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

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; on behalf of The International Parkinson Disease Genomics Consortium (IPDGC) and The Global Parkinson’s Genetics Program (GP2)

doi:10.1038/s41531-023-00472-6

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

NPJ Parkinsons Dis. 2023 Mar 4;9(1):33. doi: 10.1038/s41531-023-00472-6.

Authors

Hampton L Leonard^{1

2

3

4}, Ruqaya Murtadha⁵, Alejandro Martinez-Carrasco⁶, Alina Jama⁷, Amica Corda Müller-Nedebock^{8

9}, Ana-Luisa Gil-Martinez^{10

11}, Anastasia Illarionova¹², Anni Moore¹³, Bernabe I Bustos¹⁴, Bharati Jadhav¹⁵, Brook Huxford¹⁶, Catherine Storm⁶, Clodagh Towns⁶, Dan Vitale^{13

5

17}, Devina Chetty⁷, Eric Yu^{18

19}, Francis P Grenn¹³, Gabriela Salazar²⁰, Geoffrey Rateau²¹, Hirotaka Iwaki^{13

5

17}, Inas Elsayed^{22

23}, Isabelle Francesca Foote^{16

24}, Zuné Jansen van Rensburg⁷, Jonggeol Jeff Kim^{13

16}, Jie Yuan²⁵, Julie Lake¹³, Kajsa Brolin²⁶, Konstantin Senkevich^{18

27}, Lesley Wu⁶, Manuela M X Tan^{6

28}, María Teresa Periñán^{29

30}, Mary B Makarious^{13

6}, Michael Ta¹³, Nikita Simone Pillay³¹, Oswaldo Lorenzo Betancor^{32

33}, Paula R Reyes-Pérez³⁴, Pilar Alvarez Jerez^{13

5}, Prabhjyot Saini^{18

19}, Rami Al-Ouran³⁵, Ramiya Sivakumar³⁶, Raquel Real⁶, Regina H Reynolds^{9

10}, Ruifneg Hu²⁵, Shameemah Abrahams⁷, Shilpa C Rao^{37

38}, Tarek Antar¹³, Thiago Peixoto Leal³⁷, Vassilena Iankova³⁹, William J Scotton⁹, Yeajin Song^{13

5}, Andrew Singleton^{13

5}, Mike A Nalls^{13

5

17}, Sumit Dey¹⁶, Sara Bandres-Ciga^{13

5}, Cornelis Blauwendraat^{13

5}, Alastair J Noyce¹⁶; on behalf of The International Parkinson Disease Genomics Consortium (IPDGC) and The Global Parkinson’s Genetics Program (GP2)

Affiliations

¹ Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA. leonardhl@nih.gov.
² Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA. leonardhl@nih.gov.
³ Data Tecnica International LLC, Washington, DC, USA. leonardhl@nih.gov.
⁴ German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany. leonardhl@nih.gov.
⁵ Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
⁶ Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK.
⁷ Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK.
⁸ Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
⁹ South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa.
¹⁰ Department of Neurodegenerative Disease, University College London, London, UK.
¹¹ Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, UK.
¹² German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
¹³ Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
¹⁴ The Ken & Ruth Davee Department of Neurology and Simpson Querrey Center of Neurogenetics, Feinberg Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
¹⁵ Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, New York, NY, 10029, USA.
¹⁶ Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK.
¹⁷ Data Tecnica International LLC, Washington, DC, USA.
¹⁸ Department of Human Genetics, McGill University, Montreal, QC, Canada.
¹⁹ The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada.
²⁰ INNCOSYS, Col. Morelos Second Section, 50120, Toluca de Lerdo, México.
²¹ Institut du Cerveau - Institute of Brain and Spine (ICM), Hôpital Pitié, 47 Bd de l'Hôpital, 75013, Paris, France.
²² Faculty of pharmacy, University of Gezira, Wad Medani, P.O. Box 20, Sudan.
²³ International Parkinson Disease Genomics Consortium (IPDGC)-Africa, University of Gezira, Wad Medani, P.O. Box 20, Sudan.
²⁴ Unit for Psychological Medicine, Wolfson Institute of Population Health, Queen Mary University of London, London, UK.
²⁵ Center for Advanced Parkinson Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
²⁶ Translational Neurogenetics Unit, Wallenberg Neuroscience Center, Department of Experimental Medical Science, Lund University, Lund, Sweden.
²⁷ Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada.
²⁸ Department of Neurology, Oslo University Hospital, Oslo, Norway.
²⁹ Unidad 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.
³⁰ CIBERNED, Madrid, Spain.
³¹ South African National Bioinformatics Institute (SANBI), South African Medical Research Council Bioinformatics Unit, University of the Western Cape, Bellville, South Africa.
³² Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA.
³³ Department of Neurology, University of Washington School of Medicine, Seattle, WA, USA.
³⁴ Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de, México, Juriquilla, México.
³⁵ Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.
³⁶ University of Southern California, Los Angeles, CA, 90007, USA.
³⁷ Department of Genomic Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.
³⁸ Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
³⁹ Department of Neurology With Friedrich Baur Institut, University Hospital of Ludwig-Maximilians-Universität München, Munich, Germany.

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.

Abstract

Grants and funding