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Schultz LM, Knighton A, Huguet G, Saci Z, Jean-Louis M, Mollon J, Knowles EEM, Glahn DC, Jacquemont S, Almasy L. Copy-number variants differ in frequency across genetic ancestry groups. HGG ADVANCES 2024; 5:100340. [PMID: 39138864 DOI: 10.1016/j.xhgg.2024.100340] [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: 03/21/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Copy-number variants (CNVs) have been implicated in a variety of neuropsychiatric and cognitive phenotypes. We found that deleterious CNVs are less prevalent in non-European ancestry groups than they are in European ancestry groups of both the UK Biobank (UKBB) and a US replication cohort (SPARK). We also identified specific recurrent CNVs that consistently differ in frequency across ancestry groups in both the UKBB and SPARK. These ancestry-related differences in CNV prevalence present in both an unselected community population and a family cohort enriched with individuals diagnosed with autism spectrum disorder (ASD) strongly suggest that genetic ancestry should be considered when probing associations between CNVs and health outcomes.
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Affiliation(s)
- Laura M Schultz
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Alexys Knighton
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Zohra Saci
- CHU Sainte-Justine, Montréal, QC, Canada
| | | | - Josephine Mollon
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Emma E M Knowles
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - David C Glahn
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Sébastien Jacquemont
- CHU Sainte-Justine, Montréal, QC, Canada; Department of Pediatrics, Université de Montréal, Montréal, QC, Canada
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Sha Z, Sun KY, Jung B, Barzilay R, Moore TM, Almasy L, Forsyth JK, Prem S, Gandal MJ, Seidlitz J, Glessner JT, Alexander-Bloch AF. The copy number variant architecture of psychopathology and cognitive development in the ABCD ® study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.14.24307376. [PMID: 38798629 PMCID: PMC11118651 DOI: 10.1101/2024.05.14.24307376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Importance Childhood is a crucial developmental phase for mental health and cognitive function, both of which are commonly affected in patients with psychiatric disorders. This neurodevelopmental trajectory is shaped by a complex interplay of genetic and environmental factors. While common genetic variants account for a large proportion of inherited genetic risk, rare genetic variations, particularly copy number variants (CNVs), play a significant role in the genetic architecture of neurodevelopmental disorders. Despite their importance, the relevance of CNVs to child psychopathology and cognitive function in the general population remains underexplored. Objective Investigating CNV associations with dimensions of child psychopathology and cognitive functions. Design Setting and Participants ABCD® study focuses on a cohort of over 11,875 youth aged 9 to 10, recruited from 21 sites in the US, aiming to investigate the role of various factors, including brain, environment, and genetic factors, in the etiology of mental and physical health from middle childhood through early adulthood. Data analysis occurred from April 2023 to April 2024. Main Outcomes and Measures In this study, we utilized PennCNV and QuantiSNP algorithms to identify duplications and deletions larger than 50Kb across a cohort of 11,088 individuals from the Adolescent Brain Cognitive Development® study. CNVs meeting quality control standards were subjected to a genome-wide association scan to identify regions associated with quantitative measures of broad psychiatric symptom domains and cognitive outcomes. Additionally, a CNV risk score, reflecting the aggregated burden of genetic intolerance to inactivation and dosage sensitivity, was calculated to assess its impact on variability in overall and dimensional child psychiatric and cognitive phenotypes. Results In a final sample of 8,564 individuals (mean age=9.9 years, 4,532 males) passing quality control, we identified 4,111 individuals carrying 5,760 autosomal CNVs. Our results revealed significant associations between specific CNVs and our phenotypes of interest, psychopathology and cognitive function. For instance, a duplication at 10q26.3 was associated with overall psychopathology, and somatic complaints in particular. Additionally, deletions at 1q12.1, along with duplications at 14q11.2 and 10q26.3, were linked to overall cognitive function, with particular contributions from fluid intelligence (14q11.2), working memory (10q26.3), and reading ability (14q11.2). Moreover, individuals carrying CNVs previously associated with neurodevelopmental disorders exhibited greater impairment in social functioning and cognitive performance across multiple domains, in particular working memory. Notably, a higher deletion CNV risk score was significantly correlated with increased overall psychopathology (especially in dimensions of social functioning, thought disorder, and attention) as well as cognitive impairment across various domains. Conclusions and Relevance In summary, our findings shed light on the contributions of CNVs to interindividual variability in complex traits related to neurocognitive development and child psychopathology.
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Affiliation(s)
- Zhiqiang Sha
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Kevin Y. Sun
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Benjamin Jung
- Section on Neurobehavioral and Clinical Research, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ran Barzilay
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Tyler M. Moore
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Almasy
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Smrithi Prem
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
- Graduate Program in Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Michael J. Gandal
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jakob Seidlitz
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Joseph T. Glessner
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Aaron F. Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
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Goh CJ, Kwon HJ, Kim Y, Jung S, Park J, Lee IK, Park BR, Kim MJ, Kim MJ, Lee MS. Improving CNV Detection Performance in Microarray Data Using a Machine Learning-Based Approach. Diagnostics (Basel) 2023; 14:84. [PMID: 38201393 PMCID: PMC10871075 DOI: 10.3390/diagnostics14010084] [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: 10/17/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Copy number variation (CNV) is a primary source of structural variation in the human genome, leading to several disorders. Therefore, analyzing neonatal CNVs is crucial for managing CNV-related chromosomal disabilities. However, genomic waves can hinder accurate CNV analysis. To mitigate the influences of the waves, we adopted a machine learning approach and developed a new method that uses a modified log R ratio instead of the commonly used log R ratio. Validation results using samples with known CNVs demonstrated the superior performance of our method. We analyzed a total of 16,046 Korean newborn samples using the new method and identified CNVs related to 39 genetic disorders were identified in 342 cases. The most frequently detected CNV-related disorder was Joubert syndrome 4. The accuracy of our method was further confirmed by analyzing a subset of the detected results using NGS and comparing them with our results. The utilization of a genome-wide single nucleotide polymorphism array with wave offset was shown to be a powerful method for identifying CNVs in neonatal cases. The accurate screening and the ability to identify various disease susceptibilities offered by our new method could facilitate the identification of CNV-associated chromosomal disease etiologies.
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Affiliation(s)
- Chul Jun Goh
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Hyuk-Jung Kwon
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
- Department of Computer Science and Engineering, Incheon National University (INU), Incheon 22012, Republic of Korea
| | - Yoonhee Kim
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Seunghee Jung
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Jiwoo Park
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Isaac Kise Lee
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
- Department of Computer Science and Engineering, Incheon National University (INU), Incheon 22012, Republic of Korea
- NGENI Foundation, San Diego, CA 92127, USA
| | - Bo-Ram Park
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Myeong-Ji Kim
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
| | - Min-Jeong Kim
- Diagnomics, Inc., 5795 Kearny Villa Rd., San Diego, CA 92123, USA;
| | - Min-Seob Lee
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (C.J.G.); (H.-J.K.); (Y.K.); (S.J.); (J.P.); (I.K.L.); (B.-R.P.); (M.-J.K.)
- Diagnomics, Inc., 5795 Kearny Villa Rd., San Diego, CA 92123, USA;
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Mollon J, Schultz LM, Huguet G, Knowles EEM, Mathias SR, Rodrigue A, Alexander-Bloch A, Saci Z, Jean-Louis M, Kumar K, Douard E, Almasy L, Jacquemont S, Glahn DC. Impact of Copy Number Variants and Polygenic Risk Scores on Psychopathology in the UK Biobank. Biol Psychiatry 2023; 94:591-600. [PMID: 36764568 PMCID: PMC10409883 DOI: 10.1016/j.biopsych.2023.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Our understanding of the impact of copy number variants (CNVs) on psychopathology and their joint influence with polygenic risk scores (PRSs) remains limited. METHODS The UK Biobank recruited 502,534 individuals ages 37 to 73 years living in the United Kingdom between 2006 and 2010. After quality control, genotype data from 459,855 individuals were available for CNV calling. A total of 61 commonly studied recurrent neuropsychiatric CNVs were selected for analyses and examined individually and in aggregate (any CNV, deletion, or duplication). CNV risk scores were used to quantify intolerance of CNVs to haploinsufficiency. Major depressive disorder and generalized anxiety disorder PRSs were generated for White British individuals (N = 408,870). Mood/anxiety factor scores were generated using item-level questionnaire data (N = 501,289). RESULTS CNV carriers showed higher mood/anxiety scores than noncarriers, with the largest effects seen for intolerant deletions. A total of 11 individual deletions and 8 duplications were associated with higher mood/anxiety. Carriers of the 9p24.3 (DMRT1) duplication showed lower mood/anxiety. Associations remained significant for most CNVs when excluding individuals with psychiatric diagnoses. Nominally significant CNV × PRS interactions provided preliminary evidence that associations between select individual CNVs, but not CNVs in aggregate, and mood/anxiety may be modulated by PRSs. CONCLUSIONS CNVs associated with risk for psychiatric disorders showed small to large effects on dimensional mood/anxiety scores in a general population cohort, even when excluding individuals with psychiatric diagnoses. CNV × PRS interactions showed that associations between select CNVs and mood/anxiety may be modulated by PRSs.
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Affiliation(s)
- Josephine Mollon
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Laura M Schultz
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Guillaume Huguet
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Emma E M Knowles
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Samuel R Mathias
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amanda Rodrigue
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aaron Alexander-Bloch
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Neurodevelopment and Psychosis Section, Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zohra Saci
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Martineau Jean-Louis
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Kuldeep Kumar
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Elise Douard
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Laura Almasy
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Genetics, Perelman School of Medicine, Penn-CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sebastien Jacquemont
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Olin Neuropsychiatry Research Center, Institute of Living, Hartford, Connecticut
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5
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Molecular Mechanisms Involved in the Regulation of Neurodevelopment by miR-124. Mol Neurobiol 2023; 60:3569-3583. [PMID: 36840845 DOI: 10.1007/s12035-023-03271-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/04/2023] [Indexed: 02/26/2023]
Abstract
miR-124 is a miRNA predominantly expressed in the nervous system and accounts for more than a quarter of the total miRNAs in the brain. It regulates neurogenesis, neuronal differentiation, neuronal maturation, and synapse formation and is the most important miRNA in the brain. Furthermore, emerging evidence has suggested miR-124 may be associated with the pathogenesis of various neurodevelopmental and neuropsychiatric disorders. Here, we provide an overview of the role of miR-124 in neurodevelopment and the underling mechanisms, and finally, we prospect the significance of miR-124 research to the field of neuroscience.
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White LK, Crowley TB, Finucane B, McClellan EJ, Donoghue S, Garcia-Minaur S, Repetto GM, Fischer M, Jacquemont S, Gur RE, Maillard AM, Donald KA, Bassett AS, Swillen A, McDonald-McGinn DM. Gathering the Stakeholder's Perspective: Experiences and Opportunities in Rare Genetic Disease Research. Genes (Basel) 2023; 14:169. [PMID: 36672911 PMCID: PMC9859499 DOI: 10.3390/genes14010169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Research participant feedback is rarely collected; therefore, investigators have limited understanding regarding stakeholders' (affected individuals/caregivers) motivation to participate. Members of the Genes to Mental Health Network (G2MH) surveyed stakeholders affected by copy number variants (CNVs) regarding perceived incentives for study participation, opinions concerning research priorities, and the necessity for future funding. Respondents were also asked about feelings of preparedness, research burden, and satisfaction with research study participation. METHODS Modified validated surveys were used to assess stakeholders´ views across three domains: (1) Research Study Enrollment, Retainment, Withdrawal, and Future Participation; (2) Overall Research Experience, Burden, and Preparedness; (3) Research Priorities and Obstacles. Top box score analyses were performed. RESULTS A total of 704 stakeholders´ responded from 29 countries representing 55 CNVs. The top reasons for initial participation in the research included reasons related to education and altruism. The top reasons for leaving a research study included treatment risks and side effects. The importance of sharing research findings and laboratory results with stakeholders was underscored by participants. Most stakeholders reported positive research experiences. CONCLUSIONS This study provides important insight into how individuals and families affected with a rare CNV feel toward research participation and their overall experience in rare disease research. There are clear targets for areas of improvement for study teams, although many stakeholders reported positive research experiences. Key findings from this international survey may help advance collaborative research and improve the experience of participants, investigators, and other stakeholders moving forward.
