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Courbariaux M, De Santiago K, Dalmasso C, Danjou F, Bekadar S, Corvol JC, Martinez M, Szafranski M, Ambroise C. A Sparse Mixture-of-Experts Model With Screening of Genetic Associations to Guide Disease Subtyping. Front Genet 2022; 13:859462. [PMID: 35734430 PMCID: PMC9207464 DOI: 10.3389/fgene.2022.859462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/21/2022] [Indexed: 11/27/2022] Open
Abstract
Motivation: Identifying new genetic associations in non-Mendelian complex diseases is an increasingly difficult challenge. These diseases sometimes appear to have a significant component of heritability requiring explanation, and this missing heritability may be due to the existence of subtypes involving different genetic factors. Taking genetic information into account in clinical trials might potentially have a role in guiding the process of subtyping a complex disease. Most methods dealing with multiple sources of information rely on data transformation, and in disease subtyping, the two main strategies used are 1) the clustering of clinical data followed by posterior genetic analysis and 2) the concomitant clustering of clinical and genetic variables. Both of these strategies have limitations that we propose to address. Contribution: This work proposes an original method for disease subtyping on the basis of both longitudinal clinical variables and high-dimensional genetic markers via a sparse mixture-of-regressions model. The added value of our approach lies in its interpretability in relation to two aspects. First, our model links both clinical and genetic data with regard to their initial nature (i.e., without transformation) and does not require post-processing where the original information is accessed a second time to interpret the subtypes. Second, it can address large-scale problems because of a variable selection step that is used to discard genetic variables that may not be relevant for subtyping. Results: The proposed method was validated on simulations. A dataset from a cohort of Parkinson's disease patients was also analyzed. Several subtypes of the disease and genetic variants that potentially have a role in this typology were identified. Software availability: The R code for the proposed method, named DiSuGen, and a tutorial are available for download (see the references).
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Affiliation(s)
- Marie Courbariaux
- Université Paris-Saclay, CNRS, Université d’Évry, Laboratoire de Mathématiques et Modélisation d’Évry, Évry-Courcouronnes, France
| | - Kylliann De Santiago
- Université Paris-Saclay, CNRS, Université d’Évry, Laboratoire de Mathématiques et Modélisation d’Évry, Évry-Courcouronnes, France
| | - Cyril Dalmasso
- Université Paris-Saclay, CNRS, Université d’Évry, Laboratoire de Mathématiques et Modélisation d’Évry, Évry-Courcouronnes, France
| | - Fabrice Danjou
- Sorbonne Université, Paris Brain Institute–ICM, Inserm, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Neurology, Paris, France
| | - Samir Bekadar
- Sorbonne Université, Paris Brain Institute–ICM, Inserm, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Neurology, Paris, France
| | - Jean-Christophe Corvol
- Sorbonne Université, Paris Brain Institute–ICM, Inserm, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Neurology, Paris, France
| | - Maria Martinez
- Institut de Recherche en Santé Digestive, Inserm, CHU Purpan, Toulouse, France
| | - Marie Szafranski
- Université Paris-Saclay, CNRS, Université d’Évry, Laboratoire de Mathématiques et Modélisation d’Évry, Évry-Courcouronnes, France
- ENSIIE, Évry-Courcouronnes, France
| | - Christophe Ambroise
- Université Paris-Saclay, CNRS, Université d’Évry, Laboratoire de Mathématiques et Modélisation d’Évry, Évry-Courcouronnes, France
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Gómez-López S, Martínez-Silva AV, Montiel T, Osorio-Gómez D, Bermúdez-Rattoni F, Massieu L, Escalante-Alcalde D. Neural ablation of the PARK10 candidate Plpp3 leads to dopaminergic transmission deficits without neurodegeneration. Sci Rep 2016; 6:24028. [PMID: 27063549 PMCID: PMC4827058 DOI: 10.1038/srep24028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/18/2016] [Indexed: 01/02/2023] Open
Abstract
Parkinson’s disease (PD) is a multifactorial neurodegenerative disorder, characterised by the progressive loss of midbrain dopaminergic neurons and a variety of motor symptoms. The gene coding for the phospholipid phosphatase 3, PLPP3 (formerly PPAP2B or LPP3), maps within the PARK10 locus, a region that has been linked with increased risk to late-onset PD. PLPP3 modulates the levels of a range of bioactive lipids controlling fundamental cellular processes within the central nervous system. Here we show that PLPP3 is enriched in astroglial cells of the adult murine ventral midbrain. Conditional inactivation of Plpp3 using a Nestin::Cre driver results in reduced mesencephalic levels of sphingosine-1-phosphate receptor 1 (S1P1), a well-known mediator of pro-survival responses. Yet, adult PLPP3-deficient mice exhibited no alterations in the number of dopaminergic neurons or in the basal levels of striatal extracellular dopamine (DA). Potassium-evoked DA overflow in the striatum, however, was significantly decreased in mutant mice. Locomotor evaluation revealed that, although PLPP3-deficient mice exhibit motor impairment, this is not progressive or responsive to acute L-DOPA therapy. These findings suggest that disruption of Plpp3 during early neural development leads to dopaminergic transmission deficits in the absence of nigrostriatal degeneration, and without causing an age-related locomotor decline consistent with PD.
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Affiliation(s)
- Sandra Gómez-López
- Instituto de Fisiología Celular, División de Neurociencias, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Ana Valeria Martínez-Silva
- Instituto de Fisiología Celular, División de Neurociencias, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Teresa Montiel
- Instituto de Fisiología Celular, División de Neurociencias, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Daniel Osorio-Gómez
- Instituto de Fisiología Celular, División de Neurociencias, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Federico Bermúdez-Rattoni
- Instituto de Fisiología Celular, División de Neurociencias, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Lourdes Massieu
- Instituto de Fisiología Celular, División de Neurociencias, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Diana Escalante-Alcalde
- Instituto de Fisiología Celular, División de Neurociencias, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
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Poole E, Kuan WL, Barker R, Sinclair J. The human cytomegalovirus non-coding Beta2.7 RNA as a novel therapeutic for Parkinson's disease--Translational research with no translation. Virus Res 2015; 212:64-9. [PMID: 26003955 DOI: 10.1016/j.virusres.2015.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/01/2015] [Accepted: 05/08/2015] [Indexed: 10/23/2022]
Abstract
Human cytomegalovirus (HCMV) encodes abundant numbers of microRNAs (miRNAs) and other non-coding RNAs (ncRNAs) whose functions are presently under intense investigation. In this chapter, we discuss the function of one of the more well characterised virus-encoded ncRNAs, derived from the viral major early gene (Beta2.7). This RNA plays an anti-apoptotic role during infection by directly interacting with mitochondrial complex I to help maintain high levels of ATP production and by preventing the stress induced re-localisation of retinoid/interferon-induced mortality-19 protein, GRIM-19. We then go on to describe how an 800 nucleotide sub-domain of the Beta2.7 transcript, p137, has been exploited in the development of a novel therapeutic for the treatment of Parkinson's disease.
