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Büki G, Hadzsiev K, Bene J. Copy Number Variations in Neuropsychiatric Disorders. Int J Mol Sci 2023; 24:13671. [PMID: 37761973 PMCID: PMC10530736 DOI: 10.3390/ijms241813671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Neuropsychiatric disorders are complex conditions that represent a significant global health burden with complex and multifactorial etiologies. Technological advances in recent years have improved our understanding of the genetic architecture of the major neuropsychiatric disorders and the genetic loci involved. Previous studies mainly investigated genome-wide significant SNPs to elucidate the cross-disorder and disorder-specific genetic basis of neuropsychiatric disorders. Although copy number variations represent a major source of genetic variations, they are known risk factors in developing a variety of human disorders, including certain neuropsychiatric diseases. In this review, we demonstrate the current understanding of CNVs contributing to liability for schizophrenia, bipolar disorder, and major depressive disorder.
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Affiliation(s)
| | | | - Judit Bene
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, 7624 Pécs, Hungary; (G.B.); (K.H.)
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Hara T, Owada Y, Takata A. Genetics of bipolar disorder: insights into its complex architecture and biology from common and rare variants. J Hum Genet 2023; 68:183-191. [PMID: 35614313 DOI: 10.1038/s10038-022-01046-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 11/09/2022]
Abstract
Bipolar disorder (BD) is a common mental disorder characterized by recurrent mood episodes, which causes major socioeconomic burdens globally. Though its disease pathogenesis is largely unknown, the high heritability of BD indicates strong contributions from genetic factors. In this review, we summarize the recent achievements in the genetics of BD, particularly those from genome-wide association study (GWAS) of common variants and next-generation sequencing analysis of rare variants. These include the identification of dozens of robust disease-associated loci, deepening of our understanding of the biology of BD, objective description of correlations with other psychiatric disorders and behavioral traits, formulation of methods for predicting disease risk and drug response, and the discovery of a single gene associated with bipolar disorder and schizophrenia spectrum with a large effect size. On the other hand, the findings to date have not yet made a clear contribution to the improvement of clinical psychiatry of BD. We overview the remaining challenges as well as possible paths to resolve them, referring to studies of other major neuropsychiatric disorders.
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Affiliation(s)
- Tomonori Hara
- Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan.,Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Yuji Owada
- Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Atsushi Takata
- Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan.
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Zeng Z, Aptekmann AA, Bromberg Y. Decoding the effects of synonymous variants. Nucleic Acids Res 2021; 49:12673-12691. [PMID: 34850938 PMCID: PMC8682775 DOI: 10.1093/nar/gkab1159] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/02/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Synonymous single nucleotide variants (sSNVs) are common in the human genome but are often overlooked. However, sSNVs can have significant biological impact and may lead to disease. Existing computational methods for evaluating the effect of sSNVs suffer from the lack of gold-standard training/evaluation data and exhibit over-reliance on sequence conservation signals. We developed synVep (synonymous Variant effect predictor), a machine learning-based method that overcomes both of these limitations. Our training data was a combination of variants reported by gnomAD (observed) and those unreported, but possible in the human genome (generated). We used positive-unlabeled learning to purify the generated variant set of any likely unobservable variants. We then trained two sequential extreme gradient boosting models to identify subsets of the remaining variants putatively enriched and depleted in effect. Our method attained 90% precision/recall on a previously unseen set of variants. Furthermore, although synVep does not explicitly use conservation, its scores correlated with evolutionary distances between orthologs in cross-species variation analysis. synVep was also able to differentiate pathogenic vs. benign variants, as well as splice-site disrupting variants (SDV) vs. non-SDVs. Thus, synVep provides an important improvement in annotation of sSNVs, allowing users to focus on variants that most likely harbor effects.
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Affiliation(s)
- Zishuo Zeng
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
| | - Ariel A Aptekmann
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
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Kight KE, Argue KJ, Bumgardner JG, Bardhi K, Waddell J, McCarthy MM. Social behavior in prepubertal neurexin 1α deficient rats: A model of neurodevelopmental disorders. Behav Neurosci 2021; 135:782-803. [PMID: 34323517 PMCID: PMC8649076 DOI: 10.1037/bne0000482] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Loss-of-function mutations in the synaptic protein neurexin1α (NRXN1α) are associated with several neurodevelopmental disorders, including autism spectrum disorder (ASD), schizophrenia, and attention-deficit hyperactivity disorder (ADHD), and many of these disorders are defined by core deficits in social cognition. Mouse models of Nrxn1α deficiency are not amenable to studying aspects of social cognition because, in general, mice do not engage in complex social interactions such as social play or prosocial helping behaviors. Rats, on the contrary, engage in these complex, well-characterized social behaviors. Using the Nrxn1tm1Sage Sprague Dawley rat, we tested a range of cognitive and social behaviors in juveniles with haplo- or biallelic Nrxn1α mutation. We found a deficit in ultrasonic vocalizations (USVs) of male and female neonatal rats with Nrxn1α deficiency. A male-specific deficit in social play was observed in Nrxn1α-deficient juveniles, although sociability and social discrimination were unaltered. Nurturing behavior induced by exposure to pups was enhanced in male and female juveniles with biallelic Nrxn1α mutation. Performance in tasks of prosocial helping behavior and food retrieval indicated severe deficits in learning and cognition in juveniles with biallelic Nrxn1α mutation, and a less severe deficit in haploinsufficient rats, although Pavlovian learning was altered only in haploinsufficient males. We also observed a male-specific increase in mobility and object investigation in juveniles with complete Nrxn1α deficiency. Together, these observations more fully characterize the Nrxn1tm1Sage Sprague Dawley rat as a model for Nrxn1α-related neurodevelopmental disorders, and support a rationale for the juvenile rat as a more appropriate model for disorders that involve core deficits in complex social behaviors. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
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Affiliation(s)
- Katherine E Kight
- Department of Pharmacology, University of Maryland School of Medicine
| | - Kathryn J Argue
- Department of Pharmacology, University of Maryland School of Medicine
| | | | - Keti Bardhi
- Department of Pediatrics, University of Maryland School of Medicine
| | - Jaylyn Waddell
- Department of Pediatrics, University of Maryland School of Medicine
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The "missing heritability"-Problem in psychiatry: Is the interaction of genetics, epigenetics and transposable elements a potential solution? Neurosci Biobehav Rev 2021; 126:23-42. [PMID: 33757815 DOI: 10.1016/j.neubiorev.2021.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023]
Abstract
Psychiatric disorders exhibit an enormous burden on the health care systems worldwide accounting for around one-third of years lost due to disability among adults. Their etiology is largely unknown and diagnostic classification is based on symptomatology and course of illness and not on objective biomarkers. Most psychiatric disorders are moderately to highly heritable. However, it is still unknown what mechanisms may explain the discrepancy between heritability estimates and the present data from genetic analysis. In addition to genetic differences also epigenetic modifications are considered as potentially relevant in the transfer of susceptibility to psychiatric diseases. Though, whether or not epigenetic alterations can be inherited for many generations is highly controversial. In the present article, we will critically summarize both the genetic findings and the results from epigenetic analyses, including also those of noncoding RNAs. We will argue that one possible solution to the "missing heritability" problem in psychiatry is a potential role of retrotransposons, the exploration of which is presently only in its beginnings.
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Charney AW, Stahl EA, Green EK, Chen CY, Moran JL, Chambert K, Belliveau RA, Forty L, Gordon-Smith K, Lee PH, Bromet EJ, Buckley PF, Escamilla MA, Fanous AH, Fochtmann LJ, Lehrer DS, Malaspina D, Marder SR, Morley CP, Nicolini H, Perkins DO, Rakofsky JJ, Rapaport MH, Medeiros H, Sobell JL, Backlund L, Bergen SE, Juréus A, Schalling M, Lichtenstein P, Knowles JA, Burdick KE, Jones I, Jones LA, Hultman CM, Perlis R, Purcell SM, McCarroll SA, Pato CN, Pato MT, Di Florio A, Craddock N, Landén M, Smoller JW, Ruderfer DM, Sklar P. Contribution of Rare Copy Number Variants to Bipolar Disorder Risk Is Limited to Schizoaffective Cases. Biol Psychiatry 2019; 86:110-119. [PMID: 30686506 PMCID: PMC6586545 DOI: 10.1016/j.biopsych.2018.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/13/2018] [Accepted: 12/12/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Genetic risk for bipolar disorder (BD) is conferred through many common alleles, while a role for rare copy number variants (CNVs) is less clear. Subtypes of BD including schizoaffective disorder bipolar type (SAB), bipolar I disorder (BD I), and bipolar II disorder (BD II) differ according to the prominence and timing of psychosis, mania, and depression. The genetic factors contributing to the combination of symptoms among these subtypes are poorly understood. METHODS Rare large CNVs were analyzed in 6353 BD cases (3833 BD I [2676 with psychosis, 850 without psychosis, and 307 with unknown psychosis history], 1436 BD II, 579 SAB, and 505 BD not otherwise specified) and 8656 controls. CNV burden and a polygenic risk score (PRS) for schizophrenia were used to evaluate the relative contributions of rare and common variants to risk of BD, BD subtypes, and psychosis. RESULTS CNV burden did not differ between BD and controls when treated as a single diagnostic entity. However, burden in SAB was increased relative to controls (p = .001), BD I (p = .0003), and BD II (p = .0007). Burden and schizophrenia PRSs were increased in SAB compared with BD I with psychosis (CNV p = .0007, PRS p = .004), and BD I without psychosis (CNV p = .0004, PRS p = 3.9 × 10-5). Within BD I, psychosis was associated with increased schizophrenia PRSs (p = .005) but not CNV burden. CONCLUSIONS CNV burden in BD is limited to SAB. Rare and common genetic variants may contribute differently to risk for psychosis and perhaps other classes of psychiatric symptoms.