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Affiliation(s)
- Lauren K. White
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | - Emily J. McClellan
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah Donoghue
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sixto Garcia-Minaur
- Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, 28046 Madrid, Spain
| | | | - Matthias Fischer
- Clinic and Policlinic for Psychiatry and Psychotherapy, University of Rostock, 18147 Rostock, Germany
- Sigma-Zentrum, 79713 Bad Säckingen, Germany
| | - Sebastien Jacquemont
- Sainte Justine Research Center, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Raquel E. Gur
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Kirsten A. Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Rondebosch, Cape Town 7700, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town 7935, South Africa
| | - Anne S. Bassett
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON M5G 2C4, Canada
- Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, and Department of Psychiatry, University of Toronto, Toronto, ON M5S 2S1, Canada
- Division of Cardiology, Department of Medicine, and Centre for Mental Health, and Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2N2, Canada
| | - Ann Swillen
- Center for Human Genetics, University Hospital UZ Leuven, and Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Donna M. McDonald-McGinn
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Human Biology and Medical Genetics, Sapienza University, 00185 Roma, Italy
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7
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White LK, Crowley TB, Finucane B, Garcia-Minaur S, Repetto GM, van den Bree M, Fischer M, Jacquemont S, Barzilay R, Maillard AM, Donald KA, Gur RE, Bassett AS, Swillen A, McDonald-McGinn DM. The COVID-19 pandemic's impact on worry and medical disruptions reported by individuals with chromosome 22q11.2 copy number variants and their caregivers. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2022; 66:313-322. [PMID: 35191118 PMCID: PMC9725107 DOI: 10.1111/jir.12918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/04/2022] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The world has suffered immeasurably during the COVID-19 pandemic. Increased distress and mental and medical health concerns are collateral consequences to the disease itself. The Genes to Mental Health (G2MH) Network consortium sought to understand how individuals affected by the rare copy number variations of 22q11.2 deletion and duplication syndrome, associated with neurodevelopmental/neuropsychiatric conditions, were coping. The article focuses on worry and disruptions in medical care caused by the pandemic. METHODS The University of Pennsylvania COVID-19 Stressor List and care disruption questions were circulated by 22 advocacy groups in English and 11 other languages. RESULTS A total of 512 people from 23 countries completed the survey; most were caregivers of affected individuals. Worry about family members acquiring COVID-19 had the highest average endorsed worry, whilst currently having COVID-19 had the lowest rated worry. Total COVID-19 worries were higher in individuals completing the survey towards the end of the study (later pandemic wave); 36% (n = 186) of the sample reported a significant effect on health due to care interruption during the pandemic; 44% of individuals (n = 111) receiving care for their genetic syndrome in a hospital setting reported delaying appointments due to COVID-19 fears; 12% (n = 59) of the sample reported disruptions to treatments; and of those reporting no current disruptions, 59% (n = 269) worried about future disruptions if the pandemic continued. Higher levels of care disruptions were related to higher COVID-19 worries (Ps < 0.005). Minimal differences by respondent type or copy number variation type emerged. CONCLUSIONS Widespread medical care disruptions and pandemic-related worries were reported by individuals with 22q11.2 syndrome and their family members. Reported worries were broadly consistent with research results from prior reports in the general population. The long-term effects of COVID-19 worries, interruptions to care and hospital avoidance require further study.
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Affiliation(s)
- L K White
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - T B Crowley
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - B Finucane
- Geisinger Autism & Developmental Medicine Institute, Geisinger Health System, Lewisburg, PA, USA
| | - S Garcia-Minaur
- Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain
| | - G M Repetto
- Center for Genetics and Genomics, Facultad de Medicina Clínica Alemana - Universidad del Desarrollo, Santiago, Chile
| | - M van den Bree
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - M Fischer
- Clinic and Policlinic for Psychiatry and Psychotherapy, University of Rostock, Rostock, Germany
| | - S Jacquemont
- Sainte Justine Research Center, University of Montreal, Montreal, Canada
| | - R Barzilay
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - A M Maillard
- Service des Troubles du Spectre de l'Autisme (STSA), Lausanne University Hospital, Lausanne, Switzerland
| | - K A Donald
- Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - R E Gur
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - A S Bassett
- Centre for Addiction and Mental Health, University Health Network and Department of Psychiatry, University of Toronto, Toronto, Canada
| | - A Swillen
- Center for Human Genetics, University Hospital Leuven and Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - D M McDonald-McGinn
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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8
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Dai L, Zhang D, Wu Z, Guan X, Ma M, Li L, Zhang Y, Bai Y, Guo H. A Tiered Genetic Screening Strategy for the Molecular Diagnosis of Intellectual Disability in Chinese Patients. Front Genet 2021; 12:669217. [PMID: 34630504 PMCID: PMC8495063 DOI: 10.3389/fgene.2021.669217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 09/10/2021] [Indexed: 01/02/2023] Open
Abstract
Objective: Intellectual disability (ID) is one of the most common developmental disabilities. To identify the genetic etiology of IDs in Chongqing, we conducted a multistage study in Chinese Han patients. Methods: We collected the clinical and etiological data of 1665 ID patients, including 1,604 from the disabled children evaluation center and 61 from the pediatric rehabilitation unit. Routine genetic screening results were obtained, including karyotype and candidate gene analysis. Then 105 idiopathic cases with syndromic and severe ID/developmental delay (DD) were selected and tested by chromosomal microarray (CMA) and whole exome sequencing (WES) sequentially. The pathogenicity of the CNVs and SNVs were evaluated according to ACMG guidelines. Results: Molecular diagnosis was made by routine genetic screening in 216 patients, including 196 chromosomal syndromes. Among the 105 idiopathic patients, 49 patients with pathogenic/likely pathogenic CNVs and 21 patients with VUS were identified by CMA. Twenty-six pathogenic CNVs underlying well-known syndromic cases, such as Williams-Beuren syndrome, were confirmed by multiplex ligation-dependent probe amplification (MLPA). Nine novel mutations were identified by WES in thirty-fix CNV-negative ID cases. Conclusions: The study illustrated the genetic aberrations distribution of a large ID cohort in Chongqing. Compared with conventional or single methods, a tiered high-throughput diagnostic strategy was developed to greatly improve the diagnostic yields and extend the variation spectrum for idiopathic syndromic ID cases.
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Affiliation(s)
- Limeng Dai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Danyan Zhang
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China.,Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Zhifeng Wu
- Department of Pediatrics, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xingying Guan
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Mingfu Ma
- Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Lianbing Li
- Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Yuping Zhang
- Department of Pediatrics, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yun Bai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Hong Guo
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
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9
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Zhang Q, Zhang X, Liu J, Mao C, Chen S, Zhang Y, Leng L. Identification of copy number variation and population analysis of the sacred lotus ( Nelumbo nucifera). Biosci Biotechnol Biochem 2020; 84:2037-2044. [PMID: 32594903 DOI: 10.1080/09168451.2020.1786351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The sacred lotus (Nelumbo nucifera) is widely cultured in East Asia for its horticultural, agricultural, and medicinal values. Although many molecular markers had been used to extrapolate population genetics of the sacred lotus, a study of large variations, such as copy number variation (CNV), are absent up to now. In this study, we applied whole-genome re-sequencing to 24 lotus accessions, and use read depth information to genotype and filter original CNV call. Totally 448 duplications and 4,267 deletions were identified in the final CNV set. Further analysis of population structure revealed that the population structure patterns revealed by CNV and SNP are largely consistent with each other. Our result indicated that deep sequencing followed by genotyping is a quick and straightforward way to mine out CNV from the population, and the CNV along with SNP could enable us to better comprehend the biology of the plant.
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Affiliation(s)
- Qing Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Xueting Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Jing Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Chaoyi Mao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Sha Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Yujun Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Liang Leng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
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10
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Improving Model Performance on the Stratification of Breast Cancer Patients by Integrating Multiscale Genomic Features. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1475368. [PMID: 32908867 PMCID: PMC7471833 DOI: 10.1155/2020/1475368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/26/2020] [Accepted: 07/18/2020] [Indexed: 11/17/2022]
Abstract
In clinical cancer research, it is a hot topic on how to accurately stratify patients based on genomic data. With the development of next-generation sequencing technology, more and more types of genomic features, such as mRNA expression level, can be used to distinguish cancer patients. Previous studies commonly stratified patients by using a single type of genomic features, which can only reflect one aspect of the cancer. In fact, multiscale genomic features will provide more information and may be helpful for clinical prediction. In addition, most of the conventional machine learning algorithms use a handcrafted gene set as features to construct models, which is generally selected by a statistical method with an arbitrary cut-off, e.g., p value < 0.05. The genes in the gene set are not necessarily related to the cancer and will make the model unreliable. Therefore, in our study, we thoroughly investigated the performance of different machine learning methods on stratifying breast cancer patients with a single type of genomic features. Then, we proposed a strategy, which can take into account the degree of correlation between genes and cancer patients, to identify the features from mRNAs and microRNAs, and evaluated the performance of the models with the new combined features of the multiscale genomic features. The results showed that, compared with the models constructed with a single type of features, the models with the multiscale genomic features generated by our proposed method achieved better performance on stratifying the ER status of breast cancer patients. Moreover, we found that the identified multiscale genomic features were closely related to the cancer by gene set enrichment analysis, indicating that our proposed strategy can well reflect the biological relevance of the genes to breast cancer. In conclusion, modelling with multiscale genomic features closely related to the cancer not only can guarantee the prediction performance of the models but also can effectively provide candidate genes for interpreting the mechanisms of cancer.
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11
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Ashitha SNM, Ramachandra NB. Integrated Functional Analysis Implicates Syndromic and Rare Copy Number Variation Genes as Prominent Molecular Players in Pathogenesis of Autism Spectrum Disorders. Neuroscience 2020; 438:25-40. [DOI: 10.1016/j.neuroscience.2020.04.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 01/05/2023]
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12
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Paduano F, Colao E, Loddo S, Orlando V, Trapasso F, Novelli A, Perrotti N, Iuliano R. 7q35 Microdeletion and 15q13.3 and Xp22.33 Microduplications in a Patient with Severe Myoclonic Epilepsy, Microcephaly, Dysmorphisms, Severe Psychomotor Delay and Intellectual Disability. Genes (Basel) 2020; 11:genes11050525. [PMID: 32397165 PMCID: PMC7288449 DOI: 10.3390/genes11050525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 11/16/2022] Open
Abstract
Copy number variations (CNVs) play a key role in the pathogenesis of several diseases, including a wide range of neurodevelopmental disorders. Here, we describe the detection of three CNVs simultaneously in a female patient with evidence of severe myoclonic epilepsy, microcephaly, hypertelorism, dimorphisms as well as severe psychomotor delay and intellectual disability. Array-CGH analysis revealed a ~240 kb microdeletion at the 7q35 inherited from her father, a ∼538 kb microduplication at the 15q13.3 region and a ∼178 kb microduplication at Xp22.33 region, both transmitted from her mother. The microdeletion in 7q35 was included within an intragenic region of the contactin associated protein-like 2 (CNTNAP2) gene, whereas the microduplications at 15q13.3 and Xp22.33 involved the cholinergic receptor nicotinic α 7 subunit (CHRNA7) and the cytokine receptor-like factor 2 (CRLF2) genes, respectively. Here, we describe a female patient harbouring three CNVs whose additive contribution could be responsible for her clinical phenotypes.
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MESH Headings
- Adult
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 15/ultrastructure
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 7/ultrastructure
- Chromosomes, Human, X/genetics
- Chromosomes, Human, X/ultrastructure
- Consanguinity
- DNA Copy Number Variations
- Epilepsies, Myoclonic/genetics
- Female
- Gene Duplication
- Genetic Association Studies
- Humans
- Membrane Proteins/genetics
- Microcephaly/genetics
- Nerve Tissue Proteins/genetics
- Neurodevelopmental Disorders/genetics
- Pedigree
- Receptors, Cytokine/genetics
- Sequence Deletion
- Tissue Array Analysis
- alpha7 Nicotinic Acetylcholine Receptor/genetics
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Affiliation(s)
- Francesco Paduano
- Medical Genetics Unit, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.P.); (E.C.); (F.T.); (N.P.)
