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Zhuo C, Hou W, Lin C, Hu L, Li J. Potential Value of Genomic Copy Number Variations in Schizophrenia. Front Mol Neurosci 2017; 10:204. [PMID: 28680393 PMCID: PMC5478687 DOI: 10.3389/fnmol.2017.00204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/09/2017] [Indexed: 11/13/2022] Open
Abstract
Schizophrenia is a devastating neuropsychiatric disorder affecting approximately 1% of the global population, and the disease has imposed a considerable burden on families and society. Although, the exact cause of schizophrenia remains unknown, several lines of scientific evidence have revealed that genetic variants are strongly correlated with the development and early onset of the disease. In fact, the heritability among patients suffering from schizophrenia is as high as 80%. Genomic copy number variations (CNVs) are one of the main forms of genomic variations, ubiquitously occurring in the human genome. An increasing number of studies have shown that CNVs account for population diversity and genetically related diseases, including schizophrenia. The last decade has witnessed rapid advances in the development of novel genomic technologies, which have led to the identification of schizophrenia-associated CNVs, insight into the roles of the affected genes in their intervals in schizophrenia, and successful manipulation of the target CNVs. In this review, we focus on the recent discoveries of important CNVs that are associated with schizophrenia and outline the potential values that the study of CNVs will bring to the areas of schizophrenia research, diagnosis, and therapy. Furthermore, with the help of the novel genetic tool known as the Clustered Regularly Interspaced Short Palindromic Repeats-associated nuclease 9 (CRISPR/Cas9) system, the pathogenic CNVs as genomic defects could be corrected. In conclusion, the recent novel findings of schizophrenia-associated CNVs offer an exciting opportunity for schizophrenia research to decipher the pathological mechanisms underlying the onset and development of schizophrenia as well as to provide potential clinical applications in genetic counseling, diagnosis, and therapy for this complex mental disease.
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Affiliation(s)
- Chuanjun Zhuo
- Department of Psychological Medicine, Wenzhou Seventh People's HospitalWenzhou, China.,Department of Psychological Medicine, Tianjin Anding HospitalTianjin, China
| | - Weihong Hou
- Department of Biology, University of North Carolina at CharlotteCharlotte, NC, United States.,Department of Biochemistry and Molecular Biology, Zhengzhou UniversityZhengzhou, China
| | - Chongguang Lin
- Department of Psychological Medicine, Wenzhou Seventh People's HospitalWenzhou, China
| | - Lirong Hu
- Department of Psychological Medicine, Wenzhou Seventh People's HospitalWenzhou, China
| | - Jie Li
- Department of Psychological Medicine, Tianjin Anding HospitalTianjin, China
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2
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Detection of Turner syndrome using X-chromosome inactivation specific differentially methylated CpG sites: A pilot study. Clin Chim Acta 2017; 468:174-179. [DOI: 10.1016/j.cca.2017.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/02/2017] [Accepted: 03/07/2017] [Indexed: 11/17/2022]
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3
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Zhao Q, Li T, Zhao X, Huang K, Wang T, Li Z, Ji J, Zeng Z, Zhang Z, Li K, Feng G, St Clair D, He L, Shi Y. Rare CNVs and tag SNPs at 15q11.2 are associated with schizophrenia in the Han Chinese population. Schizophr Bull 2013; 39:712-9. [PMID: 22317777 PMCID: PMC3627771 DOI: 10.1093/schbul/sbr197] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Rare copy number variations (CNVs) were involved in the etiology of neuropsychiatric disorders, and some of them appeared to be shared risk factors for several different diseases. One of those promising loci is the CNV at 15q11.2, including 4 genes, TUBGCP5, CYFIP1, NIPA2, and NIPA1. Several studies showed that microdeletions at this locus were significant associated with schizophrenia. In the current study, we investigated the role of both rare CNVs and common single nucleotide polymorphisms (SNPs) at 15q11.2 in schizophrenia in the Chinese Han population. METHODS We screened deletions at 15q11.2 in 2058 schizophrenia patients and 3275 normal controls in Chinese Han population by Affymetrix 500K/6.0 SNP arrays and SYBR green real-time polymerase chain reaction and then validated deletions by multiplex ligation-dependent probe amplification and Taqman real-time assays. We successfully genotyped 27 tag SNPs in total and tested associations in 1144 schizophrenia cases and 1144 normal controls. RESULTS We found a triple increase of deletions in cases over controls, with OR=4.45 (95% CI=1.36-14.60) and P=.014. In the analysis of common SNPs, we found that the most significant SNP in schizophrenia was rs4778334 (OR=.72, 95% CI=0.60-0.87, allelic P=.0056 after permutation, genotypic P=.015 after permutation). We also found SNP rs1009153 in CYFIP1 was associated with schizophrenia (OR=0.82, 95% CI=0.73-0.93, allelic P=.044 after permutation). CONCLUSION We found that both rare deletions and common variants at 15q11.2 were associated with schizophrenia in the Chinese Han population.