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Affiliation(s)
- Alexander W Charney
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neurosurgery, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, New York, New York.
| | - Eli A Stahl
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, New York, New York
| | - Elaine K Green
- School of Biomedical and Health Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth University, Portland Square, Plymouth, UK
| | - Chia-Yen Chen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Boston, Massachusetts
| | - Jennifer L Moran
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Richard A Belliveau
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Liz Forty
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | | | - Phil H Lee
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts; Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts
| | - Evelyn J Bromet
- Department of Psychiatry, Stony Brook University, Stony Brook, New York
| | - Peter F Buckley
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia; Department of Psychiatry, Georgia Regents University Medical Center, Augusta, Georgia
| | - Michael A Escamilla
- Center of Excellence in Neuroscience, Department of Psychiatry, Texas Tech University Health Sciences Center at El Paso, El Paso, Texas
| | - Ayman H Fanous
- Department of Psychiatry and the Behavioral Sciences, State University of New York, Downstate Medical Center, New York, New York; Department of Psychiatry, VA New York Harbor Healthcare System, Brooklyn, New York
| | - Laura J Fochtmann
- Department of Psychiatry, Stony Brook University, Stony Brook, New York
| | | | - Dolores Malaspina
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, New York, New York; Department of Psychiatry, New York University, New York, New York
| | - Stephen R Marder
- Semel Institute for Neuroscience, University of California, Los Angeles, California
| | - Christopher P Morley
- Department of Psychiatry and Behavioral Science, State University of New York, Upstate Medical University, Syracuse, New York; Department of Family Medicine, State University of New York, Upstate Medical University, Syracuse, New York; Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, New York
| | - Humberto Nicolini
- Center for Genomic Sciences, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico; Department of Psychiatry, Carracci Medical Group, Mexico City, Mexico
| | - Diana O Perkins
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffrey J Rakofsky
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, Georgia
| | - Mark H Rapaport
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, Georgia
| | - Helena Medeiros
- Department of Psychiatry and the Behavioral Sciences, State University of New York, Downstate Medical Center, New York, New York
| | - Janet L Sobell
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Keck School of Medicine, Los Angeles, California
| | - Lena Backlund
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Sarah E Bergen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anders Juréus
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Schalling
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - James A Knowles
- Department of Cell Biology, State University of New York, Downstate Medical Center, New York, New York
| | - Katherine E Burdick
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts; Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ian Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Lisa A Jones
- Department of Psychiatry, University of Birmingham, Birmingham, UK
| | - Christina M Hultman
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Roy Perlis
- Center for Experimental Therapeutics, Massachusetts General Hospital, Boston, Massachusetts
| | - Shaun M Purcell
- Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts; Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Department of Genetics, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
| | - Carlos N Pato
- Department of Psychiatry and the Behavioral Sciences, State University of New York, Downstate Medical Center, New York, New York
| | - Michele T Pato
- Department of Psychiatry and the Behavioral Sciences, State University of New York, Downstate Medical Center, New York, New York
| | - Ariana Di Florio
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Nick Craddock
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Institute of Neuroscience and Physiology, Sahlgenska Academy at the Gothenburg University, Gothenburg, Sweden
| | - Jordan W Smoller
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Boston, Massachusetts
| | - Douglas M Ruderfer
- Division of Genetic Medicine, Departments of Medicine, Biomedical Informatics, and Psychiatry, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee.
| | - Pamela Sklar
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, New York, New York
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Comprehensive cross-disorder analyses of CNTNAP2 suggest it is unlikely to be a primary risk gene for psychiatric disorders. PLoS Genet 2018; 14:e1007535. [PMID: 30586385 PMCID: PMC6324819 DOI: 10.1371/journal.pgen.1007535] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 01/08/2019] [Accepted: 11/12/2018] [Indexed: 12/21/2022] Open
Abstract
The contactin-associated protein-like 2 (CNTNAP2) gene is a member of the neurexin superfamily. CNTNAP2 was first implicated in the cortical dysplasia-focal epilepsy (CDFE) syndrome, a recessive disease characterized by intellectual disability, epilepsy, language impairments and autistic features. Associated SNPs and heterozygous deletions in CNTNAP2 were subsequently reported in autism, schizophrenia and other psychiatric or neurological disorders. We aimed to comprehensively examine evidence for the role of CNTNAP2 in susceptibility to psychiatric disorders, by the analysis of multiple classes of genetic variation in large genomic datasets. In this study we used: i) summary statistics from the Psychiatric Genomics Consortium (PGC) GWAS for seven psychiatric disorders; ii) examined all reported CNTNAP2 structural variants in patients and controls; iii) performed cross-disorder analysis of functional or previously associated SNPs; and iv) conducted burden tests for pathogenic rare variants using sequencing data (4,483 ASD and 6,135 schizophrenia cases, and 13,042 controls). The distribution of CNVs across CNTNAP2 in psychiatric cases from previous reports was no different from controls of the database of genomic variants. Gene-based association testing did not implicate common variants in autism, schizophrenia or other psychiatric phenotypes. The association of proposed functional SNPs rs7794745 and rs2710102, reported to influence brain connectivity, was not replicated; nor did predicted functional SNPs yield significant results in meta-analysis across psychiatric disorders at either SNP-level or gene-level. Disrupting CNTNAP2 rare variant burden was not higher in autism or schizophrenia compared to controls. Finally, in a CNV mircroarray study of an extended bipolar disorder family with 5 affected relatives we previously identified a 131kb deletion in CNTNAP2 intron 1, removing a FOXP2 transcription factor binding site. Quantitative-PCR validation and segregation analysis of this CNV revealed imperfect segregation with BD. This large comprehensive study indicates that CNTNAP2 may not be a robust risk gene for psychiatric phenotypes. Genetic mutations that disrupt both copies of the CNTNAP2 gene lead to severe disease, characterized by profound intellectual disability, epilepsy, language difficulties and autistic traits, leading to the hypothesis that this gene may also be involved in autism given some overlapping clinical features with this disease. Indeed, several large DNA deletions affecting one of the two copies of CNTNAP2 were found in some patients with autism, and later also in patients with schizophrenia, bipolar disorder, ADHD and epilepsy, suggesting that this gene was implicated in several psychiatric or neurologic diseases. Other studies considered genetic sequence variations that are common in the general population, and suggested that two such sequence variations in CNTNAP2 predispose to psychiatric diseases by influencing the functionality and connectivity of the brain. To better understand the involvement of CNTNAP2 in risk of mental illness, we performed several genetic analyses using a series of large publicly available or in-house datasets, comprising many thousands of patients and controls. Furthermore, we report the deletion of one copy of CNTNAP2 in two patients with bipolar disorder and one unaffected relative from an extended family where five relatives were affected with this condition. Despite the previous consideration of CNTNAP2 as a strong candidate gene for autism or schizophrenia, we show little evidence across multiple classes of DNA variation, that CNTNAP2 is likely to play a major role in risk of psychiatric diseases.
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Toma C, Shaw AD, Allcock RJN, Heath A, Pierce KD, Mitchell PB, Schofield PR, Fullerton JM. An examination of multiple classes of rare variants in extended families with bipolar disorder. Transl Psychiatry 2018; 8:65. [PMID: 29531218 PMCID: PMC5847564 DOI: 10.1038/s41398-018-0113-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bipolar disorder (BD) is a complex psychiatric condition with high heritability, the genetic architecture of which likely comprises both common variants of small effect and rare variants of higher penetrance, the latter of which are largely unknown. Extended families with high density of illness provide an opportunity to map novel risk genes or consolidate evidence for existing candidates, by identifying genes carrying pathogenic rare variants. We performed whole-exome sequencing (WES) in 15 BD families (117 subjects, of whom 72 were affected), augmented with copy number variant (CNV) microarray data, to examine contributions of multiple classes of rare genetic variants within a familial context. Linkage analysis and haplotype reconstruction using WES-derived genotypes enabled exclusion of false-positive single-nucleotide variants (SNVs), CNV inheritance estimation, de novo variant identification and candidate gene prioritization. We found that rare predicted pathogenic variants shared among ≥3 affected relatives were overrepresented in postsynaptic density (PSD) genes (P = 0.002), with no enrichment in unaffected relatives. Genome-wide burden of likely gene-disruptive variants was no different in affected vs. unaffected relatives (P = 0.24), but correlated significantly with age of onset (P = 0.017), suggesting that a high disruptive variant burden may expedite symptom onset. The number of de novo variants was no different in affected vs. unaffected offspring (P = 0.89). We observed heterogeneity within and between families, with the most likely genetic model involving alleles of modest effect and reduced penetrance: a possible exception being a truncating X-linked mutation in IRS4 within a family-specific linkage peak. Genetic approaches combining WES, CNV and linkage analyses in extended families are promising strategies for gene discovery.
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Affiliation(s)
- Claudio Toma
- 0000 0000 8900 8842grid.250407.4Neuroscience Research Australia, Sydney, Australia ,0000 0004 4902 0432grid.1005.4School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Alex D. Shaw
- 0000 0000 8900 8842grid.250407.4Neuroscience Research Australia, Sydney, Australia ,0000 0004 4902 0432grid.1005.4School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Richard J. N. Allcock
- 0000 0004 1936 7910grid.1012.2School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - Anna Heath
- 0000 0000 8900 8842grid.250407.4Neuroscience Research Australia, Sydney, Australia
| | - Kerrie D. Pierce
- 0000 0000 8900 8842grid.250407.4Neuroscience Research Australia, Sydney, Australia
| | - Philip B. Mitchell
- 0000 0004 4902 0432grid.1005.4School of Psychiatry, University of New South Wales, Sydney, Australia ,grid.415193.bBlack Dog Institute, Prince of Wales Hospital, Sydney, Australia
| | - Peter R. Schofield
- 0000 0000 8900 8842grid.250407.4Neuroscience Research Australia, Sydney, Australia ,0000 0004 4902 0432grid.1005.4School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Janice M. Fullerton
- 0000 0000 8900 8842grid.250407.4Neuroscience Research Australia, Sydney, Australia ,0000 0004 4902 0432grid.1005.4School of Medical Sciences, University of New South Wales, Sydney, Australia
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Kasem E, Kurihara T, Tabuchi K. Neurexins and neuropsychiatric disorders. Neurosci Res 2017; 127:53-60. [PMID: 29221905 DOI: 10.1016/j.neures.2017.10.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 09/24/2017] [Accepted: 10/03/2017] [Indexed: 12/29/2022]
Abstract
Neurexins are a family of presynaptic single-pass transmembrane proteins that act as synaptic organizers in mammals. The neurexins consist of three genes (NRXN1, NRXN2, and NRXN3), each of which produces a longer α- and shorter β-form. Genomic alterations in NRXN genes have been identified in a wide variety of neuropsychiatric disorders, including autism spectrum disorders (ASD), schizophrenia, intellectual disability (ID), and addiction. Remarkably, a bi-allelic deficiency of NRXN1 was recently linked to Pitt-Hopkins syndrome. The fact that some mono-allelic functional variants of NRXNs are also found in healthy controls indicates that other genetic or environmental factors affect the penetrance of NRXN deficiency. In this review, we summarize the common research methods and representative results of human genetic studies that have implicated NRXN variants in various neuropsychiatric disorders. We also summarize studies of rodent models with NRXN deficiencies that complement our knowledge of human genetics.
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Affiliation(s)
- Enas Kasem
- Department of Molecular & Cellular Physiology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621 Japan
| | - Taiga Kurihara
- Department of Molecular & Cellular Physiology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621 Japan
| | - Katsuhiko Tabuchi
- Department of Molecular & Cellular Physiology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621 Japan; Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto 390-8621, Japan.
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Gilbert J, Man HY. Fundamental Elements in Autism: From Neurogenesis and Neurite Growth to Synaptic Plasticity. Front Cell Neurosci 2017; 11:359. [PMID: 29209173 PMCID: PMC5701944 DOI: 10.3389/fncel.2017.00359] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/31/2017] [Indexed: 01/12/2023] Open
Abstract
Autism spectrum disorder (ASD) is a set of neurodevelopmental disorders with a high prevalence and impact on society. ASDs are characterized by deficits in both social behavior and cognitive function. There is a strong genetic basis underlying ASDs that is highly heterogeneous; however, multiple studies have highlighted the involvement of key processes, including neurogenesis, neurite growth, synaptogenesis and synaptic plasticity in the pathophysiology of neurodevelopmental disorders. In this review article, we focus on the major genes and signaling pathways implicated in ASD and discuss the cellular, molecular and functional studies that have shed light on common dysregulated pathways using in vitro, in vivo and human evidence. HighlightsAutism spectrum disorder (ASD) has a prevalence of 1 in 68 children in the United States. ASDs are highly heterogeneous in their genetic basis. ASDs share common features at the cellular and molecular levels in the brain. Most ASD genes are implicated in neurogenesis, structural maturation, synaptogenesis and function.
