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213 results on '"Reynolds, Regina H."'

1. Investigation of the genetic aetiology of Lewy body diseases with and without dementia

Author

Wu, Lesley Yue, Real, Raquel, Martinez-Carrasco, Alejandro, Chia, Ruth, Lawton, Michael A, Shoai, Maryam, Bresner, Catherine, Blauwendraat, Cornelis, Singleton, Andrew B, Ryten, Mina, Abramzon, Yevgeniya, Ahmed, Sarah, Alba, Camille, Albert, Marilyn S, Bacikova, Dagmar, Barrett, Matthew J, Beach, Thomas G, Bennett, David A, Besser, Lilah M, Bigio, Eileen H, Boeve, Bradley F, Bohannan, Ryan C, Caraway, Chad A, Palma, Jose-Alberto, Dalgard, Clifton L, Dickson, Dennis, Ding, Jinhui, Faber, Kelley, Ferman, Tanis, Ferrucci, Luigi, Flanagan, Margaret E, Foroud, Tatiana M, Ghetti, Bernardino, Gibbs, J Raphael, Goate, Alison, Goldstein, David, Graff-Radford, Neill R, Hu, Heng-Chen, Hupalo, Daniel, Kaiser, Scott M, Kaufmann, Horacio, Kim, Ronald C, Klein, Gregory, Kukull, Walter, Kuzma, Amanda, Leverenz, James, Lopez, Grisel, Mao, Qinwen, Martinez-McGrath, Elisa, Masliah, Eliezer, Monuki, Ed, Newell, Kathy L, Norcliffe-Kaufmann, Lucy, Perkins, Matthew, Pletnikova, Olga, Renton, Alan E, Resnick, Susan M, Ross, Owen A, Sabir, Marya S, Scherzer, Clemens R, Scholz, Sonja W, Serrano, Geidy, Shakkotai, Vikram, Sidransky, Ellen, Tanaka, Toshiko, Tayebi, Nahid, Traynor, Bryan J, Troncoso, Juan C, Viollet, Coralie, Walton, Ronald L, Woltjer, Randy, Wszolek, Zbigniew K, Black, Sandra E, Gan-Or, Ziv, Keith, Julia, Masellis, Mario, Rogaeva, Ekaterina, Aarsland, Dag, Al-Sarraj, Safa, Attems, Johannes, Ferrari, Raffaele, Gentleman, Steve, Hardy, John A, Hodges, Angela K, Love, Seth, McKeith, Ian, Morris, Christopher M, Morris, Huw R, Palmer, Laura, Pickering-Brown, Stuart, Reynolds, Regina H, Thomas, Alan J, Tilley, Bension S, Troakes, Claire, Brett, Francesca, Brice, Alexis, and Duyckaerts, Charles

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Human Genome, Genetics, Brain Disorders, Lewy Body Dementia, Alzheimer's Disease Related Dementias (ADRD), Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Parkinson's Disease, Neurodegenerative, Dementia, Aging, Prevention, Acquired Cognitive Impairment, Clinical Research, 2.1 Biological and endogenous factors, Neurological, International Lewy Body Dementia Genomics Consortium, APOE, Lewy body diseases, dementia, genome-wide association studies, Clinical sciences, Biological psychology
Abstract

Up to 80% of Parkinson's disease patients develop dementia, but time to dementia varies widely from motor symptom onset. Dementia with Lewy bodies presents with clinical features similar to Parkinson's disease dementia, but cognitive impairment precedes or coincides with motor onset. It remains controversial whether dementia with Lewy bodies and Parkinson's disease dementia are distinct conditions or represent part of a disease spectrum. The biological mechanisms underlying disease heterogeneity, in particular the development of dementia, remain poorly understood, but will likely be the key to understanding disease pathways and, ultimately, therapy development. Previous genome-wide association studies in Parkinson's disease and dementia with Lewy bodies/Parkinson's disease dementia have identified risk loci differentiating patients from controls. We collated data for 7804 patients of European ancestry from Tracking Parkinson's, The Oxford Discovery Cohort, and Accelerating Medicine Partnership-Parkinson's Disease Initiative. We conducted a discrete phenotype genome-wide association study comparing Lewy body diseases with and without dementia to decode disease heterogeneity by investigating the genetic drivers of dementia in Lewy body diseases. We found that risk allele rs429358 tagging APOEe4 increases the odds of developing dementia, and that rs7668531 near the MMRN1 and SNCA-AS1 genes and an intronic variant rs17442721 tagging LRRK2 G2019S on chromosome 12 are protective against dementia. These results should be validated in autopsy-confirmed cases in future studies.

Published
2024

2. Genome-wide determinants of mortality and motor progression in Parkinson’s disease

Author

Tan, Manuela M. X., Lawton, Michael A., Pollard, Miriam I., Brown, Emmeline, Real, Raquel, Carrasco, Alejandro Martinez, Bekadar, Samir, Jabbari, Edwin, Reynolds, Regina H., Iwaki, Hirotaka, Blauwendraat, Cornelis, Kanavou, Sofia, Hubbard, Leon, Malek, Naveed, Grosset, Katherine A., Bajaj, Nin, Barker, Roger A., Burn, David J., Bresner, Catherine, Foltynie, Thomas, Wood, Nicholas W., Williams-Gray, Caroline H., Andreassen, Ole A., Toft, Mathias, Elbaz, Alexis, Artaud, Fanny, Brice, Alexis, Corvol, Jean-Christophe, Aasly, Jan, Farrer, Matthew J., Nalls, Michael A., Singleton, Andrew B., Williams, Nigel M., Ben-Shlomo, Yoav, Hardy, John, Hu, Michele T. M., Grosset, Donald G., Shoai, Maryam, Pihlstrøm, Lasse, and Morris, Huw R.

Published
2024
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3. ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R

Author

Fairbrother-Browne, Aine, García-Ruiz, Sonia, Reynolds, Regina H, Ryten, Mina, and Hodgkinson, Alan

Subjects
Quantitative Biology - Genomics, Computer Science - Databases
Abstract

We present ensemblQueryR, a package providing an R interface to the Ensembl REST API that facilitates flexible, fast, user-friendly and R workflow integrable querying of Ensembl REST API linkage disequilibrium (LD) endpoints, optimised for high-throughput querying. ensemblQueryR achieves this through functions that are intuitive and amenable to custom code integration, use of familiar R object types as inputs and outputs, code optimisation and optional parallelisation functionality. For each LD endpoint, ensemblQueryR provides two functions, permitting both single-query and multi-query modes of operation. The multi-query functions are optimised for large query sizes and provide optional parallelisation to leverage available computational resources and minimise processing time. We demonstrate that ensemblQueryR has improved performance in terms of random access memory (RAM) usage and speed, delivering a 10-fold speed increase over analogous software whilst using a third of the RAM. Finally, ensemblQueryR is near-agnostic to operating system and computational architecture through availability of Docker and singularity images, making this tool widely accessible to the scientific community.

Published
2023

4. Genome sequence analyses identify novel risk loci for multiple system atrophy

Author

Chia, Ruth, Ray, Anindita, Shah, Zalak, Ding, Jinhui, Ruffo, Paola, Fujita, Masashi, Menon, Vilas, Saez-Atienzar, Sara, Reho, Paolo, Kaivola, Karri, Walton, Ronald L., Reynolds, Regina H., Karra, Ramita, Sait, Shaimaa, Akcimen, Fulya, Diez-Fairen, Monica, Alvarez, Ignacio, Fanciulli, Alessandra, Stefanova, Nadia, Seppi, Klaus, Duerr, Susanne, Leys, Fabian, Krismer, Florian, Sidoroff, Victoria, Zimprich, Alexander, Pirker, Walter, Rascol, Olivier, Foubert-Samier, Alexandra, Meissner, Wassilios G., Tison, François, Pavy-Le Traon, Anne, Pellecchia, Maria Teresa, Barone, Paolo, Russillo, Maria Claudia, Marín-Lahoz, Juan, Kulisevsky, Jaime, Torres, Soraya, Mir, Pablo, Periñán, Maria Teresa, Proukakis, Christos, Chelban, Viorica, Wu, Lesley, Goh, Yee Y., Parkkinen, Laura, Hu, Michele T., Kobylecki, Christopher, Saxon, Jennifer A., Rollinson, Sara, Garland, Emily, Biaggioni, Italo, Litvan, Irene, Rubio, Ileana, Alcalay, Roy N., Kwei, Kimberly T., Lubbe, Steven J., Mao, Qinwen, Flanagan, Margaret E., Castellani, Rudolph J., Khurana, Vikram, Ndayisaba, Alain, Calvo, Andrea, Mora, Gabriele, Canosa, Antonio, Floris, Gianluca, Bohannan, Ryan C., Moore, Anni, Norcliffe-Kaufmann, Lucy, Palma, Jose-Alberto, Kaufmann, Horacio, Kim, Changyoun, Iba, Michiyo, Masliah, Eliezer, Dawson, Ted M., Rosenthal, Liana S., Pantelyat, Alexander, Albert, Marilyn S., Pletnikova, Olga, Troncoso, Juan C., Infante, Jon, Lage, Carmen, Sánchez-Juan, Pascual, Serrano, Geidy E., Beach, Thomas G., Pastor, Pau, Morris, Huw R., Albani, Diego, Clarimon, Jordi, Wenning, Gregor K., Hardy, John A., Ryten, Mina, Topol, Eric, Torkamani, Ali, Chiò, Adriano, Bennett, David A., De Jager, Philip L., Low, Philip A., Singer, Wolfgang, Cheshire, William P., Wszolek, Zbigniew K., Dickson, Dennis W., Traynor, Bryan J., Gibbs, J. Raphael, Dalgard, Clifton L., Ross, Owen A., Houlden, Henry, and Scholz, Sonja W.

Published
2024
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9. 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, Martinez-Carrasco, Alejandro, Jama, Alina, Müller-Nedebock, Amica Corda, Gil-Martinez, Ana-Luisa, Illarionova, Anastasia, Moore, Anni, Bustos, Bernabe I., Jadhav, Bharati, Huxford, Brook, Storm, Catherine, Towns, Clodagh, Vitale, Dan, Chetty, Devina, Yu, Eric, Grenn, Francis P., Salazar, Gabriela, Rateau, Geoffrey, Iwaki, Hirotaka, 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., 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, Real, Raquel, Reynolds, Regina H., Hu, Ruifneg, Abrahams, Shameemah, Rao, Shilpa C., Antar, Tarek, Leal, Thiago Peixoto, Iankova, Vassilena, Scotton, William J., Song, Yeajin, Singleton, Andrew, Nalls, Mike A., Dey, Sumit, Bandres-Ciga, Sara, Blauwendraat, Cornelis, and Noyce, Alastair J.