- Tecnologica Research Institute and Marrelli Health, Biomedical Section, Stem Cells Unit, 88900 Crotone, Italy
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus S. Venuta, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Emma Colao
- Medical Genetics Unit, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.P.); (E.C.); (F.T.); (N.P.)
| | - Sara Loddo
- Medical Genetics Laboratory, Bambino Gesù Pediatric Hospital, IRCCS, 00165 Rome, Italy; (S.L.); (V.O.); (A.N.)
| | - Valeria Orlando
- Medical Genetics Laboratory, Bambino Gesù Pediatric Hospital, IRCCS, 00165 Rome, Italy; (S.L.); (V.O.); (A.N.)
| | - Francesco Trapasso
- Medical Genetics Unit, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.P.); (E.C.); (F.T.); (N.P.)
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus S. Venuta, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Antonio Novelli
- Medical Genetics Laboratory, Bambino Gesù Pediatric Hospital, IRCCS, 00165 Rome, Italy; (S.L.); (V.O.); (A.N.)
| | - Nicola Perrotti
- Medical Genetics Unit, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.P.); (E.C.); (F.T.); (N.P.)
- Department of Health Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy
| | - Rodolfo Iuliano
- Medical Genetics Unit, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.P.); (E.C.); (F.T.); (N.P.)
- Department of Health Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy
- Correspondence:
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13
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Babbs C, Brown J, Horsley SW, Slater J, Maifoshie E, Kumar S, Ooijevaar P, Kriek M, Dixon-McIver A, Harteveld CL, Traeger-Synodinos J, Wilkie AOM, Higgs DR, Buckle VJ. ATR-16 syndrome: mechanisms linking monosomy to phenotype. J Med Genet 2020; 57:414-421. [PMID: 32005695 PMCID: PMC7279195 DOI: 10.1136/jmedgenet-2019-106528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
Abstract
Background Deletions removing 100s–1000s kb of DNA, and variable numbers of poorly characterised genes, are often found in patients with a wide range of developmental abnormalities. In such cases, understanding the contribution of the deletion to an individual’s clinical phenotype is challenging. Methods Here, as an example of this common phenomenon, we analysed 41 patients with simple deletions of ~177 to ~2000 kb affecting one allele of the well-characterised, gene dense, distal region of chromosome 16 (16p13.3), referred to as ATR-16 syndrome. We characterised deletion extents and screened for genetic background effects, telomere position effect and compensatory upregulation of hemizygous genes. Results We find the risk of developmental and neurological abnormalities arises from much smaller distal chromosome 16 deletions (~400 kb) than previously reported. Beyond this, the severity of ATR-16 syndrome increases with deletion size, but there is no evidence that critical regions determine the developmental abnormalities associated with this disorder. Surprisingly, we find no evidence of telomere position effect or compensatory upregulation of hemizygous genes; however, genetic background effects substantially modify phenotypic abnormalities. Conclusions Using ATR-16 as a general model of disorders caused by CNVs, we show the degree to which individuals with contiguous gene syndromes are affected is not simply related to the number of genes deleted but depends on their genetic background. We also show there is no critical region defining the degree of phenotypic abnormalities in ATR-16 syndrome and this has important implications for genetic counselling.
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Affiliation(s)
- Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jill Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sharon W Horsley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joanne Slater
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Evie Maifoshie
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Paul Ooijevaar
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kriek
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Cornelis L Harteveld
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Traeger-Synodinos
- Department of Medical Genetics, National and Kapodistrian University of Athens, Athens, Greece
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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14
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Yehia L, Seyfi M, Niestroj LM, Padmanabhan R, Ni Y, Frazier TW, Lal D, Eng C. Copy Number Variation and Clinical Outcomes in Patients With Germline PTEN Mutations. JAMA Netw Open 2020; 3:e1920415. [PMID: 32003824 PMCID: PMC7042875 DOI: 10.1001/jamanetworkopen.2019.20415] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
IMPORTANCE PTEN is among the most common autism spectrum disorder (ASD)-predisposition genes. Germline PTEN mutation carriers can develop malignant neoplasms and/or neurodevelopmental disorders such as ASD and developmental delay. Why a single gene contributes to disparate clinical outcomes, even in patients with identical PTEN mutations, remains unclear. OBJECTIVE To investigate the association of copy number variations (CNVs), altered numbers of copies of DNA sequences within the genome, with specific phenotypes in patients with germline PTEN mutations. DESIGN, SETTING, AND PARTICIPANTS This prospective cohort study examined genome-wide microarrays performed on blood-derived DNA to detect germline CNVs from September 1, 2005, through January 3, 2018. Multicenter accrual occurred from community and academic medical centers throughout North America, South America, Europe, Australia, and Asia. Participants included patients with PTEN hamartoma tumor syndrome (PHTS) (n = 481), molecularly defined as carrying germline pathogenic PTEN mutations. Data were analyzed from November 14, 2018, to August 1, 2019. EXPOSURES Detection of CNVs from patient-derived germline DNA. MAIN OUTCOMES AND MEASURES Prevalence of pathogenic and/or likely pathogenic CNVs in patients with PHTS and association with ASD/developmental delay and/or cancer, ascertained through medical records and pathology reports. RESULTS The study included 481 patients with PHTS (mean [SD] age, 33.2 [21.6] years; 268 female [55.7%]). The analytic series consisted of 309 patients with PHTS and genetically determined European ancestry. Patients were divided into 3 phenotypic groups, excluding family members within each group. These include 110 patients with ASD/developmental delay, 194 without ASD/developmental delay, and 121 with cancer (of whom 116 were in the no ASD/developmental delay group). Genome-wide evaluation of autosomal CNVs indicated an increased CNV burden, particularly duplications in genic regions, in patients with ASD/developmental delay compared with those without ASD/developmental delay (odds ratio [OR], 1.9; 95% CI, 1.1-3.4; P = .03) and those with cancer (OR, 2.5; 95% CI, 1.3-4.6; P = .003). Eleven of the 110 patients (10.0%) with ASD/developmental delay carried pathogenic and/or likely pathogenic CNVs associated with neurodevelopmental disorders, compared with 5 of 194 (2.6%) without ASD/developmental delay (OR, 4.2; 95% CI, 1.4-13.7; P = .008) and 2 of 121 (1.7%) with cancer (OR, 6.6; 95% CI, 1.6-44.5; P = .007). Evidence of an association between pathogenic and/or likely pathogenic CNVs and PHTS with ASD/developmental delay was further supported in a validation series of 69 patients with PHTS of genetically determined non-European ancestry. CONCLUSIONS AND RELEVANCE These findings suggest that copy number variations are associated with the ASD/developmental delay clinical phenotype in PHTS, providing proof of principle for similarly heterogeneous disorders lacking outcome-specific associations.
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Affiliation(s)
- Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Marilyn Seyfi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Roshan Padmanabhan
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Ying Ni
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Thomas W. Frazier
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Autism Speaks, Cleveland, Ohio
- Department of Psychology, John Carroll University, University Heights, Ohio
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, Ohio
- Stanley Center for Psychiatric Research, Broad Institute of MIT (Massachusetts Institute of Technology) and Harvard, Cambridge, Massachusetts
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
- Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
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15
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de Coo A, Quintela I, Blanco J, Diz P, Carracedo Á. Assessment of genotyping tools applied in genetic susceptibility studies of periodontal disease: A systematic review. Arch Oral Biol 2018; 92:38-50. [DOI: 10.1016/j.archoralbio.2018.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 12/14/2022]
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16
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Zhang X, Wang B, Zhang L, You G, Palais RA, Zhou L, Fu Q. Accurate diagnosis of spinal muscular atrophy and 22q11.2 deletion syndrome using limited deoxynucleotide triphosphates and high-resolution melting. BMC Genomics 2018; 19:485. [PMID: 29925309 PMCID: PMC6011344 DOI: 10.1186/s12864-018-4833-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/29/2018] [Indexed: 12/29/2022] Open
Abstract
Background Copy number variation (CNV) has been implicated in the genetics of multiple human diseases. Spinal muscular atrophy (SMA) and 22q11.2 deletion syndrome (22q11.2DS) are two of the most common diseases which are caused by DNA copy number variations. Genetic diagnostics for these conditions would be enhanced by more accurate and efficient methods to detect the relevant CNVs. Methods Competitive PCR with limited deoxynucleotide triphosphates (dNTPs) and high-resolution melting (HRM) analysis was used to detect 22q11.2DS, SMA and SMA carrier status. For SMA, we focused on the copy number of SMN1 gene. For 22q11.2DS, we analyzed CNV for 3 genes (CLTCL1, KLHL22, and PI4KA) which are located between different region-specific low copy repeats. CFTR was used as internal reference gene for all targets. Short PCR products with separated Tms were designed by uMelt software. Results One hundred three clinical patient samples were pretested for possible SMN1 CNV, including carrier status, using multiplex ligation-dependent probe amplification (MLPA) commercial kit as gold standard. Ninety-nine samples consisting of 56 wild-type and 43 22q11.2DS samples were analyzed for CLTCL1, KLHL22, and PI4KA CNV also using MLPA. These samples were blinded and re-analyzed for the same CNVs using the limited dNTPs PCR with HRM analysis and the results were completely consistent with MLPA. Conclusions Limited dNTPs PCR with HRM analysis is an accurate method for detecting SMN1 and 22q11.2 CNVs. This method can be used quickly, reliably, and economically in large population screening for these diseases. Electronic supplementary material The online version of this article (10.1186/s12864-018-4833-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoqing Zhang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Bo Wang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Lichen Zhang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Guoling You
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Robert A Palais
- Department of Mathematics, Utah Valley University, Orem, UT, USA.,Department of Pathology, University of Utah Medical School, 50 N. Medical Drive, Salt Lake City, UT, 84132, USA
| | - Luming Zhou
- Department of Pathology, University of Utah Medical School, 50 N. Medical Drive, Salt Lake City, UT, 84132, USA.
| | - Qihua Fu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China.
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17
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Worthey EA. Analysis and Annotation of Whole-Genome or Whole-Exome Sequencing Derived Variants for Clinical Diagnosis. ACTA ACUST UNITED AC 2017; 95:9.24.1-9.24.28. [PMID: 29044471 DOI: 10.1002/cphg.49] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over the last 10 years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing or analysis (given access to appropriate tools), but rather clinical interpretation. Interpretation of genetic findings in a complex and ever changing clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires application of appropriate interpretation tools, as well as development and application of appropriate methodologies and standard procedures. This unit provides an overview of these items. Specific challenges related to implementation of genome-wide sequencing in a clinical setting are discussed. © 2017 by John Wiley & Sons, Inc.
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Lee CT, Bendriem RM, Wu WW, Shen RF. 3D brain Organoids derived from pluripotent stem cells: promising experimental models for brain development and neurodegenerative disorders. J Biomed Sci 2017; 24:59. [PMID: 28822354 PMCID: PMC5563385 DOI: 10.1186/s12929-017-0362-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/09/2017] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional (3D) brain organoids derived from human pluripotent stem cells (hPSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), appear to recapitulate the brain's 3D cytoarchitectural arrangement and provide new opportunities to explore disease pathogenesis in the human brain. Human iPSC (hiPSC) reprogramming methods, combined with 3D brain organoid tools, may allow patient-derived organoids to serve as a preclinical platform to bridge the translational gap between animal models and human clinical trials. Studies using patient-derived brain organoids have already revealed novel insights into molecular and genetic mechanisms of certain complex human neurological disorders such as microcephaly, autism, and Alzheimer's disease. Furthermore, the combination of hiPSC technology and small-molecule high-throughput screening (HTS) facilitates the development of novel pharmacotherapeutic strategies, while transcriptome sequencing enables the transcriptional profiling of patient-derived brain organoids. Finally, the addition of CRISPR/Cas9 genome editing provides incredible potential for personalized cell replacement therapy with genetically corrected hiPSCs. This review describes the history and current state of 3D brain organoid differentiation strategies, a survey of applications of organoids towards studies of neurodevelopmental and neurodegenerative disorders, and the challenges associated with their use as in vitro models of neurological disorders.