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Affiliation(s)
- Qian Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China,Changning Mental Health Center, Bio-X Institutes Affiliated Hospital, Shanghai Jiao Tong University, 299 XieHe Road, Shanghai 200042, People's Republic of China
| | - Tao Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China,Changning Mental Health Center, Bio-X Institutes Affiliated Hospital, Shanghai Jiao Tong University, 299 XieHe Road, Shanghai 200042, People's Republic of China
| | - XinZhi Zhao
- Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Ke Huang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ti Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - ZhiQiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jue Ji
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhen Zeng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhao Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Kan Li
- East China University of Science and Technology, Shanghai, People's Republic of China
| | - GuoYin Feng
- Shanghai Institute of Mental Health, Shanghai, People's Republic of China
| | - David St Clair
- Department of Mental Health, University of Aberdeen, Aberdeen, UK
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China,Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China,Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China,Institute for Nutritional Sciences, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - YongYong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China,Changning Mental Health Center, Bio-X Institutes Affiliated Hospital, Shanghai Jiao Tong University, 299 XieHe Road, Shanghai 200042, People's Republic of China,Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China,To whom correspondence should be addressed; tel: 86-21-62933338, fax: 86-21-62933338, e-mail:
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4
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Zheng X, Bei JX, Xu H, Lee J, Chong SA, Sim K, Liany H, Shyong TE, Liu T, Foo JN, Irwan ID, Teo YY, Liu J. The association between rare large duplication of 16p11.2 and schizophrenia in the Singaporean Chinese population. Schizophr Res 2013; 146:368-9. [PMID: 23510594 DOI: 10.1016/j.schres.2013.02.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 02/19/2013] [Accepted: 02/24/2013] [Indexed: 11/25/2022]
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Abstract
In this review, we discuss some of the most recent developments in genomics research and their relevance to the field of pediatrics. In particular, we examine 3 major approaches that are being used to identify genetic correlates of disease: genome-wide association studies, copy number variation studies, and next-generation sequencing. In the past few years, these approaches have yielded major insights into the causes and pathophysiology of a wide range of diseases but are also constrained by certain limitations. This review provides an overview of the genomic landscape in complex pediatric disorders and sets the stage for translating new discoveries into clinical practice, the future of genomic medicine.
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Affiliation(s)
- John J. Connolly
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania; and
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania; and,Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
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Vyas NS, Shamsi SA, Malhotra AK, Aitchison KJ, Kumari V. Can genetics inform the management of cognitive deficits in schizophrenia? J Psychopharmacol 2012; 26:334-48. [PMID: 22328662 DOI: 10.1177/0269881111434623] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
There is no doubt that schizophrenia has a significant genetic component and a number of candidate genes have been identified for this debilitating disorder. Of note, several of these are implicated in cognition. Cognitive deficits constitute core symptoms of schizophrenia, and while current antipsychotic treatment strategies aim to help psychosis-related symptomatology, the cognitive symptom domain is largely inadequately treated. A number of other pharmacological approaches (e.g. using drugs that target specific neurotransmitter systems) have also been attempted for the amelioration of cognitive deficits in this population; however, these too have had limited success so far. Psychological interventions appear promising, though there has been speculation regarding whether or not these produce long-term functional improvements. Pharmacogenetic studies of the cognitive effects of currently available antipsychotics, although in relatively early stages, suggest that the treatment of cognitive deficits in schizophrenia may be advanced by focusing on genetic variants associated with specific cognitive dysfunctions in the general population and using this to match the most relevant pharmacological and/or psychological interventions with the genetic and cognitive profiles of the target population. Such a strategy would encourage bottom-up advances in drug development and provide a platform for individualised treatment of cognitive deficits in schizophrenia.
