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6 results on '"Prabhjyot Saini"'

1. Exploring the genetic and genomic connection underlying neurodegeneration with brain iron accumulation and the risk for Parkinson’s disease

Author

Pilar Alvarez Jerez, Jose Luis Alcantud, Lucia de los Reyes-Ramírez, Anni Moore, Clara Ruz, Francisco Vives Montero, Noela Rodriguez-Losada, Prabhjyot Saini, Ziv Gan-Or, Chelsea X. Alvarado, Mary B. Makarious, Kimberley J. Billingsley, Cornelis Blauwendraat, Alastair J. Noyce, Andrew B. Singleton, Raquel Duran, and Sara Bandres-Ciga

Subjects
Neurology. Diseases of the nervous system, RC346-429
Abstract

Abstract Neurodegeneration with brain iron accumulation (NBIA) represents a group of neurodegenerative disorders characterized by abnormal iron accumulation in the brain. In Parkinson’s Disease (PD), iron accumulation is a cardinal feature of degenerating regions in the brain and seems to be a key player in mechanisms that precipitate cell death. The aim of this study was to explore the genetic and genomic connection between NBIA and PD. We screened for known and rare pathogenic mutations in autosomal dominant and recessive genes linked to NBIA in a total of 4481 PD cases and 10,253 controls from the Accelerating Medicines Partnership Parkinsons’ Disease Program and the UKBiobank. We examined whether a genetic burden of NBIA variants contributes to PD risk through single-gene, gene-set, and single-variant association analyses. In addition, we assessed publicly available expression quantitative trait loci (eQTL) data through Summary-based Mendelian Randomization and conducted transcriptomic analyses in blood of 1886 PD cases and 1285 controls. Out of 29 previously reported NBIA screened coding variants, four were associated with PD risk at a nominal p value

Published
2023
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2. The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Author

Hampton L. Leonard, Ruqaya Murtadha, Alejandro Martinez-Carrasco, Alina Jama, Amica Corda Müller-Nedebock, Ana-Luisa Gil-Martinez, Anastasia Illarionova, Anni Moore, Bernabe I. Bustos, Bharati Jadhav, Brook Huxford, Catherine Storm, Clodagh Towns, Dan Vitale, Devina Chetty, Eric Yu, Francis P. Grenn, Gabriela Salazar, Geoffrey Rateau, Hirotaka Iwaki, Inas Elsayed, Isabelle Francesca Foote, Zuné Jansen van Rensburg, Jonggeol Jeff Kim, Jie Yuan, Julie Lake, Kajsa Brolin, Konstantin Senkevich, Lesley Wu, Manuela M. X. Tan, María Teresa Periñán, Mary B. Makarious, Michael Ta, Nikita Simone Pillay, Oswaldo Lorenzo Betancor, Paula R. Reyes-Pérez, Pilar Alvarez Jerez, Prabhjyot Saini, Rami al-Ouran, Ramiya Sivakumar, Raquel Real, Regina H. Reynolds, Ruifneg Hu, Shameemah Abrahams, Shilpa C. Rao, Tarek Antar, Thiago Peixoto Leal, Vassilena Iankova, William J. Scotton, Yeajin Song, Andrew Singleton, Mike A. Nalls, Sumit Dey, Sara Bandres-Ciga, Cornelis Blauwendraat, Alastair J. Noyce, and on behalf of The International Parkinson Disease Genomics Consortium (IPDGC) and The Global Parkinson’s Genetics Program (GP2)

Subjects
Neurology. Diseases of the nervous system, RC346-429
Abstract

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
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3. Fine mapping of the HLA locus in Parkinson’s disease in Europeans

Author

Eric Yu, Aditya Ambati, Maren Stolp Andersen, Lynne Krohn, Mehrdad A. Estiar, Prabhjyot Saini, Konstantin Senkevich, Yuri L. Sosero, Ashwin Ashok Kumar Sreelatha, Jennifer A. Ruskey, Farnaz Asayesh, Dan Spiegelman, Mathias Toft, Marte K. Viken, Manu Sharma, Cornelis Blauwendraat, Lasse Pihlstrøm, Emmanuel Mignot, and Ziv Gan-Or

Subjects
Neurology. Diseases of the nervous system, RC346-429
Abstract

Abstract We fine mapped the leukocyte antigen (HLA) region in 13,770 Parkinson’s disease (PD) patients, 20,214 proxy-cases, and 490,861 controls of European origin. Four HLA types were associated with PD after correction for multiple comparisons, HLA-DQA1*03:01, HLA-DQB1*03:02, HLA-DRB1*04:01, and HLA-DRB1*04:04. Haplotype analyses followed by amino acid analysis and conditional analyses suggested that the association is protective and primarily driven by three specific amino acid polymorphisms present in most HLA-DRB1*04 subtypes—11V, 13H, and 33H (OR = 0.87, 95% CI: 0.83–0.90, p

Published
2021
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4. Author Correction: The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Author

