franchi
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - V. Bizzarri
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Rosato
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Pollazzon
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - C. Gelmini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Malacarne
- Division of Medical Genetics, Galliera Hospital, Genoa, Italy
| | - C. Fusco
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - G. Gargano
- Neonatal Intensive Care Unit (NICU), Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Bernasconi
- Former Director Pediatric Department, University of Parma, Parma, Italy
| | - O. Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - L. Garavelli
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Santa Maria Nuova Hospital, viale Risorgimento 80, 42123 Reggio Emilia, Italy
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Brabbing-Goldstein D, Reches A, Svirsky R, Bar-Shira A, Yaron Y. Dilemmas in genetic counseling for low-penetrance neuro-susceptibility loci detected on prenatal chromosomal microarray analysis. Am J Obstet Gynecol 2018; 218:247.e1-247.e12. [PMID: 29146387 DOI: 10.1016/j.ajog.2017.11.559] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/14/2017] [Accepted: 11/06/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND Chromosomal microarray analysis is standard of care in fetuses with malformations, detecting clinically significant copy number variants in 5-7% of cases over conventional karyotyping. However, it also detects variants of uncertain significance in 1.6-4.2% of the cases, some of which are low-penetrance neuro-susceptibility loci. The interpretation of these variants in pregnancy is particularly challenging because the significance is often unclear and the clinical implications may be difficult to predict. OBJECTIVE The purpose of this study was to describe counseling dilemmas regarding low-penetrance neuro-susceptibility loci that are detected by prenatal chromosomal microarray analysis. STUDY DESIGN During the study period (January 2014 to December 2015), 700 prenatal chromosomal microarray analyses were performed. Cases were categorized as "indicated" (n=375) if there were abnormal sonographic findings or suggestive medical history and "patient choice" (n=325) in the presence of a structurally normal fetus with no other particular indication. The laboratory reported on copy number variants ≥400 Kb in size in loci known to be associated with genetic syndromes and ≥1 Mb in other areas of genome. Results were classified as gross aneuploidy, copy number variants, and normal. Copy number variants were categorized according to the American College of Medical Genetics standards and guidelines: pathogenic, variants of uncertain significance, or benign. Variants of uncertain significance were further subdivided into categories of likely pathogenic, variants of uncertain significance with no subclassification, and likely benign. Statistical analysis was performed with the use of Chi square test and Fisher's exact test to compare intergroup differences in incidence of the different result categories and demographic data. RESULTS Patient choice cases became more prevalent with time (35.5% in the beginning of the study, compared with 48.4% at the end of the study period). Clinically significant copy number variants were found in 14 of 375 (3.7%) of indicated cases vs only 2 of 325 (0.6%) of patient choice cases (P=.009). All "likely benign" variants consisted of low-penetrance neuro-susceptibility loci. The incidence thereof was similar between the indicated and patient choice groups (3.7% vs 3.4%; P=.85). In the indicated group, some variants of uncertain significance may have contributed to the abnormal anatomic findings. Conversely, in the patient choice group, the finding of low-penetrance neuro-susceptibility loci was often unexpected and confounding for prospective parents. CONCLUSION Prenatal chromosomal microarray analysis added clinically significant information in both groups. However, it also detected low-penetrance neuro-susceptibility loci in approximately 3.5% of the cases. This fact should be conveyed during pretest counseling to allow patients to make informed choices, particularly when chromosomal microarray is to be performed for patient choice.
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Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders. Twin Res Hum Genet 2018; 21:1-11. [DOI: 10.1017/thg.2017.69] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hundreds of penetrant risk loci have been identified across different neurodevelopmental disorders (NDDs), and these often involve rare (<1% frequency) copy number variations (CNVs), which can involve one or more genes. Monozygotic (MZ) twin pairs are long thought to share 100% of their genomic information. However, genetic differences in the form of postzygotic somatic variants have been reported recently both in typically developing (TD) and in clinically discordant MZ pairs. We sought to investigate the contribution of rare CNVs in 100 twin pairs enriched for NDD phenotypes with a particular focus on postzygotic CNVs in MZ pairs discordant for autism spectrum disorder (ASD) using the Illumina Infinium PsychArray. In our sample, no postzygotic de novo CNVs were found in 55 MZ twin pairs, including the 13 pairs discordant for ASD. We did detect a higher rate of CNVs overlapping genes involved in disorders of the nervous system, such as a rare deletion affecting HNRNPU, in MZ pairs discordant and concordant for ASD in comparison with TD pairs (p = .02). Our results are in concordance with earlier findings that postzygotic de novo CNV events are typically rare in genomic DNA derived from saliva or blood, and suggests that the discordance of NDDs in our sample of twins is not explained by discordant CNVs. Still, studies investigating postzygotic variation in MZ discordant twins using DNA from different tissues and single cells and higher resolution genomics are needed in the future.