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Affiliation(s)
- Chun-Ting Lee
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD 20993 USA
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Building 52, Rm 1121, 10903 New Hampshire Avenue, Silver Spring, MD 20993 USA
| | - Raphael M. Bendriem
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021 USA
| | - Wells W. Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD 20993 USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD 20993 USA
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19
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Keshavan MS, Lawler AN, Nasrallah HA, Tandon R. New drug developments in psychosis: Challenges, opportunities and strategies. Prog Neurobiol 2017; 152:3-20. [PMID: 27519538 PMCID: PMC5362348 DOI: 10.1016/j.pneurobio.2016.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/11/2016] [Indexed: 02/06/2023]
Abstract
All currently approved drugs for schizophrenia work mainly by dopaminergic antagonism. While they are efficacious for psychotic symptoms, their efficacy is limited for negative symptoms and cognitive deficits which underlie the substantive disability in this illness. Recent insights into the biological basis of schizophrenia, especially in relation to non-dopaminergic mechanisms, have raised the efforts to find novel and effective drug targets, though with relatively little success thus far. Potential impediments to novel drug discovery include the continued use of symptom based disease definitions which leads to etiological and pathophysiological heterogeneity, lack of valid preclinical models for drug testing, and design limitations in clinical trials. These roadblocks can be addressed by (i) characterizing trans-diagnostic, translational pathophysiological dimensions as potential treatment targets, (ii) efficiency, accountability and, transparency in approaches to the clinical trials process, and (iii) leveraging recent advances in genetics and in vitro phenotypes. Accomplishing these goals is urgent given the significant unmet needs in the pharmacological treatment of schizophrenia. As this happens, it is imperative that clinicians employ optimal dosing, measurement-based care, and other best practices in utilizing existing treatments to optimize outcomes for their patients today.
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Affiliation(s)
- Matcheri S Keshavan
- Department of Psychiatry, Beth Israel Deaconess Medical Center and Massachusetts Mental Health Center, Harvard Medical School, United States.
| | - Ashley N Lawler
- Department of Psychiatry, Beth Israel Deaconess Medical Center and Massachusetts Mental Health Center, Harvard Medical School, United States
| | - Henry A Nasrallah
- Department of Neurology & Psychiatry, St Louis University, United States
| | - Rajiv Tandon
- Department of Psychiatry, University of Florida, Gainsville, Florida. and the North FL/South Georgia Veterans' Administration Medical Center, Gainesville, FL 32610, United States; The North Florida/South Georgia Veterans' Administration Medical Center, Gainesville, FL, 32610, United States
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20
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Gustincich S, Zucchelli S, Mallamaci A. The Yin and Yang of nucleic acid-based therapy in the brain. Prog Neurobiol 2016; 155:194-211. [PMID: 27887908 DOI: 10.1016/j.pneurobio.2016.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 11/16/2016] [Accepted: 11/20/2016] [Indexed: 02/06/2023]
Abstract
The post-genomic era has unveiled the existence of a large repertory of non-coding RNAs and repetitive elements that play a fundamental role in cellular homeostasis and dysfunction. These may represent unprecedented opportunities to modify gene expression at the right time in the correct space in vivo, providing an almost unlimited reservoir of new potential pharmacological agents. Hijacking their mode of actions, the druggable genome can be extended to regulatory RNAs and DNA elements in a scalable fashion. Here, we discuss the state-of-the-art of nucleic acid-based drugs to treat neurodegenerative diseases. Beneficial effects can be obtained by inhibiting (Yin) and increasing (Yang) gene expression, depending on the disease and the drug target. Together with the description of the current use of inhibitory RNAs (small inhibitory RNAs and antisense oligonucleotides) in animal models and clinical trials, we discuss the molecular basis and applications of new classes of activatory RNAs at transcriptional (RNAa) and translational (SINEUP) levels.
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Affiliation(s)
- Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy; Area of Neuroscience, SISSA, Trieste, Italy.
| | - Silvia Zucchelli
- Area of Neuroscience, SISSA, Trieste, Italy; Department of Health Sciences, Universita' del Piemonte Orientale, Novara, Italy
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21
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Analysis of induced pluripotent stem cells carrying 22q11.2 deletion. Transl Psychiatry 2016; 6:e934. [PMID: 27801899 PMCID: PMC5314118 DOI: 10.1038/tp.2016.206] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/18/2022] Open
Abstract
Given the complexity and heterogeneity of the genomic architecture underlying schizophrenia, molecular analyses of these patients with defined and large effect-size genomic defects could provide valuable clues. We established human-induced pluripotent stem cells from two schizophrenia patients with the 22q11.2 deletion (two cell lines from each subject, total of four cell lines) and three controls (total of four cell lines). Neurosphere size, neural differentiation efficiency, neurite outgrowth, cellular migration and the neurogenic-to-gliogenic competence ratio were significantly reduced in patient-derived cells. As an underlying mechanism, we focused on the role of DGCR8, a key gene for microRNA (miRNA) processing and mapped in the deleted region. In mice, Dgcr8 hetero-knockout is known to show a similar phenotype of reduced neurosphere size (Ouchi et al., 2013). The miRNA profiling detected reduced expression levels of miRNAs belonging to miR-17/92 cluster and miR-106a/b in the patient-derived neurospheres. Those miRNAs are reported to target p38α, and conformingly the levels of p38α were upregulated in the patient-derived cells. p38α is known to drive gliogenic differentiation. The inhibition of p38 activity by SB203580 in patient-derived neurospheres partially restored neurogenic competence. Furthermore, we detected elevated expression of GFAP, a gliogenic (astrocyte) marker, in postmortem brains from schizophrenia patients without the 22q11.2 deletion, whereas inflammation markers (IL1B and IL6) remained unchanged. In contrast, a neuronal marker, MAP2 expressions were decreased in schizophrenia brains. These results suggest that a dysregulated balance of neurogenic-to-gliogenic competence may underlie neurodevelopmental disorders such as schizophrenia.
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22
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Wang B, Ji T, Zhou X, Wang J, Wang X, Wang J, Zhu D, Zhang X, Sham PC, Zhang X, Ma X, Jiang Y. CNV analysis in Chinese children of mental retardation highlights a sex differentiation in parental contribution to de novo and inherited mutational burdens. Sci Rep 2016; 6:25954. [PMID: 27257017 PMCID: PMC4891738 DOI: 10.1038/srep25954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/06/2016] [Indexed: 12/28/2022] Open
Abstract
Rare copy number variations (CNVs) are a known genetic etiology in neurodevelopmental disorders (NDD). Comprehensive CNV analysis was performed in 287 Chinese children with mental retardation and/or development delay (MR/DD) and their unaffected parents. When compared with 5,866 ancestry-matched controls, 11~12% more MR/DD children carried rare and large CNVs. The increased CNV burden in MR/DD was predominantly due to de novo CNVs, the majority of which (62%) arose in the paternal germline. We observed a 2~3 fold increase of large CNV burden in the mothers of affected children. By implementing an evidence-based review approach, pathogenic structural variants were identified in 14.3% patients and 2.4% parents, respectively. Pathogenic CNVs in parents were all carried by mothers. The maternal transmission bias of deleterious CNVs was further replicated in a published dataset. Our study confirms the pathogenic role of rare CNVs in MR/DD, and provides additional evidence to evaluate the dosage sensitivity of some candidate genes. It also supports a population model of MR/DD that spontaneous mutations in males' germline are major contributor to the de novo mutational burden in offspring, with higher penetrance in male than female; unaffected carriers of causative mutations, mostly females, then contribute to the inherited mutational burden.
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Affiliation(s)
- Binbin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,National Research Institute of Family Planning, Beijing, China
| | - Taoyun Ji
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xueya Zhou
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China.,Department of Psychiatry and Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jing Wang
- Department of Medical Genetics, The Capital Medical University, Beijing, China
| | - Xi Wang
- National Research Institute of Family Planning, Beijing, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | | | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology at No.1 Hospital, Anhui Medical University, Heifei, Anhui, China
| | - Pak Chung Sham
- Department of Psychiatry and Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China
| | - Xu Ma
- National Research Institute of Family Planning, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. PLoS Comput Biol 2016; 12:e1004871. [PMID: 27177143 PMCID: PMC4866742 DOI: 10.1371/journal.pcbi.1004871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
By integrating Haar wavelets with Hidden Markov Models, we achieve drastically reduced running times for Bayesian inference using Forward-Backward Gibbs sampling. We show that this improves detection of genomic copy number variants (CNV) in array CGH experiments compared to the state-of-the-art, including standard Gibbs sampling. The method concentrates computational effort on chromosomal segments which are difficult to call, by dynamically and adaptively recomputing consecutive blocks of observations likely to share a copy number. This makes routine diagnostic use and re-analysis of legacy data collections feasible; to this end, we also propose an effective automatic prior. An open source software implementation of our method is available at http://schlieplab.org/Software/HaMMLET/ (DOI: 10.5281/zenodo.46262). This paper was selected for oral presentation at RECOMB 2016, and an abstract is published in the conference proceedings.
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24
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Lin GN, Corominas R, Lemmens I, Yang X, Tavernier J, Hill DE, Vidal M, Sebat J, Iakoucheva LM. Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases. Neuron 2015; 85:742-54. [PMID: 25695269 DOI: 10.1016/j.neuron.2015.01.010] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/17/2014] [Accepted: 01/14/2015] [Indexed: 12/19/2022]
Abstract
The psychiatric disorders autism and schizophrenia have a strong genetic component, and copy number variants (CNVs) are firmly implicated. Recurrent deletions and duplications of chromosome 16p11.2 confer a high risk for both diseases, but the pathways disrupted by this CNV are poorly defined. Here we investigate the dynamics of the 16p11.2 network by integrating physical interactions of 16p11.2 proteins with spatiotemporal gene expression from the developing human brain. We observe profound changes in protein interaction networks throughout different stages of brain development and/or in different brain regions. We identify the late mid-fetal period of cortical development as most critical for establishing the connectivity of 16p11.2 proteins with their co-expressed partners. Furthermore, our results suggest that the regulation of the KCTD13-Cul3-RhoA pathway in layer 4 of the inner cortical plate is crucial for controlling brain size and connectivity and that its dysregulation by de novo mutations may be a potential determinant of 16p11.2 CNV deletion and duplication phenotypes.
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Affiliation(s)
- Guan Ning Lin
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Roser Corominas
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Irma Lemmens
- Department of Medical Protein Research, VIB, and Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Xinping Yang
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Jan Tavernier
- Department of Medical Protein Research, VIB, and Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.
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25
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Manconi A, Manca E, Moscatelli M, Gnocchi M, Orro A, Armano G, Milanesi L. G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods. Front Bioeng Biotechnol 2015; 3:28. [PMID: 25806367 PMCID: PMC4354384 DOI: 10.3389/fbioe.2015.00028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/19/2015] [Indexed: 11/23/2022] Open
Abstract
Copy number variations (CNVs) are the most prevalent types of structural variations (SVs) in the human genome and are involved in a wide range of common human diseases. Different computational methods have been devised to detect this type of SVs and to study how they are implicated in human diseases. Recently, computational methods based on high-throughput sequencing (HTS) are increasingly used. The majority of these methods focus on mapping short-read sequences generated from a donor against a reference genome to detect signatures distinctive of CNVs. In particular, read-depth based methods detect CNVs by analyzing genomic regions with significantly different read-depth from the other ones. The pipeline analysis of these methods consists of four main stages: (i) data preparation, (ii) data normalization, (iii) CNV regions identification, and (iv) copy number estimation. However, available tools do not support most of the operations required at the first two stages of this pipeline. Typically, they start the analysis by building the read-depth signal from pre-processed alignments. Therefore, third-party tools must be used to perform most of the preliminary operations required to build the read-depth signal. These data-intensive operations can be efficiently parallelized on graphics processing units (GPUs). In this article, we present G-CNV, a GPU-based tool devised to perform the common operations required at the first two stages of the analysis pipeline. G-CNV is able to filter low-quality read sequences, to mask low-quality nucleotides, to remove adapter sequences, to remove duplicated read sequences, to map the short-reads, to resolve multiple mapping ambiguities, to build the read-depth signal, and to normalize it. G-CNV can be efficiently used as a third-party tool able to prepare data for the subsequent read-depth signal generation and analysis. Moreover, it can also be integrated in CNV detection tools to generate read-depth signals.
