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Janani N, Young KA, Kinney G, Strand M, Hokanson JE, Liu Y, Butler T, Austin E. A novel application of data-consistent inversion to overcome spurious inference in genome-wide association studies. Genet Epidemiol 2024; 48:270-288. [PMID: 38644517 DOI: 10.1002/gepi.22563] [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: 05/09/2023] [Revised: 12/30/2023] [Accepted: 03/27/2024] [Indexed: 04/23/2024]
Abstract
The genome-wide association studies (GWAS) typically use linear or logistic regression models to identify associations between phenotypes (traits) and genotypes (genetic variants) of interest. However, the use of regression with the additive assumption has potential limitations. First, the normality assumption of residuals is the one that is rarely seen in practice, and deviation from normality increases the Type-I error rate. Second, building a model based on such an assumption ignores genetic structures, like, dominant, recessive, and protective-risk cases. Ignoring genetic variants may result in spurious conclusions about the associations between a variant and a trait. We propose an assumption-free model built upon data-consistent inversion (DCI), which is a recently developed measure-theoretic framework utilized for uncertainty quantification. This proposed DCI-derived model builds a nonparametric distribution on model inputs that propagates to the distribution of observed data without the required normality assumption of residuals in the regression model. This characteristic enables the proposed DCI-derived model to cover all genetic variants without emphasizing on additivity of the classic-GWAS model. Simulations and a replication GWAS with data from the COPDGene demonstrate the ability of this model to control the Type-I error rate at least as well as the classic-GWAS (additive linear model) approach while having similar or greater power to discover variants in different genetic modes of transmission.
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Affiliation(s)
- Negar Janani
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Greg Kinney
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Matthew Strand
- Division of Biostatistics, National Jewish Health, Denver, Colorado, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Yaning Liu
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA
| | - Troy Butler
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA
| | - Erin Austin
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA
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2
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Bergamin CS, Pérez-Hurtado E, Oliveira L, Gabbay M, Piveta V, Bittencourt C, Russo D, Carmona RDC, Sato M, Dib SA. Enterovirus Neutralizing Antibodies, Monocyte Toll Like Receptors Expression and Interleukin Profiles Are Similar Between Non-affected and Affected Siblings From Long-Term Discordant Type 1 Diabetes Multiplex-Sib Families: The Importance of HLA Background. Front Endocrinol (Lausanne) 2020; 11:555685. [PMID: 33071971 PMCID: PMC7538605 DOI: 10.3389/fendo.2020.555685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/14/2020] [Indexed: 12/15/2022] Open
Abstract
Enteroviruses are main candidates among environmental agents in the development of type 1 diabetes (T1D). However, the relationship between virus and the immune system response during T1D pathogenesis is heterogeneous. This is an interesting paradigm and the search for answers would help to highlight the role of viral infection in the etiology of T1D. The current data is a cross-sectional study of affected and non-affected siblings from T1D multiplex-sib families to analyze associations among T1D, genetic, islet autoantibodies and markers of innate immunity. We evaluated the prevalence of anti-virus antibodies (Coxsackie B and Echo) and its relationships with human leukocyte antigen (HLA) class II alleles, TLR expression (monocytes), serum cytokine profile and islet β cell autoantibodies in 51 individuals (40 T1D and 11 non-affected siblings) from 20 T1D multiplex-sib families and 54 healthy control subjects. The viral antibody profiles were similar among all groups, except for antibodies against CVB2, which were more prevalent in the non-affected siblings. TLR4 expression was higher in the T1D multiplex-sib family's members than in the control subjects. TLR4 expression showed a positive correlation with CBV2 antibody prevalence (rS: 0.45; P = 0.03), CXCL8 (rS: 0.65, P = 0.002) and TNF-α (rS: 0.5, P = 0.01) serum levels in both groups of T1D multiplex-sib family. Furthermore, within these families, there was a positive correlation between HLA class II alleles associated with high risk for T1D and insulinoma-associated protein 2 autoantibody (IA-2A) positivity (odds ratio: 38.8; P = 0.021). However, the HLA protective haplotypes against T1D prevalence was higher in the non-affected than the affected siblings. This study shows that although the prevalence of viral infection is similar among healthy individuals and members from the T1D multiplex-sib families, the innate immune response is higher in the affected and in the non-affected siblings from these families than in the healthy controls. However, autoimmunity against β-islet cells and an absence of protective HLA alleles were only observed in the T1D multiplex-sib members with clinical disease, supporting the importance of the genetic background in the development of T1D and heterogeneity of the interaction between environmental factors and disease pathogenesis despite the high genetic diversity of the Brazilian population.