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Affiliation(s)
- Nora S Vyas
- King's College London, Institute of Psychiatry, MRC SGDP Centre, London, UK.
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7
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Abstract
Rather than being polygenic, complex disorders probably represent umbrella terms for collections of conditions caused by rare, recent mutations in any of a large number of different genes.
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Affiliation(s)
- Kevin J Mitchell
- Smurfit Institute of Genetics and Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland.
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8
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Abstract
Psychiatric disorders are multifactorial in nature with complex genetic architecture. A number of recent studies, building upon earlier findings of copy number variants (CNVs) at the 22q11.2 locus, suggest that rare CNVs represent an important component of genetic heterogeneity in the etiology of complex psychiatric diseases, such as schizophrenia. De novo CNVs are found with higher frequency among sporadic cases, whereas inherited CNVs are enriched among familial cases. Despite substantial progress, a number of challenges remain, such as pinpointing causative relationships between specific gene(s) affected by CNVs and disease phenotypes as well as distinguishing abnormal structural mutations from neutral polymorphisms and establishing a clear association between individual pathogenic CNV and disease phenotypes.
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Affiliation(s)
- Rebecca J Levy
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
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9
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Mitchell KJ, Huang ZJ, Moghaddam B, Sawa A. Following the genes: a framework for animal modeling of psychiatric disorders. BMC Biol 2011; 9:76. [PMID: 22078115 PMCID: PMC3214139 DOI: 10.1186/1741-7007-9-76] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 11/07/2011] [Indexed: 01/19/2023] Open
Abstract
The number of individual cases of psychiatric disorders that can be ascribed to identified, rare, single mutations is increasing with great rapidity. Such mutations can be recapitulated in mice to generate animal models with direct etiological validity. Defining the underlying pathogenic mechanisms will require an experimental and theoretical framework to make the links from mutation to altered behavior in an animal or psychopathology in a human. Here, we discuss key elements of such a framework, including cell type-based phenotyping, developmental trajectories, linking circuit properties at micro and macro scales and definition of neurobiological phenotypes that are directly translatable to humans.
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Affiliation(s)
- Kevin J Mitchell
- Smurfit Institute of Genetics and Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bita Moghaddam
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Akira Sawa
- Department of Psychiatry and Behavioral Sciences and Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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10
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Hochstenbach R, Buizer-Voskamp JE, Vorstman JAS, Ophoff RA. Genome arrays for the detection of copy number variations in idiopathic mental retardation, idiopathic generalized epilepsy and neuropsychiatric disorders: lessons for diagnostic workflow and research. Cytogenet Genome Res 2011; 135:174-202. [PMID: 22056632 DOI: 10.1159/000332928] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
We review the contributions and limitations of genome-wide array-based identification of copy number variants (CNVs) in the clinical diagnostic evaluation of patients with mental retardation (MR) and other brain-related disorders. In unselected MR referrals a causative genomic gain or loss is detected in 14-18% of cases. Usually, such CNVs arise de novo, are not found in healthy subjects, and have a major impact on the phenotype by altering the dosage of multiple genes. This high diagnostic yield justifies array-based segmental aneuploidy screening as the initial genetic test in these patients. This also pertains to patients with autism (expected yield about 5-10% in nonsyndromic and 10-20% in syndromic patients) and schizophrenia (at least 5% yield). CNV studies in idiopathic generalized epilepsy, attention-deficit hyperactivity disorder, major depressive disorder and Tourette syndrome indicate that patients have, on average, a larger CNV burden as compared to controls. Collectively, the CNV studies suggest that a wide spectrum of disease-susceptibility variants exists, most of which are rare (<0.1%) and of variable and usually small effect. Notwithstanding, a rare CNV can have a major impact on the phenotype. Exome sequencing in MR and autism patients revealed de novo mutations in protein coding genes in 60 and 20% of cases, respectively. Therefore, it is likely that arrays will be supplanted by next-generation sequencing methods as the initial and perhaps ultimate diagnostic tool in patients with brain-related disorders, revealing both CNVs and mutations in a single test.