Published
2023
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10. 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, Martinez-Carrasco, Alejandro, Jama, Alina, Müller-Nedebock, Amica Corda, Gil-Martinez, Ana-Luisa, Illarionova, Anastasia, Moore, Anni, Bustos, Bernabe I., Jadhav, Bharati, Huxford, Brook, Storm, Catherine, Towns, Clodagh, Vitale, Dan, Chetty, Devina, Yu, Eric, Grenn, Francis P., Salazar, Gabriela, Rateau, Geoffrey, Iwaki, Hirotaka, 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., 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, Real, Raquel, Reynolds, Regina H., Hu, Ruifneg, Abrahams, Shameemah, Rao, Shilpa C., Antar, Tarek, Leal, Thiago Peixoto, Iankova, Vassilena, Scotton, William J., Song, Yeajin, Singleton, Andrew, Nalls, Mike A., Dey, Sumit, Bandres-Ciga, Sara, Blauwendraat, Cornelis, and Noyce, Alastair J.

Published
2023
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11. Human-lineage-specific genomic elements are associated with neurodegenerative disease and APOE transcript usage

Author

Chen, Zhongbo, Zhang, David, Reynolds, Regina H, Gustavsson, Emil K, García-Ruiz, Sonia, D’Sa, Karishma, Fairbrother-Browne, Aine, Vandrovcova, Jana, Hardy, John, Houlden, Henry, Gagliano Taliun, Sarah A, Botía, Juan, and Ryten, Mina

Subjects
Human Genome, Brain Disorders, Genetics, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Acquired Cognitive Impairment, Neurosciences, Dementia, Biotechnology, Alzheimer's Disease, Neurodegenerative, Aging, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Underpinning research, Aetiology, Neurological, Alzheimer Disease, Apolipoproteins E, Brain, Chromosomes, Human, Pair 19, Conserved Sequence, DNA, Intergenic, Gene Ontology, Genome, Human, Humans, Introns, Linkage Disequilibrium, Molecular Sequence Annotation, Neurodegenerative Diseases, Phenotype, Phylogeny, Polymorphism, Single Nucleotide, RNA, Long Noncoding, RNA, Messenger, Regression Analysis, International Parkinson’s Disease Genomics Consortium
Abstract

Knowledge of genomic features specific to the human lineage may provide insights into brain-related diseases. We leverage high-depth whole genome sequencing data to generate a combined annotation identifying regions simultaneously depleted for genetic variation (constrained regions) and poorly conserved across primates. We propose that these constrained, non-conserved regions (CNCRs) have been subject to human-specific purifying selection and are enriched for brain-specific elements. We find that CNCRs are depleted from protein-coding genes but enriched within lncRNAs. We demonstrate that per-SNP heritability of a range of brain-relevant phenotypes are enriched within CNCRs. We find that genes implicated in neurological diseases have high CNCR density, including APOE, highlighting an unannotated intron-3 retention event. Using human brain RNA-sequencing data, we show the intron-3-retaining transcript to be more abundant in Alzheimer's disease with more severe tau and amyloid pathological burden. Thus, we demonstrate potential association of human-lineage-specific sequences in brain development and neurological disease.

Published
2021

12. Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture

Author

Chia, Ruth, Sabir, Marya S, Bandres-Ciga, Sara, Saez-Atienzar, Sara, Reynolds, Regina H, Gustavsson, Emil, Walton, Ronald L, Ahmed, Sarah, Viollet, Coralie, Ding, Jinhui, Makarious, Mary B, Diez-Fairen, Monica, Portley, Makayla K, Shah, Zalak, Abramzon, Yevgeniya, Hernandez, Dena G, Blauwendraat, Cornelis, Stone, David J, Eicher, John, Parkkinen, Laura, Ansorge, Olaf, Clark, Lorraine, Honig, Lawrence S, Marder, Karen, Lemstra, Afina, St George-Hyslop, Peter, Londos, Elisabet, Morgan, Kevin, Lashley, Tammaryn, Warner, Thomas T, Jaunmuktane, Zane, Galasko, Douglas, Santana, Isabel, Tienari, Pentti J, Myllykangas, Liisa, Oinas, Minna, Cairns, Nigel J, Morris, John C, Halliday, Glenda M, Van Deerlin, Vivianna M, Trojanowski, John Q, Grassano, Maurizio, Calvo, Andrea, Mora, Gabriele, Canosa, Antonio, Floris, Gianluca, Bohannan, Ryan C, Brett, Francesca, Gan-Or, Ziv, Geiger, Joshua T, Moore, Anni, May, Patrick, Krüger, Rejko, Goldstein, David S, Lopez, Grisel, Tayebi, Nahid, Sidransky, Ellen, Norcliffe-Kaufmann, Lucy, Palma, Jose-Alberto, Kaufmann, Horacio, Shakkottai, Vikram G, Perkins, Matthew, Newell, Kathy L, Gasser, Thomas, Schulte, Claudia, Landi, Francesco, Salvi, Erika, Cusi, Daniele, Masliah, Eliezer, Kim, Ronald C, Caraway, Chad A, Monuki, Edwin S, Brunetti, Maura, Dawson, Ted M, Rosenthal, Liana S, Albert, Marilyn S, Pletnikova, Olga, Troncoso, Juan C, Flanagan, Margaret E, Mao, Qinwen, Bigio, Eileen H, Rodríguez-Rodríguez, Eloy, Infante, Jon, Lage, Carmen, González-Aramburu, Isabel, Sanchez-Juan, Pascual, Ghetti, Bernardino, Keith, Julia, Black, Sandra E, Masellis, Mario, Rogaeva, Ekaterina, Duyckaerts, Charles, Brice, Alexis, Lesage, Suzanne, Xiromerisiou, Georgia, Barrett, Matthew J, Tilley, Bension S, Gentleman, Steve, Logroscino, Giancarlo, and Serrano, Geidy E

Subjects
Biological Sciences, Genetics, Human Genome, Alzheimer's Disease Related Dementias (ADRD), Prevention, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Alzheimer's Disease, Aging, Dementia, Brain Disorders, Acquired Cognitive Impairment, Lewy Body Dementia, Biotechnology, Parkinson's Disease, Neurosciences, Neurodegenerative, 2.1 Biological and endogenous factors, Aetiology, Neurological, Adaptor Proteins, Signal Transducing, Alzheimer Disease, Case-Control Studies, Gene Expression Profiling, Genetic Predisposition to Disease, Genome, Human, Genome-Wide Association Study, Glucosylceramidase, Humans, Lewy Body Disease, Nuclear Proteins, Parkinson Disease, Polymorphism, Single Nucleotide, Tumor Suppressor Proteins, alpha-Synuclein, American Genome Center, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

The genetic basis of Lewy body dementia (LBD) is not well understood. Here, we performed whole-genome sequencing in large cohorts of LBD cases and neurologically healthy controls to study the genetic architecture of this understudied form of dementia, and to generate a resource for the scientific community. Genome-wide association analysis identified five independent risk loci, whereas genome-wide gene-aggregation tests implicated mutations in the gene GBA. Genetic risk scores demonstrate that LBD shares risk profiles and pathways with Alzheimer's disease and Parkinson's disease, providing a deeper molecular understanding of the complex genetic architecture of this age-related neurodegenerative condition.

Published
2021

13. Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information.

Author

Guelfi, Sebastian, D'Sa, Karishma, Botía, Juan A, Vandrovcova, Jana, Reynolds, Regina H, Zhang, David, Trabzuni, Daniah, Collado-Torres, Leonardo, Thomason, Andrew, Quijada Leyton, Pedro, Gagliano Taliun, Sarah A, Nalls, Mike A, International Parkinson’s Disease Genomics Consortium (IPDGC), UK Brain Expression Consortium (UKBEC), Small, Kerrin S, Smith, Colin, Ramasamy, Adaikalavan, Hardy, John, Weale, Michael E, and Ryten, Mina

Subjects
International Parkinson’s Disease Genomics Consortium, UK Brain Expression Consortium
Abstract

Genome-wide association studies have generated an increasing number of common genetic variants associated with neurological and psychiatric disease risk. An improved understanding of the genetic control of gene expression in human brain is vital considering this is the likely modus operandum for many causal variants. However, human brain sampling complexities limit the explanatory power of brain-related expression quantitative trait loci (eQTL) and allele-specific expression (ASE) signals. We address this, using paired genomic and transcriptomic data from putamen and substantia nigra from 117 human brains, interrogating regulation at different RNA processing stages and uncovering novel transcripts. We identify disease-relevant regulatory loci, find that splicing eQTLs are enriched for regulatory information of neuron-specific genes, that ASEs provide cell-specific regulatory information with evidence for cellular specificity, and that incomplete annotation of the brain transcriptome limits interpretation of risk loci for neuropsychiatric disease. This resource of regulatory data is accessible through our web server, http://braineacv2.inf.um.es/.

Published
2020

14. The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases

Author

Chen, Zhongbo, Reynolds, Regina H., Pardiñas, Antonio F., Gagliano Taliun, Sarah A., van Rheenen, Wouter, Lin, Kuang, Shatunov, Aleksey, Gustavsson, Emil K., Fogh, Isabella, Jones, Ashley R., Robberecht, Wim, Corcia, Philippe, Chiò, Adriano, Shaw, Pamela J., Morrison, Karen E., Veldink, Jan H., van den Berg, Leonard H., Shaw, Christopher E., Powell, John F., Silani, Vincenzo, Hardy, John A., Houlden, Henry, Owen, Michael J., Turner, Martin R., Ryten, Mina, and Al-Chalabi, Ammar

Published
2023
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15. Mitochondria function associated genes contribute to Parkinson’s Disease risk and later age at onset

Author

Billingsley, Kimberley J, Barbosa, Ines A, Bandrés-Ciga, Sara, Quinn, John P, Bubb, Vivien J, Deshpande, Charu, Botia, Juan A, Reynolds, Regina H, Zhang, David, Simpson, Michael A, Blauwendraat, Cornelis, Gan-Or, Ziv, Gibbs, J Raphael, Nalls, Mike A, Singleton, Andrew, Ryten, Mina, and Koks, Sulev

Subjects
Aging, Brain Disorders, Neurosciences, Parkinson's Disease, Neurodegenerative, Genetics, 2.1 Biological and endogenous factors, Aetiology, Neurological, International Parkinson’s Disease Genomics Consortium, Medical genetics, Risk factors
Abstract

Mitochondrial dysfunction has been implicated in the etiology of monogenic Parkinson's disease (PD). Yet the role that mitochondrial processes play in the most common form of the disease; sporadic PD, is yet to be fully established. Here, we comprehensively assessed the role of mitochondrial function-associated genes in sporadic PD by leveraging improvements in the scale and analysis of PD GWAS data with recent advances in our understanding of the genetics of mitochondrial disease. We calculated a mitochondrial-specific polygenic risk score (PRS) and showed that cumulative small effect variants within both our primary and secondary gene lists are significantly associated with increased PD risk. We further reported that the PRS of the secondary mitochondrial gene list was significantly associated with later age at onset. Finally, to identify possible functional genomic associations we implemented Mendelian randomization, which showed that 14 of these mitochondrial function-associated genes showed functional consequence associated with PD risk. Further analysis suggested that the 14 identified genes are not only involved in mitophagy, but implicate new mitochondrial processes. Our data suggests that therapeutics targeting mitochondrial bioenergetics and proteostasis pathways distinct from mitophagy could be beneficial to treating the early stage of PD.

