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Kwong A, Zawistowski M, Fritsche LG, Zhan X, Bragg-Gresham J, Branham KE, Advani J, Othman M, Ratnapriya R, Teslovich TM, Stambolian D, Chew EY, Abecasis GR, Swaroop A. Whole genome sequencing of 4,787 individuals identifies gene-based rare variants in age-related macular degeneration. Hum Mol Genet 2024; 33:374-385. [PMID: 37934784 PMCID: PMC10840384 DOI: 10.1093/hmg/ddad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/12/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Genome-wide association studies have contributed extensively to the discovery of disease-associated common variants. However, the genetic contribution to complex traits is still largely difficult to interpret. We report a genome-wide association study of 2394 cases and 2393 controls for age-related macular degeneration (AMD) via whole-genome sequencing, with 46.9 million genetic variants. Our study reveals significant single-variant association signals at four loci and independent gene-based signals in CFH, C2, C3, and NRTN. Using data from the Exome Aggregation Consortium (ExAC) for a gene-based test, we demonstrate an enrichment of predicted rare loss-of-function variants in CFH, CFI, and an as-yet unreported gene in AMD, ORMDL2. Our method of using a large variant list without individual-level genotypes as an external reference provides a flexible and convenient approach to leverage the publicly available variant datasets to augment the search for rare variant associations, which can explain additional disease risk in AMD.
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Affiliation(s)
- Alan Kwong
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Lars G Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Xiaowei Zhan
- Southwestern Medical Center, University of Texas, 5323 Harry Hines Blvd, Dallas, TX 75390, United States
| | - Jennifer Bragg-Gresham
- Kidney Epidemiology and Cost Center, Department of Internal Medicine-Nephrology, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan Kellogg Eye Center, 1000 Wall St, Ann Arbor, MI 48105, United States
| | - Jayshree Advani
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
| | - Mohammad Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan Kellogg Eye Center, 1000 Wall St, Ann Arbor, MI 48105, United States
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
| | - Tanya M Teslovich
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, United States
| | - Dwight Stambolian
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania Medical School, 51 N. 39th Street, Philadelphia, PA 19104, United States
| | - Emily Y Chew
- Division of Epidemiology and Clinical Application, National Eye Institute, National Institutes of Health, 10 Center Drive Building 10-CRC, Bethesda, MD 20892, United States
| | - Gonçalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, United States
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
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Song X, Li R, Wang K, Bai Y, Xiao Y, Wang YP. Joint Sparse Collaborative Regression on Imaging Genetics Study of Schizophrenia. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1137-1146. [PMID: 35503837 PMCID: PMC10321021 DOI: 10.1109/tcbb.2022.3172289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The imaging genetics approach generates large amount of high dimensional and multi-modal data, providing complementary information for comprehensive study of Schizophrenia, a complex mental disease. However, at the same time, the variety of these data in structures, resolutions, and formats makes their integrative study a forbidding task. In this paper, we propose a novel model called Joint Sparse Collaborative Regression (JSCoReg), which can extract class-specific features from different health conditions/disease classes. We first evaluate the performance of feature selection in terms of Receiver operating characteristic curve and the area under the ROC curve in the simulation experiment. We demonstrate that the JSCoReg model can achieve higher accuracy compared with similar models including Joint Sparse Canonical Correlation Analysis and Sparse Collaborative Regression. We then applied the JSCoReg model to the analysis of schizophrenia dataset collected from the Mind Clinical Imaging Consortium. The JSCoReg enables us to better identify biomarkers associated with schizophrenia, which are verified to be both biologically and statistically significant.
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Affiliation(s)
- Xueli Song
- School of Sciences, Chang’an University, Xi’an, 710064, China
| | - Rongpeng Li
- School of Sciences, Chang’an University, Xi’an, 710064, China
| | - Kaiming Wang
- School of Sciences, Chang’an University, Xi’an, 710064, China
| | - Yuntong Bai
- Biomedical Engineering Department, Tulane University, New Orleans, LA 70118, USA
| | - Yuzhu Xiao
- School of Sciences, Chang’an University, Xi’an, 710064, China
| | - Yu-ping Wang
- Biomedical Engineering Department, Tulane University, New Orleans, LA 70118, USA
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Engelbrecht HR, Dalvie S, Agenbag G, Stein DJ, Ramesar RS. Whole-exome sequencing in an Afrikaner family with bipolar disorder. J Affect Disord 2020; 276:69-75. [PMID: 32697718 DOI: 10.1016/j.jad.2020.06.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/04/2020] [Accepted: 06/16/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Bipolar disorder (BD) has considerable heritability, with genome-wide association studies indicating that multiple common genetic variants contribute to risk. Less work has been undertaken to assess the contribution of rare variation in the development of this complex disorder, particularly in isolated populations. Using whole-exome sequencing (WES), the aim of this study was to identify rare, potentially damaging variants contributing to risk for BD in the Afrikaner population. METHODS WES was performed on eight Afrikaner family members, five affected and three unaffected. The analyses focused on i) the identification of rare, damaging variation, and ii) the molecular pathways in which these rare variants play a role using in silico prediction tools such as wANNOVAR and KOBAS 3.0. RESULTS Two rare and potentially damaging missense variants in FAM71B and SLC26A9 were shared by affected family members but were absent in unaffected members. In addition, variants in genes that play a role in pathways involved in signal transduction and synaptic transmission were shared by the five affected individuals. LIMITATIONS Two main limitations affect this study: the limited number of cases and controls, and the fact that whole-exome sequencing can only capture a small fragment of the genome which may harbor mutations. CONCLUSION This is the first WES study of BD in an Afrikaner family, and findings suggest that novel candidate genes may contribute to risk for BD in this population. Future work in larger samples of this population as well as in other populations is needed to fully investigate the role of the candidate genes found here.
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Affiliation(s)
- Hannah-Ruth Engelbrecht
- SA MRC Research Unit for Genomic and Precision Medicine, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, 7925.
| | - Shareefa Dalvie
- SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town.
| | - Gloudi Agenbag
- SA MRC Research Unit for Genomic and Precision Medicine, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, 7925.
| | - Dan J Stein
- SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town.
| | - Raj S Ramesar
- SA MRC Research Unit for Genomic and Precision Medicine, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, 7925.
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Li G, Han D, Wang C, Hu W, Calhoun VD, Wang YP. Application of deep canonically correlated sparse autoencoder for the classification of schizophrenia. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 183:105073. [PMID: 31525548 DOI: 10.1016/j.cmpb.2019.105073] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/27/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND OBJECTIVE Imaging genetics has been widely used to help diagnose and treat mental illness, e.g., schizophrenia, by combining magnetic resonance imaging of the brain and genomic information for comprehensive and systematic analysis. As a result, utilizing the correlation between magnetic resonance imaging of the brain and genomic information is becoming an important challenge. METHODS In this paper, the joint analysis of single nucleotide polymorphisms and functional magnetic resonance imaging is conducted for comprehensive study of schizophrenia. We developed a deep canonically correlated sparse autoencoder to classify schizophrenia patients from healthy controls, which can address the limitation of many existing methods such as canonical correlation analysis, deep canonical correlation analysis and sparse autoencoder. RESULTS The proposed deep canonically correlated sparse autoencoder can not only use complex nonlinear transformation and dimension reduction, but also achieve more accurate classifications. Our experiments showed the proposed method achieved an accuracy of 95.65% for SNP data sets and an accuracy of 80.53% for fMRI data sets. CONCLUSIONS Experiments demonstrated higher accuracy of using the proposed method over other conventional models when classifying schizophrenia patients and healthy controls.
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Affiliation(s)
- Gang Li
- School of Electronic and Control Engineering, Chang'an University, Xi'an 710064, Shaanxi, China; Key Laboratory of Road Construction Technology and Equipment of MOE, Chang'an University, China.
| | - Depeng Han
- School of Electronic and Control Engineering, Chang'an University, Xi'an 710064, Shaanxi, China
| | - Chao Wang
- School of Electronic and Control Engineering, Chang'an University, Xi'an 710064, Shaanxi, China
| | - Wenxing Hu
- Biomedical Engineering Department, Tulane University, New Orleans, LA 70118, USA.
| | - Vince D Calhoun
- Mind Research Network and Department of ECE, University of New Mexico, Albuquerque, NM 87106, USA.
| | - Yu-Ping Wang
- Biomedical Engineering Department, Tulane University, New Orleans, LA 70118, USA.
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Goicoechea de Jorge E, López Lera A, Bayarri-Olmos R, Yebenes H, Lopez-Trascasa M, Rodríguez de Córdoba S. Common and rare genetic variants of complement components in human disease. Mol Immunol 2018; 102:42-57. [PMID: 29914697 DOI: 10.1016/j.molimm.2018.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/06/2018] [Accepted: 06/08/2018] [Indexed: 12/21/2022]
Abstract
Genetic variability in the complement system and its association with disease has been known for more than 50 years, but only during the last decade have we begun to understand how this complement genetic variability contributes to the development of diseases. A number of reports have described important genotype-phenotype correlations that associate particular diseases with genetic variants altering specific aspects of the activation and regulation of the complement system. The detailed functional characterization of some of these genetic variants provided key insights into the pathogenic mechanisms underlying these pathologies, which is facilitating the design of specific anti-complement therapies. Importantly, these analyses have sometimes revealed unknown features of the complement proteins. As a whole, these advances have delineated the functional implications of genetic variability in the complement system, which supports the implementation of a precision medicine approach based on the complement genetic makeup of the patients. Here we provide an overview of rare complement variants and common polymorphisms associated with disease and discuss what we have learned from them.
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Affiliation(s)
- Elena Goicoechea de Jorge
- Department of Immunology, Complutense University, Madrid, Spain; Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Alberto López Lera
- Research Institute Hospital Universitario La Paz (IdiPaz), Madrid, Spain; Ciber de Enfermedades Raras, Madrid, Spain
| | - Rafael Bayarri-Olmos
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Hugo Yebenes
- Ciber de Enfermedades Raras, Madrid, Spain; Molecular Pathology and Complement Genetics Unit. Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | | | - Santiago Rodríguez de Córdoba
- Ciber de Enfermedades Raras, Madrid, Spain; Molecular Pathology and Complement Genetics Unit. Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.
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Analyses of the genetic diversity and protein expression variation of the acyl: CoA medium-chain ligases, ACSM2A and ACSM2B. Mol Genet Genomics 2018; 293:1279-1292. [PMID: 29948332 DOI: 10.1007/s00438-018-1460-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 06/11/2018] [Indexed: 12/18/2022]
Abstract
Benzoate (found in milk and widely used as preservative), salicylate (present in fruits and the active component of aspirin), dietary polyphenols produced by gut microbiota, metabolites from organic acidemias, and medium-chain fatty acids (MCFAs) are all metabolised/detoxified by the glycine conjugation pathway. Xenobiotics are first activated to an acyl-CoA by the mitochondrial xenobiotic/medium-chain fatty acid: CoA ligases (ACSMs) and subsequently conjugated to glycine by glycine N-acyltransferase (GLYAT). The MCFAs are activated to acyl-CoA by the ACSMs before entering mitochondrial β-oxidation. This two-step enzymatic pathway has, however, not been thoroughly investigated and the biggest gap in the literature remains the fact that studies continuously characterise the pathway as a one-step reaction. There are no studies available on the interaction/competition of the various substrates involved in the pathway, whilst very little research has been done on the ACSM ligases. To identify variants/haplotypes that should be characterised in future detoxification association studies, this study assessed the naturally observed sequence diversity and protein expression variation of ACSM2A and ACSM2B. The allelic variation, haplotype diversity, Tajima's D values, and phylogenetic analyses indicated that ACSM2A and ACSM2B are highly conserved. This confirmed an earlier hypothesis that the glycine conjugation pathway is highly conserved and essential for life as it maintains the CoA and glycine homeostasis in the liver mitochondria. The protein expression analyses showed that ACSM2A is the predominant transcript in liver. Future studies should investigate the effect of the variants identified in this study on the substrate specificity of these proteins.
