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5 results on '"Consortium, International Parkinson Disease Genomics"'

1. A Three-groups Non-local Model for Combining Heterogeneous Data Sources to Identify Genes Associated with Parkinson's Disease

Author

Wixson, Troy P., Shaby, Benjamin A., Philtron, Daisy L., Consortium, International Parkinson Disease Genomics, Lima, Leandro A., Wyman, Stacia K., Kaye, Julia A., and Finkbeiner, Steven

Subjects
Statistics - Applications
Abstract

We seek to identify genes involved in Parkinson's Disease (PD) by combining information across different experiment types. Each experiment, taken individually, may contain too little information to distinguish some important genes from incidental ones. However, when experiments are combined using the proposed statistical framework, additional power emerges. The fundamental building block of the family of statistical models that we propose is a hierarchical three-group mixture of distributions. Each gene is modeled probabilistically as belonging to either a null group that is unassociated with PD, a deleterious group, or a beneficial group. This three-group formalism has two key features. By apportioning prior probability of group assignments with a Dirichlet distribution, the resultant posterior group probabilities automatically account for the multiplicity inherent in analyzing many genes simultaneously. By building models for experimental outcomes conditionally on the group labels, any number of data modalities may be combined in a single coherent probability model, allowing information sharing across experiment types. These two features result in parsimonious inference with few false positives, while simultaneously enhancing power to detect signals. Simulations show that our three-groups approach performs at least as well as commonly-used tools for GWAS and RNA-seq, and in some cases it performs better. We apply our proposed approach to publicly-available GWAS and RNA-seq datasets, discovering novel genes that are potential therapeutic targets., Comment: 26 pages, 6 figures, 4 tables

Published
2024

2. The Genetic Architecture of Parkinson Disease in Spain: Characterizing Population-Specific Risk, Differential Haplotype Structures, and Providing Etiologic Insight