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Affiliation(s)
- R Hochstenbach
- Division of Biomedical Genetics, Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands.
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11
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Gejman PV, Sanders AR, Kendler KS. Genetics of Schizophrenia: New Findings and Challenges. Annu Rev Genomics Hum Genet 2011; 12:121-44. [DOI: 10.1146/annurev-genom-082410-101459] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pablo V. Gejman
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute, and University of Chicago, Evanston, Illinois 60201;
| | - Alan R. Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute, and University of Chicago, Evanston, Illinois 60201;
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics and Departments of Psychiatry and Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298;
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12
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Lee KW, Woon PS, Teo YY, Sim K. Genome wide association studies (GWAS) and copy number variation (CNV) studies of the major psychoses: what have we learnt? Neurosci Biobehav Rev 2011; 36:556-71. [PMID: 21946175 DOI: 10.1016/j.neubiorev.2011.09.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 09/03/2011] [Accepted: 09/13/2011] [Indexed: 12/29/2022]
Abstract
Schizophrenia (SZ) and bipolar disorder (BPD) have high heritabilities and are clinically and genetically complex. Genome wide association studies (GWAS) and studies of copy number variations (CNV) in SZ and BPD have allowed probing of their underlying genetic risks. In this systematic review, we assess extant genetic signals from published GWAS and CNV studies of SZ and BPD up till March 2011. Risk genes associated with SZ at genome wide significance level (p value<7.2 × 10(-8)) include zinc finger binding protein 804A (ZNF804A), major histocompatibility (MHC) region on chromosome 6, neurogranin (NRGN) and transcription factor 4 (TCF4). Risk genes associated with BPD include ankyrin 3, node of Ranvier (ANK3), calcium channel, voltage dependent, L type, alpha 1C subunit (CACNA1C), diacylglycerol kinase eta (DGKH), gene locus on chromosome 16p12, and polybromo-1 (PBRM1) and very recently neurocan gene (NCAN). Possible common genes underlying psychosis include ZNF804A, CACNA1C, NRGN and PBRM1. The CNV studies suggest that whilst CNVs are found in both SZ and BPD, the large deletions and duplications are more likely found in SZ rather than BPD. The validation of any genetic signal is likely confounded by genetic and phenotypic heterogeneities which are influenced by epistatic, epigenetic and gene-environment interactions. There is a pressing need to better integrate the multiple research platforms including systems biology computational models, genomics, cross disorder phenotyping studies, transcriptomics, proteomics, metabolomics, neuroimaging and clinical correlations in order to get us closer to a more enlightened understanding of the genetic and biological basis underlying these potentially crippling conditions.
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Affiliation(s)
- Kok Wei Lee
- Institute of Mental Health/Woodbridge Hospital 10, Buangkok View, Singapore 539747, Singapore
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13
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Abstract
Copy number variants (CNVs) play an important role in human disease and population diversity. Advancements in technology have allowed for the analysis of CNVs in thousands of individuals with disease in addition to thousands of controls. These studies have identified rare CNVs associated with neuropsychiatric diseases such as autism, schizophrenia, and intellectual disability. In addition, copy number polymorphisms (CNPs) are present at higher frequencies in the population, show high diversity in copy number, sequence, and structure, and have been associated with multiple phenotypes, primarily related to immune or environmental response. However, the landscape of copy number variation still remains largely unexplored, especially for smaller CNVs and those embedded within complex regions of the human genome. An integrated approach including characterization of single nucleotide variants and CNVs in a large number of individuals with disease and normal genomes holds the promise of thoroughly elucidating the genetic basis of human disease and diversity.
