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Nord CL, Valton V, Wood J, Roiser JP. Power-up: A Reanalysis of 'Power Failure' in Neuroscience Using Mixture Modeling. J Neurosci 2017; 37:8051-8061. [PMID: 28706080 PMCID: PMC5566862 DOI: 10.1523/jneurosci.3592-16.2017] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 06/06/2017] [Accepted: 06/17/2017] [Indexed: 11/25/2022] Open
Abstract
Recently, evidence for endemically low statistical power has cast neuroscience findings into doubt. If low statistical power plagues neuroscience, then this reduces confidence in the reported effects. However, if statistical power is not uniformly low, then such blanket mistrust might not be warranted. Here, we provide a different perspective on this issue, analyzing data from an influential study reporting a median power of 21% across 49 meta-analyses (Button et al., 2013). We demonstrate, using Gaussian mixture modeling, that the sample of 730 studies included in that analysis comprises several subcomponents so the use of a single summary statistic is insufficient to characterize the nature of the distribution. We find that statistical power is extremely low for studies included in meta-analyses that reported a null result and that it varies substantially across subfields of neuroscience, with particularly low power in candidate gene association studies. Therefore, whereas power in neuroscience remains a critical issue, the notion that studies are systematically underpowered is not the full story: low power is far from a universal problem.SIGNIFICANCE STATEMENT Recently, researchers across the biomedical and psychological sciences have become concerned with the reliability of results. One marker for reliability is statistical power: the probability of finding a statistically significant result given that the effect exists. Previous evidence suggests that statistical power is low across the field of neuroscience. Our results present a more comprehensive picture of statistical power in neuroscience: on average, studies are indeed underpowered-some very seriously so-but many studies show acceptable or even exemplary statistical power. We show that this heterogeneity in statistical power is common across most subfields in neuroscience. This new, more nuanced picture of statistical power in neuroscience could affect not only scientific understanding, but potentially policy and funding decisions for neuroscience research.
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Affiliation(s)
- Camilla L Nord
- Institute of Cognitive Neuroscience, University College London, London, WC1N 3AZ, United Kingdom, and
| | - Vincent Valton
- Institute of Cognitive Neuroscience, University College London, London, WC1N 3AZ, United Kingdom, and
| | - John Wood
- Research Department of Primary Care and Population Health, University College London Medical School, London NW3 2PF, United Kingdom
| | - Jonathan P Roiser
- Institute of Cognitive Neuroscience, University College London, London, WC1N 3AZ, United Kingdom, and
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2
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Li J, Tang L, Wang Y, Li F, Bao M, Xiang J, Lei D, Tang B. Genetic Associations and Interactions Between the NR3C1 (GR) and NR3C2 (MR) Genes and Aggressive Behavior in a Central South Chinese Han Population. Genet Test Mol Biomarkers 2017; 21:497-505. [PMID: 28686058 DOI: 10.1089/gtmb.2016.0417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jianming Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Neuroscience Research Center, Changsha Medical University, Changsha, Hunan, China
- Department of Anatomy, Changsha Medical University, Changsha, Hunan, China
| | - Liang Tang
- Neuroscience Research Center, Changsha Medical University, Changsha, Hunan, China
- Department of Anatomy, Changsha Medical University, Changsha, Hunan, China
| | - Yan Wang
- Neuroscience Research Center, Changsha Medical University, Changsha, Hunan, China
- School of Basic Medical Science, Changsha Medical University, Changsha, Hunan, China
| | - Fang Li
- Neuroscience Research Center, Changsha Medical University, Changsha, Hunan, China
- Department of Anatomy, Changsha Medical University, Changsha, Hunan, China
| | - Meihua Bao