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Affiliation(s)
- Emma Poole
- Department of Medicine, Addenbrooke's Hospital, Hills Road, England CB2 0QQ UK.
| | - Wei Li Kuan
- Department of Neurology, Addenbrooke's Hospital, Hills Road, England CB2 0QQ, UK
| | - Roger Barker
- Department of Neurology, Addenbrooke's Hospital, Hills Road, England CB2 0QQ, UK
| | - John Sinclair
- Department of Medicine, Addenbrooke's Hospital, Hills Road, England CB2 0QQ UK.
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Na SJ, Lee JH, Kim SW, Kim DS, Shon EH, Park HJ, Shin HY, Kim SM, Choi YC. Whole-genome analysis in Korean patients with autoimmune myasthenia gravis. Yonsei Med J 2014; 55:660-8. [PMID: 24719132 PMCID: PMC3990093 DOI: 10.3349/ymj.2014.55.3.660] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/24/2013] [Accepted: 08/23/2013] [Indexed: 11/27/2022] Open
Abstract
PURPOSE The underlying cause of myasthenia gravis (MG) is unknown, although it likely involves a genetic component. However, no common genetic variants have been unequivocally linked to autoimmune MG. We sought to identify the genetic variants associated with an increased or decreased risk of developing MG in samples from a Korean Multicenter MG Cohort. MATERIALS AND METHODS To determine new genetic targets related to autoimmune MG, a whole genome-based single nucleotide polymorphisms (SNP) analysis was conducted using an Axiom™ Genome-Wide ASI 1 Array, comprising 598375 SNPs and samples from 109 MG patients and 150 neurologically normal controls. RESULTS In total, 641 SNPs from five case-control associations showed p-values of less than 10⁻⁵. From regional analysis, we selected seven candidate genes (RYR3, CACNA1S, SLAMF1, SOX5, FHOD3, GABRB1, and SACS) for further analysis. CONCLUSION The present study suggests that a few genetic polymorphisms, such as in RYR3, CACNA1S, and SLAMF1, might be related to autoimmune MG. Our findings also encourage further studies, particularly confirmatory studies with larger samples, to validate and analyze the association between these SNPs and autoimmune MG.
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Affiliation(s)
- Sang-Jun Na
- Department of Neurology, Konyang University College of Medicine, Daejeon, Korea
| | - Ji Hyun Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea
| | - So Won Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea
| | - Dae-Seong Kim
- Department of Neurology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Eun Hee Shon
- Department of Neurology, Chungnam University Hospital, Daejeon, Korea
| | - Hyung Jun Park
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Min Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - Young-Chul Choi
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
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Chen Y, Gondro C, Quinn K, Herd RM, Parnell PF, Vanselow B. Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake. Anim Genet 2011; 42:475-90. [DOI: 10.1111/j.1365-2052.2011.02182.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ragland M, Hutter C, Zabetian C, Edwards K. Association between the ubiquitin carboxyl-terminal esterase L1 gene (UCHL1) S18Y variant and Parkinson's Disease: a HuGE review and meta-analysis. Am J Epidemiol 2009; 170:1344-57. [PMID: 19864305 PMCID: PMC2778765 DOI: 10.1093/aje/kwp288] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 08/13/2009] [Indexed: 01/26/2023] Open
Abstract
The ubiquitin carboxyl-terminal esterase L1 gene, UCHL1, located on chromosome 4p14, has been studied as a potential candidate gene for Parkinson's disease risk. The authors conducted a Human Genome Epidemiology review and meta-analysis of published case-control studies of the UCHL1 S18Y variant and Parkinson's disease in Asian and Caucasian samples. The meta-analysis of studies in populations of Asian ancestry showed a statistically significant association between the Y allele and reduced risk of Parkinson's disease under a recessive model (odds ratio (OR) for YY vs. SY + SS = 0.79, 95% confidence interval (CI): 0.67, 0.94; P = 0.006). For a dominant model, the association was not significant in Asian populations (OR for YY + SY vs. SS = 0.88, 95% CI: 0.68, 1.14; P = 0.33). For populations of European ancestry, the meta-analysis showed a significant association between the Y allele and decreased risk of Parkinson's disease under a dominant model (OR = 0.89, 95% CI: 0.81, 0.98; P = 0.02) but not under a recessive model (OR = 0.92, 95% CI: 0.66, 1.30; P = 0.65). Using the Venice criteria, developed by the Human Genome Epidemiology Network Working Group on the assessment of cumulative evidence, the authors concluded that moderate evidence exists for an association between the S18Y variant and Parkinson's disease.
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Affiliation(s)
| | | | | | - Karen Edwards
- Correspondence to Dr. Karen Edwards, University of Washington, Center for Genomics and Public Health, Box 354921, 6200 NE 74th Street, Building 29, Suite 250, Seattle, WA 98115 (e-mail: )
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Fernández-Santiago R, Sharma M, Berg D, Illig T, Anneser J, Meyer T, Ludolph A, Gasser T. No evidence of association of FLJ10986 and ITPR2 with ALS in a large German cohort. Neurobiol Aging 2009; 32:551.e1-4. [PMID: 19464757 DOI: 10.1016/j.neurobiolaging.2009.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 04/10/2009] [Accepted: 04/19/2009] [Indexed: 12/13/2022]
Abstract
A recent genome-wide association study (GWAS) found significant association of six single nucleotide polymorphisms (SNPs) in the gene FLJ10986 with sporadic amyotrophic lateral sclerosis (SALS). Another independent GWAS reported significant association of one SNP in the gene inositol 1,4,5-triphosphate receptor 2 (ITPR2) with SALS. These studies provided conflicting results. We examined the six most significant SNPs in FLJ10986 and one SNP in ITPR2 in a large cohort consisting of 595 SALS cases and 681 controls ascertained from Germany. Our results did not provide evidence for the association of these SNPs with SALS, suggesting a possible population-specific effect for FLJ10986 and ITPR2 that do not modulate the risk for SALS in the German population.