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Affiliation(s)
- Andrea Manconi
- Institute for Biomedical Technologies, National Research Council , Milan , Italy
| | - Emanuele Manca
- Department of Electrical and Electronic Engineering, University of Cagliari , Cagliari , Italy
| | - Marco Moscatelli
- Institute for Biomedical Technologies, National Research Council , Milan , Italy
| | - Matteo Gnocchi
- Institute for Biomedical Technologies, National Research Council , Milan , Italy
| | - Alessandro Orro
- Institute for Biomedical Technologies, National Research Council , Milan , Italy
| | - Giuliano Armano
- Department of Electrical and Electronic Engineering, University of Cagliari , Cagliari , Italy
| | - Luciano Milanesi
- Institute for Biomedical Technologies, National Research Council , Milan , Italy
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26
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Association of Copy Number Variations in Autism Spectrum Disorders: A Systematic Review. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/713109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Autism spectrum disorders (ASDs) are characterized by language impairments, social deficits, and repetitive behaviors. The onset of symptoms occurs by the age of 3 and shows a lifelong persistence. Genetics plays a major role in the etiology of ASD. Except genetics, several potential risk factors (environmental factors and epigenetics) may contribute to ASD. Copy number variations (CNVs) are the most widespread structural variations in the human genome. These variations can alter the genome structure either by deletion or by duplication. CNVs can be de novo or inherited. Chromosomal rearrangements have been detected in 5–10% of the patients with ASD and recently copy number changes ranging from a few kilobases (kb) to several megabases (Mb) in size have been reported. Recent data have also revealed that submicroscopic CNVs can have a role in ASD, and de novo CNVs seem to be a more common risk factor in sporadic compared with inherited forms of ASD. CNVs are being implicated as a contributor to the pathophysiology of complex neurodevelopmental disorders and they can affect a wide range of human phenotypes including mental retardation (MR), autism, neuropsychiatric disorders, and susceptibility to other complex traits such as HIV, Crohn’s disease, and psoriasis. This review emphasizes the major CNVs reported to date in ASD.
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Cappi C, Hounie AG, Mariani DB, Diniz JB, Silva ART, Reis VNS, Busso AF, Silva AG, Fidalgo F, Rogatto SR, Miguel EC, Krepischi AC, Brentani H. An inherited small microdeletion at 15q13.3 in a patient with early-onset obsessive-compulsive disorder. PLoS One 2014; 9:e110198. [PMID: 25303678 PMCID: PMC4193873 DOI: 10.1371/journal.pone.0110198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/18/2014] [Indexed: 01/22/2023] Open
Abstract
Copy number variations (CNVs) have been previously associated with several different neurodevelopmental psychiatric disorders, such as autism, schizophrenia, and attention deficit hyperactivity disorder (ADHD). The present study consisted of a pilot genome-wide screen for CNVs in a cohort of 16 patients with early-onset obsessive-compulsive disorder (OCD) and 12 mentally healthy individuals, using array-based comparative genomic hybridization (aCGH) on 44K arrays. A small rare paternal inherited microdeletion (∼64 kb) was identified in chromosome 15q13.3 of one male patient with very early onset OCD. The father did not have OCD. The deletion encompassed part of the FMN1 gene, which is involved with the glutamatergic system. This finding supports the hypothesis of a complex network of several genes expressed in the brain contributing for the genetic risk of OCD, and also supports the glutamatergic involvement in OCD, which has been previously reported in the literature.
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Affiliation(s)
- Carolina Cappi
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
| | - Ana Gabriela Hounie
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
- Federal University of São Paulo-UPIA-UNIFESP, São Paulo, Brazil
| | - Daniel B. Mariani
- Inter-institutional Grad Program on Bioinformatics, Institute of Mathematics and Statistics, São Paulo University, São Paulo, Brazil
| | - Juliana Belo Diniz
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
| | - Aderbal R. T. Silva
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
| | - Viviane N. S. Reis
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
| | - Ariane F. Busso
- International Research Center, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Felipe Fidalgo
- International Research Center, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Euripedes C. Miguel
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
| | - Ana C. Krepischi
- International Research Center, AC Camargo Cancer Center, São Paulo, Brazil
| | - Helena Brentani
- Institute and Department of Psychiatry, São Paulo University Medical School, São Paulo, Brazil
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28
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Ono S, Domschke K, Deckert J. Genomic structural variation in affective, anxiety, and stress-related disorders. J Neural Transm (Vienna) 2014; 122:69-78. [DOI: 10.1007/s00702-014-1309-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 09/02/2014] [Indexed: 12/18/2022]
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29
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Buxbaum JD, Bolshakova N, Brownfeld JM, Anney RJL, Bender P, Bernier R, Cook EH, Coon H, Cuccaro M, Freitag CM, Hallmayer J, Geschwind D, Klauck SM, Nurnberger JI, Oliveira G, Pinto D, Poustka F, Scherer SW, Shih A, Sutcliffe JS, Szatmari P, Vicente AM, Vieland V, Gallagher L. The Autism Simplex Collection: an international, expertly phenotyped autism sample for genetic and phenotypic analyses. Mol Autism 2014; 5:34. [PMID: 25392729 PMCID: PMC4228819 DOI: 10.1186/2040-2392-5-34] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 04/11/2014] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND There is an urgent need for expanding and enhancing autism spectrum disorder (ASD) samples, in order to better understand causes of ASD. METHODS In a unique public-private partnership, 13 sites with extensive experience in both the assessment and diagnosis of ASD embarked on an ambitious, 2-year program to collect samples for genetic and phenotypic research and begin analyses on these samples. The program was called The Autism Simplex Collection (TASC). TASC sample collection began in 2008 and was completed in 2010, and included nine sites from North America and four sites from Western Europe, as well as a centralized Data Coordinating Center. RESULTS Over 1,700 trios are part of this collection, with DNA from transformed cells now available through the National Institute of Mental Health (NIMH). Autism Diagnostic Interview-Revised (ADI-R) and Autism Diagnostic Observation Schedule-Generic (ADOS-G) measures are available for all probands, as are standardized IQ measures, Vineland Adaptive Behavioral Scales (VABS), the Social Responsiveness Scale (SRS), Peabody Picture Vocabulary Test (PPVT), and physical measures (height, weight, and head circumference). At almost every site, additional phenotypic measures were collected, including the Broad Autism Phenotype Questionnaire (BAPQ) and Repetitive Behavior Scale-Revised (RBS-R), as well as the non-word repetition scale, Communication Checklist (Children's or Adult), and Aberrant Behavior Checklist (ABC). Moreover, for nearly 1,000 trios, the Autism Genome Project Consortium (AGP) has carried out Illumina 1 M SNP genotyping and called copy number variation (CNV) in the samples, with data being made available through the National Institutes of Health (NIH). Whole exome sequencing (WES) has been carried out in over 500 probands, together with ancestry matched controls, and this data is also available through the NIH. Additional WES is being carried out by the Autism Sequencing Consortium (ASC), where the focus is on sequencing complete trios. ASC sequencing for the first 1,000 samples (all from whole-blood DNA) is complete and data will be released in 2014. Data is being made available through NIH databases (database of Genotypes and Phenotypes (dbGaP) and National Database for Autism Research (NDAR)) with DNA released in Dist 11.0. Primary funding for the collection, genotyping, sequencing and distribution of TASC samples was provided by Autism Speaks and the NIH, including the National Institute of Mental Health (NIMH) and the National Human Genetics Research Institute (NHGRI). CONCLUSIONS TASC represents an important sample set that leverages expert sites. Similar approaches, leveraging expert sites and ongoing studies, represent an important path towards further enhancing available ASD samples.
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Affiliation(s)
- Joseph D Buxbaum
- The Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Nadia Bolshakova
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Jessica M Brownfeld
- The Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Richard JL Anney
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Patrick Bender
- National Institute of Mental Health (NIMH), Bethesda, MD 20892-9663, USA
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Hilary Coon
- Psychiatry Department, University of Utah Medical School, Salt Lake City, UT 84108, USA
| | - Michael Cuccaro
- The John P Hussman Institute for Human Genomics, University of Miami, Miami, FL 33101, USA
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, JW Goethe University Frankfurt, 60528 Frankfurt, Germany
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Science, Child and Adolescent Psychiatry, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel Geschwind
- Department of Neurology, University of California at Los Angeles, School of Medicine, Los Angeles, CA 90095, USA
| | - Sabine M Klauck
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
- University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, 3000-602 Coimbra, Portugal
| | - Dalila Pinto
- The Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Fritz Poustka
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, JW Goethe University Frankfurt, 60528 Frankfurt, Germany
| | - Stephen W Scherer
- Department of Molecular Genetics, The Centre for Applied Genomics, Hospital for Sick Children and McLaughlin Centre and University of Toronto, Toronto, ON, Canada
| | - Andy Shih
- Autism Speaks, New York, NY 10016, USA
| | - James S Sutcliffe
- Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, Vanderbilt University, Nashville, TN 37232, USA
- Centers for Human Genetics Research and Molecular Neuroscience, Vanderbilt University, Nashville, TN 37232, USA
| | - Peter Szatmari
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Astrid M Vicente
- Instituto Nacional de Saúde Dr Ricardo Jorge, 1649-016 Lisbon, Portugal
- Instituto Gulbenkian de Ciência, P-2781-901 Oeiras, Portugal
- BioFIG-Center for Biodiversity, Functional & Integrative Genomics, Campus da FCUL, C2.2.12, Campo Grande, 1749-016 Lisboa, Portugal
| | - Veronica Vieland
- The Research Institute at Nationwide Children’s Hospital, The Ohio State University, Columbus, OH, USA
| | - Louise Gallagher
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
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30
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Raymond LJ, Deth RC, Ralston NVC. Potential Role of Selenoenzymes and Antioxidant Metabolism in relation to Autism Etiology and Pathology. AUTISM RESEARCH AND TREATMENT 2014; 2014:164938. [PMID: 24734177 PMCID: PMC3966422 DOI: 10.1155/2014/164938] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/07/2014] [Accepted: 01/27/2014] [Indexed: 11/17/2022]
Abstract
Autism and autism spectrum disorders (ASDs) are behaviorally defined, but the biochemical pathogenesis of the underlying disease process remains uncharacterized. Studies indicate that antioxidant status is diminished in autistic subjects, suggesting its pathology is associated with augmented production of oxidative species and/or compromised antioxidant metabolism. This suggests ASD may result from defects in the metabolism of cellular antioxidants which maintain intracellular redox status by quenching reactive oxygen species (ROS). Selenium-dependent enzymes (selenoenzymes) are important in maintaining intercellular reducing conditions, particularly in the brain. Selenoenzymes are a family of ~25 genetically unique proteins, several of which have roles in preventing and reversing oxidative damage in brain and endocrine tissues. Since the brain's high rate of oxygen consumption is accompanied by high ROS production, selenoenzyme activities are particularly important in this tissue. Because selenoenzymes can be irreversibly inhibited by many electrophiles, exposure to these organic and inorganic agents can diminish selenoenzyme-dependent antioxidant functions. This can impair brain development, particularly via the adverse influence of oxidative stress on epigenetic regulation. Here we review the physiological roles of selenoproteins in relation to potential biochemical mechanisms of ASD etiology and pathology.