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Affiliation(s)
- Santhosh Girirajan
- Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
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14
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Abstract
BACKGROUND For many years, the prevailing paradigm has stated that in each individual with schizophrenia (SZ) the genetic risk is due to a combination of many genetic variants, individually of small effect. Recent empirical data are prompting a re-evaluation of this polygenic, common disease-common variant (CDCV) model. Evidence includes a lack of the expected strong positive findings from genome-wide association studies and the concurrent discovery of many different mutations that individually strongly predispose to SZ and other psychiatric disorders. This has led some to adopt a mixed model wherein some cases are caused by polygenic mechanisms and some by single mutations. This model runs counter to a substantial body of theoretical literature that had supposedly conclusively rejected Mendelian inheritance with genetic heterogeneity. Here we ask how this discrepancy between theory and data arose and propose a rationalization of the recent evidence base. METHOD In light of recent empirical findings, we reconsider the methods and conclusions of early theoretical analyses and the explicit assumptions underlying them. RESULTS We show that many of these assumptions can now be seen to be false and that the model of genetic heterogeneity is consistent with observed familial recurrence risks, endophenotype studies and other population-wide parameters. CONCLUSIONS We argue for a more biologically consilient mixed model that involves interactions between disease-causing and disease-modifying variants in each individual. We consider the implications of this model for moving SZ research beyond statistical associations to pathogenic mechanisms.
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Affiliation(s)
- K J Mitchell
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland.
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15
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Rare genomic deletions and duplications and their role in neurodevelopmental disorders. Curr Top Behav Neurosci 2011; 12:345-60. [PMID: 22241247 DOI: 10.1007/7854_2011_179] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Copy number variations (CNVs) are deletions and duplications of DNA sequences that vary in length from a few base pairs to several million. While these structural variations are often benign, they can disrupt vital biological functions and result in disease. CNVs have been identified as causal in a number of neurodevelopmental disorders (NDs), including but not limited to, autism, attention-deficit/hyperactivity disorder (ADHD), and schizophrenia. Here, we examine CNV research into these disorders, and discuss relevant methodological considerations. By identifying specific rare deletions and duplications, we may be better able to determine the etiology of neurodevelopmental disorders and identify appropriate treatments.
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Tiwari AK, Zai CC, Müller DJ, Kennedy JL. Genetics in schizophrenia: where are we and what next? DIALOGUES IN CLINICAL NEUROSCIENCE 2010. [PMID: 20954426 PMCID: PMC3181975 DOI: 10.31887/dcns.2010.12.3/atiwari] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding the genetic basis of schizophrenia continues to be major challenge. The research done during the last two decades has provided several candidate genes which unfortunately have not been consistently replicated across or within a population. The recent genome-wide association studies (GWAS) and copy number variation (CNV) studies have provided important evidence suggesting a role of both common and rare large CNVs in schizophrenia genesis. The burden of rare copy number variations appears to be increased in schizophrenia patients. A consistent observation among the GWAS studies is the association with schizophrenia of genetic markers in the major histocompatibility complex (6p22.1)-containing genes including NOTCH4 and histone protein loci. Molecular genetic studies are also demonstrating that there is more overlap between the susceptibility genes for schizophrenia and bipolar disorder than previously suspected. In this review we summarize the major findings of the past decade and suggest areas of future research.