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Complement factor H in AMD: Bridging genetic associations and pathobiology. Prog Retin Eye Res 2017; 62:38-57. [PMID: 28928087 DOI: 10.1016/j.preteyeres.2017.09.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 09/08/2017] [Accepted: 09/13/2017] [Indexed: 01/28/2023]
Abstract
Age-Related Macular Degeneration (AMD) is a complex multifactorial disease characterized in its early stages by lipoprotein accumulations in Bruch's Membrane (BrM), seen on fundoscopic exam as drusen, and in its late forms by neovascularization ("wet") or geographic atrophy of the Retinal Pigmented Epithelial (RPE) cell layer ("dry"). Genetic studies have strongly supported a relationship between the alternative complement cascade, in particular the common H402 variant in Complement Factor H (CFH) and development of AMD. However, the functional significance of the CFH Y402H polymorphism remains elusive. In this article, we critically review the literature surrounding the functional significance of this polymorphism. Furthermore, based on our group's studies we propose a model in which CFH H402 affects CFH binding to heparan sulfate proteoglycans leading to accelerated lipoprotein accumulation in BrM and drusen progression. We also review the literature on the role of other complement components in AMD pathobiologies, including C3a, C5a and the membrane attack complex (MAC), and on transgenic mouse models developed to interrogate in vivo the effects of the CFH Y402H polymorphism.
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8
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Malherbe PJ, Karayiorgou M, Ehlers R, Roos JL. Increased risk of suicide in schizophrenia patients with linkage to chromosome 13q. Psychiatry Res 2017; 251:34-35. [PMID: 28189075 DOI: 10.1016/j.psychres.2017.02.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 01/09/2017] [Accepted: 02/04/2017] [Indexed: 02/07/2023]
Abstract
We link schizophrenia in families from the genetically isolated South African Afrikaner population to chromosome 13q (n =51), 1p (n =23) and combined 13q & 1p (n =18). Patients with linkages to chromosome 13q were 4.16 times more likely to meet diagnostic criteria for schizoaffective disorder compared to patients with linkage to 1p. A third of patients with linkage to both 13q &1p met diagnostic criteria for SAD. There was a significant positive relationship between suicidality and a diagnosis of schizoaffective disorder. Identifying linkage to chromosome 13q may be informative in identifying suicide risk early and prevent morbidity and mortality in schizophrenia patients.
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Affiliation(s)
- P J Malherbe
- Department of Psychiatry, University of Pretoria, South Africa.
| | - M Karayiorgou
- Neurogenetics Laboratory, Department of Psychiatry, University of Columbia, New York
| | - R Ehlers
- Department of Statistics, University of Pretoria, South Africa
| | - J L Roos
- Department of Psychiatry, University of Pretoria, South Africa
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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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van der Sluis R, Badenhorst CPS, Erasmus E, van Dyk E, van der Westhuizen FH, van Dijk AA. Conservation of the coding regions of the glycine N-acyltransferase gene further suggests that glycine conjugation is an essential detoxification pathway. Gene 2015; 571:126-34. [PMID: 26149650 DOI: 10.1016/j.gene.2015.06.081] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 05/20/2015] [Accepted: 06/22/2015] [Indexed: 11/26/2022]
Abstract
Thorough investigation of the glycine conjugation pathway has been neglected. No defect of the glycine conjugation pathway has been reported and this could reflect the essential role of glycine conjugation in hepatic metabolism. Therefore, we hypothesised that genetic variation in the open reading frame (ORF) of the GLYAT gene should be low and that deleterious alleles would be found at low frequencies. This hypothesis was investigated by analysing the genetic variation of the human GLYAT ORF using data available in public databases. We also sequenced the GLYAT ORF of a small cohort of South African Afrikaner Caucasian individuals. In total, data from 1537 individuals was analysed. The two most prominent GLYAT haplotypes in all populations analysed, were S156 (70%) and T17S156 (20%). The S156C199 and S156H131 haplotypes, which have a negative effect on the enzyme activity of a recombinant human GLYAT, were detected at very low frequencies. In the Afrikaner Caucasian cohort a novel Q61L SNP occurring at a high frequency (12%) was detected. The results of this study indicated that the GLYAT ORF is highly conserved and supported the hypothesis that the glycine conjugation pathway is an essential detoxification pathway. These findings emphasise the importance of future investigations to determine the in vivo capacity of the glycine conjugation pathway for the detoxification of benzoate and other xenobiotics.
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Affiliation(s)
- Rencia van der Sluis
- Centre for Human Metabonomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
| | - Christoffel P S Badenhorst
- Centre for Human Metabonomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
| | - Elardus Erasmus
- Centre for Human Metabonomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
| | - Etresia van Dyk
- Centre for Human Metabonomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
| | | | - Alberdina A van Dijk
- Centre for Human Metabonomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa.
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Karayannis T, Au E, Patel JC, Kruglikov I, Markx S, Delorme R, Héron D, Salomon D, Glessner J, Restituito S, Gordon A, Rodriguez-Murillo L, Roy NC, Gogos JA, Rudy B, Rice ME, Karayiorgou M, Hakonarson H, Keren B, Huguet G, Bourgeron T, Hoeffer C, Tsien RW, Peles E, Fishell G. Cntnap4 differentially contributes to GABAergic and dopaminergic synaptic transmission. Nature 2014; 511:236-40. [PMID: 24870235 PMCID: PMC4281262 DOI: 10.1038/nature13248] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/11/2014] [Indexed: 01/08/2023]
Abstract
Although considerable evidence suggests that the chemical synapse is a lynchpin underlying affective disorders, how molecular insults differentially affect specific synaptic connections remains poorly understood. For instance, Neurexin 1a and 2 (NRXN1 and NRXN2) and CNTNAP2 (also known as CASPR2), all members of the neurexin superfamily of transmembrane molecules, have been implicated in neuropsychiatric disorders. However, their loss leads to deficits that have been best characterized with regard to their effect on excitatory cells. Notably, other disease-associated genes such as BDNF and ERBB4 implicate specific interneuron synapses in psychiatric disorders. Consistent with this, cortical interneuron dysfunction has been linked to epilepsy, schizophrenia and autism. Using a microarray screen that focused upon synapse-associated molecules, we identified Cntnap4 (contactin associated protein-like 4, also known as Caspr4) as highly enriched in developing murine interneurons. In this study we show that Cntnap4 is localized presynaptically and its loss leads to a reduction in the output of cortical parvalbumin (PV)-positive GABAergic (γ-aminobutyric acid producing) basket cells. Paradoxically, the loss of Cntnap4 augments midbrain dopaminergic release in the nucleus accumbens. In Cntnap4 mutant mice, synaptic defects in these disease-relevant neuronal populations are mirrored by sensory-motor gating and grooming endophenotypes; these symptoms could be pharmacologically reversed, providing promise for therapeutic intervention in psychiatric disorders.
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12
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Lin D, Calhoun VD, Wang YP. Correspondence between fMRI and SNP data by group sparse canonical correlation analysis. Med Image Anal 2014; 18:891-902. [PMID: 24247004 PMCID: PMC4007390 DOI: 10.1016/j.media.2013.10.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 08/27/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
Abstract
Both genetic variants and brain region abnormalities are recognized as important factors for complex diseases (e.g., schizophrenia). In this paper, we investigated the correspondence between single nucleotide polymorphism (SNP) and brain activity measured by functional magnetic resonance imaging (fMRI) to understand how genetic variation influences the brain activity. A group sparse canonical correlation analysis method (group sparse CCA) was developed to explore the correlation between these two datasets which are high dimensional-the number of SNPs/voxels is far greater than the number of samples. Different from the existing sparse CCA methods (sCCA), our approach can exploit structural information in the correlation analysis by introducing group constraints. A simulation study demonstrates that it outperforms the existing sCCA. We applied this method to the real data analysis and identified two pairs of significant canonical variates with average correlations of 0.4527 and 0.4292 respectively, which were used to identify genes and voxels associated with schizophrenia. The selected genes are mostly from 5 schizophrenia (SZ)-related signalling pathways. The brain mappings of the selected voxles also indicate the abnormal brain regions susceptible to schizophrenia. A gene and brain region of interest (ROI) correlation analysis was further performed to confirm the significant correlations between genes and ROIs.
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Affiliation(s)
- Dongdong Lin
- Biomedical Engineering Department, Tulane University, New Orleans, LA 70118, USA; Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA 70118, USA.
| | - Vince D Calhoun
- The Mind Research Network, Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Yu-Ping Wang
- Biomedical Engineering Department, Tulane University, New Orleans, LA 70118, USA; Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA 70118, USA; Center for Systems Biomedicine, Shanghai University for Science and Technology, Shanghai, China.
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13
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Rodriguez-Murillo L, Xu B, Roos JL, Abecasis GR, Gogos JA, Karayiorgou M. Fine mapping on chromosome 13q32-34 and brain expression analysis implicates MYO16 in schizophrenia. Neuropsychopharmacology 2014; 39:934-43. [PMID: 24141571 PMCID: PMC3924527 DOI: 10.1038/npp.2013.293] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/19/2013] [Accepted: 09/20/2013] [Indexed: 12/30/2022]
Abstract
We previously reported linkage of schizophrenia and schizoaffective disorder to 13q32-34 in the European descent Afrikaner population from South Africa. The nature of genetic variation underlying linkage peaks in psychiatric disorders remains largely unknown and both rare and common variants may be contributing. Here, we examine the contribution of common variants located under the 13q32-34 linkage region. We used densely spaced SNPs to fine map the linkage peak region using both a discovery sample of 415 families and a meta-analysis incorporating two additional replication family samples. In a second phase of the study, we use one family-based data set with 237 families and independent case-control data sets for fine mapping of the common variant association signal using HapMap SNPs. We report a significant association with a genetic variant (rs9583277) within the gene encoding for the myosin heavy-chain Myr 8 (MYO16), which has been implicated in neuronal phosphoinositide 3-kinase signaling. Follow-up analysis of HapMap variation within MYO16 in a second set of Afrikaner families and additional case-control data sets of European descent highlighted a region across introns 2-6 as the most likely region to harbor common MYO16 risk variants. Expression analysis revealed a significant increase in the level of MYO16 expression in the brains of schizophrenia patients. Our results suggest that common variation within MYO16 may contribute to the genetic liability to schizophrenia.
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Affiliation(s)
| | - Bin Xu
- Department of Psychiatry, Columbia University, New York, NY, USA
- Department of Physiology, Columbia University, New York, NY, USA
| | - J Louw Roos
- Department of Psychiatry and Weskoppies Hospital, University of Pretoria, Pretoria, South Africa
| | - Gonçalo R Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Joseph A Gogos
- Department of Physiology, Columbia University, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
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14
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The consequences of uniparental disomy and copy number neutral loss-of-heterozygosity during human development and cancer. Biol Cell 2011; 103:303-17. [PMID: 21651501 DOI: 10.1042/bc20110013] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
UPD (uniparental disomy) describes the inheritance of a pair of chromosomes from only one parent. Mechanisms that lead to UPD include trisomy rescue, gamete complementation, monosomy rescue and somatic recombination. Most of these mechanisms can involve aberrant chromosomes, particularly isochromosomes and Robertsonian translocations. In the last decade, the number of UPD cases reported in the literature has increased exponentially. This is partly due to the advances in genomic technologies that have allowed for high-resolution SNP (single nucleotide polymorphism) studies, which have complemented traditional methods relying on polymorphic microsatellite markers. In this review, we discuss aberrant cellular mechanisms leading to UPD and their impact on gene expression. Special emphasis is placed on the unmasking of mutant recessive alleles and the disruption of imprinted gene dosage, which give rise to specific and recurrent imprinting phenotypes. Finally, we discuss how copy number maps determined from SNP array datasets have helped identify not only deletions and duplications but also recurrent copy number neutral regions of loss-of-heterozygosity, which have been reported in many cancer types and that may constitute an important driving force in cancer. These tiny regions of UPD also alter imprinted gene dosage, which may have cumulative tumourgenic effects in addition to that of unmasking homozygous cancer-associated mutations.