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Affiliation(s)
- Rubén Fernández-Santiago
- Department for Neurodegenerative Disorders, Hertie Institute for Clinical Brain Research, Eberhard-Karls University, Otfried-Müller-Strasse 27, 72076, Tuebingen, Germany
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Srinivasan BS, Chen J, Cheng C, Conti D, Duan S, Fridley BL, Gu X, Haines JL, Jorgenson E, Kraja A, Lasky-Su J, Li L, Rodin A, Wang D, Province M, Ritchie MD. Methods for analysis in pharmacogenomics: lessons from the Pharmacogenetics Research Network Analysis Group. Pharmacogenomics 2009; 10:243-51. [PMID: 19207025 DOI: 10.2217/14622416.10.2.243] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Each year, the Pharmacogenetics Research Network (PGRN) holds an analysis workshop for the members of the PGRN to share new methodologies, study design approaches and to discuss real data applications. This event is closed to members of the PGRN, but the methods presented are relevant to others conducting pharmacogenomics research. This special report describes many of the novel approaches discussed at the workshop and provides a resource for investigators in the field performing pharmacogenomics data analysis. While the focus is pharmacogenomics, the methods discussed are far ranging and have relevance to all types of genetic association studies: identifying noncoding variants and tag-SNPs, haplotype analysis, multivariate techniques, quantitative trait analysis, gene-gene and gene-environment interactions, and genome-wide association studies. The goal is to introduce readers to the topics discussed at the workshop and provide a direction for future development of analysis tools and methods for analysis of pharmacogenomic data.
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Srinivasan BS, Doostzadeh J, Absalan F, Mohandessi S, Jalili R, Bigdeli S, Wang J, Mahadevan J, Lee CLG, Davis RW, William Langston J, Ronaghi M. Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson disease. Hum Mutat 2009; 30:228-38. [PMID: 18853455 PMCID: PMC2793088 DOI: 10.1002/humu.20840] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
It is quickly becoming apparent that situating human variation in a pathway context is crucial to understanding its phenotypic significance. Toward this end, we have developed a general method for finding pathways associated with traits that control for pathway size. We have applied this method to a new whole genome survey of coding SNP variation in 187 patients afflicted with Parkinson disease (PD) and 187 controls. We show that our dataset provides an independent replication of the axon guidance association recently reported by Lesnick et al. [PLoS Genet 2007;3:e98], and also indicates that variation in the ubiquitin-mediated proteolysis and T-cell receptor signaling pathways may predict PD susceptibility. Given this result, it is reasonable to hypothesize that pathway associations are more replicable than individual SNP associations in whole genome association studies. However, this hypothesis is complicated by a detailed comparison of our dataset to the second recent PD association study by Fung et al. [Lancet Neurol 2006;5:911–916]. Surprisingly, we find that the axon guidance pathway does not rank at the very top of the Fung dataset after controlling for pathway size. More generally, in comparing the studies, we find that SNP frequencies replicate well despite technologically different assays, but that both SNP and pathway associations are globally uncorrelated across studies. We thus have a situation in which an association between axon guidance pathway variation and PD has been found in 2 out of 3 studies. We conclude by relating this seeming inconsistency to the molecular heterogeneity of PD, and suggest future analyses that may resolve such discrepancies.
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Moore SS, Mujibi FD, Sherman EL. Molecular basis for residual feed intake in beef cattle1. J Anim Sci 2009; 87:E41-7. [DOI: 10.2527/jas.2008-1418] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wider C, Lincoln SJ, Heckman MG, Diehl NN, Stone JT, Haugarvoll K, Aasly JO, Gibson JM, Lynch T, Rajput A, Rajput ML, Uitti RJ, Wszolek ZK, Farrer MJ, Ross OA. Phactr2 and Parkinson's disease. Neurosci Lett 2009; 453:9-11. [PMID: 19429005 DOI: 10.1016/j.neulet.2009.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Revised: 01/14/2009] [Accepted: 02/04/2009] [Indexed: 11/18/2022]
Abstract
Attempts at replicating the first genome-wide association study (GWAS) in Parkinson's disease (PD) have not successfully identified genetic risk factors. The present study reevaluates data from the first GWAS and focuses on the SNP (rs11155313, located in the Phactr2 gene) with the lowest P-value in the Tier 2 patient-control series. We employed four case-control series to examine the nominated SNP rs11155313 and identified association in US (OR: 1.39, P=0.032), Canadian (OR: 1.41, P=0.014) and Irish (OR: 1.44, P=0.034) patient-control series, but not in the Norwegian series (OR: 1.15, P=0.27). When combining all four series the observed trend was statistically significant (OR: 1.30, P<0.001). This study shows that reappraisal of publicly available results of GWAS may help nominate new risk factors for PD.
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Affiliation(s)
- Christian Wider
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
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Abstract
BACKGROUND During the past decade, the genetic causes of monogenic forms of disease have been successfully defined; this work has helped the progression of basic scientific investigation into many disorders, and has helped to characterise several molecular biological processes. An important goal of genetic research is to extend this work and define genetic risk factor loci for complex disorders. The aim is for these data not only to offer further basic understanding of the disease process, but also to provide the opportunity to obtain genetic risk assessments that could be generalised to the public. RECENT DEVELOPMENTS The development of resources such as the Human Genome Project and the International Human Haplotype Map Project, coupled with technological advances in ultra-high-throughput genotyping, have provided the basis for genome-wide association studies (GWAS). This approach has been successful for several complex disorders in a short time. Although GWAS are still a new method, these studies have been used for a small number of neurological disorders and, despite varied results for these conditions, GWAS can usefully show the power and limitations of this approach. WHERE NEXT?: GWAS have the potential to show and emphasise common genetic variability associated with disease. However, a challenge of this approach is that large sample series and considerable resources are required. One important consideration will be the interpretation of the results of GWAS in a clinically meaningful way and to discern the implications for all therapy areas, including neurological disorders; this challenge will require specialised skills and resources from both the medical and the scientific communities.
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Affiliation(s)
- Javier Simón-Sánchez
- Molecular Genetics Section, Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Abstract
Herein, we investigate whether single-nucleotide polymorphisms (SNPs) across the PARK10 locus are associated with susceptibility to Parkinson's disease (PD) or age at onset (AAO) of disease. One hundred and eighty-eight SNPs were genotyped across the PARK10 locus in 180 PD patients and 180 controls from central Norway (stage 1). We then used the linkage disequilibrium (LD) structure from stage 1 to select 75 SNPs for genotyping in 186 patients and 186 controls from Ireland (stage 2). Nineteen SNPs were selected from this and previous studies for follow-up in an extended Norwegian series (530 patients and 1142 controls), the Irish series and a US series (221 patients and 221 controls) (stage 3). After correction for multiple testing, markers within ubiquitin specific peptidase 24 (USP24) are significantly associated with PD within Norwegian, Irish, and US series combined (rs13312: odds ratio (OR) 0.78, P<0.001; rs487230: OR 0.80, P=0.001). Independently, the association for rs13312 is strongest in the extended Norwegian series (OR 0.76, P=0.005), although not significant after correction for multiple testing (P< or =0.003 is considered significant). ORs in the Irish series are almost identical, and a similar but a weaker effect was observed for the US series. No marker showed consistent association with AAO. Our data indicate that genetic variability in USP24 is associated with PD. Although our work extends and confirms a previous report, the observed effect size does not explain the PARK10 linkage peak.