Published
2019

16. Moving beyond neurons: the role of cell type-specific gene regulation in Parkinson’s disease heritability

Author

Reynolds, Regina H, Botía, Juan, Nalls, Mike A, Hardy, John, Gagliano Taliun, Sarah A, and Ryten, Mina

Subjects
Genetics, Brain Disorders, Human Genome, Parkinson's Disease, Neurodegenerative, Neurosciences, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Neurological, International Parkinson’s Disease Genomics Consortium, System Genomics of Parkinson’s Disease, Neuroscience, Parkinson's disease
Abstract

Parkinson's disease (PD), with its characteristic loss of nigrostriatal dopaminergic neurons and deposition of α-synuclein in neurons, is often considered a neuronal disorder. However, in recent years substantial evidence has emerged to implicate glial cell types, such as astrocytes and microglia. In this study, we used stratified LD score regression and expression-weighted cell-type enrichment together with several brain-related and cell-type-specific genomic annotations to connect human genomic PD findings to specific brain cell types. We found that PD heritability attributable to common variation does not enrich in global and regional brain annotations or brain-related cell-type-specific annotations. Likewise, we found no enrichment of PD susceptibility genes in brain-related cell types. In contrast, we demonstrated a significant enrichment of PD heritability in a curated lysosomal gene set highly expressed in astrocytic, microglial, and oligodendrocyte subtypes, and in LoF-intolerant genes, which were found highly expressed in almost all tested cellular subtypes. Our results suggest that PD risk loci do not lie in specific cell types or individual brain regions, but rather in global cellular processes detectable across several cell types.

Published
2019

17. Genome-wide association study of REM sleep behavior disorder identifies polygenic risk and brain expression effects

Author

Krohn, Lynne, Heilbron, Karl, Blauwendraat, Cornelis, Reynolds, Regina H., Yu, Eric, Senkevich, Konstantin, Rudakou, Uladzislau, Estiar, Mehrdad A., Gustavsson, Emil K., Brolin, Kajsa, Ruskey, Jennifer A., Freeman, Kathryn, Asayesh, Farnaz, Chia, Ruth, Arnulf, Isabelle, Hu, Michele T. M., Montplaisir, Jacques Y., Gagnon, Jean-François, Desautels, Alex, Dauvilliers, Yves, Gigli, Gian Luigi, Valente, Mariarosaria, Janes, Francesco, Bernardini, Andrea, Högl, Birgit, Stefani, Ambra, Ibrahim, Abubaker, Šonka, Karel, Kemlink, David, Oertel, Wolfgang, Janzen, Annette, Plazzi, Giuseppe, Biscarini, Francesco, Antelmi, Elena, Figorilli, Michela, Puligheddu, Monica, Mollenhauer, Brit, Trenkwalder, Claudia, Sixel-Döring, Friederike, Cochen De Cock, Valérie, Monaca, Christelle Charley, Heidbreder, Anna, Ferini-Strambi, Luigi, Dijkstra, Femke, Viaene, Mineke, Abril, Beatriz, Boeve, Bradley F., Scholz, Sonja W., Ryten, Mina, Bandres-Ciga, Sara, Noyce, Alastair, Cannon, Paul, Pihlstrøm, Lasse, Nalls, Mike A., Singleton, Andrew B., Rouleau, Guy A., Postuma, Ronald B., and Gan-Or, Ziv

Published
2022
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18. An integrated genomic approach to dissect the genetic landscape regulating the cell-to-cell transfer of α-synuclein

Author

Kara, Eleanna, Crimi, Alessandro, Wiedmer, Anne, Emmenegger, Marc, Manzoni, Claudia, Bandres-Ciga, Sara, D’Sa, Karishma, Reynolds, Regina H., Botía, Juan A., Losa, Marco, Lysenko, Veronika, Carta, Manfredi, Heinzer, Daniel, Avar, Merve, Chincisan, Andra, Blauwendraat, Cornelis, García-Ruiz, Sonia, Pease, Daniel, Mottier, Lorene, Carrella, Alessandra, Beck-Schneider, Dezirae, Magalhães, Andreia D., Aemisegger, Caroline, Theocharides, Alexandre P.A., Fan, Zhanyun, Marks, Jordan D., Hopp, Sarah C., Abramov, Andrey Y., Lewis, Patrick A., Ryten, Mina, Hardy, John, Hyman, Bradley T., and Aguzzi, Adriano

Published
2021
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20. Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis

Author

Adeleye, Adelani, Alba, Camille, Bacikova, Dagmar, Hupalo, Daniel N., Martinez, Elisa McGrath, Pollard, Harvey B., Sukumar, Gauthaman, Soltis, Anthony R., Tuck, Meila, Zhang, Xijun, Wilkerson, Matthew D., Smith, Bradley N., Ticozzi, Nicola, Fallini, Claudia, Gkazi, Athina Soragia, Topp, Simon D., Kost, Jason, Scotter, Emma L., Kenna, Kevin P., Miller, Jack W., Tiloca, Cinzia, Vance, Caroline, Danielson, Eric W., Troakes, Claire, Colombrita, Claudia, Al-Sarraj, Safa, Lewis, Elizabeth A., King, Andrew, Calini, Daniela, Pensato, Viviana, Castellotti, Barbara, de Belleroche, Jacqueline, Baas, Frank, ten Asbroek, Anneloor L.M.A., Sapp, Peter C., McKenna-Yasek, Diane, McLaughlin, Russell L., Polak, Meraida, Asress, Seneshaw, Esteban-Pérez, Jesús, Muñoz-Blanco, José Luis, Stevic, Zorica, D’Alfonso, Sandra, Mazzini, Letizia, Comi, Giacomo P., Del Bo, Roberto, Ceroni, Mauro, Gagliardi, Stella, Querin, Giorgia, Bertolin, Cinzia, van Rheenen, Wouter, Diekstra, Frank P., Rademakers, Rosa, van Blitterswijk, Marka, Boylan, Kevin B., Lauria, Giuseppe, Duga, Stefano, Corti, Stefania, Cereda, Cristina, Corrado, Lucia, Sorarù, Gianni, Williams, Kelly L., Nicholson, Garth A., Blair, Ian P., Leblond-Manry, Claire, Rouleau, Guy A., Hardiman, Orla, Morrison, Karen E., Veldink, Jan H., van den Berg, Leonard H., Al-Chalabi, Ammar, Pall, Hardev, Shaw, Pamela J., Turner, Martin R., Talbot, Kevin, Taroni, Franco, García-Redondo, Alberto, Wu, Zheyang, Gellera, Cinzia, Ratti, Antonia, Brown, Robert H., Jr., Shaw, Christopher E., Ambrose, John C., Arumugam, Prabhu, Baple, Emma L., Bleda, Marta, Boardman-Pretty, Freya, Boissiere, Jeanne M., Boustred, Christopher R., Brittain, H., Caulfield, Mark J., Chan, Georgia C., Craig, Clare E.H., Daugherty, Louise C., de Burca, Anna, Devereau, Andrew, Elgar, Greg, Foulger, Rebecca E., Fowler, Tom, Furió-Tarí, Pedro, Hackett, Joanne M., Halai, Dina, Hamblin, Angela, Henderson, Shirley, Holman, James E., Hubbard, Tim J.P., Jackson, Rob, Jones, Louise J., Kasperaviciute, Dalia, Kayikci, Melis, Lahnstein, Lea, Lawson, Kay, Leigh, Sarah E.A., Leong, Ivonne U.S., Lopez, Javier F., Maleady-Crowe, Fiona, Mason, Joanne, McDonagh, Ellen M., Moutsianas, Loukas, Mueller, Michael, Murugaesu, Nirupa, Need, Anna C., Odhams, Chris A., Patch, Christine, Perez-Gil, Daniel, Polychronopoulos, Dimitris, Pullinger, John, Rahim, Tahrima, Rendon, Augusto, Riesgo-Ferreiro, Pablo, Rogers, Tim, Savage, Kevin, Sawant, Kushmita, Scott, Richard H., Siddiq, Afshan, Sieghart, Alexander, Smedley, Damian, Smith, Katherine R., Sosinsky, Alona, Spooner, William, Stevens, Helen E., Stuckey, Alexander, Sultana, Razvan, Thomas, Ellen R.A., Thompson, Simon R., Tregidgo, Carolyn, Walsh, Emma, Watters, Sarah A., Welland, Matthew J., Williams, Eleanor, Witkowska, Katarzyna, Wood, Suzanne M., Zarowiecki, Magdalena, Arepalli, Sampath, Auluck, Pavan, Baloh, Robert H., Bowser, Robert, Brice, Alexis, Broach, James, Camu, William, Chiò, Adriano, Cooper-Knock, John, Corcia, Philippe, Drepper, Carsten, Drory, Vivian E., Dunckley, Travis L., Faghri, Faraz, Farren, Jennifer, Feldman, Eva, Floeter, Mary Kay, Fratta, Pietro, Gerhard, Glenn, Gibson, Summer B., Goutman, Stephen A., Heiman-Patterson, Terry D., Hernandez, Dena G., Hoover, Ben, Jansson, Lilja, Kamel, Freya, Kirby, Janine, Kowall, Neil W., Laaksovirta, Hannu, Landi, Francesco, Le Ber, Isabelle, Lumbroso, Serge, MacGowan, Daniel JL., Maragakis, Nicholas J., Mora, Gabriele, Mouzat, Kevin, Myllykangas, Liisa, Nalls, Mike A., Orrell, Richard W., Ostrow, Lyle W., Pamphlett, Roger, Pioro, Erik, Pulst, Stefan M., Ravits, John M., Renton, Alan E., Robberecht, Wim, Robey, Ian, Rogaeva, Ekaterina, Rothstein, Jeffrey D., Sendtner, Michael, Sidle, Katie C., Simmons, Zachary, Stone, David J., Tienari, Pentti J., Trojanowski, John Q., Troncoso, Juan C., Valori, Miko, Van Damme, Philip, Van Den Bosch, Ludo, Zinman, Lorne, Albani, Diego, Borroni, Barbara, Padovani, Alessandro, Bruni, Amalia, Clarimon, Jordi, Dols-Icardo, Oriol, Illán-Gala, Ignacio, Lleó, Alberto, Danek, Adrian, Galimberti, Daniela, Scarpini, Elio, Serpente, Maria, Graff, Caroline, Chiang, Huei-Hsin, Khoshnood, Behzad, Öijerstedt, Linn, Morris, Christopher M., Nacmias, Benedetta, Sorbi, Sandro, Nielsen, Jorgen E., Hjermind, Lynne E., Novelli, Valeria, Puca, Annibale A., Pastor, Pau, Alvarez, Ignacio, Diez-Fairen, Monica, Aguilar, Miquel, Perneczky, Robert, Diehl-Schimd, Janine, Rossi, Mina, Ruiz, Agustin, Boada, Mercè, Hernández, Isabel, Moreno-Grau, Sonia, Schlachetzki, Johannes C., Aarsland, Dag, Albert, Marilyn S., Attems, Johannes, Barrett, Matthew J., Beach, Thomas G., Bekris, Lynn M., Bennett, David A., Besser, Lilah M., Bigio, Eileen H., Black, Sandra E., Boeve, Bradley F., Bohannan, Ryan C., Brett, Francesca, Brunetti, Maura, Caraway, Chad A., Palma, Jose-Alberto, Calvo, Andrea, Canosa, Antonio, Dickson, Dennis, Duyckaerts, Charles, Faber, Kelley, Ferman, Tanis, Flanagan, Margaret E., Floris, Gianluca, Foroud, Tatiana M., Fortea, Juan, Gan-Or, Ziv, Gentleman, Steve, Ghetti, Bernardino, Gibbs, Jesse Raphael, Goate, Alison, Goldstein, David, González-Aramburu, Isabel, Graff-Radford, Neill R., Hodges, Angela K., Hu, Heng-Chen, Hupalo, Daniel, Infante, Jon, Iranzo, Alex, Kaiser, Scott M., Kaufmann, Horacio, Keith, Julia, Kim, Ronald C., Klein, Gregory, Krüger, Rejko, Kukull, Walter, Kuzma, Amanda, Lage, Carmen, Lesage, Suzanne, Leverenz, James B., Logroscino, Giancarlo, Lopez, Grisel, Love, Seth, Mao, Qinwen, Marti, Maria Jose, Martinez-McGrath, Elisa, Masellis, Mario, Masliah, Eliezer, May, Patrick, McKeith, Ian, Mesulam, Marek-Marsel, Monuki, Edwin S., Newell, Kathy L., Norcliffe-Kaufmann, Lucy, Palmer, Laura, Perkins, Matthew, Pletnikova, Olga, Molina-Porcel, Laura, Reynolds, Regina H., Rodríguez-Rodríguez, Eloy, Rohrer, Jonathan D., Sanchez-Juan, Pascual, Scherzer, Clemens R., Serrano, Geidy E., Shakkottai, Vikram, Sidransky, Ellen, Tayebi, Nahid, Thomas, Alan J., Tilley, Bension S., Walton, Ronald L., Woltjer, Randy, Wszolek, Zbigniew K., Xiromerisiou, Georgia, Zecca, Chiara, Phatnani, Hemali, Kwan, Justin, Sareen, Dhruv, Broach, James R., Arcila-Londono, Ximena, Lee, Edward B., Shneider, Neil A., Fraenkel, Ernest, Zaitlen, Noah, Berry, James D., Malaspina, Andrea, Cox, Gregory A., Thompson, Leslie M., Finkbeiner, Steve, Dardiotis, Efthimios, Miller, Timothy M., Chandran, Siddharthan, Pal, Suvankar, Hornstein, Eran, MacGowan, Daniel J., Heiman-Patterson, Terry, Hammell, Molly G., Patsopoulos, Nikolaos.A., Butovsky, Oleg, Dubnau, Joshua, Nath, Avindra, Harms, Matt, Aronica, Eleonora, Poss, Mary, Phillips-Cremins, Jennifer, Crary, John, Atassi, Nazem, Lange, Dale J., Adams, Darius J., Stefanis, Leonidas, Gotkine, Marc, Babu, Suma, Raj, Towfique, Paganoni, Sabrina, Shalem, Ophir, Smith, Colin, Zhang, Bin, Harris, Brent, Broce, Iris, Drory, Vivian, Ravits, John, McMillan, Corey, Menon, Vilas, Wu, Lani, Altschuler, Steven, Amar, Khaled, Archibald, Neil, Bandmann, Oliver, Capps, Erica, Church, Alistair, Coebergh, Jan, Costantini, Alyssa, Critchley, Peter, Ghosh, Boyd CP., Hu, Michele T.M., Kobylecki, Christopher, Leigh, P. Nigel, Mann, Carl, Massey, Luke A., Morris, Huw R., Nath, Uma, Pavese, Nicola, Paviour, Dominic, Sharma, Jagdish, Vaughan, Jenny, Dewan, Ramita, Chia, Ruth, Ding, Jinhui, Hickman, Richard A., Stein, Thor D., Abramzon, Yevgeniya, Ahmed, Sarah, Sabir, Marya S., Portley, Makayla K., Tucci, Arianna, Ibáñez, Kristina, Shankaracharya, F.N.U., Keagle, Pamela, Rossi, Giacomina, Caroppo, Paola, Tagliavini, Fabrizio, Waldo, Maria L., Johansson, Per M., Nilsson, Christer F., Rowe, James B., Benussi, Luisa, Binetti, Giuliano, Ghidoni, Roberta, Jabbari, Edwin, Viollet, Coralie, Glass, Jonathan D., Singleton, Andrew B., Silani, Vincenzo, Ross, Owen A., Ryten, Mina, Torkamani, Ali, Tanaka, Toshiko, Ferrucci, Luigi, Resnick, Susan M., Pickering-Brown, Stuart, Brady, Christopher B., Kowal, Neil, Hardy, John A., Van Deerlin, Vivianna, Vonsattel, Jean Paul, Harms, Matthew B., Ferrari, Raffaele, Landers, John E., Gibbs, J. Raphael, Dalgard, Clifton L., Scholz, Sonja W., and Traynor, Bryan J.