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15
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Wessman M, Forsblom C, Kaunisto MA, Söderlund J, Ilonen J, Sallinen R, Hiekkalinna T, Parkkonen M, Maxwell AP, Tarnow L, Parving HH, Hadjadj S, Marre M, Peltonen L, Groop PH. Novel susceptibility locus at 22q11 for diabetic nephropathy in type 1 diabetes. PLoS One 2011; 6:e24053. [PMID: 21909410 PMCID: PMC3164698 DOI: 10.1371/journal.pone.0024053] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 08/03/2011] [Indexed: 01/02/2023] Open
Abstract
Background Diabetic nephropathy (DN) affects about 30% of patients with type 1 diabetes (T1D) and contributes to serious morbidity and mortality. So far only the 3q21–q25 region has repeatedly been indicated as a susceptibility region for DN. The aim of this study was to search for new DN susceptibility loci in Finnish, Danish and French T1D families. Methods and Results We performed a genome-wide linkage study using 384 microsatellite markers. A total of 175 T1D families were studied, of which 94 originated from Finland, 46 from Denmark and 35 from France. The whole sample set consisted of 556 individuals including 42 sib-pairs concordant and 84 sib-pairs discordant for DN. Two-point and multi-point non-parametric linkage analyses were performed using the Analyze package and the MERLIN software. A novel DN locus on 22q11 was identified in the joint analysis of the Finnish, Danish and French families by genome-wide multipoint non-parametric linkage analysis using the Kong and Cox linear model (NPLpairs LOD score 3.58). Nominal or suggestive evidence of linkage to this locus was also detected when the three populations were analyzed separately. Suggestive evidence of linkage was found to six additional loci in the Finnish and French sample sets. Conclusions This study identified a novel DN locus at chromosome 22q11 with significant evidence of linkage to DN. Our results suggest that this locus may be of importance in European populations. In addition, this study supports previously indicated DN loci on 3q21–q25 and 19q13.
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Affiliation(s)
- Maija Wessman
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
- Biomedicum Helsinki, Research Program in Molecular Medicine and Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- * E-mail: (MW); (P-HG)
| | - Carol Forsblom
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Mari A. Kaunisto
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
- Biomedicum Helsinki, Research Program in Molecular Medicine and Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Jenny Söderlund
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Jorma Ilonen
- Department of Clinical Microbiology, University of Eastern Finland, Kuopio, Finland
- Immunogenetics Laboratory, University of Turku, Turku, Finland
| | - Riitta Sallinen
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
| | - Tero Hiekkalinna
- Biomedicum Helsinki, Research Program in Molecular Medicine and Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Unit of Public Health Genomics, National Institute for Health and Welfare, Helsinki, Finland
| | - Maija Parkkonen
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Alexander P. Maxwell
- Nephrology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland, United Kingdom
| | | | - Hans-Henrik Parving
- Department of Medical Endocrinology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Science, Aarhus University, Aarhus, Denmark
| | - Samy Hadjadj
- Service de Médecine Interne, Endocrinologie et Maladies Métaboliques, Centre d'Investigation Clinique, Inserm CIC0802, CHU de Poitiers, Poitiers, France and Université de Poitiers, Poitiers, France
| | - Michel Marre
- Department of Endocrinology, Diabetology and Nutrition, Bichat-Claude Bernard University Hospital, Paris, France
| | - Leena Peltonen
- Biomedicum Helsinki, Research Program in Molecular Medicine and Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Unit of Public Health Genomics, National Institute for Health and Welfare, Helsinki, Finland
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hingston, United Kingdom
| | - Per-Henrik Groop
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- * E-mail: (MW); (P-HG)
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16
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Xu B, Roos JL, Dexheimer P, Boone B, Plummer B, Levy S, Gogos JA, Karayiorgou M. Exome sequencing supports a de novo mutational paradigm for schizophrenia. Nat Genet 2011; 43:864-8. [PMID: 21822266 PMCID: PMC3196550 DOI: 10.1038/ng.902] [Citation(s) in RCA: 343] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 07/12/2011] [Indexed: 02/08/2023]
Abstract
Despite high heritability, a large fraction of cases with schizophrenia do not have a family history of the disease (sporadic cases). Here, we examine the possibility that rare de novo protein-altering mutations contribute to the genetic component of schizophrenia by sequencing the exome of 53 sporadic cases, 22 unaffected controls and their parents. We identified 40 de novo mutations in 27 patients affecting 40 genes including a potentially disruptive mutation in DGCR2, a gene removed by the recurrent schizophrenia-predisposing 22q11.2 microdeletion. Comparison to rare inherited variants revealed that the identified de novo mutations show a large excess of nonsynonymous changes in cases, as well as a greater potential to affect protein structure and function. Our analysis reveals a major role of de novo mutations in schizophrenia and also a large mutational target, which together provide a plausible explanation for the high global incidence and persistence of the disease.
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Affiliation(s)
- Bin Xu
- Department of Psychiatry, Columbia University, New York, New York, USA
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17
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Ono S, Imamura A, Tasaki S, Kurotaki N, Ozawa H, Yoshiura KI, Okazaki Y. Failure to confirm CNVs as of aetiological significance in twin pairs discordant for schizophrenia. Twin Res Hum Genet 2010; 13:455-60. [PMID: 20874467 DOI: 10.1375/twin.13.5.455] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Copy number variations (CNVs) are common structural variations in the human genome that strongly affect genomic diversity and can play a role in the development of several diseases, including neurodevelopmental disorders. Recent reports indicate that monozygotic twins can show differential CNV profiles. We searched CNVs in monozygotic twins discordant for schizophrenia to identify susceptible loci for schizophrenia. Three pairs of monozygotic twins discordant for schizophrenia were subjected to analysis. Genomic DNA samples were extracted from peripheral blood lymphocytes. We adopted the Affymetrix Genome-Wide Human SNP (Single Nucleotide Polymorphism) Array 6.0 to detect copy number discordance using Partek Genomics Suite 6.5 beta. In three twin pairs, however, validations by quantitative PCR and DNA sequencing revealed that none of the regions had any discordance between the three twin pairs. Our results support the hypothesis that epigenetic changes or fluctuation in developmental process triggered by environmental factors mainly contribute to the pathogenesis of schizophrenia. Schizophrenia caused by strong genetics factors including copy number alteration or gene mutation may be a small subset of the clinical population.
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Affiliation(s)
- Shinji Ono
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Japan
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18
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Nimmo G, Monsonego S, Descartes M, Franklin J, Steinberg S, Braverman N. Rhizomelic chrondrodysplasia punctata type 2 resulting from paternal isodisomy of chromosome 1. Am J Med Genet A 2010; 152A:1812-7. [PMID: 20583171 DOI: 10.1002/ajmg.a.33489] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rhizomelic chondrodysplasia punctata (RCDP) is an autosomal-recessive disorder resulting from mutations in one of three peroxisomal genes essential for ether lipid biosynthesis, PEX7 (RCDP1), GNPAT (RCDP2), and AGPS (RCDP3). Affected patients have characteristic features including shortening of the proximal long bones, epiphyseal stippling, bilateral cataracts, growth and developmental delays. Whereas the majority of patients have RCDP type 1, around 5% have RCDP type 2 or 3. We identified a patient with RCDP type 2 and an apparent homozygous deletion, c.1428delC, after full sequencing of his GNPAT genes. The father was heterozygous for this mutation, while sequencing of the maternal GNPAT genes revealed only wild-type sequence. Southern analyses performed on parental gDNA did not show evidence of a maternal gene deletion. Amplification and fragment analysis of dinucleotide repeat markers spanning chromosome 1 in the patient and both parents revealed paternal uniparental inheritance. We discuss the potential mechanisms causing uniparental disomy (UPD) in this patient and review the literature on chromosome 1 UPD. The absence of non-RCDP clinical features in this patient was consistent with previous literature supporting the absence of imprinted genes on chromosome 1. This first description of RCDP caused by UPD dramatically changes the parental recurrence risk, highlighting the value of obtaining parental genotypes when the proband has a putative homozygous mutation by sequence analysis.
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Affiliation(s)
- Graeme Nimmo
- Montreal Children's Hospital Research Institute, McGill University, Montreal, Quebec, Canada
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19
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Whitfield JB, Dy V, McQuilty R, Zhu G, Heath AC, Montgomery GW, Martin NG. Genetic effects on toxic and essential elements in humans: arsenic, cadmium, copper, lead, mercury, selenium, and zinc in erythrocytes. ENVIRONMENTAL HEALTH PERSPECTIVES 2010; 118:776-82. [PMID: 20053595 PMCID: PMC2898853 DOI: 10.1289/ehp.0901541] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 01/05/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND OBJECTIVES An excess of toxic trace elements or a deficiency of essential ones has been implicated in many common diseases or public health problems, but little is known about causes of variation between people living within similar environments. We estimated effects of personal and socioeconomic characteristics on concentrations of arsenic (As), cadmium (Cd), copper (Cu), mercury (Hg), lead (Pb), selenium (Se), and zinc (Zn) in erythrocytes and tested for genetic effects using data from twin pairs. METHODS We used blood samples from 2,926 adult twins living in Australia (1,925 women and 1,001 men; 30-92 years of age) and determined element concentrations in erythrocytes by inductively coupled plasma-mass spectrometry. We assessed associations between element concentrations and personal and socioeconomic characteristics, as well as the sources of genetic and environmental variation and covariation in element concentrations. We evaluated the chromosomal locations of genes affecting these characteristics by linkage analysis in 501 dizygotic twin pairs. RESULTS Concentrations of Cu, Se, and Zn, and of As and Hg showed substantial correlations, concentrations of As and Hg due mainly to common genetic effects. Genetic linkage analysis showed significant linkage for Pb [chromosome 3, near SLC4A7 (solute carrier family 4, sodium bicarbonate cotransporter, member 7)] and suggestive linkage for Cd (chromosomes 2, 18, 20, and X), Hg (chromosome 5), Se (chromosomes 4 and 8), and Zn {chromosome 2, near SLC11A1 [solute carrier family 11 (proton-coupled divalent metal ion transporters)]}. CONCLUSIONS Although environmental exposure is a precondition for accumulation of toxic elements, individual characteristics and genetic factors are also important. Identification of the contributory genetic polymorphisms will improve our understanding of trace and toxic element uptake and distribution mechanisms.
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Affiliation(s)
- John B Whitfield
- Genetic Epidemiology Unit, Queensland Institute of Medical Research, Brisbane, Australia.
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20
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Hartz SM, Ho BC, Andreasen NC, Librant A, Rudd D, Epping EA, Wassink TH. G72 influences longitudinal change in frontal lobe volume in schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:640-647. [PMID: 19760675 PMCID: PMC2908546 DOI: 10.1002/ajmg.b.31033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Schizophrenia is a neurodevelopmental psychiatric disorder characterized by a variety of structural brain abnormalities that appear to progress across the course of illness. Schizophrenia also is highly heritable, and one gene that has emerged as a possible susceptibility factor is G72. G72 influences brain development and activity by an as-yet unclear mechanism, and multiple studies have reported associations between G72 and schizophrenia. We were interested in linking these domains of investigation by determining whether G72 also influences the rate of longitudinal structural brain changes in individuals with schizophrenia. As part of the Iowa Longitudinal Study of Recent Onset Psychoses, we genotyped four G72 polymorphisms previously associated with schizophrenia in 110 subjects with schizophrenia or schizoaffective disorder from whom we had obtained two brain MRI scans an average of 3 years apart. The four polymorphisms captured three haplotypes, one of which was strongly associated with an increased rate of frontal lobe volume decrement. This same haplotype was also associated with more severe psychotic symptoms at the time of the second scan. These data thus suggest that variation in G72 modulates the progressive brain changes that characterize schizophrenia.
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Affiliation(s)
- Sarah M Hartz
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Beng-Choon Ho
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Nancy C Andreasen
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Amy Librant
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Danielle Rudd
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Eric A Epping
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Thomas H Wassink
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
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21
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Keller MC, McRae AF, McGaughran JM, Visscher PM, Martin NG, Montgomery GW. Non-pathological paternal isodisomy of chromosome 2 detected from a genome-wide SNP scan. Am J Med Genet A 2009; 149A:1823-6. [PMID: 19610117 DOI: 10.1002/ajmg.a.32973] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Matthew C Keller
- Department of Psychology, University of Colorado at Boulder, 80309, USA.