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Affiliation(s)
- James Gilbert
- Department of Biology, Boston University, Boston, MA, United States
| | - Heng-Ye Man
- Department of Biology, Boston University, Boston, MA, United States.,Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
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11
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Budde M, Forstner AJ, Adorjan K, Schaupp SK, Nöthen MM, Schulze TG. Genetische Grundlagen der bipolaren Störung. DER NERVENARZT 2017; 88:755-759. [DOI: 10.1007/s00115-017-0336-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Thompson CA, Karelis J, Middleton FA, Gentile K, Coman IL, Radoeva PD, Mehta R, Fremont WP, Antshel KM, Faraone SV, Kates WR. Associations between neurodevelopmental genes, neuroanatomy, and ultra high risk symptoms of psychosis in 22q11.2 deletion syndrome. Am J Med Genet B Neuropsychiatr Genet 2017; 174:295-314. [PMID: 28139055 DOI: 10.1002/ajmg.b.32515] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 11/07/2016] [Indexed: 11/06/2022]
Abstract
22q11.2 deletion syndrome is a neurogenetic disorder resulting in the deletion of over 40 genes. Up to 40% of individuals with 22q11.2DS develop schizophrenia, though little is known about the underlying mechanisms. We hypothesized that allelic variation in functional polymorphisms in seven genes unique to the deleted region would affect lobar brain volumes, which would predict risk for psychosis in youth with 22q11.2DS. Participants included 56 individuals (30 males) with 22q11.2DS. Anatomic MR images were collected and processed using Freesurfer. Participants were genotyped for 10 SNPs in the COMT, DGCR8, GNB1L, PIK4CA, PRODH, RTN4R, and ZDHHC8 genes. All subjects were assessed for ultra high risk symptoms of psychosis. Allelic variation of the rs701428 SNP of RTN4R was significantly associated with volumetric differences in gray matter of the lingual gyrus and cuneus of the occipital lobe. Moreover, occipital gray matter volumes were robustly associated with ultra high risk symptoms of psychosis in the presence of the G allele of rs701428. Our results suggest that RTN4R, a relatively under-studied gene at the 22q11 locus, constitutes a susceptibility gene for psychosis in individuals with this syndrome through its alteration of the architecture of the brain. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Carlie A Thompson
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York
| | - Jason Karelis
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York
| | - Frank A Middleton
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York.,Department of Neuroscience, SUNY Upstate Medical University, Syracuse, New York
| | - Karen Gentile
- Department of Neuroscience, SUNY Upstate Medical University, Syracuse, New York
| | - Ioana L Coman
- Department of Computer Science, SUNY Oswego, Oswego, New York
| | - Petya D Radoeva
- Department of Psychiatry, University of Washington, Seattle, Washington
| | - Rashi Mehta
- Department of Radiology, SUNY Upstate Medical University, Syracuse, New York
| | - Wanda P Fremont
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York
| | - Kevin M Antshel
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York.,Department of Psychology, Syracuse University, Syracuse, New York
| | - Stephen V Faraone
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York
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13
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Harripaul R, Noor A, Ayub M, Vincent JB. The Use of Next-Generation Sequencing for Research and Diagnostics for Intellectual Disability. Cold Spring Harb Perspect Med 2017; 7:7/3/a026864. [PMID: 28250017 DOI: 10.1101/cshperspect.a026864] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic or genomic mutation is a major cause of intellectual disability (ID). However, despite the generally anticipated strong genotype/phenotype correlation for ID, there are huge obstacles to gene identification, except perhaps where very distinct syndromic features are observed, because of the high degree of genetic heterogeneity and wide variability of phenotype for different mutations or even with the same mutation within a single gene. A recent review estimates in excess of 2500 genes for ID. Fortunately for researchers and diagnosticians alike, the recent advent of massively parallel sequencing technologies, or next-generation sequencing (NGS) has made an apparently impossible task tractable. Here, we review the ongoing research endeavors to identify new disease genes, as well as strategies and approaches at the clinical level.
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Affiliation(s)
- Ricardo Harripaul
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 1R8, Canada
| | - Abdul Noor
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1Z5, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1Z5, Canada
| | - Muhammad Ayub
- Department of Psychiatry, Queen's University, Kingston, Ontario K7L 7X3, Canada
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 1R8, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario M5T 1R8, Canada
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14
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Greenwood TA. Positive Traits in the Bipolar Spectrum: The Space between Madness and Genius. MOLECULAR NEUROPSYCHIATRY 2017; 2:198-212. [PMID: 28277566 PMCID: PMC5318923 DOI: 10.1159/000452416] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 10/10/2016] [Indexed: 01/25/2023]
Abstract
Bipolar disorder is a severe, lifelong mood disorder for which little is currently understood of the genetic mechanisms underlying risk. By examining related dimensional phenotypes, we may further our understanding of the disorder. Creativity has a historical connection with the bipolar spectrum and is particularly enhanced among unaffected first-degree relatives and those with bipolar spectrum traits. This suggests that some aspects of the bipolar spectrum may confer advantages, while more severe expressions of symptoms negatively influence creative accomplishment. Creativity is a complex, multidimensional construct with both cognitive and affective components, many of which appear to reflect a shared genetic vulnerability with bipolar disorder. It is suggested that a subset of bipolar risk variants confer advantages as positive traits according to an inverted-U-shaped curve with clinically unaffected allele carriers benefitting from the positive traits and serving to maintain the risk alleles in the population. The association of risk genes with creativity in healthy individuals (e.g., NRG1), as well as an overall sharing of common genetic variation between bipolar patients and creative individuals, provides support for this model. Current findings are summarized from a multidisciplinary perspective to demonstrate the feasibility of research in this area to reveal the mechanisms underlying illness.
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15
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Li M, Carey J, Cristiano S, Susztak K, Coresh J, Boerwinkle E, Kao WHL, Beaty TH, Köttgen A, Scharpf RB. Genome-Wide Association of Copy Number Polymorphisms and Kidney Function. PLoS One 2017; 12:e0170815. [PMID: 28135296 PMCID: PMC5279752 DOI: 10.1371/journal.pone.0170815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 01/11/2017] [Indexed: 01/08/2023] Open
Abstract
Genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) have identified more than 50 loci associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. However, significant SNPs account for a small proportion of eGFR variability. Other forms of genetic variation have not been comprehensively evaluated for association with eGFR. In this study, we assess whether changes in germline DNA copy number are associated with GFR estimated from serum creatinine, eGFRcrea. We used hidden Markov models (HMMs) to identify copy number polymorphic regions (CNPs) from high-throughput SNP arrays for 2,514 African (AA) and 8,645 European ancestry (EA) participants in the Atherosclerosis Risk in Communities (ARIC) study. Separately for the EA and AA cohorts, we used Bayesian Gaussian mixture models to estimate copy number at regions identified by the HMM or previously reported in the HapMap Project. We identified 312 and 464 autosomal CNPs among individuals of EA and AA, respectively. Multivariate models adjusted for SNP-derived covariates of population structure identified one CNP in the EA cohort near genome-wide statistical significance (Bonferroni-adjusted p = 0.067) located on chromosome 5 (876-880kb). Overall, our findings suggest a limited role of CNPs in explaining eGFR variability.
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Affiliation(s)
- Man Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Jacob Carey
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Stephen Cristiano
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, Baltimore, Maryland, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Wen Hong L. Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Division of Genetic Epidemiology, Medical Center–University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Robert B. Scharpf
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
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16
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Long Y, Su Y, Ai H, Zhang Z, Yang B, Ruan G, Xiao S, Liao X, Ren J, Huang L, Ding N. A genome-wide association study of copy number variations with umbilical hernia in swine. Anim Genet 2016; 47:298-305. [PMID: 27028052 DOI: 10.1111/age.12402] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2015] [Indexed: 02/06/2023]
Abstract
Umbilical hernia (UH) is one of the most common congenital defects in pigs, leading to considerable economic loss and serious animal welfare problems. To test whether copy number variations (CNVs) contribute to pig UH, we performed a case-control genome-wide CNV association study on 905 pigs from the Duroc, Landrace and Yorkshire breeds using the Porcine SNP60 BeadChip and penncnv algorithm. We first constructed a genomic map comprising 6193 CNVs that pertain to 737 CNV regions. Then, we identified eight CNVs significantly associated with the risk for UH in the three pig breeds. Six of seven significantly associated CNVs were validated using quantitative real-time PCR. Notably, a rare CNV (CNV14:13030843-13059455) encompassing the NUGGC gene was strongly associated with UH (permutation-corrected P = 0.0015) in Duroc pigs. This CNV occurred exclusively in seven Duroc UH-affected individuals. SNPs surrounding the CNV did not show association signals, indicating that rare CNVs may play an important role in complex pig diseases such as UH. The NUGGC gene has been implicated in human omphalocele and inguinal hernia. Our finding supports that CNVs, including the NUGGC CNV, contribute to the pathogenesis of pig UH.
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Affiliation(s)
- Yi Long
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ying Su
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhiyan Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Guorong Ruan
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.,Fujian Vocational College of Agriculture, Fuzhou, 360119, China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xinjun Liao
- College of Life Science of Jinggangshan University, Jian, 343009, China
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Nengshui Ding
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
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17
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Green EK, Rees E, Walters JTR, Smith KG, Forty L, Grozeva D, Moran JL, Sklar P, Ripke S, Chambert KD, Genovese G, McCarroll SA, Jones I, Jones L, Owen MJ, O'Donovan MC, Craddock N, Kirov G. Copy number variation in bipolar disorder. Mol Psychiatry 2016; 21:89-93. [PMID: 25560756 PMCID: PMC5038134 DOI: 10.1038/mp.2014.174] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/26/2014] [Accepted: 11/05/2014] [Indexed: 01/19/2023]
Abstract
Large (>100 kb), rare (<1% in the population) copy number variants (CNVs) have been shown to confer risk for schizophrenia (SZ), but the findings for bipolar disorder (BD) are less clear. In a new BD sample from the United Kingdom (n=2591), we have examined the occurrence of CNVs and compared this with previously reported samples of 6882 SZ and 8842 control subjects. When combined with previous data, we find evidence for a contribution to BD for three SZ-associated CNV loci: duplications at 1q21.1 (P=0.022), deletions at 3q29 (P=0.03) and duplications at 16p11.2 (P=2.3 × 10(-4)). The latter survives multiple-testing correction for the number of recurrent large CNV loci in the genome. Genes in 20 regions (total of 55 genes) were enriched for rare exonic CNVs among BD cases, but none of these survives correction for multiple testing. Finally, our data provide strong support for the hypothesis of a lesser contribution of very large (>500 kb) CNVs in BD compared with SZ, most notably for deletions >1 Mb (P=9 × 10(-4)).