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Abstract
During the last years, remarkable progress in our understanding of molecular genetic mechanisms underlying movement disorders has been achieved. The successes of linkage studies, followed by positional cloning, have dominated the last decade and several genes underlying monogenic disorders have been discovered. The pathobiological understanding garnered from these mutations has laid the foundation for much of the search for genetic loci that confer risk for, rather than cause, disease. With the introduction of whole genome association studies as a novel tool to investigate genetic variation underlying common, complex diseases, a new era in neurogenomics has just begun. As the field rapidly moves forward several new challenges and critical questions in clinical care have to be addressed. In this review, we summarize recent advances in the discovery of susceptibility loci underlying major movement disorders, explain the newest methodologies and tools employed for finding and characterizing genes and discuss how insights into the molecular genetic basis of neurological disorders will impact therapeutic concepts in patient care.
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Affiliation(s)
- Sonja Scholz
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Department of Molecular Neuroscience, Institute of Neurology, Queen Square House, London, United Kingdom
| | - Andrew Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
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15
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Li Y, Rowland C, Xiromerisiou G, Lagier RJ, Schrodi SJ, Dradiotis E, Ross D, Bui N, Catanese J, Aggelakis K, Grupe A, Hadjigeorgiou G. Neither replication nor simulation supports a role for the axon guidance pathway in the genetics of Parkinson's disease. PLoS One 2008; 3:e2707. [PMID: 18628988 PMCID: PMC2442653 DOI: 10.1371/journal.pone.0002707] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 06/17/2008] [Indexed: 11/25/2022] Open
Abstract
Susceptibility to sporadic Parkinson's disease (PD) is thought to be influenced by both genetic and environmental factors and their interaction with each other. Statistical models including multiple variants in axon guidance pathway genes have recently been purported to be capable of predicting PD risk, survival free of the disease and age at disease onset; however the specific models have not undergone independent validation. Here we tested the best proposed risk panel of 23 single nucleotide polymorphisms (SNPs) in two PD sample sets, with a total of 525 cases and 518 controls. By single marker analysis, only one marker was significantly associated with PD risk in one of our sample sets (rs6692804: P = 0.03). Multi-marker analysis using the reported model found a mild association in one sample set (two sided P = 0.049, odds ratio for each score change = 1.07) but no significance in the other (two sided P = 0.98, odds ratio = 1), a stark contrast to the reported strong association with PD risk (P = 4.64×10−38, odds ratio as high as 90.8). Following a procedure similar to that used to build the reported model, simulated multi-marker models containing SNPs from randomly chosen genes in a genome wide PD dataset produced P-values that were highly significant and indistinguishable from similar models where disease status was permuted (3.13×10−23 to 4.90×10−64), demonstrating the potential for overfitting in the model building process. Together, these results challenge the robustness of the reported panel of genetic markers to predict PD risk in particular and a role of the axon guidance pathway in PD genetics in general.
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Affiliation(s)
- Yonghong Li
- Celera, Alameda, California, United States of America.
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García-Martín E, Ayuso P, Luengo A, Martínez C, Agúndez JA. Genetic variability of histamine receptors in patients with Parkinson's disease. BMC MEDICAL GENETICS 2008; 9:15. [PMID: 18366640 PMCID: PMC2292154 DOI: 10.1186/1471-2350-9-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 03/17/2008] [Indexed: 11/10/2022]
Abstract
Background Changes in the density and expression of histamine receptors (HRH) have been detected in Parkinson's disease (PD) patients, and HRH antagonists bring about improvements in motor and other symptoms, thus suggesting that HRH play a role in the clinical response of PD patients. This study is aimed to analyse polymorphic variations of HRH in patients with PD. Methods Leukocytary DNA from 195 PD patients and a control group of 231 unrelated healthy individuals was studied for the nonsynonymous HRH1Leu449Ser and the promoter HRH2G-1018A polymorphisms by using amplification-restriction analyses. Results The HRH1Leu449Ser amino acid substitution was identified in two women with late-onset PD whereas it was not observed among healthy subjects. The HRH2G-1018A polymorphism was observed with allele frequencies = 3.59 (95% CI = 1.74–5.44) and 5.0 (95% CI = 3.00–6.96) for patients with PD and healthy controls, respectively. These frequencies were independent of gender and age of onset of the disease. Multiple comparison analyses revealed that differences were not statistically significant. Conclusion These results indicate that the polymorphisms analyzed are not a major risk factor for PD, although the HRH1Leu449Ser amino acid substitution might be related to PD.
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Affiliation(s)
- Elena García-Martín
- Department of Biochemistry and Molecular Biology, School of Biological Sciences, University of Extremadura, Badajoz, Spain.
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Seng KC, Seng CK. The success of the genome-wide association approach: a brief story of a long struggle. Eur J Hum Genet 2008; 16:554-64. [PMID: 18285837 DOI: 10.1038/ejhg.2008.12] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The genome-wide association approach has been the most powerful and efficient study design thus far in identifying genetic variants that are associated with complex human diseases. This approach became feasible as the result of several key advancements in genetic knowledge, genotyping technologies, statistical analysis algorithms and the availability of large collections of cases and controls. With all these necessary tools in hand, many genome-wide association studies were recently completed, and many more studies which will explore the genetic basis of various complex diseases and quantitative traits are soon to come. This approach has started to reap the fruits of its labor over the past several months. Publications of genome-wide association studies in several complex diseases such as inflammatory bowel disease, type-2 diabetes, breast cancer and prostate cancer have been abundant in the first half of this year. The aims of this review are firstly, to provide a timely summary for most of the genome-wide association studies that have been published until June/July 2007 and secondly, to evaluate to what extent these results have been validated in subsequent replication studies.