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22
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Elucidating the genetic architecture of familial schizophrenia using rare copy number variant and linkage scans. Proc Natl Acad Sci U S A 2009; 106:16746-51. [PMID: 19805367 DOI: 10.1073/pnas.0908584106] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To elucidate the genetic architecture of familial schizophrenia we combine linkage analysis with studies of fine-level chromosomal variation in families recruited from the Afrikaner population in South Africa. We demonstrate that individually rare inherited copy number variants (CNVs) are more frequent in cases with familial schizophrenia as compared to unaffected controls and affect almost exclusively genic regions. Interestingly, we find that while the prevalence of rare structural variants is similar in familial and sporadic cases, the type of variants is markedly different. In addition, using a high-density linkage scan with a panel of nearly 2,000 markers, we identify a region on chromosome 13q34 that shows genome-wide significant linkage to schizophrenia and show that in the families not linked to this locus, there is evidence for linkage to chromosome 1p36. No causative CNVs were identified in either locus. Overall, our results from approaches designed to detect risk variants with relatively low frequency and high penetrance in a well-defined and relatively homogeneous population, provide strong empirical evidence supporting the notion that multiple genetic variants, including individually rare ones, that affect many different genes contribute to the genetic risk of familial schizophrenia. They also highlight differences in the genetic architecture of the familial and sporadic forms of the disease.
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23
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Ng MYM, Levinson DF, Faraone SV, Suarez BK, DeLisi LE, Arinami T, Riley B, Paunio T, Pulver AE, Irmansyah, Holmans PA, Escamilla M, Wildenauer DB, Williams NM, Laurent C, Mowry BJ, Brzustowicz LM, Maziade M, Sklar P, Garver DL, Abecasis GR, Lerer B, Fallin MD, Gurling HMD, Gejman PV, Lindholm E, Moises HW, Byerley W, Wijsman EM, Forabosco P, Tsuang MT, Hwu HG, Okazaki Y, Kendler KS, Wormley B, Fanous A, Walsh D, O’Neill FA, Peltonen L, Nestadt G, Lasseter VK, Liang KY, Papadimitriou GM, Dikeos DG, Schwab SG, Owen MJ, O’Donovan MC, Norton N, Hare E, Raventos H, Nicolini H, Albus M, Maier W, Nimgaonkar VL, Terenius L, Mallet J, Jay M, Godard S, Nertney D, Alexander M, Crowe RR, Silverman JM, Bassett AS, Roy MA, Mérette C, Pato CN, Pato MT, Roos JL, Kohn Y, Amann-Zalcenstein D, Kalsi G, McQuillin A, Curtis D, Brynjolfson J, Sigmundsson T, Petursson H, Sanders AR, Duan J, Jazin E, Myles-Worsley M, Karayiorgou M, Lewis CM. Meta-analysis of 32 genome-wide linkage studies of schizophrenia. Mol Psychiatry 2009; 14:774-85. [PMID: 19349958 PMCID: PMC2715392 DOI: 10.1038/mp.2008.135] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Accepted: 11/11/2008] [Indexed: 02/07/2023]
Abstract
A genome scan meta-analysis (GSMA) was carried out on 32 independent genome-wide linkage scan analyses that included 3255 pedigrees with 7413 genotyped cases affected with schizophrenia (SCZ) or related disorders. The primary GSMA divided the autosomes into 120 bins, rank-ordered the bins within each study according to the most positive linkage result in each bin, summed these ranks (weighted for study size) for each bin across studies and determined the empirical probability of a given summed rank (P(SR)) by simulation. Suggestive evidence for linkage was observed in two single bins, on chromosomes 5q (142-168 Mb) and 2q (103-134 Mb). Genome-wide evidence for linkage was detected on chromosome 2q (119-152 Mb) when bin boundaries were shifted to the middle of the previous bins. The primary analysis met empirical criteria for 'aggregate' genome-wide significance, indicating that some or all of 10 bins are likely to contain loci linked to SCZ, including regions of chromosomes 1, 2q, 3q, 4q, 5q, 8p and 10q. In a secondary analysis of 22 studies of European-ancestry samples, suggestive evidence for linkage was observed on chromosome 8p (16-33 Mb). Although the newer genome-wide association methodology has greater power to detect weak associations to single common DNA sequence variants, linkage analysis can detect diverse genetic effects that segregate in families, including multiple rare variants within one locus or several weakly associated loci in the same region. Therefore, the regions supported by this meta-analysis deserve close attention in future studies.
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Affiliation(s)
- MYM Ng
- King’s College London, Department of Medical and Molecular Genetics, London, UK
| | - DF Levinson
- Department of Psychiatry, Stanford University, Stanford, CA, USA
| | - SV Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - BK Suarez
- Washington University in St Louis, St Louis, MO, USA
| | - LE DeLisi
- Department of Psychiatry, The New York University Langone Medical Center, New York, NY, USA
- Nathan S Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - T Arinami
- Department of Medical Genetics, University of Tsukuba, Tsukuba, Japan
| | - B Riley
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - T Paunio
- National Public Health Institute, Helsinki, Finland
- Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland
| | - AE Pulver
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Irmansyah
- Department of Psychiatry, University of Indonesia, Jakarta, Indonesia
| | - PA Holmans
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - M Escamilla
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - DB Wildenauer
- Center for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, University of Western Australia, Perth, WA, Australia
| | - NM Williams
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - C Laurent
- Department of Child Psychiatry, Université Pierre et Marie Curie and Hôpital de la Pitiè-Salpêtrière, Paris, France
| | - BJ Mowry
- Queensland Centre for Mental Health Research and University of Queensland, Brisbane, QLD, Australia
| | - LM Brzustowicz
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - M Maziade
- Department of Psychiatry, Laval University & Centre de recherche Université Laval Robert-Giffard, Québec, QC, Canada
| | - P Sklar
- Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - DL Garver
- VA Medical Center, Asheville, NC, USA
| | - GR Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - B Lerer
- Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - MD Fallin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - HMD Gurling
- Department of Mental Health Sciences, University College London, London, UK
| | - PV Gejman
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute and Northwestern University, Evanston, IL, USA
| | - E Lindholm
- Department of Development & Genetics, Uppsala University, Uppsala, Sweden
| | | | - W Byerley
- University of California, San Francisco, CA, USA
| | - EM Wijsman
- Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - P Forabosco
- King’s College London, Department of Medical and Molecular Genetics, London, UK
| | - MT Tsuang
- Center for Behavioral Genomics and Department of Psychiatry, University of California, San Diego, CA, USA
- Harvard Institute of Psychiatric Epidemiology & Genetics, Boston, MA, USA
| | - H-G Hwu
- National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Y Okazaki
- Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - KS Kendler
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - B Wormley
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - A Fanous
- Washington VA Medical Center, Washington, DC, USA
- Department of Psychiatry, Georgetown University Medical Center, Virginia Commonwealth University, Richmond, VA, USA
| | - D Walsh
- The Health Research Board, Dublin, Ireland
| | - FA O’Neill
- Department of Psychiatry, Queens University, Belfast, Northern Ireland
| | - L Peltonen
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- The Broad Institute, MIT, Boston, MA, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - G Nestadt
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - VK Lasseter
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - KY Liang
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - GM Papadimitriou
- 1st Department of Psychiatry, University of Athens Medical School, and University Mental Health Research Institute, Athens, Greece
| | - DG Dikeos
- 1st Department of Psychiatry, University of Athens Medical School, and University Mental Health Research Institute, Athens, Greece
| | - SG Schwab
- Western Australian Institute for Medical Research, University of Western Australia, Perth, WA, Australia
- School of Psychiatry and Clinical Neurosciences, University of Western Australia, Perth, WA, Australia
- School of Medicine and Pharmacology, University of Western Australia, Perth, WA, Australia
| | - MJ Owen
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - MC O’Donovan
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - N Norton
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - E Hare
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - H Raventos
- School of Biology and CIBCM, University of Costa Rica, San Jose, Costa Rica
| | - H Nicolini
- Carracci Medical Group and Universidad Autonoma de la Ciudad de Mexico, Mexico City, Mexico
| | - M Albus
- State Mental Hospital, Haar, Germany
| | - W Maier
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | - VL Nimgaonkar
- Departments of Psychiatry and Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - L Terenius
- Department of Clinical Neuroscience, Karolinska Hospital, Stockholm, Sweden
| | - J Mallet
- Laboratoire de Génétique Moléculaire de la Neurotransmission et des Processus Neurodégénératifs, Centre National de la Recherche Scientifique, Hôpital de la Pitié Salpêtrière, Paris, France
| | - M Jay
- Department of Child Psychiatry, Université Pierre et Marie Curie and Hôpital de la Pitiè-Salpêtrière, Paris, France
| | - S Godard
- INSERM, Institut de Myologie, Hôpital de la Pitiè-Salpêtrière, Paris, France
| | - D Nertney
- Queensland Centre for Mental Health Research and University of Queensland, Brisbane, QLD, Australia
| | - M Alexander
- Department of Psychiatry, Stanford University, Stanford, CA, USA
| | - RR Crowe
- Department of Psychiatry, The University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - JM Silverman
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - AS Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - M-A Roy
- Department of Psychiatry, Laval University & Centre de recherche Université Laval Robert-Giffard, Québec, QC, Canada
| | - C Mérette
- Department of Psychiatry, Laval University & Centre de recherche Université Laval Robert-Giffard, Québec, QC, Canada
| | - CN Pato
- Center for Genomic Psychiatry, University of Southern California, Los Angeles, CA, USA
| | - MT Pato
- Center for Genomic Psychiatry, University of Southern California, Los Angeles, CA, USA
| | - J Louw Roos
- Department of Psychiatry, University of Pretoria, Weskoppies Hospital, Pretoria, Republic of South Africa
| | - Y Kohn
- Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - D Amann-Zalcenstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - G Kalsi
- Department of Mental Health Sciences, University College London, London, UK
| | - A McQuillin
- Department of Mental Health Sciences, University College London, London, UK
| | - D Curtis
- Department of Psychological Medicine, St Bartholomew’s and Royal London School of Medicine and Dentistry, London, UK
| | - J Brynjolfson
- Department of Psychiatry, General Hospital, Reykjavik, Iceland
| | - T Sigmundsson
- Department of Psychiatry, General Hospital, Reykjavik, Iceland
| | - H Petursson
- Department of Psychiatry, General Hospital, Reykjavik, Iceland
| | - AR Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute and Northwestern University, Evanston, IL, USA
| | - J Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute and Northwestern University, Evanston, IL, USA
| | - E Jazin
- Department of Development & Genetics, Uppsala University, Uppsala, Sweden
| | - M Myles-Worsley
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - M Karayiorgou
- Departments of Psychiatry and Genetics & Development, Columbia University Medical Center, New York, NY, USA
| | - CM Lewis
- King’s College London, Department of Medical and Molecular Genetics, London, UK
- King’s College London, MRC SGDP Centre, Institute of Psychiatry, London, UK
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Genome-wide study of families with absolute pitch reveals linkage to 8q24.21 and locus heterogeneity. Am J Hum Genet 2009; 85:112-9. [PMID: 19576568 DOI: 10.1016/j.ajhg.2009.06.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 06/10/2009] [Accepted: 06/12/2009] [Indexed: 11/20/2022] Open
Abstract
Absolute pitch (AP) is the rare ability to instantaneously recognize and label tones with their musical note names without using a reference pitch for comparison. The etiology of AP is complex. Prior studies have implicated both genetic and environmental factors in its genesis, yet the molecular basis for AP remains unknown. To locate regions of the human genome that may harbor AP-predisposing genetic variants, we performed a genome-wide linkage study on 73 multiplex AP families by genotyping them with 6090 SNP markers. Nonparametric multipoint linkage analyses were conducted, and the strongest evidence for linkage was observed on chromosome 8q24.21 in the subset of 45 families with European ancestry (exponential LOD score = 3.464, empirical genome-wide p = 0.03). Other regions with suggestive LOD scores included chromosomes 7q22.3, 8q21.11, and 9p21.3. Of these four regions, only the 7q22.3 linkage peak was also evident when 19 families with East Asian ancestry were analyzed separately. Though only one of these regions has yet reached statistical significance individually, we detected a larger number of independent linkage peaks than expected by chance overall, indicating that AP is genetically heterogeneous.