Author

Bandres-Ciga, Sara, Ahmed, Sarah, Gómez-Garre, Pilar, Kia, Demis A, Tan, Manuela, Houlden, Henry, Morris, Huw R, Plun-Favreau, Helene, Holmans, Peter, Hardy, John, Trabzuni, Daniah, Bras, Jose, PhD, John Quinn, Jesús, Silvia, Mok, Kin Y, Kinghorn, Kerri J, Billingsley, Kimberley, Wood, Nicholas W, Lewis, Patrick, Schreglmann, Sebastian, Guerreiro, Rita, Lovering, Ruth, R'Bibo, Lea, Manzoni, Claudia, Labrador-Espinosa, Miguel A, Rizig, Mie, Ryten, Mina, Guelfi, Sebastian, Escott-Price, Valentina, Chelban, Viorica, Foltynie, Thomas, Williams, Nigel, Morrison, Karen E, Brice, Alexis, Danjou, Fabrice, Macias, Daniel, Lesage, Suzanne, Corvol, Jean-Christophe, Martinez, Maria, Schulte, Claudia, Brockmann, Kathrin, Simón-Sánchez, Javier, Heutink, Peter, Rizzu, Patrizia, Sharma, Manu, Gasser, Thomas, Méndez-Del-Barrio, Carlota, Nicolas, Aude, Cookson, Mark R, Blauwendraat, Cornelis, Craig, David W, Faghri, Faraz, Gibbs, J Raphael, Hernandez, Dena G, Keuren-Jensen, Kendall Van, Shulman, Joshua M, Periñán-Tocino, Teresa, Iwaki, Hirotaka, Leonard, Hampton L, Nalls, Mike A, Robak, Laurie, Lubbe, Steven, Finkbeiner, Steven, Mencacci, Niccolo E, Lungu, Codrin, Singleton, Andrew B, Scholz, Sonja W, Tejera-Parrado, Cristina, Reed, Xylena, Alcalay, Roy N, Gan-Or, Ziv, Rouleau, Guy A, Krohn, Lynne, van Hilten, Jacobus J, Marinus, Johan, Adarmes-Gómez, Astrid D, Aguilar, Miquel, Alvarez, Ignacio, Vargas-González, Laura, Alvarez, Victoria, Barrero, Francisco Javier, Yarza, Jesús Alberto Bergareche, Bernal-Bernal, Inmaculada, Blazquez, Marta, Bonilla-Toribio, Marta, Botía, Juan A, Boungiorno, María Teresa, Buiza-Rueda, Dolores, Cámara, Ana, Diez-Fairen, Monica, Carrillo, Fátima, Carrión-Claro, Mario, Cerdan, Debora, Clarimón, Jordi, Compta, Yaroslau, de la Casa, Beatríz, Dols-Icardo, Oriol, Duarte, Jacinto, Duran, Raquel, Escamilla-Sevilla, Francisco, Ezquerra, Mario, Feliz, Cici, Fernández, Manel, Fernández-Santiago, Rubé, Garcia, Ciara, García-Ruiz, Pedro, Heredia, Maria Jose Gomez, Gonzalez-Aramburu, Isabel, Sabir, Marya S, Tartari, Juan Pablo, Pagola, Ana Gorostidi, Hoenicka, Janet, Infante, Jon, Jimenez-Escrig, Adriano, Kulisevsky, Jaime, Lopez-Sendon, Jose Luis, Arregui, Adolfo López de Munain, Buongiorno, Mariateresa, Torres, Irene Martínez, Marín, Juan, Marti, Maria Jose, Martínez-Castrillo, Juan Carlos, González, Manuel Menéndez, Mata, Marina, Mínguez, Adolfo, Mir, Pablo, Rezola, Elisabet Mondragon, Pagonabarraga, Javier, Pascual-Sedano, Berta, Pastor, Pau, Errazquin, Francisco Perez, Ruiz-Martínez, Javier, Ruz, Clara, Rodriguez, Antonio Sanchez, Sierra, María, Suarez-Sanmartin, Esther, Gorostidi, Ana, Tabernero, Cesar, Tolosa, Eduard, Valldeoriola, Francesc, Vela, Lydia, Vives, Francisco, Zimprich, Alexander, Pihlstrom, Lasse, Bergareche, Jesús Alberto, Toft, Mathias, Koks, Sulev, Taba, Pille, Hassin-Baer, Sharon, Dalgard, Clifton L, Adeleye, Adelani, Soltis, Anthony R, Alba, Camille, Viollet, Coralie, Bacikova, Dagmar, Mondragon, Elisabet, Hupalo, Daniel N, Sukumar, Gauthaman, Pollard, Harvey B, Wilkerson, Matthew D, Martinez, Elisa McGrath, Vinagre-Aragon, Ana, Croitoru, Ioana, Marín-Lahoz, Juan, Fernández-Santiago, Rubén, Muñoz, Esteban, Sanchez Rodriguez, Antonio, Menéndez-González, Manuel, Suarez-San Martin, Esther, Vela-Desojo, Lydia, Mínguez-Castellanos, Adolfo, Gomez Heredia, Maria Jose, Perez Errazquin, Francisco, Romero-Acebal, Manolo, Martínez Torres, Irene, Kim, Jonggeol Jeffrey, Center, American Genome, Brooks, Janet, Saez-Atienzar, Sara, Jorda, Rafael, Botia, Juan A, Bonet-Ponce, Luis, Clarke, Carl, Morris, Huw, Edsall, Connor, Hernandez, Dena, Simon Sanchez, Javier, Marti, Maria José, López de Munain, Adolfo, Singleton, Andrew, Consortium, International Parkinson Disease Genomics, Noyce, Alastair J, Kaiyrzhanov, Rauan, Middlehurst, Ben, National Institutes of Health (US), Department of Defense (US), Michael J. Fox Foundation for Parkinson's Research, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad (España), European Commission, Junta de Andalucía, Sociedad Andaluza de Neurología, Jacques and Gloria Gossweiler Foundation, Fundación Alicia Koplowitz, Fundación Mutua Madrileña, and Universidad de Sevilla