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Affiliation(s)
- Laura J. Raymond
- Energy & Environmental Research Center, University of North Dakota, 15 North 23rd Street, Stop 9018, Grand Forks, ND 58202, USA
| | - Richard C. Deth
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Nicholas V. C. Ralston
- Energy & Environmental Research Center, University of North Dakota, 15 North 23rd Street, Stop 9018, Grand Forks, ND 58202, USA
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31
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Banerjee S, Riordan M, Bhat MA. Genetic aspects of autism spectrum disorders: insights from animal models. Front Cell Neurosci 2014; 8:58. [PMID: 24605088 PMCID: PMC3932417 DOI: 10.3389/fncel.2014.00058] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 02/07/2014] [Indexed: 01/26/2023] Open
Abstract
Autism spectrum disorders (ASDs) are a complex neurodevelopmental disorder that display a triad of core behavioral deficits including restricted interests, often accompanied by repetitive behavior, deficits in language and communication, and an inability to engage in reciprocal social interactions. ASD is among the most heritable disorders but is not a simple disorder with a singular pathology and has a rather complex etiology. It is interesting to note that perturbations in synaptic growth, development, and stability underlie a variety of neuropsychiatric disorders, including ASD, schizophrenia, epilepsy, and intellectual disability. Biological characterization of an increasing repertoire of synaptic mutants in various model organisms indicates synaptic dysfunction as causal in the pathophysiology of ASD. Our understanding of the genes and genetic pathways that contribute toward the formation, stabilization, and maintenance of functional synapses coupled with an in-depth phenotypic analysis of the cellular and behavioral characteristics is therefore essential to unraveling the pathogenesis of these disorders. In this review, we discuss the genetic aspects of ASD emphasizing on the well conserved set of genes and genetic pathways implicated in this disorder, many of which contribute to synapse assembly and maintenance across species. We also review how fundamental research using animal models is providing key insights into the various facets of human ASD.
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Affiliation(s)
- Swati Banerjee
- Department of Physiology, Center for Biomedical Neuroscience, School of Medicine, University of Texas Health Science Center San Antonio, TX, USA
| | - Maeveen Riordan
- Department of Physiology, Center for Biomedical Neuroscience, School of Medicine, University of Texas Health Science Center San Antonio, TX, USA
| | - Manzoor A Bhat
- Department of Physiology, Center for Biomedical Neuroscience, School of Medicine, University of Texas Health Science Center San Antonio, TX, USA
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32
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Worthey EA. Analysis and annotation of whole-genome or whole-exome sequencing-derived variants for clinical diagnosis. CURRENT PROTOCOLS IN HUMAN GENETICS 2013; 79:9.24.1-9.24.24. [PMID: 24510652 DOI: 10.1002/0471142905.hg0924s79] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Over the last several years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test under particular circumstances in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing but rather the analysis and interpretation. Interpretation of genetic findings in a clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires the development of novel or repositioned analysis tools, methodologies, and processes. This unit provides an overview of these items. Specific challenges related to implementation in a clinical setting are discussed.
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Affiliation(s)
- Elizabeth A Worthey
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin.,The Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Computer Science, University of Wisconsin, Milwaukee, Wisconsin
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Lin CF, Naj AC, Wang LS. Analyzing copy number variation using SNP array data: protocols for calling CNV and association tests. CURRENT PROTOCOLS IN HUMAN GENETICS 2013; 79:1.27.1-1.27.15. [PMID: 24510649 PMCID: PMC4015338 DOI: 10.1002/0471142905.hg0127s79] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
High-density SNP genotyping technology provides a low-cost, effective tool for conducting Genome Wide Association (GWA) studies. The wide adoption of GWA studies has indeed led to discoveries of disease- or trait-associated SNPs, some of which were subsequently shown to be causal. However, the nearly universal shortcoming of many GWA studies--missing heritability--has prompted great interest in searching for other types of genetic variation, such as copy number variation (CNV). Certain CNVs have been reported to alter disease susceptibility. Algorithms and tools have been developed to identify CNVs using SNP array hybridization intensity data. Such an approach provides an additional source of data with almost no extra cost. In this unit, we demonstrate the steps for calling CNVs from Illumina SNP array data using PennCNV and performing association analysis using R and PLINK.
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Affiliation(s)
- Chiao-Feng Lin
- Department of Pathology and Laboratory Medicine and
Institute for Biomedical Informatics, Perelman School of Medicine at the University
of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adam C Naj
- Department of Biostatistics and Epidemiology and Center for
Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the
University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine and
Institute for Biomedical Informatics, Perelman School of Medicine at the University
of Pennsylvania, Philadelphia, PA 19104, USA
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34
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Persico AM, Napolioni V. Autism genetics. Behav Brain Res 2013; 251:95-112. [PMID: 23769996 DOI: 10.1016/j.bbr.2013.06.012] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 12/22/2022]
Abstract
Autism spectrum disorder (ASD) is a severe neuropsychiatric disease with strong genetic underpinnings. However, genetic contributions to autism are extremely heterogeneous, with many different loci underlying the disease to a different extent in different individuals. Moreover, the phenotypic expression (i.e., "penetrance") of these genetic components is also highly variable, ranging from fully penetrant point mutations to polygenic forms with multiple gene-gene and gene-environment interactions. Furthermore, many genes involved in ASD are also involved in intellectual disability, further underscoring their lack of specificity in phenotypic expression. We shall hereby review current knowledge on the genetic basis of ASD, spanning genetic/genomic syndromes associated with autism, monogenic forms due to copy number variants (CNVs) or rare point mutations, mitochondrial forms, and polygenic autisms. Finally, the recent contributions of genome-wide association and whole exome sequencing studies will be highlighted.
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Affiliation(s)
- Antonio M Persico
- Child and Adolescent Neuropsychiatry Unit, University Campus Bio-Medico, Rome, Italy.
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35
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Lahiri DK, Maloney B. Gene × environment interaction by a longitudinal epigenome-wide association study (LEWAS) overcomes limitations of genome-wide association study (GWAS). Epigenomics 2013; 4:685-99. [PMID: 23244313 DOI: 10.2217/epi.12.60] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The goal of genome-wide association studies is to identify SNPs unique to disease. It usually involves a single sampling from subjects' lifetimes. While primary DNA sequence variation influences gene-expression levels, expression is also influenced by epigenetics, including the 'somatic epitype' (G(SE)), an epigenotype acquired postnatally. While genes are inherited, and novel polymorphisms do not routinely appear, G(SE) is fluid. Furthermore, G(SE) could respond to environmental factors (such as heavy metals) and to differences in exercise, maternal care and dietary supplements - all of which postnatally modify oxidation or methylation of DNA, leading to altered gene expression. Change in epigenetic status may be critical for the development of many diseases. We propose a 'longitudinal epigenome-wide association study', wherein G(SE) are measured at multiple time points along with subjects' histories. This Longitudinal epigenome-wide association study, based on the 'dynamic' somatic epitype over the 'static' genotype, merits further investigation.
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Affiliation(s)
- Debomoy K Lahiri
- Department of Psychiatry, Laboratory of Molecular Neurogenetics, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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36
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Chen Y, Tian L, Zhang F, Liu C, Lu T, Ruan Y, Wang L, Yan H, Yan J, Liu Q, Zhang H, Ma W, Yang J, Li K, Lv L, Zhang D, Yue W. Myosin Vb gene is associated with schizophrenia in Chinese Han population. Psychiatry Res 2013; 207:13-8. [PMID: 23561489 DOI: 10.1016/j.psychres.2013.02.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 01/29/2013] [Accepted: 02/21/2013] [Indexed: 11/27/2022]
Abstract
Myosin Vb (MYO5B) has recently been implicated in the etiology of bipolar disorder in a genome-wide association study (GWAS). This gene is involved in amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor subunit glutamate receptor 1 (GluR1) recycling and plays an important role in the primary excitatory neurotransmission. Dysfunction of the brain glutamate system has been postulated to be involved in the pathophysiology in schizophrenia. To further investigate the association between MYO5B polymorphisms and schizophrenia, we genotyped nine single nucleotide polymorphisms (SNPs) in an independent sample of 1463 individuals with schizophrenia and 1563 healthy control subjects, and detected three SNPs and two haplotype blocks which displayed significant association with schizophrenia. This association was further strengthened by the results of meta-analysis. Our data strongly supported that the MYO5B gene might be associated with schizophrenia in the Chinese Han population and they have implications for understanding the glutamate hypothesis of schizophrenia.
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Affiliation(s)
- Yaguang Chen
- Institute of Mental Health, Peking University, 51 Hua Yuan Bei Road, Beijing 100191, China
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CNVrd, a read-depth algorithm for assigning copy-number at the FCGR locus: population-specific tagging of copy number variation at FCGR3B. PLoS One 2013; 8:e63219. [PMID: 23646200 PMCID: PMC3640002 DOI: 10.1371/journal.pone.0063219] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 04/04/2013] [Indexed: 01/09/2023] Open
Abstract
The extent of contribution from common gene copy number (CN) variants in human disease is currently unresolved. Part of the reason for this is the technical difficulty in directly measuring CN variation (CNV) using molecular methods, and the lack of single nucleotide polymorphisms (SNPs) that can tag complex CNV that has arisen multiple times on different SNP haplotypes. One CNV locus implicated in human disease is FCGR. Here we aimed to use next-generation sequencing (NGS) data from the 1000 Genomes Project to assign CN at FCGR3A and FCGR3B and to comprehensively assess the ability of SNPs to tag specific CN variants. A read-depth algorithm was developed (CNVrd) and validated on a subset of HapMap samples using CN assignments that had previously been determined using molecular and microarray methods. At 7 out of 9 other complex loci there was >90% concordance with microarray data. However, given that some prior knowledge of CN is required, the generalizability of CNVrd is limited and should be applied to other complex CNV loci with caution. Subsequently, CN was assigned et FCGR3B using CNVrd in a total of 952 samples from the 1000 Genomes Project, using three classes and SNPs that correlated with duplication were identified. The best tag SNP was observed in the Mexican-American sample set for duplication at FCGR3B. This SNP (rs117435514, r2 = 0.79) also tagged similar duplication in Chinese and Japanese (r2 = 0.35–0.60), but not in Caucasian or African. No tag SNP for duplication at FCGR3A or deletion at FCGR3B was identified in any population. We conclude that it is possible to tag CNV at the FCGR locus, but CN and SNPs have to be characterized and correlated on a population-specific basis.
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38
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Nag A, Bochukova EG, Kremeyer B, Campbell DD, Muller H, Valencia-Duarte AV, Cardona J, Rivas IC, Mesa SC, Cuartas M, Garcia J, Bedoya G, Cornejo W, Herrera LD, Romero R, Fournier E, Reus VI, Lowe TL, Farooqi IS, Mathews CA, McGrath LM, Yu D, Cook E, Wang K, Scharf JM, Pauls DL, Freimer NB, Plagnol V, Ruiz-Linares A. CNV analysis in Tourette syndrome implicates large genomic rearrangements in COL8A1 and NRXN1. PLoS One 2013; 8:e59061. [PMID: 23533600 PMCID: PMC3606459 DOI: 10.1371/journal.pone.0059061] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 02/11/2013] [Indexed: 12/22/2022] Open
Abstract
Tourette syndrome (TS) is a neuropsychiatric disorder with a strong genetic component. However, the genetic architecture of TS remains uncertain. Copy number variation (CNV) has been shown to contribute to the genetic make-up of several neurodevelopmental conditions, including schizophrenia and autism. Here we describe CNV calls using SNP chip genotype data from an initial sample of 210 TS cases and 285 controls ascertained in two Latin American populations. After extensive quality control, we found that cases (N = 179) have a significant excess (P = 0.006) of large CNV (>500 kb) calls compared to controls (N = 234). Amongst 24 large CNVs seen only in the cases, we observed four duplications of the COL8A1 gene region. We also found two cases with ∼400 kb deletions involving NRXN1, a gene previously implicated in neurodevelopmental disorders, including TS. Follow-up using multiplex ligation-dependent probe amplification (and including 53 more TS cases) validated the CNV calls and identified additional patients with rearrangements in COL8A1 and NRXN1, but none in controls. Examination of available parents indicates that two out of three NRXN1 deletions detected in the TS cases are de-novo mutations. Our results are consistent with the proposal that rare CNVs play a role in TS aetiology and suggest a possible role for rearrangements in the COL8A1 and NRXN1 gene regions.