- Neuroscience Research Center, Changsha Medical University, Changsha, Hunan, China
- Department of Anatomy, Changsha Medical University, Changsha, Hunan, China
| | - Ju Xiang
- Neuroscience Research Center, Changsha Medical University, Changsha, Hunan, China
- Department of Anatomy, Changsha Medical University, Changsha, Hunan, China
| | - Deliang Lei
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Bifsha P, Balsalobre A, Drouin J. Specificity of Pitx3-Dependent Gene Regulatory Networks in Subsets of Midbrain Dopamine Neurons. Mol Neurobiol 2016; 54:4921-4935. [PMID: 27514757 DOI: 10.1007/s12035-016-0040-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/05/2016] [Indexed: 01/16/2023]
Abstract
Dysfunction of midbrain dopaminergic (mDA) neurons is involved in Parkinson's disease (PD) and neuropsychiatric disorders. Pitx3 is expressed in mDA neuron subsets of the substantia nigra compacta (SNc) and of the ventral tegmental area (VTA) that are degeneration-sensitive in PD. The genetic network(s) and mode(s) of action of Pitx3 in these mDA neurons remain poorly characterized. We hypothesized that, given their distinct neuronal identities, Pitx3-expressing neurons of SNc and VTA should differ in their Pitx3-controlled gene expression networks and this may involve subset-specific co-regulators. Expression profiling of purified mDA neuronal subsets indicates that Pitx3 regulates different sets of genes in SNc and VTA, such as activating the expression of primary cilium gene products specifically in VTA neurons. Interaction network analysis pointed to the participation of differentially expressed Lhx/Lmo family members in the modulation of Pitx3 action in SNc and VTA mDA neurons. Conversely, global binding patterns of Pitx3 on genomic DNA of human dopaminergic cells revealed that Pitx3 is often co-recruited to regions that foster the formation of GATA-bHLH-BRN complexes, which usually involve Lmo co-regulatory proteins. We focused on Lmo3 for its preferential expression in SNc neurons and demonstrated that it functions as a transcriptional co-activator of Pitx3 by enhancing its activity on genomic regulatory elements. In summary, we defined the SN and VTA-specific programs of Pitx3-dependent gene expression and identified Lmo3 as a SN-specific co-regulator of Pitx3-dependent transcription.
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Affiliation(s)
- Panojot Bifsha
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM), 110, avenue des Pins Ouest, Montréal, Québec, H2W 1R7, Canada.,Division of Experimental Medicine, McGill University, Montréal, Quebec, H3A 1A3, Canada
| | - Aurelio Balsalobre
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM), 110, avenue des Pins Ouest, Montréal, Québec, H2W 1R7, Canada
| | - Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM), 110, avenue des Pins Ouest, Montréal, Québec, H2W 1R7, Canada. .,Division of Experimental Medicine, McGill University, Montréal, Quebec, H3A 1A3, Canada.
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4
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Neuroprotective Transcription Factors in Animal Models of Parkinson Disease. Neural Plast 2015; 2016:6097107. [PMID: 26881122 PMCID: PMC4736191 DOI: 10.1155/2016/6097107] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/10/2015] [Accepted: 07/14/2015] [Indexed: 11/28/2022] Open
Abstract
A number of transcription factors, including En1/2, Foxa1/2, Lmx1a/b, Nurr1, Otx2, and Pitx3, with key roles in midbrain dopaminergic (mDA) neuron development, also regulate adult mDA neuron survival and physiology. Mouse models with targeted disruption of some of these genes display several features reminiscent of Parkinson disease (PD), in particular the selective and progressive loss of mDA neurons in the substantia nigra pars compacta (SNpc). The characterization of these animal models has provided valuable insights into various mechanisms of PD pathogenesis. Therefore, the dissection of the mechanisms and survival signalling pathways engaged by these transcription factors to protect mDA neuron from degeneration can suggest novel therapeutic strategies. The work on En1/2-mediated neuroprotection also highlights the potential of protein transduction technology for neuroprotective approaches in PD.