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Affiliation(s)
- Arun K Tiwari
- Neurogenetics section, Neuroscience department, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
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17
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Bassett AS, Scherer SW, Brzustowicz LM. Copy number variations in schizophrenia: critical review and new perspectives on concepts of genetics and disease. Am J Psychiatry 2010; 167:899-914. [PMID: 20439386 PMCID: PMC3295834 DOI: 10.1176/appi.ajp.2009.09071016] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Structural variations of DNA, such as copy number variations (CNVs), are recognized to contribute both to normal genomic variability and to risk for human diseases. For example, schizophrenia has an established connection with 22q11.2 deletions. Recent genome-wide studies have provided initial evidence that CNVs at other loci may also be associated with schizophrenia. In this article, the authors provide a brief overview of CNVs, review recent findings related to schizophrenia, outline implications for clinical practice and diagnostic subtyping, and make recommendations for future reports on CNVs to improve interpretation of results. METHOD The review included genome-wide surveys of CNVs in schizophrenia that included one or more comparison groups, were published before 2009, and used newer methods. Six studies were identified. RESULTS Despite some limitations, these initial genome-wide studies of CNVs provide replicated associations of schizophrenia with rare 1q21.1 and 15q13.3 deletions. Collectively, the results point to a more general mutational mechanism involving rare CNVs that elevate risk for schizophrenia, especially more developmental forms of the disease. Including 22q11.2 deletions, rare risk-associated CNVs appear to account for up to 2% of schizophrenia. CONCLUSIONS The more penetrant CNVs have direct implications for clinical practice and diagnostic subtyping. CNVs with lower penetrance promise to contribute to our genetic understanding of pathogenesis. The findings provide insight into a broader neuropsychiatric spectrum for schizophrenia than previously conceived and indicate new directions for genetic studies.
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18
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Strong synaptic transmission impact by copy number variations in schizophrenia. Proc Natl Acad Sci U S A 2010; 107:10584-9. [PMID: 20489179 DOI: 10.1073/pnas.1000274107] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia is a psychiatric disorder with onset in late adolescence and unclear etiology characterized by both positive and negative symptoms, as well as cognitive deficits. To identify copy number variations (CNVs) that increase the risk of schizophrenia, we performed a whole-genome CNV analysis on a cohort of 977 schizophrenia cases and 2,000 healthy adults of European ancestry who were genotyped with 1.7 million probes. Positive findings were evaluated in an independent cohort of 758 schizophrenia cases and 1,485 controls. The Gene Ontology synaptic transmission family of genes was notably enriched for CNVs in the cases (P = 1.5 x 10(-7)). Among these, CACNA1B and DOC2A, both calcium-signaling genes responsible for neuronal excitation, were deleted in 16 cases and duplicated in 10 cases, respectively. In addition, RET and RIT2, both ras-related genes important for neural crest development, were significantly affected by CNVs. RET deletion was exclusive to seven cases, and RIT2 deletions were overrepresented common variant CNVs in the schizophrenia cases. Our results suggest that novel variations involving the processes of synaptic transmission contribute to the genetic susceptibility of schizophrenia.
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Ikeda M, Aleksic B, Kirov G, Kinoshita Y, Yamanouchi Y, Kitajima T, Kawashima K, Okochi T, Kishi T, Zaharieva I, Owen MJ, O'Donovan MC, Ozaki N, Iwata N. Copy number variation in schizophrenia in the Japanese population. Biol Psychiatry 2010; 67:283-6. [PMID: 19880096 DOI: 10.1016/j.biopsych.2009.08.034] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 08/12/2009] [Accepted: 08/31/2009] [Indexed: 11/27/2022]
Abstract
BACKGROUND Copy number variants (CNVs) have been shown to increase the risk to develop schizophrenia. The best supported findings are at 1q21.1, 15q11.2, 15q13.3, and 22q11.2 and deletions at the gene neurexin 1 (NRXN1). METHODS In this study, we used Affymetrix 5.0 arrays to investigate the role of rare CNVs in 575 patients with schizophrenia and 564 control subjects from Japan. RESULTS There was a nonsignificant trend for excess of rare CNVs in schizophrenia (p = .087); however, we did not confirm the previously implicated association for very large CNVs (>500 kilobase [kb]) in this population. We provide support for three previous findings in schizophrenia, as we identified one deletion in a case at 1q21.1, one deletion within NRXN1, and four duplications in cases and one in a control subject at 16p13.1, a locus first implicated in autism and later in schizophrenia. CONCLUSIONS In this population, we support some of the previous findings in schizophrenia but could not find an increased burden of very large (>500 kb) CNVs, which was proposed recently. However, we provide support for the role of CNVs at 16p13.1, 1q21.1, and NRXN1.