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Affiliation(s)
- Ku Chee Seng
- Center for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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Sharma M, Lichtner P, Kruger R, Berg D, Schulte C, Illig T, Riess O, Gasser T. Further delineation of the association signal on chromosome 5 from the first whole genome association study in Parkinson's disease. Neurobiol Aging 2008; 30:1706-9. [PMID: 18280617 DOI: 10.1016/j.neurobiolaging.2007.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 08/29/2007] [Accepted: 12/14/2007] [Indexed: 10/22/2022]
Abstract
A recently published whole genome association study showed the involvement of 13 SNPs in the pathogenesis of Parkinson disease (PD). We performed a replication study to assess their involvement in our sporadic cohort consisting of 663 cases and 1002 controls ascertained from Germany. One of the previously reported SNP, rs7723605, showed evidence of association (p value 0.04) in our sample. We further refined the signal by genotyping additional 22 SNPs around SNP rs7723605. Our refinement analysis, however, did not provide evidence for association in our sample after adjusting for multiple testing by permutation procedure. In conclusion, our study did not lend support to the finding that the reported SNPs are directly influencing the susceptibility to sporadic form of PD at least in our population.
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Affiliation(s)
- Manu Sharma
- Hertie-Institute for Clinical Brain Research, Department of Neurodegenerative Diseases, University of Tuebingen, Hoppe-Seyler Strasse 3, 72076 Tuebingen, Germany
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Kraft P, Cox DG. Study Designs for Genome‐Wide Association Studies. GENETIC DISSECTION OF COMPLEX TRAITS 2008; 60:465-504. [DOI: 10.1016/s0065-2660(07)00417-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Lesnick TG, Papapetropoulos S, Mash DC, Ffrench-Mullen J, Shehadeh L, de Andrade M, Henley JR, Rocca WA, Ahlskog JE, Maraganore DM. A genomic pathway approach to a complex disease: axon guidance and Parkinson disease. PLoS Genet 2007; 3:e98. [PMID: 17571925 PMCID: PMC1904362 DOI: 10.1371/journal.pgen.0030098] [Citation(s) in RCA: 283] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Accepted: 05/02/2007] [Indexed: 11/18/2022] Open
Abstract
While major inroads have been made in identifying the genetic causes of rare Mendelian disorders, little progress has been made in the discovery of common gene variations that predispose to complex diseases. The single gene variants that have been shown to associate reproducibly with complex diseases typically have small effect sizes or attributable risks. However, the joint actions of common gene variants within pathways may play a major role in predisposing to complex diseases (the paradigm of complex genetics). The goal of this study was to determine whether polymorphism in a candidate pathway (axon guidance) predisposed to a complex disease (Parkinson disease [PD]). We mined a whole-genome association dataset and identified single nucleotide polymorphisms (SNPs) that were within axon-guidance pathway genes. We then constructed models of axon-guidance pathway SNPs that predicted three outcomes: PD susceptibility (odds ratio = 90.8, p = 4.64 × 10−38), survival free of PD (hazards ratio = 19.0, p = 5.43 × 10−48), and PD age at onset (R2 = 0.68, p = 1.68 × 10−51). By contrast, models constructed from thousands of random selections of genomic SNPs predicted the three PD outcomes poorly. Mining of a second whole-genome association dataset and mining of an expression profiling dataset also supported a role for many axon-guidance pathway genes in PD. These findings could have important implications regarding the pathogenesis of PD. This genomic pathway approach may also offer insights into other complex diseases such as Alzheimer disease, diabetes mellitus, nicotine and alcohol dependence, and several cancers. Complex diseases are common disorders that are believed to have many causes. Examples include Alzheimer disease, diabetes mellitus, nicotine and alcohol dependence, and several cancers. This study represents a paradigm shift from single gene to pathway studies of complex diseases. We present the example of Parkinson disease (PD) and a complex array of chemical signals that wires the brain during fetal development (the axon guidance pathway). We mined a dataset that studied hundreds of thousands of DNA variations (single nucleotide polymorphisms [SNPs]) in persons with and without PD and identified SNPs that were assigned to axon-guidance pathway genes. We then identified sets of SNPs that were highly predictive of PD susceptibility, survival free of PD, and age at onset of PD. The effect sizes and the statistical significance observed for the pathway were far greater than for any single gene. We validated our findings for the pathway using a second SNP dataset for PD and also a dataset for PD that studied RNA variations. There is prior evidence that the axon guidance pathway might play a role in other brain disorders (e.g., Alzheimer disease, Tourette syndrome, dyslexia, epilepsy, and schizophrenia). A genomic pathway approach may lead to important breakthroughs for many complex diseases.
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Affiliation(s)
- Timothy G Lesnick
- Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Spiridon Papapetropoulos
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Deborah C Mash
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | | | - Lina Shehadeh
- Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Mariza de Andrade
- Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - John R Henley
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Walter A Rocca
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - J. Eric Ahlskog
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Demetrius M Maraganore
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
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Nonsynonymous Polymorphisms of Histamine-Metabolising Enzymes in Patients with Parkinson’s Disease. Neuromolecular Med 2007; 10:10-6. [DOI: 10.1007/s12017-007-8017-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2007] [Indexed: 11/25/2022]
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Goris A, Williams-Gray CH, Clark GR, Foltynie T, Lewis SJG, Brown J, Ban M, Spillantini MG, Compston A, Burn DJ, Chinnery PF, Barker RA, Sawcer SJ. Tau and alpha-synuclein in susceptibility to, and dementia in, Parkinson's disease. Ann Neurol 2007; 62:145-53. [PMID: 17683088 DOI: 10.1002/ana.21192] [Citation(s) in RCA: 228] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVE Parkinson's disease (PD) is a neurodegenerative condition that typically presents as a movement disorder but is known to be associated with variable degrees of cognitive impairment including dementia. We investigated the genetic basis of susceptibility to and cognitive heterogeneity of this disease. METHODS In 659 PD patients, 109 of which were followed up for 3.5 years from diagnosis, and 2,176 control subjects, we studied candidate genes involved in protein aggregation and inclusion body formation, the pathological hallmark of parkinsonism: microtubule-associated protein tau (MAPT), glycogen synthase kinase-3beta (GSK3B), and alpha-synuclein (SNCA). RESULTS We observed that cognitive decline and the development of PD dementia are strongly associated (p = 10(-4)) with the inversion polymorphism containing MAPT. We also found a novel synergistic interaction between the MAPT inversion polymorphism and the single nucleotide polymorphism rs356219 from the 3' region of SNCA. In our data, carrying a risk genotype at either of these loci marginally increases the risk for development of PD, whereas carrying the combination of risk genotypes at both loci approximately doubles the risk for development of the disease (p = 3 x 10(-6)). INTERPRETATION Our data support the hypothesis that tau and alpha-synuclein are involved in shared or converging pathways in the pathogenesis of PD, and suggest that the tau inversion influences the development of cognitive impairment and dementia in patients with idiopathic PD. These findings have potentially important implications for understanding the interface between tau and alpha-synuclein pathways in neurodegenerative disorders and for unraveling the biological basis for cognitive impairment and dementia in PD.