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Tang L, Wan P, Wang Y, Pan J, Wang Y, Chen B. Genetic association and interaction between the IRF5 and TYK2 genes and systemic lupus erythematosus in the Han Chinese population. Inflamm Res 2015; 64:817-24. [DOI: 10.1007/s00011-015-0865-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/17/2015] [Accepted: 08/04/2015] [Indexed: 10/23/2022] Open
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Pitx3 deficiency produces decreased dopamine signaling and induces motor deficits in Pitx3(-/-) mice. Neurobiol Aging 2015; 36:3314-3320. [PMID: 26363812 DOI: 10.1016/j.neurobiolaging.2015.08.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 11/23/2022]
Abstract
Midbrain dopamine (DA) neurons are involved in cognition, control of motor activity, and emotion-related behaviors. Degeneration of DA neurons particularly in the substantia nigra is a hallmark of Parkinson's disease. The homeobox transcription factor, Pitx3, plays a critical role in the development, function, and maintenance of midbrain DA neurons. We found that in young adult Pitx3-null mice, Pitx3(-/-), there was decreased tyrosine hydroxylase staining, indicating a loss of DA neurons particularly in the substantia nigra. In addition, fast-scan cyclic voltammetry and microdialysis assays of DA release indicated that the lack of Pitx3 caused a significant reduction of striatal DA release. Tonic DA release was impaired more significantly than the phasic DA release induced by burst firing of DA neurons. Furthermore, behavioral tests revealed that Pitx3(-/-) mice displayed abnormal motor activities, including impaired motor coordination and decreased locomotion. In summary, these data provide further evidence that Pitx3 is specifically required for DA-related function and, if impaired, Pitx3 could contribute during the pathogenesis of Parkinson's disease.
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Dang J, Shan S, Li J, Zhao H, Xin Q, Liu Y, Bian X, Liu Q. Gene-gene interactions of IRF5, STAT4, IKZF1 and ETS1 in systemic lupus erythematosus. ACTA ACUST UNITED AC 2014; 83:401-8. [PMID: 24697319 DOI: 10.1111/tan.12349] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 01/18/2014] [Accepted: 03/05/2014] [Indexed: 01/27/2023]
Abstract
Interferon (IFN) activation signaling and T helper 17 (Th17)-cell/B-cell regulation play a critical role in the pathogenesis of systemic lupus erythematosus (SLE). Several studies have provided convincing evidence that polymorphisms in IRF5, STAT4, IKZF1 and ETS1 from these pathways may be involved in SLE by affecting gene expression or epistasis. We analyzed the genetic interaction in known SLE susceptibility loci from the four genes in northern Han Chinese. A total of 946 northern Han Chinese participated in this study (370 unrelated SLE patients and 576 healthy controls). Subjects underwent genotyping for the single-nucleotide polymorphisms (SNPs) rs2004640 in IRF5, rs7574865 in STAT4, rs4917014 in IKZF1 and rs1128334 in ETS1 by use of a TaqMan SNP genotyping assay and direct sequencing. Gene-gene interaction analysis involved direct counting, multifactor dimensionality reduction (MDR) and linear regression analysis. SLE patients and controls differed in allele frequencies of rs7574865, rs1128334 (P < 0.001) and rs4917014 (P < 0.01). Direct counting revealed that the frequency of risk homozygote combinations was higher for SLE patients than controls (P < 0.01). Furthermore, 2-, 3- and 4-way gene-gene epistasis in SLE was confirmed by parametric methods and MDR analysis. Gene expression analysis partially supported the findings. Our study confirmed the association of the IFN pathway or Th17/B-cells and the pathogenesis of SLE, and gene-gene interaction in this pathway may increase the risk of SLE.
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Affiliation(s)
- J Dang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, Shandong University School of Medicine, Jinan, China; Department of Medical Genetics and Cell Biology, Ningxia Medical University, Yinchuan, China
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Qiu G, Fu C, Liang GH. Association between PITX3 promoter polymorphism and risk of Parkinson's disease: The impact of ethnicity and onset age. Neurosci Lett 2014; 561:128-33. [DOI: 10.1016/j.neulet.2013.12.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 12/21/2013] [Accepted: 12/23/2013] [Indexed: 10/25/2022]
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Jiménez-Jiménez FJ, García-Martín E, Alonso-Navarro H, Agúndez JA. PITX3 and Risk for Parkinson's Disease: A Systematic Review and Meta-Analysis. Eur Neurol 2013; 71:49-56. [DOI: 10.1159/000353981] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 06/23/2013] [Indexed: 12/13/2022]
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10
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Button KS, Ioannidis JPA, Mokrysz C, Nosek BA, Flint J, Robinson ESJ, Munafò MR. Power failure: why small sample size undermines the reliability of neuroscience. Nat Rev Neurosci 2013; 14:365-76. [PMID: 23571845 DOI: 10.1038/nrn3475] [Citation(s) in RCA: 3927] [Impact Index Per Article: 357.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A study with low statistical power has a reduced chance of detecting a true effect, but it is less well appreciated that low power also reduces the likelihood that a statistically significant result reflects a true effect. Here, we show that the average statistical power of studies in the neurosciences is very low. The consequences of this include overestimates of effect size and low reproducibility of results. There are also ethical dimensions to this problem, as unreliable research is inefficient and wasteful. Improving reproducibility in neuroscience is a key priority and requires attention to well-established but often ignored methodological principles.