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Affiliation(s)
- Masashi Ikeda
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
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Sebat J, Levy DL, McCarthy SE. Rare structural variants in schizophrenia: one disorder, multiple mutations; one mutation, multiple disorders. Trends Genet 2009; 25:528-35. [PMID: 19883952 PMCID: PMC3351381 DOI: 10.1016/j.tig.2009.10.004] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 09/30/2009] [Accepted: 10/08/2009] [Indexed: 12/18/2022]
Abstract
Recent studies have established an important role for rare genomic deletions and duplications in the etiology of schizophrenia. This research suggests that the genetic architecture of neuropsychiatric disorders includes a constellation of rare mutations in many different genes. Mutations that confer substantial risk for schizophrenia have been identified at several loci, most of which have also been implicated in other neurodevelopmental disorders, including autism. Genetic heterogeneity is a characteristic of schizophrenia; conversely, phenotypic heterogeneity is a characteristic of all schizophrenia-associated mutations. Both kinds of heterogeneity probably reflect the complexity of neurodevelopment. Research strategies must account for both genetic and clinical heterogeneity to identify the genes and pathways crucial for the development of neuropsychiatric disorders.
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Affiliation(s)
- Jonathan Sebat
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Abstract
Common variant single-nucleotide polymorphisms at the MHC locus have recently been associated with schizophrenia. Together with known associations with rare copy-number variants affecting many genes, this reveals the highly polygenic etiology of the disease.
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Affiliation(s)
- Joseph T Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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22
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Chao YL, Chien WH, Liao HM, Fang JS, Chen CH. Copy Number Variations and Psychiatric Disorders. Tzu Chi Med J 2009. [DOI: 10.1016/s1016-3190(09)60039-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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23
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Alaerts M, Del-Favero J. Searching genetic risk factors for schizophrenia and bipolar disorder: learn from the past and back to the future. Hum Mutat 2009; 30:1139-52. [DOI: 10.1002/humu.21042] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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So HC, Chen EYH, Sham PC. Genetics of Schizophrenia Spectrum Disorders: Looking Back and Peering Ahead. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2009. [DOI: 10.47102/annals-acadmedsg.v38n5p436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The genetics of schizophrenia spectrum disorders have come a long way since the early demonstration of a substantial genetic component by family, twin and adoption studies. After over a decade of intensive molecular genetic studies, initially by linkage scans and candidate gene association studies, and more recently genome-wide association studies, a picture is now emerging that susceptibility to schizophrenia spectrum disorders is determined by many genetic variants of different types, ranging from single nucleotide polymorphisms to copy number variants, including rare and de novo variants, of pleiotropic effects on multiple diagnoses and traits. Further large-scale genome-wide association studies, and the forthcoming availability of affordable whole-genome sequencing technology, will further characterise the genetic variants involved, which in turn will be translated to improved clinical practice.