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Affiliation(s)
- Carla Sanchez Bergamin
- Endocrinology Division, Department of Medicine, Diabetes Center, Escola Paulista de Medicina - Universidade Federal de São Paulo, São Paulo, Brazil
- *Correspondence: Carla Sanchez Bergamin
| | - Elizabeth Pérez-Hurtado
- Immunology Division, Microbiology, Immunology and Parasitological Department, Escola Paulista de Medicina - Universidade Federal de São Paulo, São Paulo, Brazil
| | - Luanda Oliveira
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology and Tropical Medicine Institute of São Paulo, Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
| | - Monica Gabbay
- Endocrinology Division, Department of Medicine, Diabetes Center, Escola Paulista de Medicina - Universidade Federal de São Paulo, São Paulo, Brazil
| | - Valdecira Piveta
- Endocrinology Division, Department of Medicine, Diabetes Center, Escola Paulista de Medicina - Universidade Federal de São Paulo, São Paulo, Brazil
| | - Célia Bittencourt
- Endocrinology Division, Department of Medicine, Diabetes Center, Escola Paulista de Medicina - Universidade Federal de São Paulo, São Paulo, Brazil
| | - Denise Russo
- Enteric Diseases Laboratory, Virology Center From Instituto Adolfo Lutz, São Paulo, Brazil
| | - Rita de Cássia Carmona
- Enteric Diseases Laboratory, Virology Center From Instituto Adolfo Lutz, São Paulo, Brazil
| | - Maria Sato
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology and Tropical Medicine Institute of São Paulo, Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
| | - Sergio A. Dib
- Endocrinology Division, Department of Medicine, Diabetes Center, Escola Paulista de Medicina - Universidade Federal de São Paulo, São Paulo, Brazil
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Gloaguen E, Dizier MH, Boissel M, Rocheleau G, Canouil M, Froguel P, Tichet J, Roussel R, Julier C, Balkau B, Mathieu F. General regression model: A "model-free" association test for quantitative traits allowing to test for the underlying genetic model. Ann Hum Genet 2019; 84:280-290. [PMID: 31834638 DOI: 10.1111/ahg.12372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 11/26/2022]
Abstract
Most genome-wide association studies used genetic-model-based tests assuming an additive mode of inheritance, leading to underpowered association tests in case of departure from additivity. The general regression model (GRM) association test proposed by Fisher and Wilson in 1980 makes no assumption on the genetic model. Interestingly, it also allows formal testing of the underlying genetic model. We conducted a simulation study of quantitative traits to compare the power of the GRM test to the classical linear regression tests, the maximum of the three statistics (MAX), and the allele-based (allelic) tests. Simulations were performed on two samples sizes, using a large panel of genetic models, varying genetic models, minor allele frequencies, and the percentage of explained variance. In case of departure from additivity, the GRM was more powerful than the additive regression tests (power gain reaching 80%) and had similar power when the true model is additive. GRM was also as or more powerful than the MAX or allelic tests. The true simulated model was mostly retained by the GRM test. Application of GRM to HbA1c illustrates its gain in power. To conclude, GRM increases power to detect association for quantitative traits, allows determining the genetic model and is easily applicable.