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Affiliation(s)
- An Goris
- Department of Clinical Neurosciences (Neurology Unit), University of Cambridge, Cambridge, United Kingdom.
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Tong L, Thompson E. Multilocus lod scores in large pedigrees: combination of exact and approximate calculations. Hum Hered 2007; 65:142-53. [PMID: 17934317 PMCID: PMC2701716 DOI: 10.1159/000109731] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 06/08/2007] [Indexed: 01/23/2023] Open
Abstract
To detect the positions of disease loci, lod scores are calculated at multiple chromosomal positions given trait and marker data on members of pedigrees. Exact lod score calculations are often impossible when the size of the pedigree and the number of markers are both large. In this case, a Markov Chain Monte Carlo (MCMC) approach provides an approximation. However, to provide accurate results, mixing performance is always a key issue in these MCMC methods. In this paper, we propose two methods to improve MCMC sampling and hence obtain more accurate lod score estimates in shorter computation time. The first improvement generalizes the block-Gibbs meiosis (M) sampler to multiple meiosis (MM) sampler in which multiple meioses are updated jointly, across all loci. The second one divides the computations on a large pedigree into several parts by conditioning on the haplotypes of some 'key' individuals. We perform exact calculations for the descendant parts where more data are often available, and combine this information with sampling of the hidden variables in the ancestral parts. Our approaches are expected to be most useful for data on a large pedigree with a lot of missing data.
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Affiliation(s)
- Liping Tong
- Department of Statistics, University of Washington, Seattle, WA 98195-4322, USA.
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Li YJ, Deng J, Mayhew GM, Grimsley JW, Huo X, Vance JM. Investigation of the PARK10 Gene in Parkinson Disease. Ann Hum Genet 2007; 71:639-47. [PMID: 17388942 DOI: 10.1111/j.1469-1809.2007.00353.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Two recent association mapping studies in Parkinson disease (PD) reported three candidate genes for the PARK10 locus: EIF2B3 as a modifier of age-at-onset of PD (min P= 0.0004) and HIVEP3 as a PD risk gene (P < or = 0.006) (Oliveira et al. 2005); and LOC200008 (CDCP2) identified by the whole genome association (WGA) study of PD of Maraganore et al. (2005). However, evaluation of the on-line PD WGA results revealed two significant SNPs in HIVEP3 in the two datasets, Tier 1 and Tier 2, used by Maraganore et al. (P < or = 0.008 for Tier 1 and P=0.03 for Tier 2 dataset). Here, we revisited both the HIVEP3 and CDCP2 loci by examining 47 SNPs, mostly tagging, in an expanded PD family dataset (293 multiplex and 467 singleton families). A discordant sibpair (DSP) dataset (one DSP per family), with similar data structure as the WGA Tier 1 dataset, was also tested. We confirmed our and other previous negative findings for CDCP2. However, five significant SNPs in HIVEP3 (min P=0.004) were observed, although the two significant HIVEP3 SNPs from the PD WGA study were not significant in our datasets. Even though the sets of significant HIVEP3 markers differ between studies, these findings strongly support HIVEP3 as a candidate for PARK10. Further testing of HIVEP3 by other groups is encouraged.
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Affiliation(s)
- Y J Li
- Department of Medicine and Center for Human Genetics, Duke University Medical Center, Durham, NC 27710, USA.
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26
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Bogaerts V, Engelborghs S, Kumar-Singh S, Goossens D, Pickut B, van der Zee J, Sleegers K, Peeters K, Martin JJ, Del-Favero J, Gasser T, Dickson DW, Wszolek ZK, De Deyn PP, Theuns J, Van Broeckhoven C. A novel locus for dementia with Lewy bodies: a clinically and genetically heterogeneous disorder. ACTA ACUST UNITED AC 2007; 130:2277-91. [PMID: 17681982 DOI: 10.1093/brain/awm167] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Dementia with Lewy bodies (DLB) represents the second most frequent type of neurodegenerative dementia in the elderly. Although most patients have sporadic DLB, a limited number of DLB families have been described, suggesting that genetic factors may contribute to DLB pathogenesis. Here, we describe a three-generation Belgian family with prominent dementia and parkinsonism, consistent with a diagnosis of DLB, that was autopsy confirmed for the index patient. In a genome-wide scan and subsequent finemapping of candidate loci we obtained significant linkage to 2q35-q36 (Z = 3.01 at D2S1242). Segregation analysis defined a candidate region of 9.2 Mb between D2S433 and chr2q36.3-8, adjacent to the previously reported PARK11 locus. In addition, haplotype sharing studies in another DLB family of close geographical origin with similar clinical and neuropathological features highlighted the specificity of a 2q35-q36 haplotype harbouring a pathogenic mutation that causes DLB in the Belgian family. So far, extensive sequence analysis of five candidate genes within the 2q35-q36 region has not revealed a disease-causing mutation. Together, our data re-emphasize the genetic heterogeneity of DLB, and strongly support the existence of a gene for familial DLB on 2q35-q36. Once identified this will be the first novel causal gene for DLB and can be expected to open new avenues for biological studies of the disease process.