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Affiliation(s)
- E K Green
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - E Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - J T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - K-G Smith
- Department of Psychiatry, School of Clinical and Experimental Medicine, National Centre for Mental Health, University of Birmingham, Birmingham, UK
| | - L Forty
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - D Grozeva
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - J L Moran
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - P Sklar
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - S Ripke
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Psychiatric Genomics in the Department of Psychiatry, Friedman Brain Institute, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - K D Chambert
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - G Genovese
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - S A McCarroll
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - I Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - L Jones
- Department of Psychiatry, School of Clinical and Experimental Medicine, National Centre for Mental Health, University of Birmingham, Birmingham, UK
| | - M J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - M C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - N Craddock
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - G Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
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18
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A significant risk locus on 19q13 for bipolar disorder identified using a combined genome-wide linkage and copy number variation analysis. BioData Min 2015; 8:42. [PMID: 26692414 PMCID: PMC4683747 DOI: 10.1186/s13040-015-0076-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/07/2015] [Indexed: 11/13/2022] Open
Abstract
Background The genetic background to bipolar disorder (BPD) has been attributed to different genetic and genomic risk factors. In the present study we hypothesized that inherited copy number variations (CNVs) contribute to susceptibility of BPD. We screened 637 BP-pedigrees from the NIMH Genetic Initiative and gave priority to 46 pedigrees. In this subsample we performed parametric and non-parametric genome-wide linkage analyses using ~21,000 SNP-markers. We developed an algorithm to test for linkage restricted to regions with CNVs that are shared within and across families. Results For the combined CNV and linkage analysis, one region on 19q13 survived correction for multiple comparisons and replicates a previous BPD risk locus. The shared CNV map to the pregnancy-specific glycoprotein (PSG) gene, a gene-family not previously implicated in BPD etiology. Two SNPs in the shared CNV are likely transcription factor binding sites and are linked to expression of an F-box binding gene, a key regulator of neuronal pathways suggested to be involved in BPD etiology. Conclusions Our CNV-weighted linkage approach identifies a risk locus for BPD on 19q13 and forms a useful tool to future studies to unravel part of the genetic vulnerability to BPD. Electronic supplementary material The online version of this article (doi:10.1186/s13040-015-0076-y) contains supplementary material, which is available to authorized users.
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19
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Interaction between SLC6A4 promoter variants and childhood trauma on the age at onset of bipolar disorders. Sci Rep 2015; 5:16301. [PMID: 26542422 PMCID: PMC4635347 DOI: 10.1038/srep16301] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/08/2015] [Indexed: 12/21/2022] Open
Abstract
Age at onset (AAO) of bipolar disorders (BD) could be influenced both by a repeat length polymorphism (5HTTLPR) in the promoter region of the serotonin transporter gene (SLC6A4) and exposure to childhood trauma. We assessed 308 euthymic patients with BD for the AAO of their first mood episode and childhood trauma. Patients were genotyped for the 5HTTLPR (long/short variant) and the rs25531. Genotypes were classified on functional significance (LL, LS, SS). A sample of 126 Brazilian euthymic patients with BD was used for replication. In the French sample, the correlation between AAO and trauma score was observed only among 'SS' homozygotes (p = 0.002) but not among 'L' allele carriers. A history of at least one trauma decreased the AAO only in 'SS' homozygotes (p = 0.001). These results remained significant after correction using FDR. Regression models suggested an interaction between emotional neglect and 'SS' genotype on the AAO (p = 0.009) and no further interaction with other trauma subtypes. Partial replication was obtained in the Brazilian sample, showing an interaction between emotional abuse and 'LS' genotype on the AAO (p = 0.02). In conclusion, an effect of childhood trauma on AAO of BD was observed only in patients who carry a specific stress responsiveness-related SLC6A4 promoter genotype.
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20
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Kember RL, Georgi B, Bailey-Wilson JE, Stambolian D, Paul SM, Bućan M. Copy number variants encompassing Mendelian disease genes in a large multigenerational family segregating bipolar disorder. BMC Genet 2015; 16:27. [PMID: 25887117 PMCID: PMC4382929 DOI: 10.1186/s12863-015-0184-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/19/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Bipolar affective disorder (BP) is a common, highly heritable psychiatric disorder characterized by periods of depression and mania. Using dense SNP genotype data, we characterized CNVs in 388 members of an Old Order Amish Pedigree with bipolar disorder. We identified CNV regions arising from common ancestral mutations by utilizing the pedigree information. By combining this analysis with whole genome sequence data in the same individuals, we also explored the role of compound heterozygosity. RESULTS Here we describe 541 inherited CNV regions, of which 268 are rare in a control population of European origin but present in a large number of Amish individuals. In addition, we highlight a set of CNVs found at higher frequencies in BP individuals, and within genes known to play a role in human development and disease. As in prior reports, we find no evidence for an increased burden of CNVs in BP individuals, but we report a trend towards a higher burden of CNVs in known Mendelian disease loci in bipolar individuals (BPI and BPII, p = 0.06). CONCLUSIONS We conclude that CNVs may be contributing factors in the phenotypic presentation of mood disorders and co-morbid medical conditions in this family. These results reinforce the hypothesis of a complex genetic architecture underlying BP disorder, and suggest that the role of CNVs should continue to be investigated in BP data sets.
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Affiliation(s)
- Rachel L Kember
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Benjamin Georgi
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA.
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Steven M Paul
- Appel Alzheimer's Disease Research Institute, Mind and Brain Institute, Weill Cornell Medical College, New York, NY, USA.
| | - Maja Bućan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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21
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Abstract
The last several years have been breakthrough ones in bipolar disorder (BPD) genetics, as the field has identified robust risk variants for the first time. Leading the way have been genome-wide association studies (GWAS) that have assessed common genetic markers across very large groups of patients and controls. These have resulted in findings in genes including ANK3, CACNA1C, SYNE1, ODZ4, and TRANK1. Additional studies have begun to examine the biology of these genes and how risk variants influence aspects of brain and behavior that underlie BPD. For example, carriers of the CACNA1C risk variant have been found to exhibit hippocampal and anterior cingulate dysfunction during episodic memory recall. This work has shed additional light on the relationship of bipolar susceptibility variants to other disorders, particularly schizophrenia. Even larger BPD GWAS are expected with samples now amassed of 21,035 cases and 28,758 controls. Studies have examined the pharmacogenomics of BPD with studies of lithium response, yielding high profile results that remain to be confirmed. The next frontier in the field is the identification of rare bipolar susceptibility variants through large-scale DNA sequencing. While only a couple of papers have been published to date, many studies are underway. The Bipolar Sequencing Consortium has been formed to bring together all of the groups working in this area, and to perform meta-analyses of the data generated. The consortium, with 13 member groups, now has exome data on ~3,500 cases and ~5,000 controls, and on ~162 families. The focus will likely shift within several years from exome data to whole genome data as costs of obtaining such data continue to drop. Gene-mapping studies are now providing clear results that provide insights into the pathophysiology of the disorder. Sequencing studies should extend this process further. Findings could eventually set the stage for rational therapeutic development.
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Affiliation(s)
- Gen Shinozaki
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
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22
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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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23
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Chen J, Yu S, Fu Y, Li X. Synaptic proteins and receptors defects in autism spectrum disorders. Front Cell Neurosci 2014; 8:276. [PMID: 25309321 PMCID: PMC4161164 DOI: 10.3389/fncel.2014.00276] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/21/2014] [Indexed: 12/27/2022] Open
Abstract
Recent studies have found that hundreds of genetic variants, including common and rare variants, rare and de novo mutations, and common polymorphisms contribute to the occurrence of autism spectrum disorders (ASDs). The mutations in a number of genes such as neurexin, neuroligin, postsynaptic density protein 95, SH3, and multiple ankyrin repeat domains 3 (SHANK3), synapsin, gephyrin, cadherin, and protocadherin, thousand-and-one-amino acid 2 kinase, and contactin, have been shown to play important roles in the development and function of synapses. In addition, synaptic receptors, such as gamma-aminobutyric acid receptors and glutamate receptors, have also been associated with ASDs. This review will primarily focus on the defects of synaptic proteins and receptors associated with ASDs and their roles in the pathogenesis of ASDs via synaptic pathways.
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Affiliation(s)
- Jianling Chen
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Shunying Yu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Yingmei Fu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Xiaohong Li
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities Staten Island, NY USA
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Gonzalez S, Camarillo C, Rodriguez M, Ramirez M, Zavala J, Armas R, Contreras SA, Contreras J, Dassori A, Almasy L, Flores D, Jerez A, Raventós H, Ontiveros A, Nicolini H, Escamilla M. A genome-wide linkage scan of bipolar disorder in Latino families identifies susceptibility loci at 8q24 and 14q32. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:479-91. [PMID: 25044503 DOI: 10.1002/ajmg.b.32251] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/27/2014] [Indexed: 12/14/2022]
Abstract
A genome-wide nonparametric linkage screen was performed to localize Bipolar Disorder (BP) susceptibility loci in a sample of 3757 individuals of Latino ancestry. The sample included 963 individuals with BP phenotype (704 relative pairs) from 686 families recruited from the US, Mexico, Costa Rica, and Guatemala. Non-parametric analyses were performed over a 5 cM grid with an average genetic coverage of 0.67 cM. Multipoint analyses were conducted across the genome using non-parametric Kong & Cox LOD scores along with Sall statistics for all relative pairs. Suggestive and significant genome-wide thresholds were calculated based on 1000 simulations. Single-marker association tests in the presence of linkage were performed assuming a multiplicative model with a population prevalence of 2%. We identified two genome-wide significant susceptibly loci for BP at 8q24 and 14q32, and a third suggestive locus at 2q13-q14. Within these three linkage regions, the top associated single marker (rs1847694, P = 2.40 × 10(-5)) is located 195 Kb upstream of DPP10 in Chromosome 2. DPP10 is prominently expressed in brain neuronal populations, where it has been shown to bind and regulate Kv4-mediated A-type potassium channels. Taken together, these results provide additional evidence that 8q24, 14q32, and 2q13-q14 are susceptibly loci for BP and these regions may be involved in the pathogenesis of BP in the Latino population.
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Affiliation(s)
- Suzanne Gonzalez
- Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas; Department of Psychiatry, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
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Georgieva L, Rees E, Moran JL, Chambert KD, Milanova V, Craddock N, Purcell S, Sklar P, McCarroll S, Holmans P, O'Donovan MC, Owen MJ, Kirov G. De novo CNVs in bipolar affective disorder and schizophrenia. Hum Mol Genet 2014; 23:6677-83. [PMID: 25055870 PMCID: PMC4240207 DOI: 10.1093/hmg/ddu379] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
An increased rate of de novo copy number variants (CNVs) has been found in schizophrenia (SZ), autism and developmental delay. An increased rate has also been reported in bipolar affective disorder (BD). Here, in a larger BD sample, we aimed to replicate these findings and compare de novo CNVs between SZ and BD. We used Illumina microarrays to genotype 368 BD probands, 76 SZ probands and all their parents. Copy number variants were called by PennCNV and filtered for frequency (<1%) and size (>10 kb). Putative de novo CNVs were validated with the z-score algorithm, manual inspection of log R ratios (LRR) and qPCR probes. We found 15 de novo CNVs in BD (4.1% rate) and 6 in SZ (7.9% rate). Combining results with previous studies and using a cut-off of >100 kb, the rate of de novo CNVs in BD was intermediate between controls and SZ: 1.5% in controls, 2.2% in BD and 4.3% in SZ. Only the differences between SZ and BD and SZ and controls were significant. The median size of de novo CNVs in BD (448 kb) was also intermediate between SZ (613 kb) and controls (338 kb), but only the comparison between SZ and controls was significant. Only one de novo CNV in BD was in a confirmed SZ locus (16p11.2). Sporadic or early onset cases were not more likely to have de novo CNVs. We conclude that de novo CNVs play a smaller role in BD compared with SZ. Patients with a positive family history can also harbour de novo mutations.