Subjects
0301 basic medicine, Male, Multifactorial Inheritance, Parkinson's disease, age at onset, Machine Learning, 0302 clinical medicine, Cost of Illness, genetics [Parkinson Disease], Population specific, genetics [Genetic Predisposition to Disease], Age of Onset, genetics [Ubiquitin-Protein Ligases], Aged, 80 and over, Age at onset, Chromosome Mapping, Parkinson Disease, Middle Aged, Spanish population, humanities, Neurology, Christian ministry, Female, Adult, Genotype, Ubiquitin-Protein Ligases, Article, risk haplotype, 03 medical and health sciences, Risk score risk haplotype, Political science, polygenic risk score, Humans, Genetic Predisposition to Disease, ddc:610, Risk haplotype, Parkinson's disease, Spanish population, age at onset, polygenic risk score, risk haplotype, Aged, DNA Methylation, 030104 developmental biology, Haplotypes, Spain, Case-Control Studies, Polygenic risk score, Neurology (clinical), Polygenic, Humanities, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Background: The Iberian Peninsula stands out as having variable levels of population admixture and isolation, making Spain an interesting setting for studying the genetic architecture of neurodegenerative diseases. Objectives: To perform the largest PD genome-wide association study restricted to a single country. Methods: We performed a GWAS for both risk of PD and age at onset in 7,849 Spanish individuals. Further analyses included population-specific risk haplotype assessments, polygenic risk scoring through machine learning, Mendelian randomization of expression, and methylation data to gain insight into disease-associated loci, heritability estimates, genetic correlations, and burden analyses. Results: We identified a novel population-specific genome-wide association study signal at PARK2 associated with age at onset, which was likely dependent on the c.155delA mutation. We replicated four genome-wide independent signals associated with PD risk, including SNCA, LRRK2, KANSL1/MAPT, and HLA-DQB1. A significant trend for smaller risk haplotypes at known loci was found compared to similar studies of non-Spanish origin. Seventeen PD-related genes showed functional consequence by two-sample Mendelian randomization in expression and methylation data sets. Long runs of homozygosity at 28 known genes/loci were found to be enriched in cases versus controls. Conclusions: Our data demonstrate the utility of the Spanish risk haplotype substructure for future fine-mapping efforts, showing how leveraging unique and diverse population histories can benefit genetic studies of complex diseases. The present study points to PARK2 as a major hallmark of PD etiology in Spain., This research was supported, in part, by the Intramural Research Program of the National Institutes of Health (National Institute on Aging, National Institute of Neurological Disorders and Stroke; project numbers: 1ZIA‐NS003154‐03, Z01‐AG000949‐02, and Z01‐ES101986). In addition, this work was supported by the Department of Defense (award W81XWH‐09‐2‐0128), The Michael J Fox Foundation for Parkinson's Research, and the ISCIII Grants PI 15/0878 (Fondos Feder) to V.A. and PI 15/01013 to J,H. This study was supported by grants from the Spanish Ministry of Economy and Competitiveness (PI14/01823, PI16/01575, PI18/01898, [SAF2006‐10126 (2006‐2009), SAF2010‐22329‐C02‐01 (2010‐2012), and SAF2013‐47939‐R (2013‐2018)]), co‐founded by ISCIII (Subdirección General de Evaluación y Fomento de la Investigación) and by Fondo Europeo de Desarrollo Regional (FEDER), the Consejería de Economía, Innovación, Ciencia y Empleo de la Junta de Andalucía (CVI‐02526, CTS‐7685), the Consejería de Salud y Bienestar Social de la Junta de Andalucía (PI‐0437‐2012, PI‐0471‐2013), the Sociedad Andaluza de Neurología, the Jacques and Gloria Gossweiler Foundation, the Fundación Alicia Koplowitz, and the Fundación Mutua Madrileña. Pilar Gómez‐Garre was supported by the “Miguel Servet” (from ISCIII16 FEDER) and “Nicolás Monardes” (from Andalusian Ministry of Health) programmes. Silvia Jesús Maestre was supported by the “Juan Rodés” programme, and Daniel Macías‐García was supported by the “Río Hortega” programme (both from ISCIII‐FEDER). Cristina Tejera Parrado was supported by VPPI‐US from the Universidad de Sevilla. This research has been conducted using samples from the HUVR‐IBiS Biobank (Andalusian Public Health System Biobank and ISCIII‐Red de Biobancos PT13/0010/0056). This work was also supported by the grant PSI2014‐57643 from the Junta de Andalucía to the CTS‐438 group and a research award from the Andalusian Society of Neurology.