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Abstract
Peptidylarginine deiminases (PADIs), five isoforms of which have been identified, catalyze the conversion of arginine residues to citrulline residues in proteins. Recent studies have revealed that abnormal activation of PADI2, the gene for which is expressed throughout the nervous system, is likely to be related to the pathogenesis of neuropsychiatric diseases with neurodegenerative processes, such as Alzheimer's disease and multiple sclerosis. Such a progressive neurodegenerative process could be involved in the etiology and/or course of schizophrenia, and PADI2 may be a candidate gene for schizophrenia. To assess whether PADI2 has a role in vulnerability to schizophrenia, we conducted a two-stage case-control association study in Japanese individuals. In a screening population of 534 patients and 559 control individuals, we examined eight single-nucleotide polymorphisms (SNPs) including four haplotype tag SNPs and four coding SNPs in PADI2. There was a potential association of a synonymous SNP in exon 7 with schizophrenia. However, we could not replicate this association in a confirmatory population of 2126 patients and 2228 control individuals. The results of this study suggest that PADI2 does not contribute to genetic susceptibility to schizophrenia.
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Maziade M, Chagnon YC, Roy MA, Bureau A, Fournier A, Mérette C. Chromosome 13q13-q14 locus overlaps mood and psychotic disorders: the relevance for redefining phenotype. Eur J Hum Genet 2009; 17:1034-42. [PMID: 19172987 DOI: 10.1038/ejhg.2008.268] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The nosology of major psychoses is challenged by the findings that schizophrenia (SZ) and bipolar disorder (BP) share several neurobiological, neuropsychological and clinical phenotypic characteristics. Moreover, several vulnerability loci or genes may be common to the two DSM disorders. We previously reported, in a sample of 21 kindreds (sample 1), a genome-wide suggestive linkage in 13q13-q14 with a common locus (CL) phenotype that crossed the diagnostic boundaries by combining SZ, BP and schizoaffective disorders. Our objectives were to test phenotype specificity in a separate sample (sample 2) of 27 kindreds from Eastern Quebec and to also analyze the combined sample of 48 kindreds (1274 family members). We performed nonparametric and parametric analyses and tested as phenotypes: SZ alone, BP alone, and a CL phenotype. We replicated in sample 2 our initial finding with CL with a maximum NPL(pair) score of 3.36 at D13S1272 (44 Mb), only 2.1 Mb telomeric to our previous maximum result. In the combined sample, the peak with CL was at marker D13S1297 (42.1 Mb) with a NPL(pair) score reaching 5.21, exceeding that obtained in each sample and indicating consistency across the two samples. Our data suggest a susceptibility locus in 13q13-q14 that is shared by schizophrenia and mood disorder. That locus would be additional to another well documented and more distal 13q locus where the G72/G30 gene is mapped.
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Affiliation(s)
- Michel Maziade
- Department of Psychiatry, Laval University, Québec, QC, Canada.
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Schwab SG, Handoko HY, Kusumawardhani A, Widyawati I, Amir N, Nasrun MWS, Holmans P, Knapp M, Wildenauer DB. Genome-wide scan in 124 Indonesian sib-pair families with schizophrenia reveals genome-wide significant linkage to a locus on chromosome 3p26-21. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:1245-52. [PMID: 18449910 DOI: 10.1002/ajmg.b.30763] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Variation in incidence of schizophrenia between populations with different ethnical background may reflect population specific differences in nature and composition of genetic and environmental factors. In order to investigate whether there are population specific susceptibility genes for schizophrenia, we collected in Indonesia families with two or more affected siblings and, as far as available, parents and unaffected siblings, suitable for genetic linkage- and association studies. After checking extensively for incompatibilities with Mendelian inheritance as well as for errors in sampling, we used 124 families from the sample of 152 originally ascertained families for linkage analysis. Genotyping was performed at the NHLBI Mammalian Genotyping Service at Marshfield Research Organisation using the Screening Set 16, which comprises 402 Short Tandem Repeat Polymorphisms (STRPs). The genotypes of 540 individuals including 267 affected with schizophrenia were used for analysis. Multipoint sib-pair linkage analysis was carried out by estimation of--allele sharing derived--maximum likelihood LOD scores (MLS) in 154 sib-pair combinations. We obtained a genome-wide significant MLS of 3.76 on chromosome 3p26.2-25.3. Genome-wide significance was estimated by performing 10,000 simulated genomescans. Additional loci were detected on 1p12, which produced suggestive evidence for linkage (MLS = 2.35), as well as on 5q14.1 (MLS = 1.56), 5q33.3 (MLS = 1.11), and 10q (MLS = 1.17), where linkage had been reported previously. In conclusion, our study detected a region with genome-wide significant linkage, which will serve as starting point for identification of schizophrenia susceptibility genes in the Indonesian population.
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Affiliation(s)
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- Department of Psychiatry, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
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Holliday EG, Mowry BJ, Nyholt DR. A reanalysis of 409 European-Ancestry and African American schizophrenia pedigrees reveals significant linkage to 8p23.3 with evidence of locus heterogeneity. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:1080-8. [PMID: 18361422 DOI: 10.1002/ajmg.b.30722] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The detection and replication of schizophrenia risk loci can require substantial sample sizes, which has prompted various collaborative efforts for combining multiple samples. However, pooled samples may comprise sub-samples with substantial population genetic differences, including allele frequency differences. We investigated the impact of population differences via linkage reanalysis of Molecular Genetics of Schizophrenia 1 (MGS1) affected sibling-pair data, comprising two samples of distinct ancestral origin: European (EA: 263 pedigrees) and African-American (AA: 146 pedigrees). To exploit the linkage information contained within these distinct continental samples, we performed separate analyses of the individual samples, allowing for within-sample locus heterogeneity, and the pooled sample, allowing for both within-sample and between-sample heterogeneity. Significance levels, corrected for the multiple tests, were determined empirically. For all suggestive peaks, stronger linkage evidence was obtained in either the EA or AA sample than the combined sample, regardless of how heterogeneity was modeled for the latter. Notably, we report genomewide significant linkage of schizophrenia to 8p23.3 and evidence for a second, independent susceptibility locus, reaching suggestive linkage, 29 cM away on 8p21.3. We also detected suggestive linkage on chromosomes 5p13.3 and 7q36.2. Many regions showed pronounced differences in the extent of linkage between the EA and AA samples. This reanalysis highlights the potential impact of population differences upon linkage evidence in pooled data and demonstrates a useful approach for the analysis of samples drawn from distinct continental groups.
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Affiliation(s)
- E G Holliday
- Queensland Centre for Mental Health Research, The Park, Centre for Mental Health, Wacol, Queensland, Australia.
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Crespi B. Genomic imprinting in the development and evolution of psychotic spectrum conditions. Biol Rev Camb Philos Soc 2008; 83:441-93. [PMID: 18783362 DOI: 10.1111/j.1469-185x.2008.00050.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
I review and evaluate genetic and genomic evidence salient to the hypothesis that the development and evolution of psychotic spectrum conditions have been mediated in part by alterations of imprinted genes expressed in the brain. Evidence from the genetics and genomics of schizophrenia, bipolar disorder, major depression, Prader-Willi syndrome, Klinefelter syndrome, and other neurogenetic conditions support the hypothesis that the etiologies of psychotic spectrum conditions commonly involve genetic and epigenetic imbalances in the effects of imprinted genes, with a bias towards increased relative effects from imprinted genes with maternal expression or other genes favouring maternal interests. By contrast, autistic spectrum conditions, including Kanner autism, Asperger syndrome, Rett syndrome, Turner syndrome, Angelman syndrome, and Beckwith-Wiedemann syndrome, commonly engender increased relative effects from paternally expressed imprinted genes, or reduced effects from genes favouring maternal interests. Imprinted-gene effects on the etiologies of autistic and psychotic spectrum conditions parallel the diametric effects of imprinted genes in placental and foetal development, in that psychotic spectrum conditions tend to be associated with undergrowth and relatively-slow brain development, whereas some autistic spectrum conditions involve brain and body overgrowth, especially in foetal development and early childhood. An important role for imprinted genes in the etiologies of psychotic and autistic spectrum conditions is consistent with neurodevelopmental models of these disorders, and with predictions from the conflict theory of genomic imprinting.
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Affiliation(s)
- Bernard Crespi
- Department of Biosciences, Simon Fraser University, Burnaby BCV5A1S6, Canada.
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De Mars G, Windelinckx A, Huygens W, Peeters MW, Beunen GP, Aerssens J, Vlietinck R, Thomis MAI. Genome-wide linkage scan for contraction velocity characteristics of knee musculature in the Leuven Genes for Muscular Strength Study. Physiol Genomics 2008; 35:36-44. [PMID: 18682575 DOI: 10.1152/physiolgenomics.90252.2008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The torque-velocity relationship is known to be affected by ageing, decreasing its protective role in the prevention of falls. Interindividual variability in this torque-velocity relationship is partly determined by genetic factors (h(2): 44-67%). As a first attempt, this genome-wide linkage study aimed to identify chromosomal regions linked to the torque-velocity relationship of the knee flexors and extensors. A selection of 283 informative male siblings (17-36 yr), belonging to 105 families, was used to conduct a genome-wide SNP-based (Illumina Linkage IVb panel) multipoint linkage analysis for the torque-velocity relationship of the knee flexors and extensors. The strongest evidence for linkage was found at 15q23 for the torque-velocity slope of the knee extensors (TVSE). Other interesting linkage regions with LOD scores >2 were found at 7p12.3 [logarithm of the odds ratio (LOD) = 2.03, P = 0.0011] for the torque-velocity ratio of the knee flexors (TVRF), at 2q14.3 (LOD = 2.25, P = 0.0006) for TVSE, and at 4p14 and 18q23 for the torque-velocity ratio of the knee extensors TVRE (LOD = 2.23 and 2.08; P = 0.0007 and 0.001, respectively). We conclude that many small contributing genes are involved in causing variation in the torque-velocity relationship of the knee flexor and extensor muscles. Several earlier reported candidate genes for muscle strength and muscle mass and new candidates are harbored within or in close vicinity of the linkage regions reported in the present study.
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Affiliation(s)
- Gunther De Mars
- Department of Biomedical Kinesiology, Research Center for Exercise and Health, Faculty of Kinesiology and Rehabilitation Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
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Opgen-Rhein C, Lencz T, Burdick KE, Neuhaus AH, DeRosse P, Goldberg TE, Malhotra AK. Genetic variation in the DAOA gene complex: impact on susceptibility for schizophrenia and on cognitive performance. Schizophr Res 2008; 103:169-77. [PMID: 18541412 PMCID: PMC2605318 DOI: 10.1016/j.schres.2008.04.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 02/28/2008] [Accepted: 04/04/2008] [Indexed: 01/19/2023]
Abstract
INTRODUCTION The genetic region coding for d-amino acid oxidase activator (DAOA) is considered an intriguing susceptibility locus for schizophrenia. However, association studies have often resulted in conflicting findings, and the risk-conferring variants and their biological impact remain elusive. Our aim in this study was to investigate the relationship between DAOA variation and schizophrenia, and the influence of DAOA on cognitive performance. METHODS We analyzed block structure and association patterns of an approximately 173 kb region on chromosome 13q33, applying genotype data of 55 SNPs derived from Caucasian North American sample (178 cases, 144 healthy controls). Haplotypes were assigned using the program PHASE and frequencies compared between cases and controls. We applied MANOVA to investigate the relationship between the identified risk haplotype on cognitive performance. RESULTS We identified multiple haplotypes within the region containing the DAOA gene. Of these, one was significantly associated with schizophrenia, being over-represented in schizophrenia versus healthy controls. This haplotype was also associated with one aspect of cognitive performance, semantic fluency. Carriers of the risk haplotype showed better semantic fluency than non-carriers. CONCLUSIONS We report a significant effect of DAOA variation on risk for schizophrenia. Moreover, we identified a relationship between DAOA genetic variation and specific aspects of neurocognitive function. As the identified DAOA risk haplotype was associated with better performance on a semantic fluency measure, further work is required to identify the mechanism of DAOA action on CNS function, including the possibility of a role for balanced selection at this locus.