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Affiliation(s)
- Lyudmila Georgieva
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Elliott Rees
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Jennifer L Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kimberly D Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vihra Milanova
- Department of Psychiatry, Medical University, Sofia, Bulgaria
| | - Nicholas Craddock
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Shaun Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA and Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA and Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Steven McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Michael C O'Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - George Kirov
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK,
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The neurobiology of bipolar disorder: identifying targets for specific agents and synergies for combination treatment. Int J Neuropsychopharmacol 2014; 17:1039-52. [PMID: 23449044 DOI: 10.1017/s1461145713000096] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bipolar disorder (BD) is a chronic psychiatric illness described by severe changes in mood. Extensive research has been carried out to understand the aetiology and pathophysiology of BD. Several hypotheses have been postulated, including alteration in genetic factors, protein expression, calcium signalling, neuropathological alteration, mitochondrial dysfunction and oxidative stress in BD. In the following paper, we will attempt to integrate these data in a manner which is to understand targets of treatment and how they may be, in particular, relevant to combination treatment. In summary, the data suggested that BD might be associated with neuronal and glial cellular impairment in specific brain areas, including the prefrontal cortex. From molecular and genetics: (1) alterations in dopaminergic system, through catechol-O-aminotransferase; (2) decreased expression and polymorphism on brain-derived neurotrophic factor; (3) alterations cyclic-AMP responsive element binding; (4) dysregulation of calcium signalling, including genome-wide finding for voltage-dependent calcium channel α-1 subunit are relevant findings in BD. Future studies are now necessary to understand how these molecular pathways interact and their connection to the complex clinical manifestations observed in BD.
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Kandaswamy R, McQuillin A, Curtis D, Gurling H. Allelic association, DNA resequencing and copy number variation at the metabotropic glutamate receptor GRM7 gene locus in bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:365-72. [PMID: 24804643 PMCID: PMC4231221 DOI: 10.1002/ajmg.b.32239] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 04/14/2014] [Indexed: 12/12/2022]
Abstract
Genetic markers at the GRM7 gene have shown allelic association with bipolar disorder (BP) in several case-control samples including our own sample. In this report, we present results of resequencing the GRM7 gene in 32 bipolar samples and 32 random controls selected from 553 bipolar cases and 547 control samples (UCL1). Novel and potential etiological base pair changes discovered by resequencing were genotyped in the entire UCL case-control sample. We also report on the association between GRM7 and BP in a second sample of 593 patients and 642 controls (UCL2). The three most significantly associated SNPs in the original UCL1 BP GWAS sample were genotyped in the UCL2 sample, of which none were associated. After combining the genotype data for the two samples only two (rs1508724 and rs6769814) of the original three SNP markers remained significantly associated with BP. DNA sequencing revealed mutations in three cases which were absent in control subjects. A 3'-UTR SNP rs56173829 was found to be significantly associated with BP in the whole UCL sample (P = 0.035; OR = 0.482), the rare allele being less common in cases compared to controls. Bioinformatic analyses predicted a change in the centroid secondary structure of RNA and alterations in the miRNA binding sites for the mutated base of rs56173829. We also validated two deletions and a duplication within GRM7 using quantitative-PCR which provides further support for the pre-existing evidence that copy number variants at GRM7 may have a role in the etiology of BP.
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Affiliation(s)
- Radhika Kandaswamy
- Molecular Psychiatry Laboratory, Mental Health Sciences Unit, Faculty of Brain Sciences, University College LondonLondon, UK
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Mental Health Sciences Unit, Faculty of Brain Sciences, University College LondonLondon, UK,* Correspondence to: Andrew McQuillin, Molecular Psychiatry Laboratory, Mental Health Sciences Unit, Faculty of Brain Sciences, University College London, Rockefeller Building, 21 University Street, London WC1E 6BT, UK. E-mail:
| | - David Curtis
- Department of Psychological Medicine, St. Bartholomew's and the Royal London School of Medicine and Dentistry, Queen Mary University of LondonLondon, UK
| | - Hugh Gurling
- Molecular Psychiatry Laboratory, Mental Health Sciences Unit, Faculty of Brain Sciences, University College LondonLondon, UK
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Noor A, Lionel AC, Cohen-Woods S, Moghimi N, Rucker J, Fennell A, Thiruvahindrapuram B, Kaufman L, Degagne B, Wei J, Parikh SV, Muglia P, Forte J, Scherer SW, Kennedy JL, Xu W, McGuffin P, Farmer A, Strauss J, Vincent JB. Copy number variant study of bipolar disorder in Canadian and UK populations implicates synaptic genes. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:303-13. [PMID: 24700553 DOI: 10.1002/ajmg.b.32232] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 03/10/2014] [Indexed: 01/03/2023]
Abstract
Genome-wide single nucleotide polymorphism (SNP) data from 936 bipolar disorder (BD) individuals and 940 psychiatrically healthy comparison individuals of North European descent were analyzed for copy number variation (CNV). Using multiple CNV calling algorithms, and validating using in vitro molecular analyses, we identified CNVs implicating several candidate genes that encode synaptic proteins, such as DLG1, DLG2, DPP6, NRXN1, NRXN2, NRXN3, SHANK2, and EPHA5, as well as the neuronal splicing regulator RBFOX1 (A2BP1), and neuronal cell adhesion molecule CHL1. We have also identified recurrent CNVs on 15q13.3 and 16p11.2-regions previously reported as risk loci for neuropsychiatric disorders. In addition, we performed CNV analysis of individuals from 215 BD trios and identified de novo CNVs involving the NRXN1 and DRD5 genes. Our study provides further evidence of the occasional involvement of genomic mutations in the etiology of BD, however, there is no evidence of an increased burden of CNVs in BD. Further, the identification of CNVs at multiple members of the neurexin gene family in BD individuals, supports the role of synaptic disruption in the etiology of BD.
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Affiliation(s)
- Abdul Noor
- Molecular Neuropsychiatry & Development Lab, Campbell Family Mental Health Research Institute, The Centre for Addiction & Mental Health, Toronto, Ontario, Canada
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Cardno AG, Owen MJ. Genetic relationships between schizophrenia, bipolar disorder, and schizoaffective disorder. Schizophr Bull 2014; 40:504-15. [PMID: 24567502 PMCID: PMC3984527 DOI: 10.1093/schbul/sbu016] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There is substantial evidence for partial overlap of genetic influences on schizophrenia and bipolar disorder, with family, twin, and adoption studies showing a genetic correlation between the disorders of around 0.6. Results of genome-wide association studies are consistent with commonly occurring genetic risk variants, contributing to both the shared and nonshared aspects, while studies of large, rare chromosomal structural variants, particularly copy number variants, show a stronger influence on schizophrenia than bipolar disorder to date. Schizoaffective disorder has been less investigated but shows substantial familial overlap with both schizophrenia and bipolar disorder. A twin analysis is consistent with genetic influences on schizoaffective episodes being entirely shared with genetic influences on schizophrenic and manic episodes, while association studies suggest the possibility of some relatively specific genetic influences on broadly defined schizoaffective disorder, bipolar subtype. Further insights into genetic relationships between these disorders are expected as studies continue to increase in sample size and in technical and analytical sophistication, information on phenotypes beyond clinical diagnoses are increasingly incorporated, and approaches such as next-generation sequencing identify additional types of genetic risk variant.
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Affiliation(s)
- Alastair G. Cardno
- Academic Unit of Psychiatry and Behavioural Sciences, University of Leeds, Leeds, UK;,*To whom correspondence should be addressed; Academic Unit of Psychiatry and Behavioural Sciences, Leeds Institute of Health Sciences, University of Leeds, Charles Thackrah Building, 101 Clarendon Road, Leeds LS2 9LJ, UK; tel: +44 113 3437260, fax: +44 113 3436997, e-mail:
| | - Michael J. Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
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Doherty JL, Owen MJ. Genomic insights into the overlap between psychiatric disorders: implications for research and clinical practice. Genome Med 2014; 6:29. [PMID: 24944580 PMCID: PMC4062063 DOI: 10.1186/gm546] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Psychiatric disorders such as schizophrenia, bipolar disorder, major depressive disorder, attention-deficit/hyperactivity disorder and autism spectrum disorder are common and result in significant morbidity and mortality. Although currently classified into distinct disorder categories, they show clinical overlap and familial co-aggregation, and share genetic risk factors. Recent advances in psychiatric genomics have provided insight into the potential mechanisms underlying the overlap between these disorders, implicating genes involved in neurodevelopment, synaptic plasticity, learning and memory. Furthermore, evidence from copy number variant, exome sequencing and genome-wide association studies supports a gradient of neurodevelopmental psychopathology indexed by mutational load or mutational severity, and cognitive impairment. These findings have important implications for psychiatric research, highlighting the need for new approaches to stratifying patients for research. They also point the way for work aiming to advance our understanding of the pathways from genotype to clinical phenotype, which will be required in order to inform new classification systems and to develop novel therapeutic strategies.
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Affiliation(s)
- Joanne L Doherty
- The MRC Centre for Neuropsychiatric Genetics and Genomics and The Neuroscience and Mental Health Research Institute, Cardiff University, Hadyn Ellis Buildin, Maindy Road, Cardiff CF24 4HQ, UK
| | - Michael J Owen
- The MRC Centre for Neuropsychiatric Genetics and Genomics and The Neuroscience and Mental Health Research Institute, Cardiff University, Hadyn Ellis Buildin, Maindy Road, Cardiff CF24 4HQ, UK
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Kodama S, Yamada T, Imai J, Sawada S, Takahashi K, Tsukita S, Kaneko K, Uno K, Ishigaki Y, Oka Y, Katagiri H. Simultaneous copy number losses within multiple subtelomeric regions in early-onset type 2 diabetes mellitus. PLoS One 2014; 9:e88602. [PMID: 24709989 PMCID: PMC3977841 DOI: 10.1371/journal.pone.0088602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/13/2014] [Indexed: 11/23/2022] Open
Abstract
Genetic factors play very important roles in the onset and progression of type 2 diabetes mellitus (T2DM). However, the genetic factors correlating with T2DM onset have not as yet been fully clarified. We previously found that copy number losses in the subtelomeric region on chromosome 4p16.3 were detected in early-onset Japanese T2DM patients (onset age <35 years) at a high frequency. Herein, we additionally found two novel copy number losses within the subtelomeric regions on chromosomes 16q24.2-3 and 22q13.31-33, which have significant associations with early-onset Japanese T2DM. The associations were statistically significant by Fisher's exact tests with P values of 5.19×10−3 and 1.81×10−3 and odds ratios of 5.7 and 4.4 for 16q24.2-3 and 22q13.31-33, respectively. Furthermore, copy number variation (CNV) analysis of the whole genome using the CNV BeadChip system verified simultaneous copy number losses in all three subtelomeric regions in 11 of our 100 T2DM subjects, while none of 100 non-diabetic controls showed the copy number losses in all three regions. Our results suggest that the mechanism underlying induction of CNVs is involved in the pathogenesis of early-onset T2DM. Thus, copy number losses within multiple subtelomeric regions are strongly associated with early-onset T2DM and examination of simultaneous CNVs in these three regions may lead to the development of an accurate and selective procedure for detecting genetic susceptibility to T2DM.