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Affiliation(s)
- Emilie Gloaguen
- Inserm UMRS-958, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Marie-Hélène Dizier
- Inserm UMR-946, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mathilde Boissel
- Université de Lille, UMR 8199 - EGID, Lille, France.,CNRS, Paris, France.,Institut Pasteur de Lille, Lille, France
| | - Ghislain Rocheleau
- Université de Lille, UMR 8199 - EGID, Lille, France.,CNRS, Paris, France.,Institut Pasteur de Lille, Lille, France
| | - Mickaël Canouil
- Université de Lille, UMR 8199 - EGID, Lille, France.,CNRS, Paris, France.,Institut Pasteur de Lille, Lille, France
| | - Philippe Froguel
- Université de Lille, UMR 8199 - EGID, Lille, France.,CNRS, Paris, France.,Institut Pasteur de Lille, Lille, France.,Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
| | | | - Ronan Roussel
- Inserm U1138, Centre de Recherche des Cordeliers, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Diabetology, Endocrinology and Nutrition Department, DHU FIRE, Hôpital Bichat, AP-HP, Paris, France
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- Inserm UMRS-958, Paris, France
| | - Cécile Julier
- Inserm UMRS-958, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Flavie Mathieu
- Mission Associations Recherche & Société - Inserm Siège, DISC, Paris, France.,Paris Diderot, Sorbonne Paris Cité, Paris, France
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Moutal A, Li W, Wang Y, Ju W, Luo S, Cai S, François-Moutal L, Perez-Miller S, Hu J, Dustrude ET, Vanderah TW, Gokhale V, Khanna M, Khanna R. Homology-guided mutational analysis reveals the functional requirements for antinociceptive specificity of collapsin response mediator protein 2-derived peptides. Br J Pharmacol 2017; 175:2244-2260. [PMID: 28161890 DOI: 10.1111/bph.13737] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/26/2017] [Accepted: 01/31/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AND PURPOSE N-type voltage-gated calcium (Cav 2.2) channels are critical determinants of increased neuronal excitability and neurotransmission accompanying persistent neuropathic pain. Although Cav 2.2 channel antagonists are recommended as first-line treatment for neuropathic pain, calcium-current blocking gabapentinoids inadequately alleviate chronic pain symptoms and often exhibit numerous side effects. Collapsin response mediator protein 2 (CRMP2) targets Cav 2.2 channels to the sensory neuron membrane and allosterically modulates their function. A 15-amino-acid peptide (CBD3), derived from CRMP2, disrupts the functional protein-protein interaction between CRMP2 and Cav 2.2 channels to inhibit calcium influx, transmitter release and acute, inflammatory and neuropathic pain. Here, we have mapped the minimal domain of CBD3 necessary for its antinociceptive potential. EXPERIMENTAL APPROACH Truncated as well as homology-guided mutant versions of CBD3 were generated and assessed using depolarization-evoked calcium influx in rat dorsal root ganglion neurons, binding between CRMP2 and Cav 2.2 channels, whole-cell voltage clamp electrophysiology and behavioural effects in two models of experimental pain: post-surgical pain and HIV-induced sensory neuropathy induced by the viral glycoprotein 120. KEY RESULTS The first six amino acids within CBD3 accounted for all in vitro activity and antinociception. Spinal administration of a prototypical peptide (TAT-CBD3-L5M) reversed pain behaviours. Homology-guided mutational analyses of these six amino acids identified at least two residues, Ala1 and Arg4, as being critical for antinociception in two pain models. CONCLUSIONS AND IMPLICATIONS These results identify an antinociceptive scaffold core in CBD3 that can be used for development of low MW mimetics of CBD3. LINKED ARTICLES This article is part of a themed section on Recent Advances in Targeting Ion Channels to Treat Chronic Pain. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.12/issuetoc.
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Affiliation(s)
- Aubin Moutal
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Wennan Li
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Yue Wang
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Weina Ju
- Department of Neurology, The First Hospital of Jilin University, Jilin University, Changchun, Jilin Province, China.,Department of Pharmacology, The First Hospital of Jilin University, Jilin University, Changchun, Jilin Province, China
| | - Shizhen Luo
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Song Cai
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | | | | | - Jackie Hu
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Erik T Dustrude
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Todd W Vanderah
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Vijay Gokhale
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | - May Khanna
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - Rajesh Khanna
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA.,Neuroscience Graduate Interdisciplinary Program, College of Medicine, University of Arizona, Tucson, AZ, USA
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Mobuchon L, Battistella A, Bardel C, Scelo G, Renoud A, Houy A, Cassoux N, Milder M, Cancel-Tassin G, Cussenot O, Delattre O, Besse C, Boland A, Deleuze JF, Cox DG, Stern MH. A GWAS in uveal melanoma identifies risk polymorphisms in the CLPTM1L locus. NPJ Genom Med 2017; 2:5. [PMID: 28781888 PMCID: PMC5542017 DOI: 10.1038/s41525-017-0008-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 02/03/2023] Open
Abstract
Uveal melanoma, a rare malignant tumor of the eye, is predominantly observed in populations of European ancestry. A genome-wide association study of 259 uveal melanoma patients compared to 401 controls all of European ancestry revealed a candidate locus at chromosome 5p15.33 (region rs421284: OR = 1.7, CI 1.43-2.05). This locus was replicated in an independent set of 276 cases and 184 controls. In addition, risk variants from this region were positively associated with higher expression of CLPTM1L. In conclusion, the CLPTM1L region contains risk alleles for uveal melanoma susceptibility, suggesting that CLPTM1L could play a role in uveal melanoma oncogenesis.