Published
2021
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21. Genetic determinants of survival in progressive supranuclear palsy: a genome-wide association study

Author

Mok, Kin Y., Murphy, David P., Al-Sarraj, Safa, Troakes, Claire, Gentleman, Steve M., Allinson, Kieren S.J., Jaunmuktane, Zane, Holton, Janice L., Lees, Andrew J., Morris, Christopher M., Compta, Yaroslau, Gelpi, Ellen, van Swieten, John C., Rajput, Alex, Ferguson, Leslie, Cookson, Mark R., Gibbs, J. Raphael, Blauwendraat, Cornelis, Ding, Jinhui, Chia, Ruth, Traynor, Bryan J., Pantelyat, Alexander, Viollet, Coralie, Pletnikova, Olga, Troncoso, Juan C., Rosenthal, Liana S., Boxer, Adam L., Respondek, Gesine, Arzberger, Thomas, Roeber, Sigrun, Giese, Armin, Burn, David J., Pavese, Nicola, Gerhard, Alexander, Kobylecki, Christopher, Leigh, P. Nigel, Church, Alistair, T.M. Hu, Michele, Jabbari, Edwin, Koga, Shunsuke, Valentino, Rebecca R, Reynolds, Regina H, Ferrari, Raffaele, Tan, Manuela M X, Rowe, James B, Dalgard, Clifton L, Scholz, Sonja W, Dickson, Dennis W, Warner, Thomas T, Revesz, Tamas, Höglinger, Günter U, Ross, Owen A, Ryten, Mina, Hardy, John, Shoai, Maryam, and Morris, Huw R

Published
2021
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22. Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes

Author

D'Sa, Karishma, primary, Choi, Minee L., additional, Wagen, Aaron Z., additional, Setó-Salvia, Núria, additional, Kopach, Olga, additional, Evans, James R., additional, Rodrigues, Margarida, additional, Lopez-Garcia, Patricia, additional, Ghareeb, Ali, additional, Bayne, James, additional, Grant-Peters, Melissa, additional, Garcia-Ruiz, Sonia, additional, Chen, Zhongbo, additional, Rodriques, Samuel, additional, Athauda, Dilan, additional, Gustavsson, Emil, additional, Gagliano Taliun, Sarah A., additional, Reynolds, Regina H., additional, Young, George, additional, Strohbuecker, Stephanie, additional, Warner, Tom, additional, Rusakov, Dmitri A., additional, Patani, Rickie, additional, Bryant, Clare, additional, Klenerman, David A., additional, Gandhi, Sonia, additional, and Ryten, Mina, additional

Published
2024
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25. The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson's disease data