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Affiliation(s)
- Shinjiro Kodama
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuya Yamada
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Junta Imai
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shojiro Sawada
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kei Takahashi
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Sohei Tsukita
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Keizo Kaneko
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kenji Uno
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasushi Ishigaki
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitomo Oka
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hideki Katagiri
- Division of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Sendai, Japan
- Japan Science and Technology Agency, CREST, Tokyo, Japan
- * E-mail:
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Chen YH, Lu RB, Hung H, Kuo PH. Identifying Potential Regions of Copy Number Variation for Bipolar Disorder. MICROARRAYS 2014; 3:52-71. [PMID: 27605030 PMCID: PMC5003455 DOI: 10.3390/microarrays3010052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 11/16/2022]
Abstract
Bipolar disorder is a complex psychiatric disorder with high heritability, but its genetic determinants are still largely unknown. Copy number variation (CNV) is one of the sources to explain part of the heritability. However, it is a challenge to estimate discrete values of the copy numbers using continuous signals calling from a set of markers, and to simultaneously perform association testing between CNVs and phenotypic outcomes. The goal of the present study is to perform a series of data filtering and analysis procedures using a DNA pooling strategy to identify potential CNV regions that are related to bipolar disorder. A total of 200 normal controls and 200 clinically diagnosed bipolar patients were recruited in this study, and were randomly divided into eight control and eight case pools. Genome-wide genotyping was employed using Illumina Human Omni1-Quad array with approximately one million markers for CNV calling. We aimed at setting a series of criteria to filter out the signal noise of marker data and to reduce the chance of false-positive findings for CNV regions. We first defined CNV regions for each pool. Potential CNV regions were reported based on the different patterns of CNV status between cases and controls. Genes that were mapped into the potential CNV regions were examined with association testing, Gene Ontology enrichment analysis, and checked with existing literature for their associations with bipolar disorder. We reported several CNV regions that are related to bipolar disorder. Two CNV regions on chromosome 11 and 22 showed significant signal differences between cases and controls (p < 0.05). Another five CNV regions on chromosome 6, 9, and 19 were overlapped with results in previous CNV studies. Experimental validation of two CNV regions lent some support to our reported findings. Further experimental and replication studies could be designed for these selected regions.
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Affiliation(s)
- Yi-Hsuan Chen
- Department of Public Health & Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan.
| | - Ru-Band Lu
- Department of Psychiatry, College of Medicine & Hospital, National Cheng Kung University, Tainan 704, Taiwan.
| | - Hung Hung
- Department of Public Health & Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan.
- Research Center for Genes, Environment and Human Health, National Taiwan University, Taipei 100, Taiwan.
| | - Po-Hsiu Kuo
- Department of Public Health & Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan.
- Research Center for Genes, Environment and Human Health, National Taiwan University, Taipei 100, Taiwan.
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34
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Grozeva D, Kirov G, Conrad DF, Barnes CP, Hurles M, Owen MJ, O'Donovan MC, Craddock N. Reduced burden of very large and rare CNVs in bipolar affective disorder. Bipolar Disord 2013; 15:893-8. [PMID: 24127788 DOI: 10.1111/bdi.12125] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 08/15/2013] [Indexed: 01/21/2023]
Abstract
OBJECTIVES Large, rare chromosomal copy number variants (CNVs) have been shown to increase the risk for schizophrenia and other neuropsychiatric disorders including autism, attention-deficit hyperactivity disorder, learning difficulties, and epilepsy. Their role in bipolar disorder (BD) is less clear. There are no reports of an increase in large, rare CNVs in BD in general, but some have reported an increase in early-onset cases. We previously found that the rate of such CNVs in individuals with BD was not increased, even in early-onset cases. Our aim here was to examine the rate of large rare CNVs in BD in comparison with a new large independent reference sample from the same country. METHODS We studied the CNVs in a case-control sample consisting of 1,650 BD cases (reported previously) and 10,259 reference individuals without a known psychiatric disorder who took part in the original Wellcome Trust Case Control Consortium (WTCCC) study. The 10,259 reference individuals were affected with six non-psychiatric disorders (coronary artery disease, types 1 and 2 diabetes, hypertension, Crohn's disease, and rheumatoid arthritis). Affymetrix 500K array genotyping data were used to call the CNVs. RESULTS The rate of CNVs > 100 kb was not statistically different between cases and controls. The rate of very large (defined as > 1 Mb) and rare (< 1%) CNVs was significantly lower in patients with BD compared with the reference group. CNV loci associated with schizophrenia were not enriched in BD and, in fact, cases of BD had the lowest number of such CNVs compared with any of the WTCCC cohorts; this finding held even for the early-onset BD cases. CONCLUSIONS Schizophrenia and BD differ with respect to CNV burden and association with specific CNVs. Our findings support the hypothesis that BD is etiologically distinct from schizophrenia with respect to large, rare CNVs and the accompanying associated neurodevelopmental abnormalities.
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Mehta D, Iwamoto K, Ueda J, Bundo M, Adati N, Kojima T, Kato T. Comprehensive survey of CNVs influencing gene expression in the human brain and its implications for pathophysiology. Neurosci Res 2013; 79:22-33. [PMID: 24211644 DOI: 10.1016/j.neures.2013.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/22/2013] [Accepted: 10/29/2013] [Indexed: 01/20/2023]
Abstract
Copy number variations (CNVs) contribute to neuropsychiatric diseases, which may be partly mediated by their effects on gene expression. However, few studies have assessed the influence of CNVs on gene expression in the brain. The objective was to perform an unbiased comprehensive survey of influence of CNVs on gene expression in human brain tissues. CNV regions (CNVRs) were identified in 72 individuals (23 schizophrenia, 23 bipolar disorder and 26 controls). Significant associations between the CNVRs and gene expression levels were observed for 583 CNVR-expression probe pairs (293 unique eCNVRs and 429 unique transcripts), after corrections for multiple testing and controlling the effect of the number of subjects with CNVRs by label swapping permutations. These CNVRs affecting gene expression (eCNVRs) were significantly enriched for rare/low frequency (p=1.087×10(-10)) and gene-harboring CNVRs (p=1.4×10(-6)). Transcripts overlapping CNVRs were significantly enriched for glutathione metabolism and oxidative stress only for cases but not for controls. Moreover, 72 (24.6%) of eCNVRs were located within the chromosomal aberration regions implicated in psychiatric-disorders: 16p11.2, 1q21.1, 22q11.2, 3q29, 15q11.2, 17q12 and 16p13.1. These results shed light on the mechanism of how CNVs confer a risk for psychiatric disorders.
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Affiliation(s)
- Divya Mehta
- Max Planck Institute of Psychiatry, Munich 80804, Germany; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama 351-0198, Japan
| | - Kazuya Iwamoto
- Department of Molecular Psychiatry, Graduate School of Medicine, University of Tokyo, Tokyo 113-8654, Japan
| | - Junko Ueda
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama 351-0198, Japan
| | - Miki Bundo
- Department of Molecular Psychiatry, Graduate School of Medicine, University of Tokyo, Tokyo 113-8654, Japan
| | - Naoki Adati
- Comparative Systems Biology Team, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
| | - Toshio Kojima
- Comparative Systems Biology Team, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama 351-0198, Japan.
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36
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Niculescu AB. Convergent functional genomics of psychiatric disorders. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:587-94. [PMID: 23728881 DOI: 10.1002/ajmg.b.32163] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 03/19/2013] [Indexed: 12/27/2022]
Abstract
Genetic and gene expression studies, in humans and animal models of psychiatric and other medical disorders, are becoming increasingly integrated. Particularly for genomics, the convergence and integration of data across species, experimental modalities and technical platforms is providing a fit-to-disease way of extracting reproducible and biologically important signal, in contrast to the fit-to-cohort effect and limited reproducibility of human genetic analyses alone. With the advent of whole-genome sequencing and the realization that a major portion of the non-coding genome may contain regulatory variants, Convergent Functional Genomics (CFG) approaches are going to be essential to identify disease-relevant signal from the tremendous polymorphic variation present in the general population. Such work in psychiatry can provide an example of how to address other genetically complex disorders, and in turn will benefit by incorporating concepts from other areas, such as cancer, cardiovascular diseases, and diabetes.
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Affiliation(s)
- Alexander B Niculescu
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana; Indianapolis VA Medical Center, Indianapolis, Indiana
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Abstract
Studies of families and twins show the importance of genetic factors affecting susceptibility to bipolar disorder and suggest substantial genetic and phenotypic complexity. Robust and replicable genome-wide significant associations have recently been reported in genome-wide association studies at several common polymorphisms, including variants within the genes CACNA1C, ODZ4, and NCAN. Strong evidence exists for a polygenic contribution to risk (ie, many risk alleles of small effect). A notable finding is the overlap of susceptibility between bipolar disorder and schizophrenia for several individual risk alleles and for the polygenic risk. By contrast, genomic structural variation seems to play a smaller part in bipolar disorder than it does in schizophrenia. Together, these genetic findings suggest directions for future studies to delineate the aetiology and pathogenesis of bipolar disorder, indicate the need to re-evaluate our diagnostic classifications, and might eventually pave the way for major improvements in clinical management.
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Affiliation(s)
- Nick Craddock
- Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
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Pescosolido MF, Gamsiz ED, Nagpal S, Morrow EM. Distribution of disease-associated copy number variants across distinct disorders of cognitive development. J Am Acad Child Adolesc Psychiatry 2013; 52:414-430.e14. [PMID: 23582872 PMCID: PMC3774163 DOI: 10.1016/j.jaac.2013.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Revised: 12/09/2012] [Accepted: 01/11/2012] [Indexed: 11/18/2022]
Abstract
OBJECTIVE The purpose of the present study was to discover the extent to which distinct DSM disorders share large, highly recurrent copy number variants (CNVs) as susceptibility factors. We also sought to identify gene mechanisms common to groups of diagnoses and/or specific to a given diagnosis based on associations with CNVs. METHOD Systematic review of 820 PubMed articles on autism spectrum disorder (ASD), intellectual disability (ID), schizophrenia, and epilepsy produced 54 CNVs associated with one or several disorders. Pathway analysis on genes implicated by CNVs in different groupings was conducted. RESULTS The majority of CNVs were found in ID with the other disorders somewhat subsumed, yet certain CNVs were associated with isolated or groups of disorders. Based on genes implicated by CNVs, ID encompassed 96.8% of genes in ASD, 92.8% of genes in schizophrenia, and 100.0% of genes in epilepsy. Pathway analysis revealed that synapse processes were enriched in ASD, ID, and schizophrenia. Disease-specific processes were identified in ID (actin cytoskeleton processes), schizophrenia (ubiquitin-related processes), and ASD (synaptic vesicle transport and exocytosis). CONCLUSIONS Intellectual disability may arise from the broadest range of genetic pathways, and specific subsets of these pathways appear to be relevant to other disorders or combinations of these disorders. It is clear that statistically significant CNVs across disorders of cognitive development are highly enriched for biological processes related to the synapse. There are also disorder-specific processes that may aid in understanding the distinct presentations and pathophysiology of these disorders.