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Affiliation(s)
- Lenha Mobuchon
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | - Aude Battistella
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | - Claire Bardel
- UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Université Claude Bernard-Lyon 1, Lyon, France
- Service de Biostatistique-bioinformatique, Hospices Civils de Lyon, Lyon, France
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Alexia Renoud
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Alexandre Houy
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | - Nathalie Cassoux
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | - Maud Milder
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | | | - Olivier Cussenot
- UPMC University Paris 06 GRC n°5, CeRePP, Hôpital Tenon, Paris, France
| | - Olivier Delattre
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | - Céline Besse
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - Anne Boland
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | | | - David G. Cox
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Marc-Henri Stern
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
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6
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Kitsche A, Ritz C, Hothorn LA. A General Framework for the Evaluation of Genetic Association Studies Using Multiple Marginal Models. Hum Hered 2016; 81:150-172. [DOI: 10.1159/000448477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 07/14/2016] [Indexed: 12/29/2022] Open
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Heilbronner U, Malzahn D, Strohmaier J, Maier S, Frank J, Treutlein J, Mühleisen TW, Forstner AJ, Witt SH, Cichon S, Falkai P, Nöthen MM, Rietschel M, Schulze TG. A common risk variant in CACNA1C supports a sex-dependent effect on longitudinal functioning and functional recovery from episodes of schizophrenia-spectrum but not bipolar disorder. Eur Neuropsychopharmacol 2015; 25:2262-70. [PMID: 26475575 DOI: 10.1016/j.euroneuro.2015.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/26/2015] [Accepted: 09/24/2015] [Indexed: 12/13/2022]
Abstract
Sex is a powerful modulator of disease susceptibility, course and outcome. The gene CACNA1C is among the best replicated vulnerability genes of bipolar disorder and schizophrenia. The aim of the present study was to investigate whether sex and a variant in CACNA1C (rs10774035 as a proxy for the well-acknowledged risk variant rs1006737) influence psychosocial adaptation in a large German patient sample with schizophrenia-spectrum (n=297) and bipolar (n=516) disorders. We analyzed Global Assessment of Functioning (GAF) scores, retrospectively collected for different time points during disease course. We investigated whether CACNA1C sex-dependently modulates longitudinal GAF scores and recovery from episodes of psychiatric disturbance in the above mentioned disorders. Psychosocial recovery was measured as difference score between the current GAF score (assessing the last remission) and the worst GAF score ever during an illness episode. Covariate- adjusted association analyses revealed a sex × rs10774035 genotype interaction on longitudinal GAF and recovery from illness episodes only in schizophrenia-spectrum but not in bipolar disorders. In schizophrenia-spectrum affected males, rs10774035 minor allele (T) carriers had higher GAF scores at three time points (premorbid, worst ever, current). In contrast, females carrying rs10774035 minor alleles had impaired recovery from schizophrenia-spectrum episodes. These results encourage further investigations of gene × sex interactions and longitudinal quantitative phenotypes to unravel the rich variety of behavioral consequences of genetic individuality.