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Affiliation(s)
- Abhishek Nag
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Elena G. Bochukova
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Barbara Kremeyer
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Desmond D. Campbell
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Heike Muller
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ana V. Valencia-Duarte
- Laboratorio de Genética Molecular, SIU, Universidad de Antioquia, Medellín, Colombia
- Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Julio Cardona
- Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Isabel C. Rivas
- Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Sandra C. Mesa
- Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Mauricio Cuartas
- Laboratorio de Genética Molecular, SIU, Universidad de Antioquia, Medellín, Colombia
| | - Jharley Garcia
- Laboratorio de Genética Molecular, SIU, Universidad de Antioquia, Medellín, Colombia
| | - Gabriel Bedoya
- Laboratorio de Genética Molecular, SIU, Universidad de Antioquia, Medellín, Colombia
| | - William Cornejo
- Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana, Medellín, Colombia
- Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | | | | | | | - Victor I. Reus
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
| | - Thomas L. Lowe
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
| | - I. Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | | | - Carol A. Mathews
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
| | - Lauren M. McGrath
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Boston, Massachusetts, United States of America
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Dongmei Yu
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Ed Cook
- University of Illinois, Chicago, Illinois, United States of America
| | - Kai Wang
- University of Southern California, Los Angeles, California, United States of America
| | - Jeremiah M. Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Boston, Massachusetts, United States of America
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - David L. Pauls
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Boston, Massachusetts, United States of America
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Nelson B. Freimer
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Vincent Plagnol
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Andrés Ruiz-Linares
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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Ku CS, Polychronakos C, Tan EK, Naidoo N, Pawitan Y, Roukos DH, Mort M, Cooper DN. A new paradigm emerges from the study of de novo mutations in the context of neurodevelopmental disease. Mol Psychiatry 2013; 18:141-53. [PMID: 22641181 DOI: 10.1038/mp.2012.58] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The study of de novo point mutations (new germline mutations arising from the gametes of the parents) remained largely static until the arrival of next-generation sequencing technologies, which made both whole-exome sequencing (WES) and whole-genome sequencing (WGS) feasible in practical terms. Single nucleotide polymorphism genotyping arrays have been used to identify de novo copy-number variants in a number of common neurodevelopmental conditions such as schizophrenia and autism. By contrast, as point mutations and microlesions occurring de novo are refractory to analysis by these microarray-based methods, little was known about either their frequency or impact upon neurodevelopmental disease, until the advent of WES. De novo point mutations have recently been implicated in schizophrenia, autism and mental retardation through the WES of case-parent trios. Taken together, these findings strengthen the hypothesis that the occurrence of de novo mutations could account for the high prevalence of such diseases that are associated with a marked reduction in fecundity. De novo point mutations are also known to be responsible for many sporadic cases of rare dominant mendelian disorders such as Kabuki syndrome, Schinzel-Giedion syndrome and Bohring-Opitz syndrome. These disorders share a common feature in that they are all characterized by intellectual disability. In summary, recent WES studies of neurodevelopmental and neuropsychiatric disease have provided new insights into the role of de novo mutations in these disorders. Our knowledge of de novo mutations is likely to be further accelerated by WGS. However, the collection of case-parent trios will be a prerequisite for such studies. This review aims to discuss recent developments in the study of de novo mutations made possible by technological advances in DNA sequencing.
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Affiliation(s)
- C S Ku
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
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40
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Edsgärd D, Dalgaard MD, Weinhold N, Wesolowska-Andersen A, Rajpert-De Meyts E, Ottesen AM, Juul A, Skakkebæk NE, Skøt Jensen T, Gupta R, Leffers H, Brunak S. Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer. Front Endocrinol (Lausanne) 2013; 4:2. [PMID: 23372565 PMCID: PMC3557397 DOI: 10.3389/fendo.2013.00002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 01/07/2013] [Indexed: 01/09/2023] Open
Abstract
Testicular germ cell cancer (TGCC) is one of the most heritable forms of cancer. Previous genome-wide association studies have focused on single nucleotide polymorphisms, largely ignoring the influence of copy number variants (CNVs). Here we present a genome-wide study of CNV on a cohort of 212 cases and 437 controls from Denmark, which was genotyped at ∼1.8 million markers, half of which were non-polymorphic copy number markers. No association of common variants were found, whereas analysis of rare variants (present in less than 1% of the samples) initially indicated a single gene with significantly higher accumulation of rare CNVs in cases as compared to controls, at the gene PTPN1 (P = 3.8 × 10(-2), 0.9% of cases and 0% of controls). However, the CNV could not be verified by qPCR in the affected samples. Further, the CNV calling of the array-data was validated by sequencing of the GSTM1 gene, which showed that the CNV frequency was in complete agreement between the two platforms. This study therefore disconfirms the hypothesis that there exists a single CNV locus with a major effect size that predisposes to TGCC. Genome-wide pathway association analysis indicated a weak association of rare CNVs related to cell migration (false-discovery rate = 0.021, 1.8% of cases and 1.1% of controls). Dysregulation during migration of primordial germ cells has previously been suspected to be a part of TGCC development and this set of multiple rare variants may thereby have a minor contribution to an increased susceptibility of TGCCs.
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Affiliation(s)
- Daniel Edsgärd
- Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
| | | | - Nils Weinhold
- Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
| | | | | | - Anne Marie Ottesen
- Department of Growth and Reproduction, RigshospitaletCopenhagen, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, RigshospitaletCopenhagen, Denmark
| | - Niels E. Skakkebæk
- Department of Growth and Reproduction, RigshospitaletCopenhagen, Denmark
| | - Thomas Skøt Jensen
- Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
| | - Ramneek Gupta
- Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
| | - Henrik Leffers
- Department of Growth and Reproduction, RigshospitaletCopenhagen, Denmark
| | - Søren Brunak
- Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
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41
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Vorstman JAS, Anney RJL, Derks EM, Gallagher L, Gill M, de Jonge MV, van Engeland H, Kahn RS, Ophoff RA. No evidence that common genetic risk variation is shared between schizophrenia and autism. Am J Med Genet B Neuropsychiatr Genet 2013. [PMID: 23193033 DOI: 10.1002/ajmg.b.32121] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The similarity between aspects of the clinical presentation of schizophrenia and autism spectrum disorders (ASD) suggests that elements of the biological etiology may also be shared between these two disorders. Recently, an increasing number of rare, mostly structural genetic variants are reported to increase the risk of both schizophrenia and ASD. We hypothesized that given this evidence for a shared genetic background based on rare genetic variants, common risk alleles may also be shared between ASD and schizophrenia. To test this hypothesis, the polygenic score, which summarizes the collective effect of a large number of common risk alleles, was used. We examined whether the polygenic score derived from a schizophrenia case-control dataset, previously reported by Purcell et al., was able to differentiate ASD cases from controls. The results demonstrate that the schizophrenia-derived polygenic score is not different between ASD cases and controls, indicating that there is no important sharing of common risk alleles between the two neuropsychiatric disorders. Possibly, common risk alleles are less important in ASD in comparison to their more prominent role in schizophrenia and bipolar disorders. These findings provide important novel insights into shared and distinct elements of the genetic architecture of autism and schizophrenia.
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Affiliation(s)
- Jacob A S Vorstman
- Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands.
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42
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MacLeod AK, Davies G, Payton A, Tenesa A, Harris SE, Liewald D, Ke X, Luciano M, Lopez LM, Gow AJ, Corley J, Redmond P, McNeill G, Pickles A, Ollier W, Horan M, Starr JM, Pendleton N, Thomson PA, Porteous DJ, Deary IJ. Genetic copy number variation and general cognitive ability. PLoS One 2012; 7:e37385. [PMID: 23300510 PMCID: PMC3530597 DOI: 10.1371/journal.pone.0037385] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 04/18/2012] [Indexed: 01/06/2023] Open
Abstract
Differences in genomic structure between individuals are ubiquitous features of human genetic variation. Specific copy number variants (CNVs) have been associated with susceptibility to numerous complex psychiatric disorders, including attention-deficit-hyperactivity disorder, autism-spectrum disorders and schizophrenia. These disorders often display co-morbidity with low intelligence. Rare chromosomal deletions and duplications are associated with these disorders, so it has been suggested that these deletions or duplications may be associated with differences in intelligence. Here we investigate associations between large (≥500kb), rare (<1% population frequency) CNVs and both fluid and crystallized intelligence in community-dwelling older people. We observe no significant associations between intelligence and total CNV load. Examining individual CNV regions previously implicated in neuropsychological disorders, we find suggestive evidence that CNV regions around SHANK3 are associated with fluid intelligence as derived from a battery of cognitive tests. This is the first study to examine the effects of rare CNVs as called by multiple algorithms on cognition in a large non-clinical sample, and finds no effects of such variants on general cognitive ability.
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Affiliation(s)
- Andrew K. MacLeod
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Gail Davies
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Antony Payton
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, United Kingdom
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Xiayi Ke
- Medical Research Council Centre of Epidemiology for Child Health, University College London Institute of Child Health, London, United Kingdom
| | - Michelle Luciano
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Lorna M. Lopez
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alan J. Gow
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Janie Corley
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Redmond
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Geraldine McNeill
- Institute of Applied Health Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Andrew Pickles
- School of Epidemiology and Health Science, Department of Medicine, University of Manchester, Manchester, United Kingdom
| | - William Ollier
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, United Kingdom
| | - Michael Horan
- School of Community-Based Medicine, Neurodegeneration Research Group, University of Manchester, Manchester, United Kingdom
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Geriatric Medicine Unit, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil Pendleton
- School of Community-Based Medicine, Neurodegeneration Research Group, University of Manchester, Manchester, United Kingdom
| | - Pippa A. Thomson
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David J. Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
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43
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Millan MJ. An epigenetic framework for neurodevelopmental disorders: from pathogenesis to potential therapy. Neuropharmacology 2012; 68:2-82. [PMID: 23246909 DOI: 10.1016/j.neuropharm.2012.11.015] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 11/11/2012] [Accepted: 11/22/2012] [Indexed: 12/12/2022]
Abstract
Neurodevelopmental disorders (NDDs) are characterized by aberrant and delayed early-life development of the brain, leading to deficits in language, cognition, motor behaviour and other functional domains, often accompanied by somatic symptoms. Environmental factors like perinatal infection, malnutrition and trauma can increase the risk of the heterogeneous, multifactorial and polygenic disorders, autism and schizophrenia. Conversely, discrete genetic anomalies are involved in Down, Rett and Fragile X syndromes, tuberous sclerosis and neurofibromatosis, the less familiar Phelan-McDermid, Sotos, Kleefstra, Coffin-Lowry and "ATRX" syndromes, and the disorders of imprinting, Angelman and Prader-Willi syndromes. NDDs have been termed "synaptopathies" in reference to structural and functional disturbance of synaptic plasticity, several involve abnormal Ras-Kinase signalling ("rasopathies"), and many are characterized by disrupted cerebral connectivity and an imbalance between excitatory and inhibitory transmission. However, at a different level of integration, NDDs are accompanied by aberrant "epigenetic" regulation of processes critical for normal and orderly development of the brain. Epigenetics refers to potentially-heritable (by mitosis and/or meiosis) mechanisms controlling gene expression without changes in DNA sequence. In certain NDDs, prototypical epigenetic processes of DNA methylation and covalent histone marking are impacted. Conversely, others involve anomalies in chromatin-modelling, mRNA splicing/editing, mRNA translation, ribosome biogenesis and/or the regulatory actions of small nucleolar RNAs and micro-RNAs. Since epigenetic mechanisms are modifiable, this raises the hope of novel therapy, though questions remain concerning efficacy and safety. The above issues are critically surveyed in this review, which advocates a broad-based epigenetic framework for understanding and ultimately treating a diverse assemblage of NDDs ("epigenopathies") lying at the interface of genetic, developmental and environmental processes. This article is part of the Special Issue entitled 'Neurodevelopmental Disorders'.
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Affiliation(s)
- Mark J Millan
- Unit for Research and Discovery in Neuroscience, IDR Servier, 125 chemin de ronde, 78290 Croissy sur Seine, Paris, France.