Published
2019

3. Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies

Author

Consortium, International Parkinson Disease Genomics, Nalls, Michael A, Sveinbjörnsdóttir, Sigurlaug, Pollak, Pierre, Post, Bart, Potter, Simon, Ravina, Bernard, Revesz, Tamas, Riess, Olaf, Rivadeneira, Fernando, Rizzu, Patrizia, Ryten, Mina, Sawcer, Stephen, Stefánsson, Kári, Schapira, Anthony, Scheffer, Hans, Shaw, Karen, Shoulson, Ira, Sidransky, Ellen, Smith, Colin, Spencer, Chris C A, Stefánsson, Hreinn, Steinberg, Stacy, Stockton, Joanna D, Martinez, Maria, Strange, Amy, Talbot, Kevin, Tanner, Carlie M, Tashakkori-Ghanbaria, Avazeh, Tison, François, Trabzuni, Daniah, Traynor, Bryan J, Utterlinden, André G, Velseboer, Daan, Vidailhet, Marie, Hardy, John, Walker, Robert, van de Warrenburg, Bart, Wickremaratchi, Mirdhu, Williams, Nigel, Williams-Gray, Caroline H, Winder-Rhodes, Sophie, Heutink, Peter, Brice, Alexis, Gasser, Thomas, Singleton, Andrew B, Wood, Nicholas W, Plagnol, Vincent, Hernandez, Dena G, Sheerin, Una-Marie, Saad, Mohamad, Simón-Sánchez, Javier, Schulte, Claudia, Lesage, Suzanne, Arepalli, Sampath, Barker, Roger, Ben-Shlomo, Yoav, Berendse, Henk W, Berg, Daniela, Bhatia, Kailash, de Bie, Rob M A, Biffi, Alessandro, Bloem, Bas, Bochdanovits, Zoltan, Bonin, Michael, Bras, Jose M, Sharma, Manu, Brockmann, Kathrin, Brooks, Janet, Burn, David J, Charlesworth, Gavin, Chen, Honglei, Chinnery, Patrick F, Chong, Sean, Clarke, Carl E, Cookson, Mark R, Cooper, Mark, Corvol, Jean Christophe, Counsell, Carl, Damier, Philippe, Dartigues, Jean-François, Deloukas, Panos, Deuschl, Günther, Dexter, David T, van Dijk, Karin D, Dillman, Alissa, Durif, Frank, Dürr, Alexandra, Edkins, Sarah, Evans, Jonathan R, Foltynie, Thomas, Gao, Jianjun, Gardner, Michelle, Gibbs, J Raphael, Goate, Alison, Gray, Emma, Guerreiro, Rita, Simón-Sánchez, J., Gústafsson, Ómar, Harris, Clare, van Hilten, Jacobus J, Hofman, Albert, Hollenbeck, Albert, Hu, Michele, Huang, Xuemei, Huber, Heiko, Hudson, Gavin, Hunt, Sarah E, Huttenlocher, Johanna, Illig, Thomas, Jónsson, Pálmi V, Lambert, Jean-Charles, Langford, Cordelia, Lees, Andrew, Lichtner, Peter, Limousin, Patricia, Lopez, Grisel, Lorenz, Delia, McNeill, Alisdair, Moorby, Catriona, Moore, Matthew, Morris, Huw R, Morrison, Karen E, Mudanohwo, Ese, O'Sullivan, Sean, Pearson, Justin, Perlmutter, Joel S, Pétursson, Hjörvar, ANS - Amsterdam Neuroscience, Neurology, ACS - Amsterdam Cardiovascular Sciences, Graduate School, Human genetics, Anatomy and neurosciences, NCA - Neurodegeneration, Pollak, Pierre, and Neuroscience Campus Amsterdam - Neurodegeneration

Subjects
Male, Genome-wide association study, Genomic disorders and inherited multi-system disorders Functional Neurogenomics [IGMD 3], 0302 clinical medicine, genetics [Parkinson Disease], Parkinson Disease/genetics, Age of Onset, genetics [Genetic Predisposition to Disease], Genetics, 0303 health sciences, Genetic Predisposition to Disease/genetics, Parkinson Disease, General Medicine, Middle Aged, Polymorphism, Single Nucleotide/genetics, LRRK2, genetics [Genetic Variation], 3. Good health, Genetic Variation/genetics, Meta-analysis, Genetic Loci/genetics, genetics [Polymorphism, Single Nucleotide], Female, Functional Neurogenomics [DCN 2], Sequence Analysis, Adult, Genotype, Single-nucleotide polymorphism, genetics [Genetic Loci], Biology, Polymorphism, Single Nucleotide, Risk Assessment, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Genetic variation, Humans, Genetic Predisposition to Disease, ddc:610, Alleles, 030304 developmental biology, Aged, Genetic Variation, Odds ratio, nervous system diseases, ddc:616.8, Genetic Loci, Age of onset, 030217 neurology & neurosurgery, Imputation (genetics), Genome-Wide Association Study
Abstract

Item does not contain fulltext BACKGROUND: Genome-wide association studies (GWAS) for Parkinson's disease have linked two loci (MAPT and SNCA) to risk of Parkinson's disease. We aimed to identify novel risk loci for Parkinson's disease. METHODS: We did a meta-analysis of datasets from five Parkinson's disease GWAS from the USA and Europe to identify loci associated with Parkinson's disease (discovery phase). We then did replication analyses of significantly associated loci in an independent sample series. Estimates of population-attributable risk were calculated from estimates from the discovery and replication phases combined, and risk-profile estimates for loci identified in the discovery phase were calculated. FINDINGS: The discovery phase consisted of 5333 case and 12 019 control samples, with genotyped and imputed data at 7 689 524 SNPs. The replication phase consisted of 7053 case and 9007 control samples. We identified 11 loci that surpassed the threshold for genome-wide significance (p