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Affiliation(s)
- Urs Heilbronner
- Institute of Psychiatric Phenomics and Genomics, Ludwig-Maximilians-University Munich, Germany.
| | - Dörthe Malzahn
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
| | - Sandra Maier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
| | - Thomas W Mühleisen
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich (FZJ), Jülich, Germany; Institute of Human Genetics, University of Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Germany; Division of Medical Genetics, University Hospital Basel, University of Basel, Switzerland; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilians-University Munich, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics, Ludwig-Maximilians-University Munich, Germany; Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany; Department of Psychiatry and Psychotherapy, University Medical Center, Georg-August-University, Göttingen, Germany
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8
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Zhang W, Li Q. Nonparametric Risk and Nonparametric Odds in Quantitative Genetic Association Studies. Sci Rep 2015; 5:12105. [PMID: 26174851 PMCID: PMC5378889 DOI: 10.1038/srep12105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 06/17/2015] [Indexed: 12/30/2022] Open
Abstract
The coefficient in a linear regression model is commonly employed to evaluate the genetic effect of a single nucleotide polymorphism associated with a quantitative trait under the assumption that the trait value follows a normal distribution or is appropriately normally distributed after a certain transformation. When this assumption is violated, the distribution-free tests are preferred. In this work, we propose the nonparametric risk (NR) and nonparametric odds (NO), obtain the asymptotic normal distribution of estimated NR and then construct the confidence intervals. We also define the genetic models using NR, construct the test statistic under a given genetic model and a robust test, which are free of the genetic uncertainty. Simulation studies show that the proposed confidence intervals have satisfactory cover probabilities and the proposed test can control the type I error rates and is more powerful than the exiting ones under most of the considered scenarios. Application to gene of PTPN22 and genomic region of 6p21.33 from the Genetic Analysis Workshop 16 for association with the anticyclic citrullinated protein antibody further show their performances.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Systems Control, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Qizhai Li
- Key Laboratory of Systems Control, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
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9
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Bensussan M, Lefebvre V, Ducamp A, Trouverie J, Gineau E, Fortabat MN, Guillebaux A, Baldy A, Naquin D, Herbette S, Lapierre C, Mouille G, Horlow C, Durand-Tardif M. Suppression of Dwarf and irregular xylem Phenotypes Generates Low-Acetylated Biomass Lines in Arabidopsis. PLANT PHYSIOLOGY 2015; 168:452-63. [PMID: 25888614 PMCID: PMC4453781 DOI: 10.1104/pp.15.00122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/15/2015] [Indexed: 05/17/2023]
Abstract
eskimo1-5 (esk1-5) is a dwarf Arabidopsis (Arabidopsis thaliana) mutant that has a constitutive drought syndrome and collapsed xylem vessels, along with low acetylation levels in xylan and mannan. ESK1 has xylan O-acetyltransferase activity in vitro. We used a suppressor strategy on esk1-5 to screen for variants with wild-type growth and low acetylation levels, a favorable combination for ethanol production. We found a recessive mutation in the KAKTUS (KAK) gene that suppressed dwarfism and the collapsed xylem character, the cause of decreased hydraulic conductivity in the esk1-5 mutant. Backcrosses between esk1-5 and two independent knockout kak mutants confirmed suppression of the esk1-5 effect. kak single mutants showed larger stem diameters than the wild type. The KAK promoter fused with a reporter gene showed activity in the vascular cambium, phloem, and primary xylem in the stem and hypocotyl. However, suppression of the collapsed xylem phenotype in esk1 kak double mutants was not associated with the recovery of cell wall O-acetylation or any major cell wall modifications. Therefore, our results indicate that, in addition to its described activity as a repressor of endoreduplication, KAK may play a role in vascular development. Furthermore, orthologous esk1 kak double mutants may hold promise for ethanol production in crop plants.