Author

Michael J. Fox Foundation for Parkinson's Research, Aligning Science Against Parkinson's, National Institutes of Health (US), National Institute on Aging (US), National Institute of Neurological Disorders and Stroke (US), Leonard, Hampton [0000-0003-2390-8110], Illarionova, Anastasia [0000-0002-1711-7155], Moore, Anni [0000-0003-1953-6449], Bustos, Bernabé I. [0000-0003-2679-9503], Huxford, Brook [0000-0002-5908-6983], Storm, Catherine S. [0000-0003-4957-1712], Towns, Clodagh [0000-0001-8418-6241], Yu, Eric [0000-0003-3525-4564], Elsayed, Inas [0000-0003-4646-8218], Lake, Julie [0000-0002-3441-2455], Brolin, Kajsa [0000-0003-4832-922X], Senkevich, Konstantin [0000-0003-3407-5716], Tan, Manuela M. X. [0000-0001-5835-669X], Makarious, Mary B [.0000-0002-7978-1051], Pillay, Nikita Simone [0000-0002-9058-0920], Betancor, Oswaldo Lorenzo [0000-0002-5607-8363], Real, Raquel [0000-0001-8117-742X], Reynolds, Regina H. [0000-0001-6470-7919], Scotton, William J. [0000-0003-0607-3190], Singleton, Andrew [0000-0001-5606-700X], Dey, Sumit [0000-0002-9087-4486], Blauwendraat, Cornelis [0000-0001-9358-8111], Noyce, Alastair [0000-0003-3027-5497], Leonard, Hampton, Murtadha, Ruqaya, Martínez-Carrasco, Alejandro, Jama, Alina, Müller-Nedebock, Amica Corda, Gil-Martínez, Ana Luisa, Illarionova, Anastasia, Moore, Anni, Bustos, Bernabé I., Jadhav, Bharati, Huxford, Brook, Storm, Catherine S., Towns, Clodagh, Vitale, Dan, Chetty, Devina, Yu, Eric, Grenn, Francis P., Salazar, Gabriela, Rateau, Geoffrey, Iwaki, Hirotaka, 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., Periñán, María Teresa, Makarious, Mary B., Ta, Michael, Pillay, Nikita Simone, Betancor, Oswaldo Lorenzo, Reyes-Pérez, Paula R., Álvarez Jerez, Pilar, Saini, Prabhjyot, Al-Ouran, Rami, Sivakumar, Ramiya, Real, Raquel, Reynolds, Regina H., Hu, Ruifneg, Abrahams, Shameemah, Rao, Shilpa C., Antar, Tarek, Leal, Thiago Peixoto, Iankova, Vassilena, Scotton, William J., Song, Yeajin, Singleton, Andrew, Nalls, Mike A., Dey, Sumit, Bandres-Ciga, Sara, Blauwendraat, Cornelis, Noyce, Alastair, International Parkinson’s Disease Genomics Consortium, Global Parkinson’s Genetics Program, Michael J. Fox Foundation for Parkinson's Research, Aligning Science Against Parkinson's, National Institutes of Health (US), National Institute on Aging (US), National Institute of Neurological Disorders and Stroke (US), Leonard, Hampton [0000-0003-2390-8110], Illarionova, Anastasia [0000-0002-1711-7155], Moore, Anni [0000-0003-1953-6449], Bustos, Bernabé I. [0000-0003-2679-9503], Huxford, Brook [0000-0002-5908-6983], Storm, Catherine S. [0000-0003-4957-1712], Towns, Clodagh [0000-0001-8418-6241], Yu, Eric [0000-0003-3525-4564], Elsayed, Inas [0000-0003-4646-8218], Lake, Julie [0000-0002-3441-2455], Brolin, Kajsa [0000-0003-4832-922X], Senkevich, Konstantin [0000-0003-3407-5716], Tan, Manuela M. X. [0000-0001-5835-669X], Makarious, Mary B [.0000-0002-7978-1051], Pillay, Nikita Simone [0000-0002-9058-0920], Betancor, Oswaldo Lorenzo [0000-0002-5607-8363], Real, Raquel [0000-0001-8117-742X], Reynolds, Regina H. [0000-0001-6470-7919], Scotton, William J. [0000-0003-0607-3190], Singleton, Andrew [0000-0001-5606-700X], Dey, Sumit [0000-0002-9087-4486], Blauwendraat, Cornelis [0000-0001-9358-8111], Noyce, Alastair [0000-0003-3027-5497], Leonard, Hampton, Murtadha, Ruqaya, Martínez-Carrasco, Alejandro, Jama, Alina, Müller-Nedebock, Amica Corda, Gil-Martínez, Ana Luisa, Illarionova, Anastasia, Moore, Anni, Bustos, Bernabé I., Jadhav, Bharati, Huxford, Brook, Storm, Catherine S., Towns, Clodagh, Vitale, Dan, Chetty, Devina, Yu, Eric, Grenn, Francis P., Salazar, Gabriela, Rateau, Geoffrey, Iwaki, Hirotaka, 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., Periñán, María Teresa, Makarious, Mary B., Ta, Michael, Pillay, Nikita Simone, Betancor, Oswaldo Lorenzo, Reyes-Pérez, Paula R., Álvarez Jerez, Pilar, Saini, Prabhjyot, Al-Ouran, Rami, Sivakumar, Ramiya, Real, Raquel, Reynolds, Regina H., Hu, Ruifneg, Abrahams, Shameemah, Rao, Shilpa C., Antar, Tarek, Leal, Thiago Peixoto, Iankova, Vassilena, Scotton, William J., Song, Yeajin, Singleton, Andrew, Nalls, Mike A., Dey, Sumit, Bandres-Ciga, Sara, Blauwendraat, Cornelis, Noyce, Alastair, International Parkinson’s Disease Genomics Consortium, and Global Parkinson’s Genetics Program

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

27. The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases

Author

Neurologen, Brain, Neuromuscular Disorders, Genetic Risks, Projectafdeling ALS, Regenerative Medicine and Stem Cells, Chen, Zhongbo, Reynolds, Regina H, Pardiñas, Antonio F, Gagliano Taliun, Sarah A, van Rheenen, Wouter, Lin, Kuang, Shatunov, Aleksey, Gustavsson, Emil K, Fogh, Isabella, Jones, Ashley R, Robberecht, Wim, Corcia, Philippe, Chiò, Adriano, Shaw, Pamela J, Morrison, Karen E, Veldink, Jan H, van den Berg, Leonard H, Shaw, Christopher E, Powell, John F, Silani, Vincenzo, Hardy, John A, Houlden, Henry, Owen, Michael J, Turner, Martin R, Ryten, Mina, Al-Chalabi, Ammar, Neurologen, Brain, Neuromuscular Disorders, Genetic Risks, Projectafdeling ALS, Regenerative Medicine and Stem Cells, Chen, Zhongbo, Reynolds, Regina H, Pardiñas, Antonio F, Gagliano Taliun, Sarah A, van Rheenen, Wouter, Lin, Kuang, Shatunov, Aleksey, Gustavsson, Emil K, Fogh, Isabella, Jones, Ashley R, Robberecht, Wim, Corcia, Philippe, Chiò, Adriano, Shaw, Pamela J, Morrison, Karen E, Veldink, Jan H, van den Berg, Leonard H, Shaw, Christopher E, Powell, John F, Silani, Vincenzo, Hardy, John A, Houlden, Henry, Owen, Michael J, Turner, Martin R, Ryten, Mina, and Al-Chalabi, Ammar

Published
2023

29. IntroVerse: a comprehensive database of introns across human tissues

Author

García-Ruiz, Sonia, primary, Gustavsson, Emil K, additional, Zhang, David, additional, Reynolds, Regina H, additional, Chen, Zhongbo, additional, Fairbrother-Browne, Aine, additional, Gil-Martínez, Ana Luisa, additional, Botia, Juan A, additional, Collado-Torres, Leonardo, additional, and Ryten, Mina, additional

Published
2022
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30. Association between the LRP1B and APOE loci and the development of Parkinson’s disease dementia

Author

Real, Raquel, primary, Martinez-Carrasco, Alejandro, additional, Reynolds, Regina H, additional, Lawton, Michael A, additional, Tan, Manuela M X, additional, Shoai, Maryam, additional, Corvol, Jean-Christophe, additional, Ryten, Mina, additional, Bresner, Catherine, additional, Hubbard, Leon, additional, Brice, Alexis, additional, Lesage, Suzanne, additional, Faouzi, Johann, additional, Elbaz, Alexis, additional, Artaud, Fanny, additional, Williams, Nigel, additional, Hu, Michele T M, additional, Ben-Shlomo, Yoav, additional, Grosset, Donald G, additional, Hardy, John, additional, and Morris, Huw R, additional

Published
2022
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31. Association of genetic variation at the GJA5/ACP6 locus with motor progression in Parkinson’s

Author

Martinez-Carrasco, Alejandro, primary, Real, Raquel, additional, Lawton, Michael, additional, Reynolds, Regina H, additional, Tan, Manuela M. X., additional, Wu, Lesley, additional, Williams, Nigel M., additional, Carroll, Camille, additional, Corvol, Jean-Christophe, additional, Hu, Michele T.M., additional, Grosset, Donald G., additional, Hardy, John, additional, Ryten, Mina, additional, Ben-Shlomo, Yoav, additional, Shoai, Maryam, additional, and Morris, Huw R., additional

Published
2022
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32. Analysis of subcellular RNA fractions demonstrates significant genetic regulation of gene expression in human brain post-transcriptionally.

Author

D'Sa, Karishma, Guelfi, Sebastian, Vandrovcova, Jana, Reynolds, Regina H., Zhang, David, Hardy, John, Botía, Juan A., Weale, Michael E., Taliun, Sarah A. Gagliano, Small, Kerrin S., and Ryten, Mina

Subjects
GENETIC regulation, RNA analysis, GENE expression, RNA regulation, GENOMICS, POSTMORTEM changes, BRAIN physiology
Abstract

Gaining insight into the genetic regulation of gene expression in human brain is key to the interpretation of genome-wide association studies for major neurological and neuropsychiatric diseases. Expression quantitative trait loci (eQTL) analyses have largely been used to achieve this, providing valuable insights into the genetic regulation of steady-state RNA in human brain, but not distinguishing between molecular processes regulating transcription and stability. RNA quantification within cellular fractions can disentangle these processes in cell types and tissues which are challenging to model in vitro. We investigated the underlying molecular processes driving the genetic regulation of gene expression specific to a cellular fraction using allele-specific expression (ASE). Applying ASE analysis to genomic and transcriptomic data from paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control human brains, we demonstrate that a significant proportion of genetic regulation of gene expression occurs post-transcriptionally in the cytoplasm, with genes undergoing this form of regulation more likely to be synaptic. These findings have implications for understanding the structure of gene expression regulation in human brain, and importantly the interpretation of rapidly growing single-nucleus brain RNA-sequencing and eQTL datasets, where cytoplasm-specific regulatory events could be missed. [ABSTRACT FROM AUTHOR]

Published
2023
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33. The annotation and function of the Parkinson’s and Gaucher disease-linked geneGBA1has been concealed by its protein-coding pseudogeneGBAP1

Author

Gustavsson, Emil K., primary, Sethi, Siddharth, additional, Gao, Yujing, additional, Brenton, Jonathan W., additional, García-Ruiz, Sonia, additional, Zhang, David, additional, Garza, Raquel, additional, Reynolds, Regina H., additional, Evans, James R., additional, Chen, Zhongbo, additional, Grant-Peters, Melissa, additional, Macpherson, Hannah, additional, Montgomery, Kylie, additional, Dore, Rhys, additional, Wernick, Anna I., additional, Arber, Charles, additional, Wray, Selina, additional, Gandhi, Sonia, additional, Esselborn, Julian, additional, Blauwendraat, Cornelis, additional, Douse, Christopher H., additional, Adami, Anita, additional, Atacho, Diahann A.M., additional, Kouli, Antonina, additional, Quaegebeur, Annelies, additional, Barker, Roger A., additional, Englund, Elisabet, additional, Platt, Frances, additional, Jakobsson, Johan, additional, Wood, Nicholas W., additional, Houlden, Henry, additional, Saini, Harpreet, additional, Bento, Carla F., additional, Hardy, John, additional, and Ryten, Mina, additional

Published
2022
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34. Functional genomics provide key insights to improve the diagnostic yield of hereditary ataxia.