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Luk KC, Rymar VV, van den Munckhof P, Nicolau S, Steriade C, Bifsha P, Drouin J, Sadikot AF. The transcription factor Pitx3 is expressed selectively in midbrain dopaminergic neurons susceptible to neurodegenerative stress. J Neurochem 2013; 125:932-43. [DOI: 10.1111/jnc.12160] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 12/17/2012] [Accepted: 01/09/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Kelvin C. Luk
- Department of Neurology and Neurosurgery; Montreal Neurological Institute; McGill University; Montreal Quebec Canada
| | - Vladimir V. Rymar
- Department of Neurology and Neurosurgery; Montreal Neurological Institute; McGill University; Montreal Quebec Canada
| | - Pepijn van den Munckhof
- Unité genetique moleculaire; Institut de recherches cliniques de Montreal; Montreal Quebec Canada
| | - Stefan Nicolau
- Department of Neurology and Neurosurgery; Montreal Neurological Institute; McGill University; Montreal Quebec Canada
| | - Claude Steriade
- Department of Neurology and Neurosurgery; Montreal Neurological Institute; McGill University; Montreal Quebec Canada
| | - Panojot Bifsha
- Unité genetique moleculaire; Institut de recherches cliniques de Montreal; Montreal Quebec Canada
| | - Jacques Drouin
- Unité genetique moleculaire; Institut de recherches cliniques de Montreal; Montreal Quebec Canada
| | - Abbas F. Sadikot
- Department of Neurology and Neurosurgery; Montreal Neurological Institute; McGill University; Montreal Quebec Canada
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Fuchs H, Gailus-Durner V, Neschen S, Adler T, Afonso LC, Aguilar-Pimentel JA, Becker L, Bohla A, Calzada-Wack J, Cohrs C, Dewert A, Fridrich B, Garrett L, Glasl L, Götz A, Hans W, Hölter SM, Horsch M, Hurt A, Janas E, Janik D, Kahle M, Kistler M, Klein-Rodewald T, Lengger C, Ludwig T, Maier H, Marschall S, Micklich K, Möller G, Naton B, Prehn C, Puk O, Rácz I, Räss M, Rathkolb B, Rozman J, Scheerer M, Schiller E, Schrewe A, Steinkamp R, Stöger C, Sun M, Szymczak W, Treise I, Vargas Panesso IL, Vernaleken AM, Willershäuser M, Wolff-Muscate A, Zeh R, Adamski J, Beckers J, Bekeredjian R, Busch DH, Eickelberg O, Favor J, Graw J, Höfler H, Höschen C, Katus H, Klingenspor M, Klopstock T, Neff F, Ollert M, Schulz H, Stöger T, Wolf E, Wurst W, Yildirim AÖ, Zimmer A, Hrabě de Angelis M. Innovations in phenotyping of mouse models in the German Mouse Clinic. Mamm Genome 2012; 23:611-22. [PMID: 22926221 PMCID: PMC3463795 DOI: 10.1007/s00335-012-9415-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 07/05/2012] [Indexed: 01/29/2023]
Abstract
Under the label of the German Mouse Clinic (GMC), a concept has been developed and implemented that allows the better understanding of human diseases on the pathophysiological and molecular level. This includes better understanding of the crosstalk between different organs, pleiotropy of genes, and the systemic impact of envirotypes and drugs. In the GMC, experts from various fields of mouse genetics and physiology, in close collaboration with clinicians, work side by side under one roof. The GMC is an open-access platform for the scientific community by providing phenotypic analysis in bilateral collaborations ("bottom-up projects") and as a partner and driver in international large-scale biology projects ("top-down projects"). Furthermore, technology development is a major topic in the GMC. Innovative techniques for primary and secondary screens are developed and implemented into the phenotyping pipelines (e.g., detection of volatile organic compounds, VOCs).