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Affiliation(s)
- Matthieu Bensussan
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Valérie Lefebvre
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Aloïse Ducamp
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Jacques Trouverie
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Emilie Gineau
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Marie-Noëlle Fortabat
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Alexia Guillebaux
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Aurélie Baldy
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Delphine Naquin
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Stéphane Herbette
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Catherine Lapierre
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Gregory Mouille
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Christine Horlow
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Mylène Durand-Tardif
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
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(S)-Lacosamide Binding to Collapsin Response Mediator Protein 2 (CRMP2) Regulates CaV2.2 Activity by Subverting Its Phosphorylation by Cdk5. Mol Neurobiol 2015; 53:1959-1976. [PMID: 25846820 DOI: 10.1007/s12035-015-9141-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/09/2015] [Indexed: 12/22/2022]
Abstract
The neuronal circuit remodels during development as well as in human neuropathologies such as epilepsy. Neurite outgrowth is an obligatory step in these events. We recently reported that alterations in the phosphorylation state of an axon specification/guidance protein, the collapsin response mediator protein 2 (CRMP2), play a major role in the activity-dependent regulation of neurite outgrowth. We also identified (S)-LCM, an inactive stereoisomer of the clinically used antiepileptic drug (R)-LCM (Vimpat®), as a novel tool for preferentially targeting CRMP2-mediated neurite outgrowth. Here, we investigated the mechanism by which (S)-LCM affects CRMP2 phosphorylation by two key kinases, cyclin-dependent kinase 5 (Cdk5) and glycogen synthase kinase 3β (GSK-3β). (S)-LCM application to embryonic cortical neurons resulted in reduced levels of Cdk5- and GSK-3β-phosphorylated CRMP2. Mechanistically, (S)-LCM increased CRMP2 binding to both Cdk5- and GSK-3β without affecting binding of CRMP2 to its canonical partner tubulin. Saturation transfer difference nuclear magnetic resonance (STD NMR) and differential scanning fluorimetry (DSF) experiments demonstrated direct binding of (S)-LCM to CRMP2. Using an in vitro luminescent kinase assay, we observed that (S)-LCM specifically inhibited Cdk5-mediated phosphorylation of CRMP2. Cross-linking experiments and analytical ultracentrifugation showed no effect of (S)-LCM on the oligomerization state of CRMP2. The increased association between Cdk5-phosphorylated CRMP2 and CaV2.2 was reduced by (S)-LCM in vitro and in vivo. This reduction translated into a decrease of calcium influx via CaV2.2 in (S)-LCM-treated neurons compared to controls. (S)-LCM, to our knowledge, is the first molecule described to directly inhibit CRMP2 phosphorylation and may be useful for delineating CRMP2-facilitated functions.
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Maciukiewicz M, Dmitrzak-Weglarz M, Pawlak J, Leszczynska-Rodziewicz A, Zaremba D, Skibinska M, Hauser J. Analysis of genetic association and epistasis interactions between circadian clock genes and symptom dimensions of bipolar affective disorder. Chronobiol Int 2014; 31:770-8. [PMID: 24673294 DOI: 10.3109/07420528.2014.899244] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bipolar affective disorder (BD) is a severe psychiatric disorder characterized by periodic changes in mood from depression to mania. Disruptions of biological rhythms increase risk of mood disorders. Because clinical representation of disease is heterogeneous, homogenous sets of patients are suggested to use in the association analyses. In our study, we aimed to apply previously computed structure of bipolar disorder symptom dimension for analyses of genetic association. We based quantitative trait on: main depression, sleep disturbances, appetite disturbances, excitement and psychotic dimensions consisted of OPCRIT checklist items. We genotyped 42 polymorphisms from circadian clock genes: PER3, ARNTL, CLOCK and TIMELSSS from 511 patients BD (n = 292 women and n = 219 men). As quantitative trait we used clinical dimensions, described above. Genetic associations between alleles and quantitative trait were performed using applied regression models applied in PLINK. In addition, we used the Kruskal-Wallis test to look for associations between genotypes and quantitative trait. During second stage of our analyses, we used multidimensional scaling (multifactor dimensionality reduction) for quantitative trait to compute pairwise epistatic interactions between circadian gene variants. We found association between ARNTL variant rs11022778 main depression (p = 0.00047) and appetite disturbances (p = 0.004). In epistatic interaction analyses, we observed two locus interactions between sleep disturbances (p = 0.007; rs11824092 of ARNTL and rs11932595 of CLOCK) as well as interactions of subdimension in main depression and ARNTL variants (p = 0.0011; rs3789327, rs10766075) and appetite disturbances in depression and ARNTL polymorphism (p = 7 × 10(-4); rs11022778, rs156243).