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Affiliation(s)
- Carolin Opgen-Rhein
- Division of Psychiatry Research, The Zucker Hillside Hospital, North Shore-Long Island Jewish Health System, Glen Oaks, New York, United States.,Department of Psychiatry and Psychotherapy, Charité -University Medicine Berlin, Campus Benjamin Franklin, Germany
| | - Todd Lencz
- Division of Psychiatry Research, The Zucker Hillside Hospital, North Shore-Long Island Jewish Health System, Glen Oaks, New York, United States.,Department of Psychiatry and Behavioral Health, Albert Einstein College of Medicine, Bronx, NY, USA.,Center for Translational Psychiatry, Feinstein Institute for Medical Research, Manhasset, NY, USA
| | - Katherine E. Burdick
- Division of Psychiatry Research, The Zucker Hillside Hospital, North Shore-Long Island Jewish Health System, Glen Oaks, New York, United States.,Department of Psychiatry and Behavioral Health, Albert Einstein College of Medicine, Bronx, NY, USA.,Center for Translational Psychiatry, Feinstein Institute for Medical Research, Manhasset, NY, USA
| | - Andres H Neuhaus
- Division of Psychiatry Research, The Zucker Hillside Hospital, North Shore-Long Island Jewish Health System, Glen Oaks, New York, United States.,Department of Psychiatry and Psychotherapy, Charité -University Medicine Berlin, Campus Benjamin Franklin, Germany
| | - Pamela DeRosse
- Division of Psychiatry Research, The Zucker Hillside Hospital, North Shore-Long Island Jewish Health System, Glen Oaks, New York, United States
| | - Terry E. Goldberg
- Division of Psychiatry Research, The Zucker Hillside Hospital, North Shore-Long Island Jewish Health System, Glen Oaks, New York, United States
| | - Anil K. Malhotra
- Division of Psychiatry Research, The Zucker Hillside Hospital, North Shore-Long Island Jewish Health System, Glen Oaks, New York, United States.,Department of Psychiatry and Behavioral Health, Albert Einstein College of Medicine, Bronx, NY, USA.,Center for Translational Psychiatry, Feinstein Institute for Medical Research, Manhasset, NY, USA
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O'Connor DT, Zhu G, Rao F, Taupenot L, Fung MM, Das M, Mahata SK, Mahata M, Wang L, Zhang K, Greenwood TA, Shih PAB, Cockburn MG, Ziegler MG, Stridsberg M, Martin NG, Whitfield JB. Heritability and genome-wide linkage in US and australian twins identify novel genomic regions controlling chromogranin a: implications for secretion and blood pressure. Circulation 2008; 118:247-57. [PMID: 18591442 DOI: 10.1161/circulationaha.107.709105] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Chromogranin A (CHGA) triggers catecholamine secretory granule biogenesis, and its catestatin fragment inhibits catecholamine release. We approached catestatin heritability using twin pairs, coupled with genome-wide linkage, in a series of twin and sibling pairs from 2 continents. METHODS AND RESULTS Hypertensive patients had elevated CHGA coupled with reduction in catestatin, suggesting diminished conversion of precursor to catestatin. Heritability for catestatin in twins was 44% to 60%. Six hundred fifteen nuclear families yielded 870 sib pairs for linkage, with significant logarithm of odds peaks on chromosomes 4p, 4q, and 17q. Because acidification of catecholamine secretory vesicles determines CHGA trafficking and processing to catestatin, we genotyped at positional candidate ATP6N1, bracketed by peak linkage markers on chromosome 17q, encoding a subunit of vesicular H(+)-translocating ATPase. The minor allele diminished CHGA secretion and processing to catestatin. The ATP6N1 variant also influenced blood pressure in 1178 individuals with the most extreme blood pressure values in the population. In chromaffin cells, inhibition of H(+)-ATPase diverted CHGA from regulated to constitutive secretory pathways. CONCLUSIONS We established heritability of catestatin in twins from 2 continents. Linkage identified 3 regions contributing to catestatin, likely novel determinants of sympathochromaffin exocytosis. At 1 such positional candidate (ATP6N1), variation influenced CHGA secretion and processing to catestatin, confirming the mechanism of a novel trans-QTL for sympathochromaffin activity and blood pressure.
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Affiliation(s)
- Daniel T O'Connor
- Departments of Medicine and Pharmacology and Center for Human Genetics and Genomics, University of California at San Diego School of Medicine, Veterans Affairs San Diego Healthcare System, La Jolla, CA 92093-0838, USA.
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Xu B, Roos JL, Levy S, van Rensburg EJ, Gogos JA, Karayiorgou M. Strong association of de novo copy number mutations with sporadic schizophrenia. Nat Genet 2008; 40:880-5. [PMID: 18511947 DOI: 10.1038/ng.162] [Citation(s) in RCA: 604] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 04/29/2008] [Indexed: 01/30/2023]
Abstract
Schizophrenia is an etiologically heterogeneous psychiatric disease, which exists in familial and nonfamilial (sporadic) forms. Here, we examine the possibility that rare de novo copy number (CN) mutations with relatively high penetrance contribute to the genetic component of schizophrenia. We carried out a whole-genome scan and implemented a number of steps for finding and confirming CN mutations. Confirmed de novo mutations were significantly associated with schizophrenia (P = 0.00078) and were collectively approximately 8 times more frequent in sporadic (but not familial) cases with schizophrenia than in unaffected controls. In comparison, rare inherited CN mutations were only modestly enriched in sporadic cases. Our results suggest that rare de novo germline mutations contribute to schizophrenia vulnerability in sporadic cases and that rare genetic lesions at many different loci can account, at least in part, for the genetic heterogeneity of this disease.
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Affiliation(s)
- Bin Xu
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
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Anttila V, Nyholt DR, Kallela M, Artto V, Vepsäläinen S, Jakkula E, Wennerström A, Tikka-Kleemola P, Kaunisto MA, Hämäläinen E, Widén E, Terwilliger J, Merikangas K, Montgomery GW, Martin NG, Daly M, Kaprio J, Peltonen L, Färkkilä M, Wessman M, Palotie A. Consistently replicating locus linked to migraine on 10q22-q23. Am J Hum Genet 2008; 82:1051-63. [PMID: 18423523 DOI: 10.1016/j.ajhg.2008.03.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 02/04/2008] [Accepted: 03/03/2008] [Indexed: 10/22/2022] Open
Abstract
Here, we present the results of two genome-wide scans in two diverse populations in which a consistent use of recently introduced migraine-phenotyping methods detects and replicates a locus on 10q22-q23, with an additional independent replication. No genetic variants have been convincingly established in migraine, and although several loci have been reported, none of them has been consistently replicated. We employed the three known migraine-phenotyping methods (clinical end diagnosis, latent-class analysis, and trait-component analysis) with robust multiple testing correction in a large sample set of 1675 individuals from 210 migraine families from Finland and Australia. Genome-wide multipoint linkage analysis that used the Kong and Cox exponential model in Finns detected a locus on 10q22-q23 with highly significant evidence of linkage (LOD 7.68 at 103 cM in female-specific analysis). The Australian sample showed a LOD score of 3.50 at the same locus (100 cM), as did the independent Finnish replication study (LOD score 2.41, at 102 cM). In addition, four previously reported loci on 8q21, 14q21, 18q12, and Xp21 were also replicated. A shared-segment analysis of 10q22-q23 linked Finnish families identified a 1.6-9.5 cM segment, centered on 101 cM, which shows in-family homology in 95% of affected Finns. This region was further studied with 1323 SNPs. Although no significant association was observed, four regions warranting follow-up studies were identified. These results support the use of symptomology-based phenotyping in migraine and suggest that the 10q22-q23 locus probably contains one or more migraine susceptibility variants.
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De Mars G, Windelinckx A, Huygens W, Peeters MW, Beunen GP, Aerssens J, Vlietinck R, Thomis MAI. Genome-wide linkage scan for maximum and length-dependent knee muscle strength in young men: significant evidence for linkage at chromosome 14q24.3. J Med Genet 2008; 45:275-83. [PMID: 18178634 PMCID: PMC2564859 DOI: 10.1136/jmg.2007.055277] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background: Maintenance of high muscular fitness is positively related to bone health, functionality in daily life and increasing insulin sensitivity, and negatively related to falls and fractures, morbidity and mortality. Heritability of muscle strength phenotypes ranges between 31% and 95%, but little is known about the identity of the genes underlying this complex trait. As a first attempt, this genome-wide linkage study aimed to identify chromosomal regions linked to muscle and bone cross-sectional area, isometric knee flexion and extension torque, and torque–length relationship for knee flexors and extensors. Methods: In total, 283 informative male siblings (17–36 years old), belonging to 105 families, were used to conduct a genome-wide SNP-based multipoint linkage analysis. Results: The strongest evidence for linkage was found for the torque–length relationship of the knee flexors at 14q24.3 (LOD = 4.09; p<10−5). Suggestive evidence for linkage was found at 14q32.2 (LOD = 3.00; P = 0.005) for muscle and bone cross-sectional area, at 2p24.2 (LOD = 2.57; p = 0.01) for isometric knee torque at 30° flexion, at 1q21.3, 2p23.3 and 18q11.2 (LOD = 2.33, 2.69 and 2.21; p<10−4 for all) for the torque–length relationship of the knee extensors and at 18p11.31 (LOD = 2.39; p = 0.0004) for muscle-mass adjusted isometric knee extension torque. Conclusions: We conclude that many small contributing genes rather than a few important genes are involved in causing variation in different underlying phenotypes of muscle strength. Furthermore, some overlap in promising genomic regions were identified among different strength phenotypes.
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Affiliation(s)
- G De Mars
- Department of Biomedical Kinesiology, Research Center for Exercise and Health, Faculty of Kinesiology and Rehabilitation Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
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Francks C, Maegawa S, Laurén J, Abrahams BS, Velayos-Baeza A, Medland SE, Colella S, Groszer M, McAuley EZ, Caffrey TM, Timmusk T, Pruunsild P, Koppel I, Lind PA, Matsumoto-Itaba N, Nicod J, Xiong L, Joober R, Enard W, Krinsky B, Nanba E, Richardson AJ, Riley BP, Martin NG, Strittmatter SM, Möller HJ, Rujescu D, St Clair D, Muglia P, Roos JL, Fisher SE, Wade-Martins R, Rouleau GA, Stein JF, Karayiorgou M, Geschwind DH, Ragoussis J, Kendler KS, Airaksinen MS, Oshimura M, DeLisi LE, Monaco AP. LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia. Mol Psychiatry 2007; 12:1129-39, 1057. [PMID: 17667961 PMCID: PMC2990633 DOI: 10.1038/sj.mp.4002053] [Citation(s) in RCA: 227] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Left-right asymmetrical brain function underlies much of human cognition, behavior and emotion. Abnormalities of cerebral asymmetry are associated with schizophrenia and other neuropsychiatric disorders. The molecular, developmental and evolutionary origins of human brain asymmetry are unknown. We found significant association of a haplotype upstream of the gene LRRTM1 (Leucine-rich repeat transmembrane neuronal 1) with a quantitative measure of human handedness in a set of dyslexic siblings, when the haplotype was inherited paternally (P=0.00002). While we were unable to find this effect in an epidemiological set of twin-based sibships, we did find that the same haplotype is overtransmitted paternally to individuals with schizophrenia/schizoaffective disorder in a study of 1002 affected families (P=0.0014). We then found direct confirmatory evidence that LRRTM1 is an imprinted gene in humans that shows a variable pattern of maternal downregulation. We also showed that LRRTM1 is expressed during the development of specific forebrain structures, and thus could influence neuronal differentiation and connectivity. This is the first potential genetic influence on human handedness to be identified, and the first putative genetic effect on variability in human brain asymmetry. LRRTM1 is a candidate gene for involvement in several common neurodevelopmental disorders, and may have played a role in human cognitive and behavioral evolution.