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Affiliation(s)
- Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg/Munich, Germany
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13
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Meta-analysis of association between PITX3 gene polymorphism and Parkinson's disease. J Neurol Sci 2012; 317:80-6. [DOI: 10.1016/j.jns.2012.02.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 01/14/2012] [Accepted: 02/23/2012] [Indexed: 11/17/2022]
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Derwińska K, Mierzewska H, Goszczańska A, Szczepanik E, Xia Z, Kuśmierska K, Tryfon J, Kutkowska-Kaźmierczak A, Bocian E, Mazurczak T, Obersztyn E, Stankiewicz P. Clinical improvement of the aggressive neurobehavioral phenotype in a patient with a deletion of PITX3 and the absence of L-DOPA in the cerebrospinal fluid. Am J Med Genet B Neuropsychiatr Genet 2012; 159B:236-42. [PMID: 22223473 DOI: 10.1002/ajmg.b.32020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 12/09/2011] [Indexed: 11/07/2022]
Abstract
The development of midbrain dopamine (DA) neurons is regulated by several transcription factors, including Nurr1, Wnt1, Lmx1a/1b, En1, En2, Foxa1, Foxa2, and Pitx3. PITX3 is an upstream co-activator of the TH (tyrosine hydroxylase) promoter. Pitx3(-/-) mice have a selective loss of dopaminergic neurons in the substantia nigra and ventral tegmental area, leading to the significantly reduced DA levels in the nigrostriatal pathway and in the dorsal striatum and manifest anomalous striatum-dependent cognitive impairment and neurobehavioral activity. Treatment with L-DOPA, dopamine, or dopamine receptor agonists in these mice reversed several of their sensorimotor impairments. Heterozygous missense mutations in PITX3 have been reported in patients with autosomal dominant congenital cataract and anterior segment (ocular) mesenchymal dysgenesis (ASMD) whereas homozygous missense mutations have been found in patients with microphthalmia and neurological impairment. Using a clinical oligonucleotide array comparative genomic hybridization (aCGH), we have identified an ∼317 kb hemizygous deletion in 10q24.32, involving PITX3 in a 17-year-old male with a Smith-Magenis syndrome-like phenotype, including mild intellectual impairment, sleep disturbance, hyperactivity, and aggressive and self-destructive behavior. Interestingly, no eye anomalies were found in our patient. Analysis of neurotransmitters in his cerebrospinal fluid revealed an absence of L-DOPA and significantly decreased levels of catecholamine metabolites. Importantly, L-DOPA treatment of our patient has led to mild mitigation of his aggressive behavior and mild improvement of his attention span, extended time periods of concentration, and better sleep.
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Affiliation(s)
- Katarzyna Derwińska
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
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PITX3 polymorphism is not associated with Parkinson's disease in a Chinese population. Neurosci Lett 2011; 505:260-2. [PMID: 22037506 DOI: 10.1016/j.neulet.2011.10.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 10/06/2011] [Accepted: 10/15/2011] [Indexed: 10/16/2022]
Abstract
Several studies have indicated that three PITX3 single nucleotide polymorphisms (SNPs), rs2281983, rs4919621 and rs3758549, are likely to be associated with Parkinson's disease (PD) in Caucasians. Some studies also suggested an age-of-onset effect. We recently reported that allele and genotype frequencies did not differ between late-onset PD (LOPD) patients and controls for all three SNPs. To extend the analysis to early-onset PD (EOPD) patients, and to test whether an age-of-onset effect exists in Chinese, we genotyped these SNPs in 290 Chinese EOPD patients using a ligase detection reaction (LDR). For all three SNPs, allele and genotype frequencies did not differ between total PD patients and controls, between LOPD patients and controls, between EOPD patients and controls, or between LOPD and EOPD patients. Our results suggest that these PITX3 SNPs do not contribute to the risk of developing PD in EOPD or LOPD in Chinese.
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