Hampton L. Leonard, Ruqaya Murtadha, Alejandro Martinez-Carrasco, Alina Jama, Amica Corda Müller-Nedebock, Ana-Luisa Gil-Martinez, Anastasia Illarionova, Anni Moore, Bernabe I. Bustos, Bharati Jadhav, Brook Huxford, Catherine Storm, Clodagh Towns, Dan Vitale, Devina Chetty, Eric Yu, Francis P. Grenn, Gabriela Salazar, Geoffrey Rateau, Hirotaka Iwaki, Inas Elsayed, Isabelle Francesca Foote, Zuné Jansen van Rensburg, Jonggeol Jeff Kim, Jie Yuan, Julie Lake, Kajsa Brolin, Konstantin Senkevich, Lesley Wu, Manuela M. X. Tan, María Teresa Periñán, Mary B. Makarious, Michael Ta, Nikita Simone Pillay, Oswaldo Lorenzo Betancor, Paula R. Reyes-Pérez, Pilar Alvarez Jerez, Prabhjyot Saini, Rami al-Ouran, Ramiya Sivakumar, Raquel Real, Regina H. Reynolds, Ruifneg Hu, Shameemah Abrahams, Shilpa C. Rao, Tarek Antar, Thiago Peixoto Leal, Vassilena Iankova, William J. Scotton, Yeajin Song, Andrew Singleton, Mike A. Nalls, Sumit Dey, Sara Bandres-Ciga, Cornelis Blauwendraat, Alastair J. Noyce, and on behalf of The International Parkinson Disease Genomics Consortium (IPDGC) and The Global Parkinson’s Genetics Program (GP2)

Subjects
Neurology. Diseases of the nervous system, RC346-429
Published
2023
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5. Large genome-wide association study identifies three novel risk variants for restless legs syndrome

Author

Maria Didriksen, Muhammad Sulaman Nawaz, Joseph Dowsett, Steven Bell, Christian Erikstrup, Ole B. Pedersen, Erik Sørensen, Poul J. Jennum, Kristoffer S. Burgdorf, Brendan Burchell, Adam S. Butterworth, Nicole Soranzo, David B. Rye, Lynn Marie Trotti, Prabhjyot Saini, Lilja Stefansdottir, Sigurdur H. Magnusson, Gudmar Thorleifsson, Thordur Sigmundsson, Albert P. Sigurdsson, Katja Van Den Hurk, Franke Quee, Michael W. T. Tanck, Willem H. Ouwehand, David J. Roberts, Eric J. Earley, Michael P. Busch, Alan E. Mast, Grier P. Page, John Danesh, Emanuele Di Angelantonio, Hreinn Stefansson, Henrik Ullum, and Kari Stefansson

Subjects
Biology (General), QH301-705.5
Abstract

Didriksen, Nawaz, et al. identify three novel genetic risk variants for restless legs syndrome and confirm 19 out of 20 previously reported variants through a genome-wide association meta-analysis including nearly half a million individuals. Using expression QTL analysis, they also find that a subset of these loci may have a causal effect on nearby gene expression.

Published
2020
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6. Fine mapping of the HLA locus in Parkinson’s disease in Europeans

Author

Konstantin Senkevich, Marte K. Viken, Ashwin Ashok Kumar Sreelatha, Mathias Toft, Farnaz Asayesh, Jennifer A. Ruskey, Maren Stolp Andersen, Lynne Krohn, Aditya Ambati, Mehrdad Asghari Estiar, Lasse Pihlstrøm, Prabhjyot Saini, Eric Yu, Ziv Gan-Or, Manu Sharma, Yuri L. Sosero, Dan Spiegelman, Cornelis Blauwendraat, and Emmanuel Mignot

Subjects
Genetics, chemistry.chemical_classification, Parkinson's disease, Haplotype, Locus (genetics), Genomics, Disease, Human leukocyte antigen, Biology, medicine.disease, Article, Amino acid, Cellular and Molecular Neuroscience, Immune system, Neurology, chemistry, Multiple comparisons problem, medicine, Neurology. Diseases of the nervous system, Neurology (clinical), RC346-429
Abstract

We fine mapped the leukocyte antigen (HLA) region in 13,770 Parkinson’s disease (PD) patients, 20,214 proxy-cases, and 490,861 controls of European origin. Four HLA types were associated with PD after correction for multiple comparisons, HLA-DQA1*03:01, HLA-DQB1*03:02, HLA-DRB1*04:01, and HLA-DRB1*04:04. Haplotype analyses followed by amino acid analysis and conditional analyses suggested that the association is protective and primarily driven by three specific amino acid polymorphisms present in most HLA-DRB1*04 subtypes—11V, 13H, and 33H (OR = 0.87, 95% CI: 0.83–0.90, p −9 for all three variants). No other effects were present after adjustment for these amino acids. Our results suggest that specific HLA-DRB1 variants are associated with reduced risk of PD, providing additional evidence for the role of the immune system in PD. Although effect size is small and has no diagnostic significance, understanding the mechanism underlying this association may lead to the identification of new targets for therapeutics development.

Published
2021

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