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Affiliation(s)
- C Francks
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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Hsu R, Woodroffe A, Lai WS, Cook MN, Mukai J, Dunning JP, Swanson DJ, Roos JL, Abecasis GR, Karayiorgou M, Gogos JA. Nogo Receptor 1 (RTN4R) as a candidate gene for schizophrenia: analysis using human and mouse genetic approaches. PLoS One 2007; 2:e1234. [PMID: 18043741 PMCID: PMC2077930 DOI: 10.1371/journal.pone.0001234] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2007] [Accepted: 11/01/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND NOGO Receptor 1 (RTN4R) regulates axonal growth, as well as axon regeneration after injury. The gene maps to the 22q11.2 schizophrenia susceptibility locus and is thus a strong functional and positional candidate gene. METHODOLOGY/PRINCIPAL FINDINGS We evaluate evidence for genetic association between common RTN4R polymorphisms and schizophrenia in a large family sample of Afrikaner origin and screen the exonic sequence of RTN4R for rare variants in an independent sample from the U.S. We also employ animal model studies to assay a panel of schizophrenia-related behavioral tasks in an Rtn4r-deficient mouse model. We found weak sex-specific evidence for association between common RTN4R polymorphisms and schizophrenia in the Afrikaner patients. In the U.S. sample, we identified two novel non-conservative RTN4R coding variants in two patients with schizophrenia that were absent in 600 control chromosomes. In our complementary mouse model studies, we identified a haploinsufficient effect of Rtn4r on locomotor activity, but normal performance in schizophrenia-related behavioral tasks. We also provide evidence that Rtn4r deficiency can modulate the long-term behavioral effects of transient postnatal N-methyl-D-aspartate (NMDA) receptor hypofunction. CONCLUSIONS Our results do not support a major role of RTN4R in susceptibility to schizophrenia or the cognitive and behavioral deficits observed in individuals with 22q11 microdeletions. However, they suggest that RTN4R may modulate the genetic risk or clinical expression of schizophrenia in a subset of patients and identify additional studies that will be necessary to clarify the role of RTN4R in psychiatric phenotypes. In addition, our results raise interesting issues about evaluating the significance of rare genetic variants in disease and their role in causation.
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Affiliation(s)
- Ruby Hsu
- Department of Neuroscience, Columbia University, New York, New York, United States of America
| | - Abigail Woodroffe
- Department of Epidemiology, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Wen-Sung Lai
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Melloni N. Cook
- Department of Psychology, The University of Memphis, Memphis, Tennessee, United States of America
| | - Jun Mukai
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Jonathan P. Dunning
- Department of Psychology, The University of Memphis, Memphis, Tennessee, United States of America
| | - Douglas J. Swanson
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - J. Louw Roos
- Department of Psychiatry, University of Pretoria and Weskoppies Hospital, Pretoria, Republic of South Africa
| | - Gonçalo R. Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Maria Karayiorgou
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- * To whom correspondence should be addressed. E-mail: (MK); (JG)
| | - Joseph A. Gogos
- Department of Neuroscience, Columbia University, New York, New York, United States of America
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- * To whom correspondence should be addressed. E-mail: (MK); (JG)
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Detera-Wadleigh SD, Liu CY, Maheshwari M, Cardona I, Corona W, Akula N, Steele CJM, Badner JA, Kundu M, Kassem L, Potash JB, Gibbs R, Gershon ES, McMahon FJ. Sequence variation in DOCK9 and heterogeneity in bipolar disorder. Psychiatr Genet 2007; 17:274-86. [PMID: 17728666 DOI: 10.1097/ypg.0b013e328133f352] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Linkage of bipolar disorder to a broad region on chromosome 13q has been supported in several studies including a meta-analysis on genome scans. Subsequent reports have shown that variations in the DAOA (G72) locus on 13q33 display association with bipolar disorder but these may not account for all of the linkage evidence in the region. OBJECTIVE To identify additional susceptibility loci on 13q32-q33 by linkage disequilibrium mapping and explore the impact of phenotypic heterogeneity on association. METHODS In the initial phase, 98 single nucleotide polymorphism (SNPs) located on 13q32-q33 were genotyped on 285 probands with bipolar disorder and their parents were drawn from families in the NIMH Genetics Initiative consortium for bipolar disorder (NIMH1-4) and two other series. Fine scale mapping using one family series (NIMH1-2) as the test sample was targeted on a gene that displayed the highest evidence of association. A secondary analysis of familial component phenotypes of bipolar disorder was conducted. RESULTS Three of seven SNPs in DOCK9, a gene that encodes an activator of the Rho-GTPase Cdc42, showed significant excess allelic transmission (P=0.0477-0.00067). Fine scale mapping on DOCK9 yielded evidence of association at nine SNPs in the gene (P=0.02-0.006). Follow-up tests detected excess transmission of the same allele of rs1340 in two out of three other sets of families. The association signals were largely attributable to maternally transmitted alleles (rs1927568: P=0.000083; odds ratio=3.778). A secondary analysis of familial component phenotypes of bipolar disorder detected significant association across multiple DOCK9 markers for racing thoughts, psychosis, delusion during mania and course of illness indicators. CONCLUSION These results suggest that DOCK9 contributes to both risk and increased illness severity in bipolar disorder. We found evidence for the effect of phenotypic heterogeneity on association. To our knowledge this is the first report to implicate DOCK9 or the Rho-GTPase pathway in the etiology of bipolar disorder.
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Affiliation(s)
- Sevilla D Detera-Wadleigh
- Genetic Basis of Mood and Anxiety Disorders, Mood and Anxiety Program, National Institute of Mental Health Intramural Research Program, National Institutes of Health/U.S. DHHS, 35 Convent Drive, Bethesda, MD 20892, USA.
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Whitfield JB, Dy V, McQuilty R, Zhu G, Montgomery GW, Ferreira MAR, Duffy DL, Neale MC, Heijmans BT, Heath AC, Martin NG. Evidence of genetic effects on blood lead concentration. ENVIRONMENTAL HEALTH PERSPECTIVES 2007; 115:1224-30. [PMID: 17687451 PMCID: PMC1940084 DOI: 10.1289/ehp.8847] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Accepted: 06/14/2007] [Indexed: 05/04/2023]
Abstract
BACKGROUND Lead is an environmental pollutant that causes acute and chronic toxicity. Surveys have related mean blood lead concentrations to exogenous sources, including industrial activity, use of lead-based paints, or traffic density. However, there has been little investigation of individual differences in lead absorption, distribution, or toxicity, or of genetic causes of such variation. OBJECTIVES We assessed the genetic contribution to variation in blood lead concentration in adults and conducted a preliminary search for genes producing such variation. METHODS Erythrocyte lead concentration was measured by inductively coupled plasma mass spectrometry in venous blood samples from 2,926 Australian adult male and female twins. Mean lead concentrations were compared by place of residence, social class and education, and by the subjects' age, sex, alcohol intake, smoking habits, iron status, and HFE genotype. RESULTS After adjustment for these covariates, there was strong evidence of genetic effects but not for shared environmental effects persisting into adult life. Linkage analysis showed suggestive evidence (logarithm of odds = 2.63, genome-wide p = 0.170) for a quantitative trait locus affecting blood lead values on chromosome 3 with the linkage peak close to SLC4A7, a gene whose product affects lead transport. CONCLUSIONS We conclude that genetic variation plays a significant role in determining lead absorption, lead distribution within the body, or both.
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Affiliation(s)
- John B Whitfield
- Department of Clinical Biochemistry, Royal Prince Alfred Hospital, Sydney, Australia.
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40
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Escamilla MA, Ontiveros A, Nicolini H, Raventos H, Mendoza R, Medina R, Munoz R, Levinson D, Peralta JM, Dassori A, Almasy L. A genome-wide scan for schizophrenia and psychosis susceptibility loci in families of Mexican and Central American ancestry. Am J Med Genet B Neuropsychiatr Genet 2007; 144B:193-9. [PMID: 17044102 DOI: 10.1002/ajmg.b.30411] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Schizophrenia is a complex psychiatric disorder, likely to be caused in part by multiple genes. In this study, linkage analyses were performed to identify chromosomal regions most likely to be associated with schizophrenia and psychosis in multiplex families of Mexican and Central American origin. Four hundred and fifty-nine individuals from 99 families, containing at least two siblings with hospital diagnoses of schizophrenia or schizoaffective disorder, were genotyped. Four hundred and four microsatellite markers were genotyped for all individuals and multipoint non-parametric linkage analyses were performed using broad (any psychosis) and narrow (schizophrenia and schizoaffective disorder) models. Under the broad model, three chromosomal regions (1pter-p36, 5q35, and 18p11) exhibited evidence of linkage with non-parametric lod (NPL) scores greater than 2.7 (equivalent to empirical P values of less than 0.001) with the peak multipoint NPL = 3.42 (empirical P value = 0.00003), meeting genomewide evidence for significant linkage in the 1pter-p36 region. Under the narrow model, the same three loci showed (non-significant) evidence of linkage. These linkage findings (1pter-p36, 18p11, and 5q35) highlight where genes for psychosis and schizophrenia are most likely to be found in persons of Mexican and Central American ancestry, and correspond to recent linkages of schizophrenia or psychosis in other populations which were formed in part from emigrants from the Spanish empire of the 15th and 16th centuries.
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Affiliation(s)
- M A Escamilla
- Department of Psychiatry, University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, Texas, 78229-3900, USA.
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Savitz J, van der Merwe L, Solms M, Ramesar R. Neurocognitive function in an extended Afrikaner-ancestry family with affective illness. J Psychiatry Neurosci 2007; 32:116-20. [PMID: 17353940 PMCID: PMC1810583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
OBJECTIVE To characterize the neuropsychological profile of an extended family with unipolar depression (UPD) and other forms of affective illness. METHOD We administered a battery of neuropsychological tasks measuring various aspects of executive function and visual and verbal memory to 49 individuals in 1 extended family. Six participants had 1 lifetime episode of major depression (MDE-S), 15 were diagnosed with recurrent major depression (MDE-R), 11 had another DSM-IV diagnosis and 17 subjects were unaffected. RESULTS After controlling for multiple confounding factors, including mood and medication, the MDE-R sample made significantly more errors than unaffected relatives on the Stroop Task, a measure of cognitive control. CONCLUSION There may be at least 1 subtype of UPD characterized by a state-independent deficit in cognitive control.
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Affiliation(s)
- Jonathan Savitz
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.
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Turner CLS, Bunyan DJ, Thomas NS, Mackay DJG, Jones HP, Waterham HR, Wanders RJA, Temple IK. Zellweger syndrome resulting from maternal isodisomy of chromosome 1. Am J Med Genet A 2007; 143A:2172-7. [PMID: 17702006 DOI: 10.1002/ajmg.a.31912] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Zellweger syndrome (ZS) is an autosomal recessive peroxisomal disorder that results from mutations in one of the peroxisome biogenesis (PEX) genes. This is the first patient reported with uniparental disomy (UPD) resulting in ZS, in this case maternal isodisomy of chromosome 1 involving reduction to homoallelism of a frameshift mutation within PEX 10. Other reported cases of UPD1, and evidence for the imprinting of genes on chromosome 1, are reviewed. The molecular findings in this patient have important implications for molecular testing and genetic counseling in ZS.
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Affiliation(s)
- Claire L S Turner
- Wessex Clinical Genetics Service, Southampton University Hospital NHS Trust, Princess Anne Hospital, Coxford Road, Southampton, UK.
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Aliyu MH, Calkins ME, Swanson CL, Lyons PD, Savage RM, May R, Wiener H, McLeod-Bryant S, Devlin B, Nimgaonkar VL, Ragland JD, Gur RE, Gur RC, Bradford LD, Edwards N, Kwentus J, McEvoy JP, Santos AB, McCleod-Bryant S, Tennison C, Go RCP, Allen TB. Project among African-Americans to explore risks for schizophrenia (PAARTNERS): recruitment and assessment methods. Schizophr Res 2006; 87:32-44. [PMID: 16887335 DOI: 10.1016/j.schres.2006.06.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2006] [Revised: 06/16/2006] [Accepted: 06/19/2006] [Indexed: 11/21/2022]
Abstract
The Project among African-Americans to Explore Risks for Schizophrenia (PAARTNERS) is a multi-site, NIMH-funded study that seeks to identify genetic polymorphisms that confer susceptibility to schizophrenia among African-Americans by linkage mapping and targeted association analyses. Because deficits in certain dimensions of cognitive ability are thought to underlie liability to schizophrenia, the project also examines cognitive abilities in individuals affected by schizophrenia and their extended family members. This article describes PAARTNERS study design, ascertainment methods and preliminary sample characteristics. We aim to recruit a sample of 1260 African-American families, all of whom have at least one proband with schizophrenia or schizoaffective disorder. The data collection protocol includes a structured Diagnostic Interview for Genetic Studies, Family Interview for Genetic Studies, focused neurocognitive assessment, medical records review, and the collection of blood or buccal cells for genetic analyses. We have currently completed study procedures for 106 affected sib-pair, 457 case-parent trio and 23 multiplex families. A total of 289 probands have completed the best estimate final diagnosis process and 1153 probands and family members have been administered the computerized neuropsychological battery. This project lays the foundation for future analysis of cognitive and behavioral endophenotypes. This novel integration of diagnostic, neurocognitive and genetic data will also generate valuable information for future phenotypic and genetic studies of schizophrenia.