Author

Chen, Zhongbo, Tucci, Arianna, Cipriani, Valentina, Gustavsson, Emil K, Ibañez, Kristina, Reynolds, Regina H, Zhang, David, Vestito, Letizia, García, Alejandro Cisterna, Sethi, Siddharth, Brenton, Jonathan W, García-Ruiz, Sonia, Fairbrother-Browne, Aine, Gil-Martinez, Ana-Luisa, Consortium, Genomics England Research, Wood, Nick, Hardy, John A, Smedley, Damian, Houlden, Henry, and Botía, Juan

Subjects
FRIEDREICH'S ataxia, SPINOCEREBELLAR ataxia, FUNCTIONAL genomics, MICROSATELLITE repeats, GENE expression, WHOLE genome sequencing
Abstract

Improvements in functional genomic annotation have led to a critical mass of neurogenetic discoveries. This is exemplified in hereditary ataxia, a heterogeneous group of disorders characterised by incoordination from cerebellar dysfunction. Associated pathogenic variants in more than 300 genes have been described, leading to a detailed genetic classification partitioned by age-of-onset. Despite these advances, up to 75% of patients with ataxia remain molecularly undiagnosed even following whole genome sequencing, as exemplified in the 100 000 Genomes Project. This study aimed to understand whether we can improve our knowledge of the genetic architecture of hereditary ataxia by leveraging functional genomic annotations, and as a result, generate insights and strategies that raise the diagnostic yield. To achieve these aims, we used publicly-available multi-omics data to generate 294 genic features, capturing information relating to a gene's structure, genetic variation, tissue-specific, cell-type-specific and temporal expression, as well as protein products of a gene. We studied these features across genes typically causing childhood-onset, adult-onset or both types of disease first individually, then collectively. This led to the generation of testable hypotheses which we investigated using whole genome sequencing data from up to 2182 individuals presenting with ataxia and 6658 non-neurological probands recruited in the 100 000 Genomes Project. Using this approach, we demonstrated a high short tandem repeat (STR) density within childhood-onset genes suggesting that we may be missing pathogenic repeat expansions within this cohort. This was verified in both childhood- and adult-onset ataxia patients from the 100 000 Genomes Project who were unexpectedly found to have a trend for higher repeat sizes even at naturally-occurring STRs within known ataxia genes, implying a role for STRs in pathogenesis. Using unsupervised analysis, we found significant similarities in genomic annotation across the gene panels, which suggested adult- and childhood-onset patients should be screened using a common diagnostic gene set. We tested this within the 100 000 Genomes Project by assessing the burden of pathogenic variants among childhood-onset genes in adult-onset patients and vice versa. This demonstrated a significantly higher burden of rare, potentially pathogenic variants in conventional childhood-onset genes among individuals with adult-onset ataxia. Our analysis has implications for the current clinical practice in genetic testing for hereditary ataxia. We suggest that the diagnostic rate for hereditary ataxia could be increased by removing the age-of-onset partition, and through a modified screening for repeat expansions in naturally-occurring STRs within known ataxia-associated genes, in effect treating these regions as candidate pathogenic loci. [ABSTRACT FROM AUTHOR]

Published
2023
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35. Association between the LRP1B and APOE loci in the development of Parkinson's disease dementia.

Author

Real, Raquel, Martinez-Carrasco, Alejandro, Reynolds, Regina H, Lawton, Michael A, Tan, Manuela M X, Shoai, Maryam, Corvol, Jean-Christophe, Ryten, Mina, Bresner, Catherine, Hubbard, Leon, Brice, Alexis, Lesage, Suzanne, Faouzi, Johann, Elbaz, Alexis, Artaud, Fanny, Williams, Nigel, Hu, Michele T M, Ben-Shlomo, Yoav, Grosset, Donald G, and Hardy, John

Subjects
PARKINSON'S disease, MOVEMENT disorders, DEMENTIA, APOLIPOPROTEIN E, LOCUS (Genetics), COGNITION disorders
Abstract

Parkinson's disease is one of the most common age-related neurodegenerative disorders. Although predominantly a motor disorder, cognitive impairment and dementia are important features of Parkinson's disease, particularly in the later stages of the disease. However, the rate of cognitive decline varies among Parkinson's disease patients, and the genetic basis for this heterogeneity is incompletely understood. To explore the genetic factors associated with rate of progression to Parkinson's disease dementia, we performed a genome-wide survival meta-analysis of 3,923 clinically diagnosed Parkinson's disease cases of European ancestry from four longitudinal cohorts. In total, 6.7% of individuals with Parkinson's disease developed dementia during study follow-up, on average 4.4 ± 2.4 years from disease diagnosis. We have identified the APOE ε4 allele as a major risk factor for the conversion to Parkinson's disease dementia [hazards ratio = 2.41 (1.94-3.00), P = 2.32 × 10-15], as well as a new locus within the ApoE and APP receptor LRP1B gene [hazards ratio = 3.23 (2.17-4.81), P = 7.07 × 10-09]. In a candidate gene analysis, GBA variants were also identified to be associated with higher risk of progression to dementia [hazards ratio = 2.02 (1.21-3.32), P = 0.007]. CSF biomarker analysis also implicated the amyloid pathway in Parkinson's disease dementia, with significantly reduced levels of amyloid β42 (P = 0.0012) in Parkinson's disease dementia compared to Parkinson's disease without dementia. These results identify a new candidate gene associated with faster conversion to dementia in Parkinson's disease and suggest that amyloid-targeting therapy may have a role in preventing Parkinson's disease dementia. [ABSTRACT FROM AUTHOR]

Published
2023
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36. Genome-wide determinants of mortality and motor progression in Parkinson’s disease

Author

Tan, Manuela MX, primary, Lawton, Michael A, additional, Pollard, Miriam I, additional, Brown, Emmeline, additional, Real, Raquel, additional, Martinez Carrasco, Alejandro, additional, Bekadar, Samir, additional, Jabbari, Edwin, additional, Reynolds, Regina H, additional, Iwaki, Hirotaka, additional, Blauwendraat, Cornelis, additional, Kanavou, Sofia, additional, Hubbard, Leon, additional, Malek, Naveed, additional, Grosset, Katherine A, additional, Bajaj, Nin, additional, Barker, Roger A, additional, Burn, David J, additional, Bresner, Catherine, additional, Foltynie, Thomas, additional, Wood, Nicholas W, additional, Williams-Gray, Caroline H, additional, Andreassen, Ole A, additional, Toft, Mathias, additional, Elbaz, Alexis, additional, Artaud, Fanny, additional, Brice, Alexis, additional, Corvol, Jean-Christophe, additional, Aasly, Jan, additional, Farrer, Matthew J, additional, Nalls, Michael A, additional, Singleton, Andrew B, additional, Williams, Nigel M, additional, Ben-Shlomo, Yoav, additional, Hardy, John, additional, Hu, Michele TM, additional, Grosset, Donald G, additional, Shoai, Maryam, additional, Pihlstrøm, Lasse, additional, and Morris, Huw R, additional

Published
2022
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37. Analysis of nucleus and cytoplasm-specific RNA fractions demonstrates that a significant proportion of the genetic regulation of gene expression across the human brain occurs post-transcriptionally

Author

D'Sa, Karishma, primary, Guelfi, Sebastian, additional, Vandrovcova, Jana, additional, Reynolds, Regina H., additional, Zhang, David, additional, Hardy, John, additional, Botía, Juan A., additional, Weale, Michael E., additional, Taliun, Sarah A. Gagliano, additional, Small, Kerrin S., additional, and Ryten, Mina, additional

Published
2022
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40. Association between the LRP1B and APOEloci and the development of Parkinson's disease dementia

Author

Real, Raquel, primary, Martinez-Carrasco, Alejandro, additional, Reynolds, Regina H., additional, Lawton, Michael A., additional, Tan, Manuela M. X., additional, Shoai, Maryam, additional, Corvol, Jean-Christophe, additional, Ryten, Mina, additional, Bresner, Catherine, additional, Hubbard, Leon, additional, Brice, Alexis, additional, Lesage, Suzanne, additional, Faouzi, Johann, additional, Elbaz, Alexis, additional, Artaud, Fanny, additional, Williams, Nigel, additional, Hu, Michele T. M., additional, Ben-Shlomo, Yoav, additional, Grosset, Donald G., additional, Hardy, John, additional, and Morris, Huw R., additional

Published
2022
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41. 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., primary, Murtadha, Ruqaya, additional, Martinez-Carrasco, Alejandro, additional, Muller-Nedebock, Amica, additional, Gil-Martinez, Ana-Luisa, additional, Illarionova, Anastasia, additional, Moore, Anni, additional, Bustos, Bernabe I., additional, Jadhav, Bharati, additional, Huxford, Brook, additional, Storm, Catherine, additional, Towns, Clodagh, additional, Vitale, Dan, additional, Chetty, Devina, additional, Yu, Eric, additional, Jama, Fatumah, additional, Grenn, Francis P., additional, Salazar, Gabriela, additional, Rateau, Geoffrey, additional, Iwaki, Hirotaka, additional, Elsayed, Inas, additional, Foote, Isabelle, additional, van Rensburg, Zuné Jansen, additional, Kim, Jonggeol Jeff, additional, Yuan, Jie, additional, Lake, Julie, additional, Brolin, Kajsa, additional, Senkevich, Konstantin, additional, Wu, Lesley, additional, Tan, Manuela M.X., additional, Periñán, María Teresa, additional, Makarious, Mary B, additional, Ta, Michael, additional, Pillay, Nikita Simone, additional, Betancor, Oswaldo Lorenzo, additional, Reyes-Pérez, Paula R., additional, Jerez, Pilar Alvarez, additional, Saini, Prabhjyot, additional, al-Ouran, Rami, additional, Sivakumar, Ramiya, additional, Real, Raquel, additional, Reynolds, Regina H., additional, Hu, Ruifneg, additional, Abrahams, Shameemah, additional, Rao, Shilpa C., additional, Antar, Tarek, additional, Leal, Thiago Peixoto, additional, Iankova, Vassilena, additional, Scotton, William J., additional, Song, Yeajin, additional, Singleton, Andrew, additional, Nalls, Mike A., additional, Dey, Sumit, additional, Bandres-Ciga, Sara, additional, Blauwendraat, Cornelis, additional, and Noyce, Alastair J., additional

Published
2022
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42. The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases

Author

Chen, Zhongbo, primary, Reynolds, Regina H., additional, Pardiñas, Antonio F., additional, Gagliano Taliun, Sarah A., additional, van Rheenen, Wouter, additional, Lin, Kuang, additional, Shatunov, Aleksey, additional, Gustavsson, Emil K., additional, Fogh, Isabella, additional, Jones, Ashley R., additional, Robberecht, Wim, additional, Corcia, Philippe, additional, Chiò, Adriano, additional, Shaw, Pamela J., additional, Morrison, Karen E., additional, Veldink, Jan H., additional, van den Berg, Leonard H., additional, Shaw, Christopher E., additional, Powell, John F., additional, Silani, Vincenzo, additional, Hardy, John A., additional, Houlden, Henry, additional, Owen, Michael J., additional, Turner, Martin R., additional, Ryten, Mina, additional, and Al-Chalabi, Ammar, additional

Published
2022
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45. A genetic link between risk for Alzheimer's disease and severe COVID-19 outcomes via the OAS1 gene

Author

Magusali, Naciye, primary, Graham, Andrew C, additional, Piers, Thomas M, additional, Panichnantakul, Pantila, additional, Yaman, Umran, additional, Shoai, Maryam, additional, Reynolds, Regina H, additional, Botia, Juan A, additional, Brookes, Keeley J, additional, Guetta-Baranes, Tamar, additional, Bellou, Eftychia, additional, Bayram, Sevinc, additional, Sokolova, Dimitra, additional, Ryten, Mina, additional, Sala Frigerio, Carlo, additional, Escott-Price, Valentina, additional, Morgan, Kevin, additional, Pocock, Jennifer M, additional, Hardy, John, additional, and Salih, Dervis A, additional

Published
2021
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46. Identification of candidate parkinson disease genes by integrating genome-wide association study, expression, and epigenetic data sets