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Affiliation(s)
- Malgorzata Maciukiewicz
- Laboratory of Psychiatric Genetics, Department of Psychiatry, Poznan University of Medical Sciences , Poznan , Poland
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Kubo M, Imai A, Nishiyama T, Ishikawa M, Sato Y, Kurata T, Hiwatashi Y, Reski R, Hasebe M. System for stable β-estradiol-inducible gene expression in the moss Physcomitrella patens. PLoS One 2013; 8:e77356. [PMID: 24086772 PMCID: PMC3785464 DOI: 10.1371/journal.pone.0077356] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 09/02/2013] [Indexed: 01/02/2023] Open
Abstract
Inducible transgene expression provides a useful tool to analyze gene function. The moss Physcomitrellapatens is a model basal land plant with well-developed research tools, including a high efficiency of gene targeting and substantial genomics resources. However, current systems for controlled transgene expression remain limited. Here we report the development of an estrogen receptor mediated inducible gene expression system, based on the system used in flowering plants. After identifying the appropriate promoters to drive the chimeric transducer, we succeeded in inducing transcription over 1,000-fold after 24 h incubation with β-estradiol. The P. patens system was also effective for high-level long-term induction of gene expression; transcript levels of the activated gene were maintained for at least seven days on medium containing β-estradiol. We also established two potentially neutral targeting sites and a set of vectors for reproducible expression of two transgenes. This β-estradiol-dependent system will be useful to test genes individually or in combination, allowing stable, inducible transgenic expression in P. patens.
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Affiliation(s)
- Minoru Kubo
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- FRIAS – Freiburg Institute for Advanced Studies, Freiburg, Germany
- * E-mail: (MK); (MH)
| | - Akihiro Imai
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Tomoaki Nishiyama
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Masaki Ishikawa
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | | | - Tetsuya Kurata
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
| | - Yuji Hiwatashi
- National Institute for Basic Biology, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- FRIAS – Freiburg Institute for Advanced Studies, Freiburg, Germany
- BIOSS – Centre for Biological Signalling Studies, Freiburg, Germany
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, Japan Science and Technology Agency, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
- * E-mail: (MK); (MH)
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The psychiatric vulnerability gene CACNA1C and its sex-specific relationship with personality traits, resilience factors and depressive symptoms in the general population. Mol Psychiatry 2013; 18:607-13. [PMID: 22665259 DOI: 10.1038/mp.2012.53] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome-wide association studies have reported an association between the A-allele of rs1006737 within CACNA1C and affective disorders and schizophrenia. The aim of the present study was to investigate the relationship between rs1006737 and established and potential endophenotypes for these disorders in a population-based cohort of 3793 subjects, using an analytical method designed to assess a previously reported sex-specific effect of CACNA1C. The investigated endophenotypes included personality traits and resilience factors. At 10-year follow-up, subjects were screened for depressive symptoms. All subjects were genotyped for rs1006737. The direction of the effect and mode of inheritance of rs1006737 differed between the sexes. In men, the A-allele was associated with higher emotional lability and lower resilience, that is, lower sense of coherence (P=0.021), lower perceived social support (P=0.018), lower dispositional optimism (P=0.032) and more depressive symptoms at follow-up (P=0.007). In women, the A-allele was associated with lower emotional lability and stronger resilience, that is, higher sense of coherence (P=0.00028), higher perceived social support (P=0.010), lower neuroticism (P=0.022) and fewer depressive symptoms at follow-up (P=0.035). After conservative Bonferroni correction for 32 tests, results only remained significant for sense of coherence in women (P=0.009). These results suggest that CACNA1C is involved in the genetic architecture of endophenotypes for affective disorders and schizophrenia, and that it shows a distinct sex-specific effect. Comprehensive phenotype characterization in case-control samples and the general population, as well as an adequate modeling of sex-specific genetic effects, may be warranted to elucidate the pathogenetic mechanisms conferred by robustly identified susceptibility genes.
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Are Multiple Contrast Tests Superior to the ANOVA? Int J Biostat 2013; 9:/j/ijb.2013.9.issue-1/ijb-2012-0020/ijb-2012-0020.xml. [DOI: 10.1515/ijb-2012-0020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Konietschke F, Hothorn LA, Brunner E. Rank-based multiple test procedures and simultaneous confidence intervals. Electron J Stat 2012. [DOI: 10.1214/12-ejs691] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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