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Affiliation(s)
- Muktar H Aliyu
- Department of Psychiatry, University of Alabama at Birmingham, Birmingham, AL 35294-2041, and Duke University Medical Center-John Umstead Hospital, Butner, NC, United States.
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Abou Jamra R, Schmael C, Cichon S, Rietschel M, Schumacher J, Nöthen MM. The G72/G30 gene locus in psychiatric disorders: a challenge to diagnostic boundaries? Schizophr Bull 2006; 32:599-608. [PMID: 16914640 PMCID: PMC2632259 DOI: 10.1093/schbul/sbl028] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In follow-up from evidence obtained in linkage studies, systematic linkage disequilibrium mapping within chromosomal region 13q33 has led to the identification of a schizophrenia susceptibility locus which harbors the genes G72 and G30. These association findings have been replicated in several independent schizophrenia samples. Association has also been found between genetic variants at the G72/G30 locus and bipolar affective disorder (BPAD), with replication in independent studies. Results from studies of more detailed psychiatric phenotypes show that association exists with symptom clusters that are common to several disorders as well as with specific psychiatric diagnoses. These findings may indicate that the association lies not with the diagnostic categories per se but with more specific aspects of the phenotype, such as affective symptoms and cognitive effects, which cross traditional psychiatric diagnostic boundaries. At the molecular level, the picture remains far from clear. No putative functional variants have been identified in the coding regions of G72 or G30, and it is therefore likely that disease susceptibility is caused by as yet unidentified variants which alter gene expression or splicing. A further complication is the fact that inconsistencies are evident in the risk alleles and haplotypes observed to be associated across different samples and studies, which may suggest the presence of multiple susceptibility variants at this locus. Functional analyses indicate that the G72 gene product plays a role in the activation of N-methyl-D-aspartate receptors, a molecular pathway implicated in both schizophrenia and BPAD, making it the most plausible candidate gene at this locus.
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Affiliation(s)
- Rami Abou Jamra
- Institute of Human Genetics, University of Bonn, Wilhelmstrasse 31, D-53111 Bonn, Germany.
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Wigginton JE, Abecasis GR. An evaluation of the replicate pool method: quick estimation of genome-wide linkage peak p-values. Genet Epidemiol 2006; 30:320-32. [PMID: 16832873 DOI: 10.1002/gepi.20147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The calculation of empirical p-values for genome-wide non-parametric linkage tests continues to present significant computational challenges for many complex disease mapping studies. The gold standard approach is to use gene dropping to simulate null genome scans. Unfortunately, this approach is too computationally expensive for many data sets of interest. An alternative, more efficient method for sampling null genome scans is to pre-calculate pools of family-specific statistics and then resample from these replicate pools to generate "pseudo-replicate" genome scans. In this study, we use simulations to explore properties of the replicate pool p-value estimator pRP and show that it provides an excellent approximation to the traditional gene-dropping estimator for significantly less computational effort. While the computational efficiency of the replicate pool estimator is noticeable in almost all data sets, by applying the replicate pool method to several previously characterized data sets we show that savings in computational effort can be especially significant (on the order of 10,000-fold or more) when one or more large families are analyzed. We also estimate replicate pool p-values for the schizophrenia data described by Abecasis et al. and show that pRP closely approximates gene-drop p-values for all linkage peaks reported for this study. Lastly, we expand upon Song et al.'s previous work by deriving a conservative estimator of the variance for PRP that can easily be computed in practical settings. We have implemented the replicate pool method along with our variance estimator in a new program called Pseudo, which is the first widely available automated implementation of the replicate pool method.
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Affiliation(s)
- Janis E Wigginton
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
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Xiao P, Liu P, Weber JL, Papasian CJ, Recker RR, Deng HW. Paternal uniparental isodisomy of the entire chromosome 3 revealed in a person with no apparent phenotypic disorders. Hum Mutat 2006; 27:133-7. [PMID: 16429396 DOI: 10.1002/humu.20302] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Uniparental disomy (UPD) is a rare genetic abnormality. During a whole genome linkage study we identified a case of paternal uniparental isodisomy 3 serendipitously. This is the first ascertained human paternal UPD for chromosome 3 (UPD3pat). The finding of this paternal UPD case of the entire chromosome 3 with no apparent phenotypic disorders suggests that there are no paternal imprinted genes causing rare genetic disorders on chromosome 3.
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Affiliation(s)
- Peng Xiao
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, Nebraska, USA
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Detera-Wadleigh SD, McMahon FJ. G72/G30 in schizophrenia and bipolar disorder: review and meta-analysis. Biol Psychiatry 2006; 60:106-14. [PMID: 16581030 DOI: 10.1016/j.biopsych.2006.01.019] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 01/19/2006] [Accepted: 01/28/2006] [Indexed: 01/31/2023]
Abstract
Association of the G72/G30 locus with schizophrenia and bipolar disorder has now been reported in several studies. The G72/G30 locus may be one of several that account for the evidence of linkage that spans a broad region of chromosome 13q. However, the story of G72/G30 is complex. Our meta-analysis of published association studies shows highly significant evidence of association between nucleotide variations in the G72/G30 region and schizophrenia, along with compelling evidence of association with bipolar disorder. But the associated alleles and haplotypes are not identical across studies, and some strongly associated variants are located approximately 50 kb telomeric of G72. Interestingly, G72 and G30 are transcribed in opposite directions; hence, their transcripts could cross-regulate translation. A functional native protein and functional motifs for G72 or G30 remain to be demonstrated. The interaction of G72 with d-amino acid oxidase, itself of interest as a modulator of N-methyl-d-aspartate receptors through regulation of d-serine levels, has been reported in one study and could be a key functional link that deserves further investigation. The association findings in the G72/G30 region, among the most compelling in psychiatry, may expose an important molecular pathway involved in susceptibility to schizophrenia and bipolar disorder.
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Affiliation(s)
- Sevilla D Detera-Wadleigh
- National Institute of Mental Health Intramural Research Program, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland 20892-3719, USA.
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Valle A, O'Connor DT, Taylor P, Zhu G, Montgomery GW, Slagboom PE, Martin NG, Whitfield JB. Butyrylcholinesterase: association with the metabolic syndrome and identification of 2 gene loci affecting activity. Clin Chem 2006; 52:1014-20. [PMID: 16574762 DOI: 10.1373/clinchem.2005.065052] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Plasma cholinesterase activity is known to be correlated with plasma triglycerides, HDL- and LDL-cholesterol, and other features of the metabolic syndrome. A role in triglyceride metabolism has been proposed. Genetic variants that decrease activity have been studied extensively, but the factors contributing to overall variation in the population are poorly understood. We studied plasma cholinesterase activity in a sample of 2200 adult twins to assess covariation with cardiovascular risk factors and components of the metabolic syndrome, to determine the degree of genetic effects on enzyme activity, and to search for quantitative trait loci affecting activity. METHODS AND RESULTS Cholinesterase activity was lower in women than in men before the age of 50, but increased to activity values similar to those in males after that age. There were highly significant correlations with variables associated with the metabolic syndrome: plasma triglyceride, HDL- and LDL-cholesterol, apolipoprotein B and E, urate, and insulin concentrations; gamma-glutamyltransferase and aspartate and alanine aminotransferase activities; body mass index; and blood pressure. The heritability of plasma cholinesterase activity was 65%. Linkage analysis with data from the dizygotic twin pairs showed suggestive linkage on chromosome 3 at the location of the cholinesterase (BCHE) gene and also on chromosome 5. CONCLUSIONS Our results confirm and extend the connection between cholinesterase, cardiovascular risk factors, and metabolic syndrome. They establish a substantial heritability for plasma cholinesterase activity that might be attributable to variation near the structural gene and at an independent locus.
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Affiliation(s)
- Anne Valle
- Department of Pharmacology, University of California at San Diego School of Medicine, and VA San Diego Healthcare System, La Jolla, CA, USA
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Hansell NK, Medland SE, Ferreira MAR, Geffen GM, Zhu G, Montgomery GW, Duffy DL, Wright MJ, Martin NG. Linkage Analyses of Event-Related Potential Slow Wave Phenotypes Recorded in a Working Memory Task. Behav Genet 2005; 36:29-44. [PMID: 16331531 DOI: 10.1007/s10519-005-9002-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Accepted: 06/20/2005] [Indexed: 10/25/2022]
Abstract
Working memory is an essential component of wide-ranging cognitive functions. It is a complex genetic trait probably influenced by numerous genes that individually have only a small influence. These genes may have an amplified influence on phenotypes closer to the gene action. In this study, event-related potential (ERP) phenotypes recorded during a working-memory task were collected from 656 adolescents from 299 families for whom genotypes were available. Univariate linkage analyses using the MERLIN variance-components method were conducted on slow wave phenotypes recorded at multiple sites while participants were required to remember the location of a target. Suggestive linkage (LOD > 2.2) was found on chromosomes 4, 5, 6, 10, 17, and 20. After correcting for multiple testing, suggestive linkage remained on chromosome 10. Empirical thresholds were computed for the most promising phenotypes. Those on chromosome 10 remained suggestive. A number of genes reported to regulate neural differentiation and function (i.e. NRP1, ANK3, and CHAT) were found under these linkage peaks and may influence the levels of neural activity occurring in individuals participating in a spatial working-memory task.
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Affiliation(s)
- N K Hansell
- Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
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Petryshen TL, Middleton FA, Tahl AR, Rockwell GN, Purcell S, Aldinger KA, Kirby A, Morley CP, McGann L, Gentile KL, Waggoner SG, Medeiros HM, Carvalho C, Macedo A, Albus M, Maier W, Trixler M, Eichhammer P, Schwab SG, Wildenauer DB, Azevedo MH, Pato MT, Pato CN, Daly MJ, Sklar P. Genetic investigation of chromosome 5q GABAA receptor subunit genes in schizophrenia. Mol Psychiatry 2005; 10:1074-88, 1057. [PMID: 16172613 DOI: 10.1038/sj.mp.4001739] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We previously performed a genome-wide linkage scan in Portuguese schizophrenia families that identified a risk locus on chromosome 5q31-q35. This finding was supported by meta-analysis of 20 other schizophrenia genome-wide scans that identified 5q23.2-q34 as the second most compelling susceptibility locus in the genome. In the present report, we took a two-stage candidate gene association approach to investigate a group of gamma-aminobutyric acid (GABA) A receptor subunit genes (GABRA1, GABRA6, GABRB2, GABRG2, and GABRP) within our linkage peak. These genes are plausible candidates based on prior evidence for GABA system involvement in schizophrenia. In the first stage, associations were detected in a Portuguese patient sample with single nucleotide polymorphisms (SNPs) and haplotypes in GABRA1 (P=0.00062-0.048), GABRP (P=0.0024-0.042), and GABRA6 (P=0.0065-0.0088). The GABRA1 and GABRP findings were replicated in the second stage in an independent German family-based sample (P=0.0015-0.043). Supportive evidence for association was also obtained for a previously reported GABRB2 risk haplotype. Exploratory analyses of the effects of associated GABRA1 haplotypes on transcript levels found altered expression of GABRA6 and coexpressed genes of GABRA1 and GABRB2. Comparison of transcript levels in schizophrenia patients and unaffected siblings found lower patient expression of GABRA6 and coexpressed genes of GABRA1. Interestingly, the GABRA1 coexpressed genes include synaptic and vesicle-associated genes previously found altered in schizophrenia prefrontal cortex. Taken together, these results support the involvement of the chromosome 5q GABAA receptor gene cluster in schizophrenia, and suggest that schizophrenia-associated haplotypes may alter expression of GABA-related genes.
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Affiliation(s)
- T L Petryshen
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
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