Author

Kia, Demis A., Zhang, David, Guelfi, Sebastian, Manzoni, Claudia, Hubbard, Leon, Reynolds, Regina H., Botía, Juan, Ryten, Mina, Ferrari, Raffaele, Lewis, Patrick A., Williams, Nigel, Trabzuni, Daniah, Hardy, John, Wood, Nicholas W., Noyce, Alastair J., Kaiyrzhanov, Rauan, Middlehurst, Ben, Tan, Manuela, Houlden, Henry, Morris, Huw R., Plun-Favreau, Helene, Holmans, Peter, Bras, Jose, PhD, John Quinn, Mok, Kin Y., Kinghorn, Kerri J., Billingsley, Kimberley, Lewis, Patrick, Schreglmann, Sebastian, Guerreiro, Rita, Lovering, Ruth, R'Bibo, Lea, Rizig, Mie, Escott-Price, Valentina, Chelban, Viorica, Foltynie, Thomas, Brice, Alexis, Danjou, Fabrice, Lesage, Suzanne, Corvol, Jean-Christophe, Martinez, Maria, Schulte, Claudia, Brockmann, Kathrin, Simón-Sánchez, Javier, Heutink, Peter, Rizzu, Patrizia, Sharma, Manu, Gasser, Thomas, Nicolas, Aude, Cookson, Mark R., Bandres-Ciga, Sara, Blauwendraat, Cornelis, Craig, David W., Faghri, Faraz, Gibbs, J. Raphael, Hernandez, Dena G., Van Keuren-Jensen, Kendall, Shulman, Joshua M., Leonard, Hampton L., Nalls, Mike A., Robak, Laurie, Lubbe, Steven, Finkbeiner, Steven, Mencacci, Niccolo E., Lungu, Codrin, Singleton, Andrew B, Scholz, Sonja W., 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, Alvarez, Victoria, Javier Barrero, Francisco, Bergareche Yarza, Jesús A., Bernal-Bernal, Inmaculada, Blazquez, Marta, Bonilla-Toribio, Marta, Botía, Juan A., Boungiorno, María T., Buiza-Rueda, Dolores, Càmara, Ana, Carrillo, Fátima, Carrión-Claro, Mario, Cerdan, Debora, Clarimón, Jordi, Compta, Yaroslau, Diez-Fairen, Monica, Dols-Icardo, Oriol, Duarte, Jacinto, Duran, Raquel, Escamilla-Sevilla, Francisco, Ezquerra, Mario, Feliz, Cici, Fernàndez, Manel, Fernàndez-Santiago, Rubén, Garcia, Ciara, García-Ruiz, Pedro, Gómez-Garre, Pilar, Gomez Heredia, Maria J., Gonzalez-Aramburu, Isabel, Pagola, Ana G., Hoenicka, Janet, Infante, Jon, Jimenez-Escrig, Adriano, Kulisevsky, Jaime, Labrador-Espinosa, Miguel A., Lopez-Sendon, Jose Luis, Arregui, Adolfo López de Munain, Macias, Daniel, Torres, Irene Martínez, Marín, Juan, Marti, Maria Jose, Martínez-Castrillo, Juan Carlos, Mèndez-del-Barrio, Carlota, González, Manuel Menéndez, Adolfo Mínguez, Marina Mata, Mir, Pablo, Rezola, Elisabet Mondragon, Muñoz, Esteban, Pagonabarraga, Javier, Pastor, Pau, Errazquin, Francisco Perez, Perinán-Tocino, Teresa, Ruiz-Martínez, Javier, Ruz, Clara, Rodriguez, Antonio Sanchez, Sierra, María, Suarez-Sanmartin, Esther, Tabernero, Cesar, Tartari, Juan Pablo, Tejera-Parrado, Cristina, Tolosa, Eduard, Valldeoriola, Francesc, Vargas-González, Laura, Vela, Lydia, Vives, Francisco, Zimprich, Alexander, Pihlstrom, Lasse, Toft, Mathias, Koks, Sulev, Taba, Pille, Hassin-Baer, Sharon, Weale, Michael, Ramasamy, Adaikalavan, Smith, Colin, Guelfi, Manuel Sebastian, D'sa, Karishma, Forabosco, Paola, Botiá, Juan A., and Universidad de Cantabria

Subjects
Candidate gene, Protein catabolic process, Gene Expression, Genome-wide association study, Computational biology, Biology, Epigenesis, Genetic, 03 medical and health sciences, 0302 clinical medicine, Databases, Genetic, Humans, Online First, 030212 general & internal medicine, Epigenetics, Gene, Genetic Association Studies, Genetic association, Original Investigation, Research, Parkinson Disease, Protein ubiquitination, Neurology (clinical), Candidate Disease Gene, 030217 neurology & neurosurgery, Comments, Genome-Wide Association Study
Abstract

Key Points Question What genes and genomic processes underlie risk of sporadic Parkinson disease? Findings This genetic association study integrated Parkinson disease genome-wide association study data and brain-derived gene regulation data using various complementary bioinformatic tools and identified 11 candidate genes with evidence of disease-associated regulatory changes. Coexpression and protein level analyses of these genes demonstrated a significant functional association with known mendelian Parkinson disease genes. Meaning This study suggests that gene regulation data may be used to identify candidate genes and pathways involved in sporadic Parkinson disease., Importance Substantial genome-wide association study (GWAS) work in Parkinson disease (PD) has led to the discovery of an increasing number of loci shown reliably to be associated with increased risk of disease. Improved understanding of the underlying genes and mechanisms at these loci will be key to understanding the pathogenesis of PD. Objective To investigate what genes and genomic processes underlie the risk of sporadic PD. Design and Setting This genetic association study used the bioinformatic tools Coloc and transcriptome-wide association study (TWAS) to integrate PD case-control GWAS data published in 2017 with expression data (from Braineac, the Genotype-Tissue Expression [GTEx], and CommonMind) and methylation data (derived from UK Parkinson brain samples) to uncover putative gene expression and splicing mechanisms associated with PD GWAS signals. Candidate genes were further characterized using cell-type specificity, weighted gene coexpression networks, and weighted protein-protein interaction networks. Main Outcomes and Measures It was hypothesized a priori that some genes underlying PD loci would alter PD risk through changes to expression, splicing, or methylation. Candidate genes are presented whose change in expression, splicing, or methylation are associated with risk of PD as well as the functional pathways and cell types in which these genes have an important role. Results Gene-level analysis of expression revealed 5 genes (WDR6 [OMIM 606031], CD38 [OMIM 107270], GPNMB [OMIM 604368], RAB29 [OMIM 603949], and TMEM163 [OMIM 618978]) that replicated using both Coloc and TWAS analyses in both the GTEx and Braineac expression data sets. A further 6 genes (ZRANB3 [OMIM 615655], PCGF3 [OMIM 617543], NEK1 [OMIM 604588], NUPL2 [NCBI 11097], GALC [OMIM 606890], and CTSB [OMIM 116810]) showed evidence of disease-associated splicing effects. Cell-type specificity analysis revealed that gene expression was overall more prevalent in glial cell types compared with neurons. The weighted gene coexpression performed on the GTEx data set showed that NUPL2 is a key gene in 3 modules implicated in catabolic processes associated with protein ubiquitination and in the ubiquitin-dependent protein catabolic process in the nucleus accumbens, caudate, and putamen. TMEM163 and ZRANB3 were both important in modules in the frontal cortex and caudate, respectively, indicating regulation of signaling and cell communication. Protein interactor analysis and simulations using random networks demonstrated that the candidate genes interact significantly more with known mendelian PD and parkinsonism proteins than would be expected by chance. Conclusions and Relevance Together, these results suggest that several candidate genes and pathways are associated with the findings observed in PD GWAS studies., This genetic association study investigates what genes and genomic processes underlie the risk of sporadic Parkinson disease.

Published
2021

47. Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into the complex genetic architecture

Author

Chia, Ruth, Sabir, Marya S., Bandres-Ciga, Sara, Saez-Atienzar, Sara, Reynolds, Regina H., Gustavsson, Emil, Walton, Ronald L., Ahmed, Sarah, Viollet, Coralie, Ding, Jinhui, Makarious, Mary B., Diez-Fairen, Monica, Portley, Makayla K., Shah, Zalak, Abramzon, Yevgeniya, Hernandez, Dena G., Blauwendraat, Cornelis, Stone, David J., Eicher, John, Parkkinen, Laura, Ansorge, Olaf, Clark, Lorraine, Honig, Lawrence S., Marder, Karen, Lemstra, Afina, George-Hyslop, Peter St, Londos, Elisabet, Morgan, Kevin, Lashley, Tammaryn, Warner, Thomas T., Jaunmuktane, Zane, Galasko, Douglas, Santana, Isabel, Tienari, Pentti J., Myllykangas, Liisa, Oinas, Minna, Cairns, Nigel J., Morris, John C., Halliday, Glenda M., Van Deerlin, Vivianna M., Trojanowski, John Q., Grassano, Maurizio, Calvo, Andrea, Mora, Gabriele, Canosa, Antonio, Floris, Gianluca, Bohannan, Ryan C., Brett, Francesca, Gan-Or, Ziv, Geiger, Joshua T., Moore, Anni, May, Patrick, Krüger, Rejko, Goldstein, David, Lopez, Grisel, Tayebi, Nahid, Sidransky, Ellen, Palma, Jose-Alberto, Kaufmann, Horacio, Shakkottai, Vikram, Perkins, Matthew, Newell, Kathy L., Gasser, Thomas, Schulte, Claudia, Landi, Francesco, Salvi, Erika, Cusi, Daniele, Masliah, Eliezer, Kim, Ronald C., Caraway, Chad A., Monuki, Ed, Brunetti, Maura, Dawson, Ted M., Rosenthal, Liana S., Albert, Marilyn S., Pletnikova, Olga, Troncoso, Juan C., Flanagan, Margaret E., Mao, Qinwen, Bigio, Eileen H., Rodríguez-Rodríguez, Eloy, Infante, Jon, Lage, Carmen, González-Aramburu, Isabel, Sanchez-Juan, Pascual, Ghetti, Bernardino, Keith, Julia, Black, Sandra E., Masellis, Mario, Rogaeva, Ekaterina, Duyckaerts, Charles, Brice, Alexis, Lesage, Suzanne, Xiromerisiou, Georgia, Barrett, Matthew J., Tilley, Bension S., Gentleman, Steve, Logroscino, Giancarlo, Serrano, Geidy E., Beach, Thomas G., McKeith, Ian G., Thomas, Alan J., Attems, Johannes, Morris, Christopher M., Palmer, Laura, Love, Seth, Troakes, Claire, Al-Sarraj, Safa, Hodges, Angela K., Aarsland, Dag, Klein, Gregory, Kaiser, Scott M., Woltjer, Randy, Pastor, Pau, Bekris, Lynn M., Leverenz, James, Besser, Lilah M., Kuzma, Amanda, Renton, Alan E., Goate, Alison, Bennett, David A., Scherzer, Clemens R., Morris, Huw R., Ferrari, Raffaele, Albani, Diego, Brown, Stuart Pickering, Faber, Kelley, Kukull, Walter, Morenas-Rodriguez, Estrella, Lleó, Alberto, Fortea, Juan, Alcolea, Daniel, Clarimon, Jordi, Nalls, Michael A., Ferrucci, Luigi, Resnick, Susan M., Tanaka, Toshiko, Foroud, Tatiana M., Graff-Radford, Neill R., Wszolek, Zbigniew K., Ferman, Tanis, Boeve, Bradley F., Hardy, John A., Topol, Eric, Torkamani, Ali, Singleton, Andrew B., Ryten, Mina, Dickson, Dennis, Chiò, Adriano, Ross, Owen A., Gibbs, J. Raphael, Dalgard, Clifton L., Traynor, Bryan J., and Scholz, Sonja W.