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Affiliation(s)
- Veerle Bogaerts
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Institute Born-Bunge, Antwerpen, Belgium
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Chanock SJ, Manolio T, Boehnke M, Boerwinkle E, Hunter DJ, Thomas G, Hirschhorn JN, Abecasis G, Altshuler D, Bailey-Wilson JE, Brooks LD, Cardon LR, Daly M, Donnelly P, Fraumeni JF, Freimer NB, Gerhard DS, Gunter C, Guttmacher AE, Guyer MS, Harris EL, Hoh J, Hoover R, Kong CA, Merikangas KR, Morton CC, Palmer LJ, Phimister EG, Rice JP, Roberts J, Rotimi C, Tucker MA, Vogan KJ, Wacholder S, Wijsman EM, Winn DM, Collins FS. Replicating genotype–phenotype associations. Nature 2007; 447:655-60. [PMID: 17554299 DOI: 10.1038/447655a] [Citation(s) in RCA: 1013] [Impact Index Per Article: 59.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Barendse W, Reverter A, Bunch RJ, Harrison BE, Barris W, Thomas MB. A validated whole-genome association study of efficient food conversion in cattle. Genetics 2007; 176:1893-905. [PMID: 17507676 PMCID: PMC1931545 DOI: 10.1534/genetics.107.072637] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The genetic factors that contribute to efficient food conversion are largely unknown. Several physiological systems are likely to be important, including basal metabolic rate, the generation of ATP, the regulation of growth and development, and the homeostatic control of body mass. Using whole-genome association, we found that DNA variants in or near proteins contributing to the background use of energy of the cell were 10 times as common as those affecting appetite and body-mass homeostasis. In addition, there was a genic contribution from the extracellular matrix and tissue structure, suggesting a trade-off between efficiency and tissue construction. Nevertheless, the largest group consisted of those involved in gene regulation or control of the phenotype. We found that the distribution of micro-RNA motifs was significantly different for the genetic variants associated with residual feed intake than for the genetic variants in total, although the distribution of promoter sequence motifs was not different. This suggests that certain subsets of micro-RNA are more important for the regulation of this trait. Successful validation depended on the sign of the allelic association in different populations rather than on the strength of the initial association or its size of effect.
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Affiliation(s)
- W Barendse
- CSIRO Livestock Industries, Queensland Bioscience Precinct, St. Lucia 4067, Australia
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Schymick JC, Scholz SW, Fung HC, Britton A, Arepalli S, Gibbs JR, Lombardo F, Matarin M, Kasperaviciute D, Hernandez DG, Crews C, Bruijn L, Rothstein J, Mora G, Restagno G, Chiò A, Singleton A, Hardy J, Traynor BJ. Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 2007; 6:322-8. [PMID: 17362836 DOI: 10.1016/s1474-4422(07)70037-6] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND The cause of sporadic ALS is currently unknown. Despite evidence for a role for genetics, no common genetic variants have been unequivocally linked to sporadic ALS. We sought to identify genetic variants associated with an increased or decreased risk for developing ALS in a cohort of American sporadic cases. METHODS We undertook a genome-wide association study using publicly available samples from 276 patients with sporadic ALS and 271 neurologically normal controls. 555 352 unique SNPs were assayed in each sample using the Illumina Infinium II HumanHap550 SNP chip. FINDINGS More than 300 million genotypes were produced in 547 participants. These raw genotype data are freely available on the internet and represent the first publicly accessible SNP data for ALS cases. 34 SNPs with a p value less than 0.0001 (two degrees of freedom) were found, although none of these reached significance after Bonferroni correction. INTERPRETATION We generated publicly available genotype data for sporadic ALS patients and controls. No single locus was definitively associated with increased risk of developing disease, although potentially associated candidate SNPs were identified.
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Affiliation(s)
- Jennifer C Schymick
- Laboratory of Neurogenetics, National Institute on Aging, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
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Melquist S, Craig DW, Huentelman MJ, Crook R, Pearson JV, Baker M, Zismann VL, Gass J, Adamson J, Szelinger S, Corneveaux J, Cannon A, Coon KD, Lincoln S, Adler C, Tuite P, Calne DB, Bigio EH, Uitti RJ, Wszolek ZK, Golbe LI, Caselli RJ, Graff-Radford N, Litvan I, Farrer MJ, Dickson DW, Hutton M, Stephan DA. Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms. Am J Hum Genet 2007; 80:769-78. [PMID: 17357082 PMCID: PMC1852701 DOI: 10.1086/513320] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Accepted: 01/12/2007] [Indexed: 01/06/2023] Open
Abstract
To date, only the H1 MAPT haplotype has been consistently associated with risk of developing the neurodegenerative disease progressive supranuclear palsy (PSP). We hypothesized that additional genetic loci may be involved in conferring risk of PSP that could be identified through a pooling-based genomewide association study of >500,000 SNPs. Candidate SNPs with large differences in allelic frequency were identified by ranking all SNPs by their probe-intensity difference between cohorts. The MAPT H1 haplotype was strongly detected by this methodology, as was a second major locus on chromosome 11p12-p11 that showed evidence of association at allelic (P<.001), genotypic (P<.001), and haplotypic (P<.001) levels and was narrowed to a single haplotype block containing the DNA damage-binding protein 2 (DDB2) and lysosomal acid phosphatase 2 (ACP2) genes. Since DNA damage and lysosomal dysfunction have been implicated in aging and neurodegenerative processes, both genes are viable candidates for conferring risk of disease.
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Affiliation(s)
- Stacey Melquist
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL 32224, USA
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Grupe A, Abraham R, Li Y, Rowland C, Hollingworth P, Morgan A, Jehu L, Segurado R, Stone D, Schadt E, Karnoub M, Nowotny P, Tacey K, Catanese J, Sninsky J, Brayne C, Rubinsztein D, Gill M, Lawlor B, Lovestone S, Holmans P, O'Donovan M, Morris JC, Thal L, Goate A, Owen MJ, Williams J. Evidence for novel susceptibility genes for late-onset Alzheimer's disease from a genome-wide association study of putative functional variants. Hum Mol Genet 2007; 16:865-73. [PMID: 17317784 DOI: 10.1093/hmg/ddm031] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This study sets out to identify novel susceptibility genes for late-onset Alzheimer's disease (LOAD) in a powerful set of samples from the UK and USA (1808 LOAD cases and 2062 controls). Allele frequencies of 17 343 gene-based putative functional single nucleotide polymorphisms (SNPs) were tested for association with LOAD in a discovery case-control sample from the UK. A tiered strategy was used to follow-up significant variants from the discovery sample in four independent sample sets. Here, we report the identification of several candidate SNPs that show significant association with LOAD. Three of the identified markers are located on chromosome 19 (meta-analysis: full sample P = 6.94E - 81 to 0.0001), close to the APOE gene and exhibit linkage disequilibrium (LD) with the APOEepsilon4 and epsilon2/3 variants (0.09 < D'<1). Two of the three SNPs can be regarded as study-wide significant (expected number of false positives reaching the observed significance level less than 0.05 per study). Sixteen additional SNPs show evidence for association with LOAD [P = 0.0010-0.00006; odds ratio (OR) = 1.07-1.45], several of which map to known linkage regions, biological candidate genes and novel genes. Four SNPs not in LD with APOE show a false positive rate of less than 2 per study, one of which shows study-wide suggestive evidence taking account of 17 343 tests. This is a missense mutation in the galanin-like peptide precursor gene (P = 0.00005, OR = 1.2, false positive rate = 0.87).