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Abstract
BACKGROUND It has been well established that both genes and non-shared environment contribute substantially to the underlying aetiology of major depressive disorder (MDD). A comprehensive overview of genetic research in MDD is presented. Method Papers were retrieved from PubMed up to December 2011, using many keywords including: depression, major depressive disorder, genetics, rare variants, gene-environment, whole genome, epigenetics, and specific candidate genes and variants. These were combined in a variety of permutations. RESULTS Linkage studies have yielded some promising chromosomal regions in MDD. However, there is a continued lack of consistency in association studies, in both candidate gene and genome-wide association studies (GWAS). Numerous factors may account for variable results including the use of different diagnostic approaches, small samples in early studies, population stratification, epigenetic phenomena, copy number variation (CNV), rare variation, and phenotypic and allelic heterogeneity. The conflicting results are also probably, in part, a consequence of environmental factors not being considered or controlled for. CONCLUSIONS Each research group has to identify what issues their sample may best address. We suggest that, where possible, more emphasis should be placed on the environment in molecular behavioural genetics to identify individuals at environmental high risk in addition to genetic high risk. Sequencing should be used to identify rare and alternative variation that may act as a risk factor, and a systems biology approach including gene-gene interactions and pathway analyses would be advantageous. GWAS may require even larger samples with reliably defined (sub)phenotypes.
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Affiliation(s)
- S Cohen-Woods
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, UK.
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McRae AF, Wright MJ, Hansell NK, Montgomery GW, Martin NG. No association between general cognitive ability and rare copy number variation. Behav Genet 2013; 43:202-7. [PMID: 23417127 DOI: 10.1007/s10519-013-9587-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 02/06/2013] [Indexed: 11/26/2022]
Abstract
There is increasing evidence for the role of rare copy-number variation (CNV) in the development of neuropsychiatric disorders. It is likely that such variants also have an effect on the variation of cognition in what is considered the "normal" phenotypic range. The role of rare CNV (>20 KB in length; frequency <5 %) on general cognitive ability is investigated in a sample of 800 individuals (mean age = 16.5, SD = 1.2) using copy-number variants called from the Illumina 610K SNP genotyping array with the software QuantiSNP. We assessed three measures of CNV burden--total CNV length, number of CNV and average CNV length--for both deletions and duplications in combination and separately. No correlation was found between any of the measures of CNV burden and IQ, or when comparing the top and bottom 10 % of the sample for IQ, both on a genome-wide scale and at individual positions across the genome.
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Affiliation(s)
- Allan F McRae
- University of Queensland Diamantina Institute, Brisbane, QLD, Australia.
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Chen X, Shen Y, Gao Y, Zhao H, Sheng X, Zou J, Lip V, Xie H, Guo J, Shao H, Bao Y, Shen J, Niu B, Gusella JF, Wu BL, Zhang T. Detection of copy number variants reveals association of cilia genes with neural tube defects. PLoS One 2013; 8:e54492. [PMID: 23349908 PMCID: PMC3547935 DOI: 10.1371/journal.pone.0054492] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 12/12/2012] [Indexed: 11/19/2022] Open
Abstract
Background Neural tube defects (NTDs) are one of the most common birth defects caused by a combination of genetic and environmental factors. Currently, little is known about the genetic basis of NTDs although up to 70% of human NTDs were reported to be attributed to genetic factors. Here we performed genome-wide copy number variants (CNVs) detection in a cohort of Chinese NTD patients in order to exam the potential role of CNVs in the pathogenesis of NTDs. Methods The genomic DNA from eighty-five NTD cases and seventy-five matched normal controls were subjected for whole genome CNVs analysis. Non-DGV (the Database of Genomic Variants) CNVs from each group were further analyzed for their associations with NTDs. Gene content in non-DGV CNVs as well as participating pathways were examined. Results Fifty-five and twenty-six non-DGV CNVs were detected in cases and controls respectively. Among them, forty and nineteen CNVs involve genes (genic CNV). Significantly more non-DGV CNVs and non-DGV genic CNVs were detected in NTD patients than in control (41.2% vs. 25.3%, p<0.05 and 37.6% vs. 20%, p<0.05). Non-DGV genic CNVs are associated with a 2.65-fold increased risk for NTDs (95% CI: 1.24–5.87). Interestingly, there are 41 cilia genes involved in non-DGV CNVs from NTD patients which is significantly enriched in cases compared with that in controls (24.7% vs. 9.3%, p<0.05), corresponding with a 3.19-fold increased risk for NTDs (95% CI: 1.27–8.01). Pathway analyses further suggested that two ciliogenesis pathways, tight junction and protein kinase A signaling, are top canonical pathways implicated in NTD-specific CNVs, and these two novel pathways interact with known NTD pathways. Conclusions Evidence from the genome-wide CNV study suggests that genic CNVs, particularly ciliogenic CNVs are associated with NTDs and two ciliogenesis pathways, tight junction and protein kinase A signaling, are potential pathways involved in NTD pathogenesis.
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Affiliation(s)
- Xiaoli Chen
- Capital Institute of Pediatrics, Beijing, China
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Yiping Shen
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Shanghai Children's Medical Center, Jiaotong University, Shanghai, China
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yonghui Gao
- Capital Institute of Pediatrics, Beijing, China
- Institute of Acu-moxibustion, China Academy of Chinese Medical Sciences, Beijing, China
| | - Huizhi Zhao
- Capital Institute of Pediatrics, Beijing, China
| | - Xiaoming Sheng
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Jizhen Zou
- Department of Pathology, Capital Institute of Pediatrics, Beijing, China
| | - Va Lip
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Hua Xie
- Capital Institute of Pediatrics, Beijing, China
| | - Jin Guo
- Capital Institute of Pediatrics, Beijing, China
| | - Hong Shao
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Yihua Bao
- Capital Institute of Pediatrics, Beijing, China
| | - Jianliang Shen
- Department of Hematology, Navy General Hospital of PLA, Beijing, China
| | - Bo Niu
- Department of Biotechnology, Capital Institute of Pediatrics, Beijing, China
| | - James F. Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bai-Lin Wu
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Children's Hospital and Institutes of Biomedical Science, Shanghai Medical College, Fudan University, Shanghai, China
- * E-mail: (BLW); (TZ)
| | - Ting Zhang
- Capital Institute of Pediatrics, Beijing, China
- * E-mail: (BLW); (TZ)
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Greenwood TA, Kelsoe JR. Genome-wide association study of irritable vs. elated mania suggests genetic differences between clinical subtypes of bipolar disorder. PLoS One 2013; 8:e53804. [PMID: 23326512 PMCID: PMC3542199 DOI: 10.1371/journal.pone.0053804] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 12/04/2012] [Indexed: 11/25/2022] Open
Abstract
The use of clinical features to define subtypes of a disorder may aid in gene identification for complex diseases. In particular, clinical subtypes of mania may distinguish phenotypic subgroups of bipolar subjects that may also differ genetically. To assess this possibility, we performed a genome-wide association study using genotype data from the Bipolar Genome Study (BiGS) and subjects that were categorized as having either irritable or elated mania during their most severe episode. A bipolar case-only analysis in the GAIN bipolar sample identified several genomic regions that differed between irritable and elated subjects, the most significant of which was for 33 SNPs on chromosome 13q31 (peak p = 2×10(-7)). This broad peak is in a relative gene desert over an unknown EST and between the SLITRK1 and SLITRK6 genes. Evidence for association to this region came predominantly from subjects in the sample that were originally collected as part of a family-based bipolar linkage study, rather than those collected as bipolar singletons. We then genotyped an additional sample of bipolar singleton cases and controls, and the analysis of irritable vs. elated mania in this new sample did not replicate our previous findings. However, this lack of replication is likely due to the presence of significant differences in terms of clinical co-morbity that were identified between these singleton bipolar cases and those that were selected from families segregating the disorder. Despite these clinical differences, analysis of the combined sample provided continued support for 13q31 and other regions from our initial analysis. Though genome-wide significance was not achieved, our results suggest that irritable mania results from a distinct set of genes, including a region on chromosome 13q31.
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Affiliation(s)
- Tiffany A. Greenwood
- Department of Psychiatry, University of San Diego, La Jolla, California, United States of America
| | | | - John R. Kelsoe
- Department of Psychiatry, University of San Diego, La Jolla, California, United States of America
- San Diego Veterans Administration Healthcare System, San Diego, California, United States of America
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Abstract
AbstractCopy number variants (CNVs) are submicroscopic deletions and duplications of genomic material that were previously thought to be rare phenomena. They have now been robustly associated with a variety of disorders such as autism, schizophrenia, and attention-deficit/hyperactivity disorder through an emerging research base in affective disorders. A complex picture is emerging of a polygenic, heterogeneous model of disease, with CNVs conferring broad susceptibility to a variety of neurodevelopmental disorders, rather than specific disorders per se. Although the insights gleaned thus far only represent a small piece of a much larger puzzle, progress has been rapid and new technologies promise even more insights into these hitherto opaque brain disorders. We will discuss CNVs, the current state of evidence for their role in the pathogenesis of classical psychiatric disorders, and the application of such knowledge in clinical settings.
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Van Den Bossche MJ, Johnstone M, Strazisar M, Pickard BS, Goossens D, Lenaerts AS, De Zutter S, Nordin A, Norrback KF, Mendlewicz J, Souery D, De Rijk P, Sabbe BG, Adolfsson R, Blackwood D, Del-Favero J. Rare copy number variants in neuropsychiatric disorders: Specific phenotype or not? Am J Med Genet B Neuropsychiatr Genet 2012; 159B:812-22. [PMID: 22911887 DOI: 10.1002/ajmg.b.32088] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/11/2012] [Indexed: 12/31/2022]
Abstract
From a number of genome-wide association studies it was shown that de novo and/or rare copy number variants (CNVs) are found at an increased frequency in neuropsychiatric diseases. In this study we examined the prevalence of CNVs in six genomic regions (1q21.1, 2p16.3, 3q29, 15q11.2, 15q13.3, and 16p11.2) previously implicated in neuropsychiatric diseases. Hereto, a cohort of four neuropsychiatric disorders (schizophrenia, bipolar disorder, major depressive disorder, and intellectual disability) and control individuals from three different populations was used in combination with Multilpex Amplicon Quantifiaction (MAQ) assays, capable of high resolution (kb range) and custom-tailored CNV detection. Our results confirm the etiological candidacy of the six selected CNV regions for neuropsychiatric diseases. It is possible that CNVs in these regions can result in disturbed brain development and in this way lead to an increased susceptibility for different neuropsychiatric disorders, dependent on additional genetic and environmental factors. Our results also suggest that the neurodevelopmental component is larger in the etiology of schizophrenia and intellectual disability than in mood disorders. Finally, our data suggest that deletions are in general more pathogenic than duplications. Given the high frequency of the examined CNVs (1-2%) in patients of different neuropsychiatric disorders, screening of large cohorts with an affordable and feasible method like the MAQ assays used in this study is likely to result in important progress in unraveling the genetic factors leading to an increased susceptibility for several psychiatric disorders.