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Harel T, Lupski JR. Genomic disorders 20 years on-mechanisms for clinical manifestations. Clin Genet 2017; 93:439-449. [PMID: 28950406 DOI: 10.1111/cge.13146] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/01/2017] [Accepted: 09/21/2017] [Indexed: 12/18/2022]
Abstract
Genomic disorders result from copy-number variants (CNVs) or submicroscopic rearrangements of the genome rather than from single nucleotide variants (SNVs). Diverse technologies, including array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) microarrays, and more recently, whole genome sequencing and whole-exome sequencing, have enabled robust genome-wide unbiased detection of CNVs in affected individuals and in reportedly healthy controls. Sequencing of breakpoint junctions has allowed for elucidation of upstream mechanisms leading to genomic instability and resultant structural variation, whereas studies of the association between CNVs and specific diseases or susceptibility to morbid traits have enhanced our understanding of the downstream effects. In this review, we discuss the hallmarks of genomic disorders as they were defined during the first decade of the field, including genomic instability and the mechanism for rearrangement defined as nonallelic homologous recombination (NAHR); recurrent vs nonrecurrent rearrangements; and gene dosage sensitivity. Moreover, we highlight the exciting advances of the second decade of this field, including a deeper understanding of genomic instability and the mechanisms underlying complex rearrangements, mechanisms for constitutional and somatic chromosomal rearrangements, structural intra-species polymorphisms and susceptibility to NAHR, the role of CNVs in the context of genome-wide copy number and single nucleotide variation, and the contribution of noncoding CNVs to human disease.
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Affiliation(s)
- T Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - J R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
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Grünblatt E, Oneda B, Ekici AB, Ball J, Geissler J, Uebe S, Romanos M, Rauch A, Walitza S. High resolution chromosomal microarray analysis in paediatric obsessive-compulsive disorder. BMC Med Genomics 2017; 10:68. [PMID: 29179725 PMCID: PMC5704537 DOI: 10.1186/s12920-017-0299-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 11/06/2017] [Indexed: 02/16/2023] Open
Abstract
Background Obsessive-Compulsive Disorder (OCD) is a common and chronic disorder in which a person has uncontrollable, reoccurring thoughts and behaviours. It is a complex genetic condition and, in case of early onset (EO), the patients manifest a more severe phenotype, and an increased heritability. Large (>500 kb) copy number variations (CNVs) previously associated with autism and schizophrenia have been reported in OCD. Recently, rare CNVs smaller than 500 kb overlapping risk loci for other neurodevelopmental conditions have also been reported in OCD, stressing the importance of examining CNVs of any size range. The aim of this study was to further investigate the role of rare and small CNVs in the aetiology of EO-OCD. Methods We performed high-resolution chromosomal microarray analysis in 121 paediatric OCD patients and in 124 random controls to identify rare CNVs (>50 kb) which might contribute to EO-OCD. Results The frequencies and the size of the observed rare CNVs in the patients did not differ from the controls. However, we observed a significantly higher frequency of rare CNVs affecting brain related genes, especially deletions, in the patients (OR = 1.98, 95% CI 1.02–3.84; OR = 3.61, 95% CI 1.14–11.41, respectively). Similarly, enrichment-analysis of CNVs gene content, performed with three independent methods, confirmed significant clustering of predefined genes involved in synaptic/brain related functional pathways in the patients but not in the controls. In two patients we detected de-novo CNVs encompassing genes previously associated with different neurodevelopmental disorders (NRXN1, ANKS1B, UHRF1BP1). Conclusions Our results further strengthen the role of small rare CNVs, particularly deletions, as susceptibility factors for paediatric OCD. Electronic supplementary material The online version of this article (10.1186/s12920-017-0299-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Neumünsterallee 9, 8032, Zürich, Switzerland. .,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland. .,Department of Psychiatry, Psychosomatic and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland. .,Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland.
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich-Schlieren, Switzerland
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
| | - Juliane Ball
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Neumünsterallee 9, 8032, Zürich, Switzerland
| | - Julia Geissler
- Center of Mental Health, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
| | - Steffen Uebe
- Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
| | - Marcel Romanos
- Center of Mental Health, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
| | - Anita Rauch
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Institute of Medical Genetics, University of Zurich, Zurich-Schlieren, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Neumünsterallee 9, 8032, Zürich, Switzerland. .,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
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Advani HV, Barrett AN, Evans MI, Choolani M. Challenges in non-invasive prenatal screening for sub-chromosomal copy number variations using cell-free DNA. Prenat Diagn 2017; 37:1067-1075. [PMID: 28950403 DOI: 10.1002/pd.5161] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/23/2017] [Accepted: 09/16/2017] [Indexed: 12/14/2022]
Abstract
Non-invasive prenatal screening (NIPS) has revolutionized the approach to prenatal fetal aneuploidy screening. Many commercial providers now offer analyses for sub-chromosomal copy number variations (CNVs). Here, we review the use of NIPS in the context of screening for microdeletions and microduplications, issues surrounding the choice of disorders tested for, and the advantages and disadvantages associated with the inclusion of microdeletions to current NIPS. Several studies have claimed benefits; however, we suggest that microdeletions have not demonstrated a low enough false positive rate to be deemed practical or ethically acceptable, especially considering their low positive predictive values. Because a positive NIPS result should be confirmed using diagnostic techniques, and false positive rates are as high as 90% for some microdeletions, diagnostic testing seems preferable when the goal is to maximize the detection of microdeletion or microduplication syndromes.
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Affiliation(s)
- Henna V Advani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mark I Evans
- Department of Obstetrics and Gynecology, Mt. Sinai School of Medicine, New York, NY, USA.,Comprehensive Genetics and Fetal Medicine Foundation of America, New York, NY, USA
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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