Subjects
whole-genome sequencing, GBA, Lewy body dementia, Biochemistry, biophysics & molecular biology [F05] [Life sciences], Biochimie, biophysique & biologie moléculaire [F05] [Sciences du vivant]
Abstract

The genetic basis of Lewy body dementia (LBD) is not well understood. Here, we performed whole-genome sequencing in large cohorts of LBD cases and neurologically healthy controls to study the genetic architecture of this understudied form of dementia and to generate a resource for the scientific community. Genome-wide association analysis identified five independent risk loci, whereas genome-wide gene-aggregation tests implicated mutations in the gene GBA. Genetic risk scores demonstrate that LBD shares risk profiles and pathways with Alzheimer’s and Parkinson’s disease, providing a deeper molecular understanding of the complex genetic architecture of this age-related neurodegenerative condition.Competing Interest StatementThomas G. Beach is a consultant for Prothena, Vivid Genomics and Avid Radiopharmaceuticals. He is a scientific advisory board member for Vivid Genomics. John A. Hardy, Huw R. Morris, Stuart Pickering-Brown, Andrew B. Singleton, and Bryan J. Traynor hold US, EU and Canadian patents on the clinical testing and therapeutic intervention for the hexanucleotide repeat expansion of C9orf72. Michael A. Nalls is supported by a consulting contract between Data Tecnica International and the National Institute on Aging, NIH, Bethesda, MD, USA; as a possible conflict of interest Dr. Nalls also consults for Neuron23 Inc., Lysosomal Therapeutics Inc., Illumina Inc., the Michael J. Fox Foundation and Vivid Genomics among others. Jose A. Palma is an editorial board member of Movement Disorders, Parkinsonism & Related Disorders, BMC Neurology, and Clinical Autonomic Research. Bradley F. Boeve, James Leverenz, and Sonja W. Scholz serve on the Scientific Advisory Council of the Lewy Body Dementia Association. Sonja W. Scholz is an editorial board member for the Journal of Parkinson's Disease. Bryan J. Traynor is an editorial board member for JAMA Neurology; Journal of Neurology, Neurosurgery, and Psychiatry; Brain; and Neurobiology of Aging. Zbigniew K. Wszolek serves as a principal investigator or co-principal investigator on Abbvie, Inc. (M15-562 and M15-563), Biogen, Inc. (228PD201) grant, and Biohaven Pharmaceuticals, Inc. (BHV4157-206 and BHV3241-301). Zbigniew K. Wszolek serves as the principal investigator of the Mayo Clinic American Parkinson Disease Association (APDA) Information and Referral Center, and as co-principal investigator of the Mayo Clinic APDA Center for Advanced Research. All other authors report no competing interests.

Published
2020

48. CoExp: A Web Tool for the Exploitation of Co-expression Networks

Author

Garcia-Ruiz, Sonia, Gil-Martinez, Ana L., Cisterna, Alejandro, Jurado-Ruiz, Federico, Reynolds, Regina H., NABEC North Amer Brain Expression, Cookson, Mark R., Hardy, John, Ryten, Mina, Botia, Juan A., Garcia-Ruiz, Sonia, Gil-Martinez, Ana L., Cisterna, Alejandro, Jurado-Ruiz, Federico, Reynolds, Regina H., NABEC North Amer Brain Expression, Cookson, Mark R., Hardy, John, Ryten, Mina, and Botia, Juan A.

Abstract

Gene co-expression networks are a powerful type of analysis to construct gene groupings based on transcriptomic profiling. Co-expression networks make it possible to discover modules of genes whose mRNA levels are highly correlated across samples. Subsequent annotation of modules often reveals biological functions and/or evidence of cellular specificity for cell types implicated in the tissue being studied. There are multiple ways to perform such analyses with weighted gene co-expression network analysis (WGCNA) amongst one of the most widely used R packages. While managing a few network models can be done manually, it is often more advantageous to study a wider set of models derived from multiple independently generated transcriptomic data sets (e.g., multiple networks built from many transcriptomic sources). However, there is no software tool available that allows this to be easily achieved. Furthermore, the visual nature of co-expression networks in combination with the coding skills required to explore networks, makes the construction of a web-based platform for their management highly desirable. Here, we present the CoExp Web application, a user-friendly online tool that allows the exploitation of the full collection of 109 co-expression networks provided by the CoExpNets suite of R packages. We describe the usage of CoExp, including its contents and the functionality available through the family of CoExpNets packages. All the tools presented, including the web front- and back-ends are available for the research community so any research group can build its own suite of networks and make them accessible through their own CoExp Web application. Therefore, this paper is of interest to both researchers wishing to annotate their genes of interest across different brain network models and specialists interested in the creation of GCNs looking for a tool to appropriately manage, use, publish, and share their networks in a consistent and productive manner.

Published
2021

49. Human-lineage-specific genomic elements are associated with neurodegenerative disease and APOE transcript usage

Author

Universidad de Sevilla. Departamento de Medicina, Chen, Zhongbo, Zhang, David, Reynolds, Regina H., Labrador-Espinosa, Miguel Á., Periñán Tocino, María Teresa, Mir Rivera, Pablo, Ryten, Mina, Universidad de Sevilla. Departamento de Medicina, Chen, Zhongbo, Zhang, David, Reynolds, Regina H., Labrador-Espinosa, Miguel Á., Periñán Tocino, María Teresa, Mir Rivera, Pablo, and Ryten, Mina

Abstract

Knowledge of genomic features specific to the human lineage may provide insights into brain-related diseases. We leverage high-depth whole genome sequencing data to generate a combined annotation identifying regions simultaneously depleted for genetic variation (constrained regions) and poorly conserved across primates. We propose that these constrained, non-conserved regions (CNCRs) have been subject to human-specific purifying selection and are enriched for brain-specific elements. We find that CNCRs are depleted from protein-coding genes but enriched within lncRNAs. We demonstrate that per-SNP heritability of a range of brain-relevant phenotypes are enriched within CNCRs. We find that genes implicated in neurological diseases have high CNCR density, including APOE, highlighting an unannotated intron-3 retention event. Using human brain RNA-sequencing data, we show the intron-3-retaining transcript to be more abundant in Alzheimer’s disease with more severe tau and amyloid pathological burden. Thus, we demonstrate potential association of human-lineage-specific sequences in brain development and neurological disease.

Published
2021

50. Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis

Author

Dewan, Ramita, Chia, Ruth, Ding, Jinhui, Hickman, Richard A., Stein, Thor D., Abramzon, Yevgeniya, Ahmed, Sarah, Sabir, Marya S., Portley, Makayla K., Tucci, Arianna, Ibáñez, Kristina, Shankaracharya, F. N.U., Keagle, Pamela, Rossi, Giacomina, Caroppo, Paola, Tagliavini, Fabrizio, Waldo, Maria L., Johansson, Per M., Nilsson, Christer F., Adeleye, Adelani, Alba, Camille, Bacikova, Dagmar, Hupalo, Daniel N., Martinez, Elisa Mc Grath, Pollard, Harvey B., Sukumar, Gauthaman, Soltis, Anthony R., Tuck, Meila, Zhang, Xijun, Wilkerson, Matthew D., Smith, Bradley N., Ticozzi, Nicola, Fallini, Claudia, Gkazi, Athina Soragia, Topp, Simon D., Kost, Jason, Scotter, Emma L., Kenna, Kevin P., Miller, Jack W., Tiloca, Cinzia, Vance, Caroline, Danielson, Eric W., Troakes, Claire, Colombrita, Claudia, Al-Sarraj, Safa, Lewis, Elizabeth A., Nielsen, Jorgen E., Hjermind, Lynne E., Reynolds, Regina H., Rowe, James B., Dewan, Ramita, Chia, Ruth, Ding, Jinhui, Hickman, Richard A., Stein, Thor D., Abramzon, Yevgeniya, Ahmed, Sarah, Sabir, Marya S., Portley, Makayla K., Tucci, Arianna, Ibáñez, Kristina, Shankaracharya, F. N.U., Keagle, Pamela, Rossi, Giacomina, Caroppo, Paola, Tagliavini, Fabrizio, Waldo, Maria L., Johansson, Per M., Nilsson, Christer F., Adeleye, Adelani, Alba, Camille, Bacikova, Dagmar, Hupalo, Daniel N., Martinez, Elisa Mc Grath, Pollard, Harvey B., Sukumar, Gauthaman, Soltis, Anthony R., Tuck, Meila, Zhang, Xijun, Wilkerson, Matthew D., Smith, Bradley N., Ticozzi, Nicola, Fallini, Claudia, Gkazi, Athina Soragia, Topp, Simon D., Kost, Jason, Scotter, Emma L., Kenna, Kevin P., Miller, Jack W., Tiloca, Cinzia, Vance, Caroline, Danielson, Eric W., Troakes, Claire, Colombrita, Claudia, Al-Sarraj, Safa, Lewis, Elizabeth A., Nielsen, Jorgen E., Hjermind, Lynne E., Reynolds, Regina H., and Rowe, James B.

Abstract

We examined the role of repeat expansions in the pathogenesis of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) by analyzing whole-genome sequence data from 2,442 FTD/ALS patients, 2,599 Lewy body dementia (LBD) patients, and 3,158 neurologically healthy subjects. Pathogenic expansions (range, 40–64 CAG repeats) in the huntingtin (HTT) gene were found in three (0.12%) patients diagnosed with pure FTD/ALS syndromes but were not present in the LBD or healthy cohorts. We replicated our findings in an independent collection of 3,674 FTD/ALS patients. Postmortem evaluations of two patients revealed the classical TDP-43 pathology of FTD/ALS, as well as huntingtin-positive, ubiquitin-positive aggregates in the frontal cortex. The neostriatal atrophy that pathologically defines Huntington's disease was absent in both cases. Our findings reveal an etiological relationship between HTT repeat expansions and FTD/ALS syndromes and indicate that genetic screening of FTD/ALS patients for HTT repeat expansions should be considered.

Published
2021

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