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Affiliation(s)
- Andrew Grupe
- Celera Diagnostics, 1401 Harbor Bay Parkway, Alameda, CA 94502, USA
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Fung HC, Scholz S, Matarin M, Simón-Sánchez J, Hernandez D, Britton A, Gibbs JR, Langefeld C, Stiegert ML, Schymick J, Okun MS, Mandel RJ, Fernandez HH, Foote KD, Rodríguez RL, Peckham E, De Vrieze FW, Gwinn-Hardy K, Hardy JA, Singleton A. Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 2006; 5:911-6. [PMID: 17052657 DOI: 10.1016/s1474-4422(06)70578-6] [Citation(s) in RCA: 285] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND Several genes underlying rare monogenic forms of Parkinson's disease have been identified over the past decade. Despite evidence for a role for genetics in sporadic Parkinson's disease, few common genetic variants have been unequivocally linked to this disorder. We sought to identify any common genetic variability exerting a large effect in risk for Parkinson's disease in a population cohort and to produce publicly available genome-wide genotype data that can be openly mined by interested researchers and readily augmented by genotyping of additional repository subjects. METHODS We did genome-wide, single-nucleotide-polymorphism (SNP) genotyping of publicly available samples from a cohort of Parkinson's disease patients (n=267) and neurologically normal controls (n=270). More than 408,000 unique SNPs were used from the Illumina Infinium I and HumanHap300 assays. FINDINGS We have produced around 220 million genotypes in 537 participants. This raw genotype data has been and as such is the first publicly accessible high-density SNP data outside of the International HapMap Project. We also provide here the results of genotype and allele association tests. INTERPRETATION We generated publicly available genotype data for Parkinson's disease patients and controls so that these data can be mined and augmented by other researchers to identify common genetic variability that results in minor and moderate risk for disease.
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Affiliation(s)
- Hon-Chung Fung
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
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Elbaz A, Nelson LM, Payami H, Ioannidis JPA, Fiske BK, Annesi G, Carmine Belin A, Factor SA, Ferrarese C, Hadjigeorgiou GM, Higgins DS, Kawakami H, Krüger R, Marder KS, Mayeux RP, Mellick GD, Nutt JG, Ritz B, Samii A, Tanner CM, Van Broeckhoven C, Van Den Eeden SK, Wirdefeldt K, Zabetian CP, Dehem M, Montimurro JS, Southwick A, Myers RM, Trikalinos TA. Lack of replication of thirteen single-nucleotide polymorphisms implicated in Parkinson's disease: a large-scale international study. Lancet Neurol 2006; 5:917-23. [PMID: 17052658 PMCID: PMC3636768 DOI: 10.1016/s1474-4422(06)70579-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND A genome-wide association study identified 13 single-nucleotide polymorphisms (SNPs) significantly associated with Parkinson's disease. Small-scale replication studies were largely non-confirmatory, but a meta-analysis that included data from the original study could not exclude all SNP associations, leaving relevance of several markers uncertain. METHODS Investigators from three Michael J Fox Foundation for Parkinson's Research-funded genetics consortia-comprising 14 teams-contributed DNA samples from 5526 patients with Parkinson's disease and 6682 controls, which were genotyped for the 13 SNPs. Most (88%) participants were of white, non-Hispanic descent. We assessed log-additive genetic effects using fixed and random effects models stratified by team and ethnic origin, and tested for heterogeneity across strata. A meta-analysis was undertaken that incorporated data from the original genome-wide study as well as subsequent replication studies. FINDINGS In fixed and random-effects models no associations with any of the 13 SNPs were identified (odds ratios 0.89 to 1.09). Heterogeneity between studies and between ethnic groups was low for all SNPs. Subgroup analyses by age at study entry, ethnic origin, sex, and family history did not show any consistent associations. In our meta-analysis, no SNP showed significant association (summary odds ratios 0.95 to 1.08); there was little heterogeneity except for SNP rs7520966. INTERPRETATION Our results do not lend support to the finding that the 13 SNPs reported in the original genome-wide association study are genetic susceptibility factors for Parkinson's disease.
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Li Y, Schrodi S, Rowland C, Tacey K, Catanese J, Grupe A. Genetic evidence for ubiquitin-specific proteases USP24 and USP40 as candidate genes for late-onset Parkinson disease. Hum Mutat 2006; 27:1017-23. [PMID: 16917932 DOI: 10.1002/humu.20382] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Linkage studies have defined susceptibility regions for late-onset Parkinson disease (PD) on chromosomes 1 and 2, but specific genetic variants have not been definitively identified. Here we report the results of a case-control study to identify disease-associated single nucleotide polymorphisms (SNPs) in these loci. In the initial phase of our study, we genotyped two putative functional SNPs in ubiquitin-specific protease 24 (USP24), a biological candidate gene within the chromosome 1 linkage region, and scanned the chromosome 2 linkage peak with 43 SNPs in a sample set of 224 PD cases and 186 matched controls. Both USP24 SNPs were significantly associated with disease risk (p = 0.0037 for rs1165222:T > C, p.Thr195ILe, and p = 0.037 for rs13312:C > G, a SNP in the 3'-untranslated region), and one marker, rs1048603:C > T, p.Arg1123Cys, in USP40 was significant from the chromosome 2 scan (p = 0.038). Further genotyping of the region surrounding these initial markers led us to identify 19 additional SNPs with strong disease association. In the second phase, we genotyped the 22 significant markers in an additional 110 cases and 162 controls, which together with part of the initial sample set (201 cases and 149 controls) constitute an expanded sample set of 311 age- and gender-matched case-control pairs. Twenty-one markers were significant in the expanded sample set (most significant allelic p-value: 0.0006 for rs287235:C > G on chromosome 1, and 0.005 for rs838552:T > C on chromosome 2), and six SNPs in USP24 remained significant after conservatively adjusting for testing 27 markers (pBonferroni = 0.017-0.049). It is unlikely that population stratification contributed to this finding, as population stratification was undetectable in our sample set using 78 null markers. Our data suggest that genetic variants in USP24 and USP40 affect the risk for late-onset PD, which is consistent with the predicted role of the ubiquitination pathway in PD etiology.
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Affiliation(s)
- Yonghong Li
- Celera Diagnostics, Alameda, California 94502, USA.
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Maraganore DM, Andrade MD, Lesnick TG, Pant PVK, Cox DR, Ballinger DG. Response from Maraganore et al. Am J Hum Genet 2006. [DOI: 10.1086/504731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Myers RH. Considerations for genomewide association studies in Parkinson disease. Am J Hum Genet 2006; 78:1081-2. [PMID: 16685659 PMCID: PMC1474090 DOI: 10.1086/504730] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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