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44
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An environmental analysis of genes associated with schizophrenia: hypoxia and vascular factors as interacting elements in the neurodevelopmental model. Mol Psychiatry 2012; 17:1194-205. [PMID: 22290124 DOI: 10.1038/mp.2011.183] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Investigating and understanding gene-environment interaction (G × E) in a neurodevelopmentally and biologically plausible manner is a major challenge for schizophrenia research. Hypoxia during neurodevelopment is one of several environmental factors related to the risk of schizophrenia, and links between schizophrenia candidate genes and hypoxia regulation or vascular expression have been proposed. Given the availability of a wealth of complex genetic information on schizophrenia in the literature without knowledge on the connections to environmental factors, we now systematically collected genes from candidate studies (using SzGene), genome-wide association studies (GWAS) and copy number variation (CNV) analyses, and then applied four criteria to test for a (theoretical) link to ischemia-hypoxia and/or vascular factors. In all, 55% of the schizophrenia candidate genes (n=42 genes) met the criteria for a link to ischemia-hypoxia and/or vascular factors. Genes associated with schizophrenia showed a significant, threefold enrichment among genes that were derived from microarray studies of the ischemia-hypoxia response (IHR) in the brain. Thus, the finding of a considerable match between genes associated with the risk of schizophrenia and IHR and/or vascular factors is reproducible. An additional survey of genes identified by GWAS and CNV analyses suggested novel genes that match the criteria. Findings for interactions between specific variants of genes proposed to be IHR and/or vascular factors with obstetric complications in patients with schizophrenia have been reported in the literature. Therefore, the extended gene set defined here may form a reasonable and evidence-based starting point for hypothesis-based testing of G × E interactions in clinical genetic and translational neuroscience studies.
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Dixon-Salazar TJ, Silhavy JL, Udpa N, Schroth J, Bielas S, Schaffer AE, Olvera J, Bafna V, Zaki MS, Abdel-Salam GH, Mansour LA, Selim L, Abdel-Hadi S, Marzouki N, Ben-Omran T, Al-Saana NA, Sonmez FM, Celep F, Azam M, Hill KJ, Collazo A, Fenstermaker AG, Novarino G, Akizu N, Garimella KV, Sougnez C, Russ C, Gabriel SB, Gleeson JG. Exome sequencing can improve diagnosis and alter patient management. Sci Transl Med 2012; 4:138ra78. [PMID: 22700954 DOI: 10.1126/scitranslmed.3003544] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The translation of "next-generation" sequencing directly to the clinic is still being assessed but has the potential for genetic diseases to reduce costs, advance accuracy, and point to unsuspected yet treatable conditions. To study its capability in the clinic, we performed whole-exome sequencing in 118 probands with a diagnosis of a pediatric-onset neurodevelopmental disease in which most known causes had been excluded. Twenty-two genes not previously identified as disease-causing were identified in this study (19% of cohort), further establishing exome sequencing as a useful tool for gene discovery. New genes identified included EXOC8 in Joubert syndrome and GFM2 in a patient with microcephaly, simplified gyral pattern, and insulin-dependent diabetes. Exome sequencing uncovered 10 probands (8% of cohort) with mutations in genes known to cause a disease different from the initial diagnosis. Upon further medical evaluation, these mutations were found to account for each proband's disease, leading to a change in diagnosis, some of which led to changes in patient management. Our data provide proof of principle that genomic strategies are useful in clarifying diagnosis in a proportion of patients with neurodevelopmental disorders.
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Affiliation(s)
- Tracy J Dixon-Salazar
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Jennifer L Silhavy
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Nitin Udpa
- Department of Computer Sciences, School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jana Schroth
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Stephanie Bielas
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Ashleigh E Schaffer
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Jesus Olvera
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Vineet Bafna
- Department of Computer Sciences, School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Ghada H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | | | - Laila Selim
- Cairo University Children's Hospital, Cairo 406, Egypt
| | | | - Naima Marzouki
- Laboratoire Génétique Moléculaire, El Razi University Hospital, Marrakech 2360, Morocco
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics Division, Department of Pediatrics, Hamad Medical Corporation, Doha 3050, Qatar
| | - Nouriya A Al-Saana
- Department of Pediatrics, Dhahran Health Center, Saudi Aramco Corporation, Dhahran 31311, KSA
| | - F Müjgan Sonmez
- Child Neurology Department, Medical School of Karadeniz Technical University, Trabzon 61080, Turkey
| | - Figen Celep
- Medical Biology Department, Medical School of Karadeniz Technical University, Trabzon 61080, Turkey
| | - Matloob Azam
- Department of Paediatrics and Child Neurology, Wah Medical College, Wah Cantt, Pakistan
| | - Kiley J Hill
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Adrienne Collazo
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Ali G Fenstermaker
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Gaia Novarino
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Naiara Akizu
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Kiran V Garimella
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Carrie Sougnez
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Carsten Russ
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Stacey B Gabriel
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
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Abstract
The adult form of attention deficit/hyperactivity disorder (aADHD) has a prevalence of up to 5% and is the most severe long-term outcome of this common neurodevelopmental disorder. Family studies in clinical samples suggest an increased familial liability for aADHD compared with childhood ADHD (cADHD), whereas twin studies based on self-rated symptoms in adult population samples show moderate heritability estimates of 30-40%. However, using multiple sources of information, the heritability of clinically diagnosed aADHD and cADHD is very similar. Results of candidate gene as well as genome-wide molecular genetic studies in aADHD samples implicate some of the same genes involved in ADHD in children, although in some cases different alleles and different genes may be responsible for adult versus childhood ADHD. Linkage studies have been successful in identifying loci for aADHD and led to the identification of LPHN3 and CDH13 as novel genes associated with ADHD across the lifespan. In addition, studies of rare genetic variants have identified probable causative mutations for aADHD. Use of endophenotypes based on neuropsychology and neuroimaging, as well as next-generation genome analysis and improved statistical and bioinformatic analysis methods hold the promise of identifying additional genetic variants involved in disease etiology. Large, international collaborations have paved the way for well-powered studies. Progress in identifying aADHD risk genes may provide us with tools for the prediction of disease progression in the clinic and better treatment, and ultimately may help to prevent persistence of ADHD into adulthood.
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Liao HM, Chao YL, Huang AL, Cheng MC, Chen YJ, Lee KF, Fang JS, Hsu CH, Chen CH. Identification and characterization of three inherited genomic copy number variations associated with familial schizophrenia. Schizophr Res 2012; 139:229-36. [PMID: 22682706 DOI: 10.1016/j.schres.2012.05.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 04/26/2012] [Accepted: 05/15/2012] [Indexed: 12/23/2022]
Abstract
Schizophrenia is a complex mental disorder with high degree of genetic influence in its etiology. Several recent studies revealed that copy number variations (CNVs) of genomic DNA contributed significantly to the genetic architecture of sporadic schizophrenia. This study aimed to investigate whether CNVs also contribute to the familial forms of schizophrenia. Using array-based comparative genomic hybridization technology, we searched for pathogenic CNV associated with schizophrenia in a sample of 60 index cases from multiplex schizophrenia families. We detected three inherited CNVs that were associated with schizophrenia in three families, including a microdeletion of ~4.4Mb at chromosome 6q12-q13, a microduplication of ~1Mb at chromosome 18q12.3, and an interstitial duplication of ~5Mb at chromosome 15q11.2-q13.1. Our data indicate that CNVs contribute to the genetic underpinnings of the familial forms of schizophrenia as well as of the sporadic form. As 15q11-13 duplication is a well-known recurrent CNV associated with autism in the literature, the detection of the 15q11.2-q13.1 duplication in our schizophrenia patients provides additional support to other studies reporting that schizophrenia is part of the clinical spectrum of 15q11-q13 duplication syndrome.
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Affiliation(s)
- Hsiao-Mei Liao
- Institute of Biotechnology and Graduate Program of Biotechnology in Medicine, National Tsing-Hua University, Hsinchu, Taiwan
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48
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Animal models of psychiatric disorders that reflect human copy number variation. Neural Plast 2012; 2012:589524. [PMID: 22900207 PMCID: PMC3414062 DOI: 10.1155/2012/589524] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 12/04/2022] Open
Abstract
The development of genetic technologies has led to the identification of several copy number variations (CNVs) in the human genome. Genome rearrangements affect dosage-sensitive gene expression in normal brain development. There is strong evidence associating human psychiatric disorders, especially autism spectrum disorders (ASDs) and schizophrenia to genetic risk factors and accumulated CNV risk loci. Deletions in 1q21, 3q29, 15q13, 17p12, and 22q11, as well as duplications in 16p11, 16p13, and 15q11-13 have been reported as recurrent CNVs in ASD and/or schizophrenia. Chromosome engineering can be a useful technology to reflect human diseases in animal models, especially CNV-based psychiatric disorders. This system, based on the Cre/loxP strategy, uses large chromosome rearrangement such as deletion, duplication, inversion, and translocation. Although it is hard to reflect human pathophysiology in animal models, some aspects of molecular pathways, brain anatomy, cognitive, and behavioral phenotypes can be addressed. Some groups have created animal models of psychiatric disorders, ASD, and schizophrenia, which are based on human CNV. These mouse models display some brain anatomical and behavioral abnormalities, providing insight into human neuropsychiatric disorders that will contribute to novel drug screening for these devastating disorders.
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Qiu S, Aldinger KA, Levitt P. Modeling of autism genetic variations in mice: focusing on synaptic and microcircuit dysfunctions. Dev Neurosci 2012; 34:88-100. [PMID: 22572629 DOI: 10.1159/000336644] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/21/2011] [Indexed: 12/24/2022] Open
Abstract
Autism spectrum disorders (ASD) are heterogeneous neurodevelopmental disorders that are characterized by deficits in social interaction, verbal and nonverbal communication, and restrictive interests and repetitive behaviors. While human genetic studies have revealed marked heritability in ASD, it has been challenging to translate this genetic risk into a biological mechanism that influences brain development relevant to the disorder phenotypes. This is partly due to the complex genetic architecture of ASD, which involves de novo gene mutations, genomic abnormalities, and common genetic variants. Rather than trying to reconstitute the clinical disorder, using genetic model animals to examine specific features of core ASD pathophysiology offers unique opportunities for refining our understanding of neurodevelopmental mechanisms in ASD. A variety of ASD-relevant phenotypes can now be investigated in rodents, including stereotyped and repetitive behaviors, and deficits in social interaction and communication. In this review, we focus on several prevailing mouse models and discuss how studies have advanced our understanding of synaptic mechanisms that may underlie ASD pathophysiology. Although synaptic perturbations are not the only alterations relevant for ASD, we reason that understanding the synaptic underpinnings of ASD using mouse models may provide mechanistic insights into its etiology and lead to novel therapeutic and interventional strategies.
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Affiliation(s)
- Shenfeng Qiu
- Department of Cell and Neurobiology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, Calif., USA
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50
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Abstract
Molecular mechanisms underlying brain structure and function are affected by nutrition throughout the life cycle, with profound implications for health and disease. Responses to nutrition are in turn influenced by individual differences in multiple target genes. Recent advances in genomics and epigenomics are increasing understanding of mechanisms by which nutrition and genes interact. This review starts with a short account of current knowledge on nutrition-gene interactions, focusing on the significance of epigenetics to nutritional regulation of gene expression, and the roles of SNP and copy number variants (CNV) in determining individual responses to nutrition. A critical assessment is then provided of recent advances in nutrition-gene interactions, and especially energy status, in three related areas: (i) mental health and well-being, (ii) mental disorders and schizophrenia, (iii) neurological (neurodevelopmental and neurodegenerative) disorders and Alzheimer's disease. Optimal energy status, including physical activity, has a positive role in mental health. By contrast, sub-optimal energy status, including undernutrition and overnutrition, is implicated in many disorders of mental health and neurology. These actions are mediated by changes in energy metabolism and multiple signalling molecules, e.g. brain-derived neurotrophic factor (BDNF). They often involve epigenetic mechanisms, including DNA methylation and histone modifications. Recent advances show that many brain disorders result from a sophisticated network of interactions between numerous environmental and genetic factors. Personal, social and economic costs of sub-optimal brain health are immense. Future advances in understanding the complex interactions between nutrition, genes and the brain should help to reduce these costs and enhance quality of life.
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