Published
2011

4. The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson's disease data

Author

Leonard, Hampton L, Murtadha, Ruqaya, Huxford, Brook, Storm, Catherine, Towns, Clodagh, Vitale, Dan, Chetty, Devina, Yu, Eric, Grenn, Francis P, Salazar, Gabriela, Rateau, Geoffrey, Iwaki, Hirotaka, Martinez-Carrasco, Alejandro, Elsayed, Inas, Foote, Isabelle Francesca, Jansen van Rensburg, Zuné, Kim, Jonggeol Jeff, Yuan, Jie, Lake, Julie, Brolin, Kajsa, Senkevich, Konstantin, Wu, Lesley, Tan, Manuela M X, Jama, Alina, Periñán, María Teresa, Makarious, Mary B, Ta, Michael, Pillay, Nikita Simone, Betancor, Oswaldo Lorenzo, Reyes-Pérez, Paula R, Alvarez Jerez, Pilar, Saini, Prabhjyot, Al-Ouran, Rami, Sivakumar, Ramiya, Müller-Nedebock, Amica Corda, Real, Raquel, Reynolds, Regina H, Hu, Ruifneg, Abrahams, Shameemah, Rao, Shilpa C, Antar, Tarek, Leal, Thiago Peixoto, Iankova, Vassilena, Scotton, William J, Song, Yeajin, Gil-Martinez, Ana-Luisa, Singleton, Andrew, Nalls, Mike A, Dey, Sumit, Bandres-Ciga, Sara, Blauwendraat, Cornelis, Noyce, Alastair J, Program, The Global Parkinson’s Genetics, Illarionova, Anastasia, Moore, Anni, Bustos, Bernabe I, Jadhav, Bharati, and Consortium, International Parkinson Disease Genomics

Subjects
Cellular and Molecular Neuroscience, Neurology, Neurology (clinical), ddc:610
Abstract

Open science and collaboration are necessary to facilitate the advancement of Parkinson’s disease (PD) research. Hackathons are collaborative events that bring together people with different skill sets and backgrounds to generate resources and creative solutions to problems. These events can be used as training and networking opportunities, thus we coordinated a virtual 3-day hackathon event, during which 49 early-career scientists from 12 countries built tools and pipelines with a focus on PD. Resources were created with the goal of helping scientists accelerate their own research by having access to the necessary code and tools. Each team was allocated one of nine different projects, each with a different goal. These included developing post-genome-wide association studies (GWAS) analysis pipelines, downstream analysis of genetic variation pipelines, and various visualization tools. Hackathons are a valuable approach to inspire creative thinking, supplement training in data science, and foster collaborative scientific relationships, which are foundational practices for early-career researchers. The resources generated can be used to accelerate research on the genetics of PD.

Published
2023

5. Author Correction: The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson's disease data

Author

Leonard, Hampton L, Murtadha, Ruqaya, Huxford, Brook, Storm, Catherine, Towns, Clodagh, Vitale, Dan, Chetty, Devina, Yu, Eric, Grenn, Francis P, Salazar, Gabriela, Rateau, Geoffrey, Iwaki, Hirotaka, Martinez-Carrasco, Alejandro, Elsayed, Inas, Foote, Isabelle Francesca, Jansen van Rensburg, Zuné, Kim, Jonggeol Jeff, Yuan, Jie, Lake, Julie, Brolin, Kajsa, Senkevich, Konstantin, Wu, Lesley, Tan, Manuela M X, Jama, Alina, Periñán, María Teresa, Makarious, Mary B, Ta, Michael, Pillay, Nikita Simone, Betancor, Oswaldo Lorenzo, Reyes-Pérez, Paula R, Alvarez Jerez, Pilar, Saini, Prabhjyot, Al-Ouran, Rami, Sivakumar, Ramiya, Müller-Nedebock, Amica Corda, Real, Raquel, Reynolds, Regina H, Hu, Ruifneg, Abrahams, Shameemah, Rao, Shilpa C, Antar, Tarek, Leal, Thiago Peixoto, Iankova, Vassilena, Scotton, William J, Song, Yeajin, Gil-Martinez, Ana-Luisa, Singleton, Andrew, Nalls, Mike A, Dey, Sumit, Bandres-Ciga, Sara, Blauwendraat, Cornelis, Noyce, Alastair J, Program, The Global Parkinson’s Genetics, Illarionova, Anastasia, Moore, Anni, Bustos, Bernabe I, Jadhav, Bharati, and Consortium, International Parkinson Disease Genomics

Subjects
ddc:610
Published
2023

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