Key words: Copy number variation, Genome-wide association, Linkage
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Affiliation(s)
- Hon-Cheong So
- Department of Psychiatry, the University of Hong Kong
| | - Eric YH Chen
- Department of Psychiatry, the University of Hong Kong
| | - Pak C Sham
- Department of Psychiatry, the University of Hong Kong
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25
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Need AC, Ge D, Weale ME, Maia J, Feng S, Heinzen EL, Shianna KV, Yoon W, Kasperavičiūtė D, Gennarelli M, Strittmatter WJ, Bonvicini C, Rossi G, Jayathilake K, Cola PA, McEvoy JP, Keefe RSE, Fisher EMC, St. Jean PL, Giegling I, Hartmann AM, Möller HJ, Ruppert A, Fraser G, Crombie C, Middleton LT, St. Clair D, Roses AD, Muglia P, Francks C, Rujescu D, Meltzer HY, Goldstein DB. A genome-wide investigation of SNPs and CNVs in schizophrenia. PLoS Genet 2009; 5:e1000373. [PMID: 19197363 PMCID: PMC2631150 DOI: 10.1371/journal.pgen.1000373] [Citation(s) in RCA: 361] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 01/07/2009] [Indexed: 12/13/2022] Open
Abstract
We report a genome-wide assessment of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) in schizophrenia. We investigated SNPs using 871 patients and 863 controls, following up the top hits in four independent cohorts comprising 1,460 patients and 12,995 controls, all of European origin. We found no genome-wide significant associations, nor could we provide support for any previously reported candidate gene or genome-wide associations. We went on to examine CNVs using a subset of 1,013 cases and 1,084 controls of European ancestry, and a further set of 60 cases and 64 controls of African ancestry. We found that eight cases and zero controls carried deletions greater than 2 Mb, of which two, at 8p22 and 16p13.11-p12.4, are newly reported here. A further evaluation of 1,378 controls identified no deletions greater than 2 Mb, suggesting a high prior probability of disease involvement when such deletions are observed in cases. We also provide further evidence for some smaller, previously reported, schizophrenia-associated CNVs, such as those in NRXN1 and APBA2. We could not provide strong support for the hypothesis that schizophrenia patients have a significantly greater "load" of large (>100 kb), rare CNVs, nor could we find common CNVs that associate with schizophrenia. Finally, we did not provide support for the suggestion that schizophrenia-associated CNVs may preferentially disrupt genes in neurodevelopmental pathways. Collectively, these analyses provide the first integrated study of SNPs and CNVs in schizophrenia and support the emerging view that rare deleterious variants may be more important in schizophrenia predisposition than common polymorphisms. While our analyses do not suggest that implicated CNVs impinge on particular key pathways, we do support the contribution of specific genomic regions in schizophrenia, presumably due to recurrent mutation. On balance, these data suggest that very few schizophrenia patients share identical genomic causation, potentially complicating efforts to personalize treatment regimens.
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Affiliation(s)
- Anna C. Need
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Dongliang Ge
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Michael E. Weale
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Jessica Maia
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Sheng Feng
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Erin L. Heinzen
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Kevin V. Shianna
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Woohyun Yoon
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | | | - Massimo Gennarelli
- Genetic Unit, IRCCS San Giovanni di Dio Fatebenefratelli, Brescia, Italy
- Department of Biomedical Science and Biotech, University of Brescia, Brescia, Italy
| | - Warren J. Strittmatter
- Division of Neurology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Cristian Bonvicini
- Genetic Unit, IRCCS San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Giuseppe Rossi
- Psychiatric Unit, IRCCS San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Karu Jayathilake
- Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Philip A. Cola
- University Hospitals Case Medical Center, Cleveland, Ohio, United States of America
| | - Joseph P. McEvoy
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Richard S. E. Keefe
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina, United States of America
| | | | - Pamela L. St. Jean
- Genetics Division, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - Ina Giegling
- Division of Molecular and Clinical Neurobiology, Department of Psychiatry, Ludwig-Maximilians-University, Munich, Germany
| | - Annette M. Hartmann
- Division of Molecular and Clinical Neurobiology, Department of Psychiatry, Ludwig-Maximilians-University, Munich, Germany
| | - Hans-Jürgen Möller
- Department of Psychiatry, Ludwig-Maximilians-University, Munich, Germany
| | | | - Gillian Fraser
- Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Caroline Crombie
- Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Lefkos T. Middleton
- Division of Neuroscience and Mental Health, Neuroscience Laboratories, Burlington Danes, Hammersmith Hospital, London, United Kingdom
| | - David St. Clair
- Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Allen D. Roses
- Deane Drug Discovery Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | | | - Clyde Francks
- Medical Genetics, GlaxoSmithKline R&D, Verona, Italy
| | - Dan Rujescu
- Division of Molecular and Clinical Neurobiology, Department of Psychiatry, Ludwig-Maximilians-University, Munich, Germany
| | - Herbert Y. Meltzer
- Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - David B. Goldstein
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
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