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Soemedi R, Wilson I, Bentham J, Darlay R, Töpf A, Zelenika D, Cosgrove C, Setchfield K, Thornborough C, Granados-Riveron J, Blue G, Breckpot J, Hellens S, Zwolinkski S, Glen E, Mamasoula C, Rahman T, Hall D, Rauch A, Devriendt K, Gewillig M, O’ Sullivan J, Winlaw D, Bu’Lock F, Brook J, Bhattacharya S, Lathrop M, Santibanez-Koref M, Cordell H, Goodship J, Keavney B. Contribution of global rare copy-number variants to the risk of sporadic congenital heart disease. Am J Hum Genet 2012; 91:489-501. [PMID: 22939634 DOI: 10.1016/j.ajhg.2012.08.003] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/25/2012] [Accepted: 08/02/2012] [Indexed: 10/28/2022] Open
Abstract
Previous studies have shown that copy-number variants (CNVs) contribute to the risk of complex developmental phenotypes. However, the contribution of global CNV burden to the risk of sporadic congenital heart disease (CHD) remains incompletely defined. We generated genome-wide CNV data by using Illumina 660W-Quad SNP arrays in 2,256 individuals with CHD, 283 trio CHD-affected families, and 1,538 controls. We found association of rare genic deletions with CHD risk (odds ratio [OR] = 1.8, p = 0.0008). Rare deletions in study participants with CHD had higher gene content (p = 0.001) with higher haploinsufficiency scores (p = 0.03) than they did in controls, and they were enriched with Wnt-signaling genes (p = 1 × 10(-5)). Recurrent 15q11.2 deletions were associated with CHD risk (OR = 8.2, p = 0.02). Rare de novo CNVs were observed in ~5% of CHD trios; 10 out of 11 occurred on the paternally transmitted chromosome (p = 0.01). Some of the rare de novo CNVs spanned genes known to be involved in heart development (e.g., HAND2 and GJA5). Rare genic deletions contribute ~4% of the population-attributable risk of sporadic CHD. Second to previously described CNVs at 1q21.1, deletions at 15q11.2 and those implicating Wnt signaling are the most significant contributors to the risk of sporadic CHD. Rare de novo CNVs identified in CHD trios exhibit paternal origin bias.
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Bergen SE, O'Dushlaine CT, Ripke S, Lee PH, Ruderfer DM, Akterin S, Moran JL, Chambert KD, Handsaker RE, Backlund L, Ösby U, McCarroll S, Landen M, Scolnick EM, Magnusson PKE, Lichtenstein P, Hultman CM, Purcell SM, Sklar P, Sullivan PF. Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder. Mol Psychiatry 2012; 17:880-6. [PMID: 22688191 PMCID: PMC3724337 DOI: 10.1038/mp.2012.73] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 04/02/2012] [Accepted: 04/23/2012] [Indexed: 12/21/2022]
Abstract
Schizophrenia (SCZ) and bipolar disorder (BD) are highly heritable psychiatric disorders with overlapping susceptibility loci and symptomatology. We conducted a genome-wide association study (GWAS) of these disorders in a large Swedish sample. We report a new and independent case-control analysis of 1507 SCZ cases, 836 BD cases and 2093 controls. No single-nucleotide polymorphisms (SNPs) achieved significance in these new samples; however, combining new and previously reported SCZ samples (2111 SCZ and 2535 controls) revealed a genome-wide significant association in the major histocompatibility complex (MHC) region (rs886424, P=4.54 × 10(-8)). Imputation using multiple reference panels and meta-analysis with the Psychiatric Genomics Consortium SCZ results underscored the broad, significant association in the MHC region in the full SCZ sample. We evaluated the role of copy number variants (CNVs) in these subjects. As in prior reports, deletions were enriched in SCZ, but not BD cases compared with controls. Singleton deletions were more frequent in both case groups compared with controls (SCZ: P=0.003, BD: P=0.013), whereas the largest CNVs (>500 kb) were significantly enriched only in SCZ cases (P=0.0035). Two CNVs with previously reported SCZ associations were also overrepresented in this SCZ sample: 16p11.2 duplications (P=0.0035) and 22q11 deletions (P=0.03). These results reinforce prior reports of significant MHC and CNV associations in SCZ, but not BD.
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Affiliation(s)
- S E Bergen
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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Hucthagowder V, Liu TC, Paciorkowski AR, Thio LL, Keller MS, Anderson CD, Herman T, Dehner LP, Grange DK, Kulkarni S. Chromosome 2p15p16.1 microdeletion syndrome: 2.5 Mb deletion in a patient with renal anomalies, intractable seizures and a choledochal cyst. Eur J Med Genet 2012; 55:485-9. [DOI: 10.1016/j.ejmg.2012.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 04/06/2012] [Indexed: 10/28/2022]
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Pandey A, Davis NA, White BC, Pajewski NM, Savitz J, Drevets WC, McKinney BA. Epistasis network centrality analysis yields pathway replication across two GWAS cohorts for bipolar disorder. Transl Psychiatry 2012; 2:e154. [PMID: 22892719 PMCID: PMC3432194 DOI: 10.1038/tp.2012.80] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most pathway and gene-set enrichment methods prioritize genes by their main effect and do not account for variation due to interactions in the pathway. A portion of the presumed missing heritability in genome-wide association studies (GWAS) may be accounted for through gene-gene interactions and additive genetic variability. In this study, we prioritize genes for pathway enrichment in GWAS of bipolar disorder (BD) by aggregating gene-gene interaction information with main effect associations through a machine learning (evaporative cooling) feature selection and epistasis network centrality analysis. We validate this approach in a two-stage (discovery/replication) pathway analysis of GWAS of BD. The discovery cohort comes from the Wellcome Trust Case Control Consortium (WTCCC) GWAS of BD, and the replication cohort comes from the National Institute of Mental Health (NIMH) GWAS of BD in European Ancestry individuals. Epistasis network centrality yields replicated enrichment of Cadherin signaling pathway, whose genes have been hypothesized to have an important role in BD pathophysiology but have not demonstrated enrichment in previous analysis. Other enriched pathways include Wnt signaling, circadian rhythm pathway, axon guidance and neuroactive ligand-receptor interaction. In addition to pathway enrichment, the collective network approach elevates the importance of ANK3, DGKH and ODZ4 for BD susceptibility in the WTCCC GWAS, despite their weak single-locus effect in the data. These results provide evidence that numerous small interactions among common alleles may contribute to the diathesis for BD and demonstrate the importance of including information from the network of gene-gene interactions as well as main effects when prioritizing genes for pathway analysis.
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Affiliation(s)
- A Pandey
- Tandy School of Computer Science, Department of Mathematics, University of Tulsa, Tulsa, OK, USA
| | - N A Davis
- Tandy School of Computer Science, Department of Mathematics, University of Tulsa, Tulsa, OK, USA
| | - B C White
- Tandy School of Computer Science, Department of Mathematics, University of Tulsa, Tulsa, OK, USA
| | - N M Pajewski
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - J Savitz
- Laureate Institute for Brain Research, Tulsa, OK, USA,Department of Medicine, Tulsa School of Community Medicine, University of Tulsa, Tulsa, OK, USA
| | - W C Drevets
- Laureate Institute for Brain Research, Tulsa, OK, USA,Department of Psychiatry, University of Oklahoma College of Medicine Tulsa, Tulsa, OK, USA
| | - B A McKinney
- Tandy School of Computer Science, Department of Mathematics, University of Tulsa, Tulsa, OK, USA,Laureate Institute for Brain Research, Tulsa, OK, USA,Tandy School of Computer Science, Department of Mathematics, University of Tulsa, Rayzor Hall, 800 South Tucker Drive, Tulsa, OK 74104, USA. E-mail:
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Sullivan PF, Daly MJ, O'Donovan M. Genetic architectures of psychiatric disorders: the emerging picture and its implications. Nat Rev Genet 2012; 13:537-51. [PMID: 22777127 PMCID: PMC4110909 DOI: 10.1038/nrg3240] [Citation(s) in RCA: 824] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Psychiatric disorders are among the most intractable enigmas in medicine. In the past 5 years, there has been unprecedented progress on the genetics of many of these conditions. In this Review, we discuss the genetics of nine cardinal psychiatric disorders (namely, Alzheimer's disease, attention-deficit hyperactivity disorder, alcohol dependence, anorexia nervosa, autism spectrum disorder, bipolar disorder, major depressive disorder, nicotine dependence and schizophrenia). Empirical approaches have yielded new hypotheses about aetiology and now provide data on the often debated genetic architectures of these conditions, which have implications for future research strategies. Further study using a balanced portfolio of methods to assess multiple forms of genetic variation is likely to yield many additional new findings.
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Affiliation(s)
- Patrick F Sullivan
- Departments of Genetics and Psychiatry, CB# 7264, 5097 Genomic Medicine, University of North Carolina at Chapel Hill, North Carolina 27599-27264, USA.
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50
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Abstract
Because of the high costs associated with ascertainment of families, most linkage studies of Bipolar I disorder (BPI) have used relatively small samples. Moreover, the genetic information content reported in most studies has been less than 0.6. Although microsatellite markers spaced every 10 cM typically extract most of the genetic information content for larger multiplex families, they can be less informative for smaller pedigrees especially for affected sib pair kindreds. For these reasons we collaborated to pool family resources and carried out higher density genotyping. Approximately 1100 pedigrees of European ancestry were initially selected for study and were genotyped by the Center for Inherited Disease Research using the Illumina Linkage Panel 12 set of 6090 single-nucleotide polymorphisms. Of the ~1100 families, 972 were informative for further analyses, and mean information content was 0.86 after pruning for linkage disequilibrium. The 972 kindreds include 2284 cases of BPI disorder, 498 individuals with bipolar II disorder (BPII) and 702 subjects with recurrent major depression. Three affection status models (ASMs) were considered: ASM1 (BPI and schizoaffective disorder, BP cases (SABP) only), ASM2 (ASM1 cases plus BPII) and ASM3 (ASM2 cases plus recurrent major depression). Both parametric and non-parametric linkage methods were carried out. The strongest findings occurred at 6q21 (non-parametric pairs LOD 3.4 for rs1046943 at 119 cM) and 9q21 (non-parametric pairs logarithm of odds (LOD) 3.4 for rs722642 at 78 cM) using only BPI and schizoaffective (SA), BP cases. Both results met genome-wide significant criteria, although neither was significant after correction for multiple analyses. We also inspected parametric scores for the larger multiplex families to identify possible rare susceptibility loci. In this analysis, we observed 59 parametric LODs of 2 or greater, many of which are likely to be close to maximum possible scores. Although some linkage findings may be false positives, the results could help prioritize the search for rare variants using whole exome or genome sequencing.
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