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The Parkinson’s Disease GWAS Locus Browser

Francis P. Grenn, Jonggeol J. Kim, Mary B. Makarious, Hirotaka Iwaki, Anastasia Illarionova, Kajsa Brolin, Jillian H. Kluss, Artur F. Schumacher-Schuh, Hampton Leonard, View ORCID ProfileFaraz Faghri, Kimberley Billingsley, Lynne Krohn, Ashley Hall, Monica Diez-Fairen, Maria Teresa Periñán, Cynthia Sandor, Caleb Webber, J. Raphael Gibbs, Mike A. Nalls, Andrew B. Singleton, Sara Bandres-Ciga, Xylena Reed, Cornelis Blauwendraat, on behalf of the International Parkinson’s Disease Genomics Consortium (IPDGC)
doi: https://doi.org/10.1101/2020.04.01.020404
Francis P. Grenn
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Jonggeol J. Kim
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Mary B. Makarious
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Hirotaka Iwaki
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
2Data Tecnica International, Glen Echo, MD, USA
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Anastasia Illarionova
3German Center for Neurodegenerative Diseases, Tubingen, Germany
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Kajsa Brolin
4Lund University, Translational Neurogenetics Unit, Department of Experimental Medical Science, Lund, Sweden
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Jillian H. Kluss
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Artur F. Schumacher-Schuh
5Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
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Hampton Leonard
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
2Data Tecnica International, Glen Echo, MD, USA
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Faraz Faghri
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
2Data Tecnica International, Glen Echo, MD, USA
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  • ORCID record for Faraz Faghri
Kimberley Billingsley
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Lynne Krohn
6Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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Ashley Hall
7Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool
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Monica Diez-Fairen
8Fundació Docència i Recerca Mútua Terrassa and Movement Disorders Unit, Department of Neurology, University Hospital Mútua Terrassa, Barcelona, Spain
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Maria Teresa Periñán
9Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
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Cynthia Sandor
10UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
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Caleb Webber
10UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
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J. Raphael Gibbs
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Mike A. Nalls
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
2Data Tecnica International, Glen Echo, MD, USA
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Andrew B. Singleton
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Sara Bandres-Ciga
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Xylena Reed
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Cornelis Blauwendraat
1Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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  • For correspondence: cornelis.blauwendraat@nih.gov
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Abstract

Parkinson’s disease (PD) is a neurodegenerative disease with an often complex genetic component identifiable by genome-wide association studies (GWAS). The most recent large scale PD GWASes have identified more than 90 independent risk variants for PD risk and progression across 80 loci. One major challenge in current genomics is identifying the causal gene(s) and variant(s) from each GWAS locus. Here we present a GWAS locus browser application that combines data from multiple databases to aid in the prioritization of genes associated with PD GWAS loci. We included 92 independent genome-wide significant signals from multiple recent PD GWAS studies including the PD risk GWAS, age-at-onset GWAS and progression GWAS. We gathered data for all 2336 genes within 1Mb up and downstream of each variant to allow users to assess which gene(s) are most associated with the variant of interest based on a set of self-ranked criteria. Our aim is that the information contained in this browser (https://pdgenetics.shinyapps.io/GWASBrowser/) will assist the PD research community with the prioritization of genes for follow-up functional studies and as potential therapeutic targets.

Footnotes

  • https://pdgenetics.shinyapps.io/GWASBrowser/

  • https://github.com/neurogenetics/GWAS_locus_browser

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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Posted April 03, 2020.
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The Parkinson’s Disease GWAS Locus Browser
Francis P. Grenn, Jonggeol J. Kim, Mary B. Makarious, Hirotaka Iwaki, Anastasia Illarionova, Kajsa Brolin, Jillian H. Kluss, Artur F. Schumacher-Schuh, Hampton Leonard, Faraz Faghri, Kimberley Billingsley, Lynne Krohn, Ashley Hall, Monica Diez-Fairen, Maria Teresa Periñán, Cynthia Sandor, Caleb Webber, J. Raphael Gibbs, Mike A. Nalls, Andrew B. Singleton, Sara Bandres-Ciga, Xylena Reed, Cornelis Blauwendraat, on behalf of the International Parkinson’s Disease Genomics Consortium (IPDGC)
bioRxiv 2020.04.01.020404; doi: https://doi.org/10.1101/2020.04.01.020404
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The Parkinson’s Disease GWAS Locus Browser
Francis P. Grenn, Jonggeol J. Kim, Mary B. Makarious, Hirotaka Iwaki, Anastasia Illarionova, Kajsa Brolin, Jillian H. Kluss, Artur F. Schumacher-Schuh, Hampton Leonard, Faraz Faghri, Kimberley Billingsley, Lynne Krohn, Ashley Hall, Monica Diez-Fairen, Maria Teresa Periñán, Cynthia Sandor, Caleb Webber, J. Raphael Gibbs, Mike A. Nalls, Andrew B. Singleton, Sara Bandres-Ciga, Xylena Reed, Cornelis Blauwendraat, on behalf of the International Parkinson’s Disease Genomics Consortium (IPDGC)
bioRxiv 2020.04.01.020404; doi: https://doi.org/10.1101/2020.04.01.020404

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