Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology
Authors: Wouter van Rheenen, Rick A. A. van der Spek, Mark K. Bakker, Joke J. F. A. van Vugt, Paul J. Hop, Ramona A. J. Zwamborn, Niek de Klein, Harm-Jan Westra, Olivier B. Bakker, Patrick Deelen, Gemma Shireby, Eilis Hannon, Matthieu Moisse, Denis Baird, Restuadi Restuadi, Egor Dolzhenko, Annelot M. Dekker, Klara Gawor, Henk-Jan Westeneng, Gijs H. P. Tazelaar, Kristel R. van Eijk, Maarten Kooyman, Ross P. Byrne, Mark Doherty, Mark Heverin, Ahmad Al Khleifat, Alfredo Iacoangeli, Aleksey Shatunov, Nicola Ticozzi, Johnathan Cooper-Knock, Bradley N. Smith, Marta Gromicho, Siddharthan Chandran, Suvankar Pal, Karen E. Morrison, Pamela J. Shaw, John Hardy, Richard W. Orrell, Michael Sendtner, Thomas Meyer, Nazli Başak, Anneke J. van der Kooi, Antonia Ratti, Isabella Fogh, Cinzia Gellera, Giuseppe Lauria, Stefania Corti, Cristina Cereda, Daisy Sproviero, Sandra D’Alfonso, Gianni Sorarù, Gabriele Siciliano, Massimiliano Filosto, Alessandro Padovani, Adriano Chiò, Andrea Calvo, Cristina Moglia, Maura Brunetti, Antonio Canosa, Maurizio Grassano, Ettore Beghi, Elisabetta Pupillo, Giancarlo Logroscino, Beatrice Nefussy, Alma Osmanovic, Angelica Nordin, Yossef Lerner, Michal Zabari, Marc Gotkine, Robert H. Baloh, Shaughn Bell, Patrick Vourc’h, Philippe Corcia, Philippe Couratier, Stéphanie Millecamps, Vincent Meininger, François Salachas, Jesus S. Mora Pardina, Abdelilah Assialioui, Ricardo Rojas-García, Patrick A. Dion, Jay P. Ross, Albert C. Ludolph, Jochen H. Weishaupt, David Brenner, Axel Freischmidt, Gilbert Bensimon, Alexis Brice, Alexandra Durr, Christine A. M. Payan, Safa Saker-Delye, Nicholas W. Wood, Simon Topp, Rosa Rademakers, Lukas Tittmann, Wolfgang Lieb, Andre Franke, Stephan Ripke, Alice Braun, Julia Kraft, David C. Whiteman, Catherine M. Olsen, Andre G. Uitterlinden, Albert Hofman, Marcella Rietschel, Sven Cichon, Markus M. Nöthen, Philippe Amouyel, Giancarlo Comi, Nilo Riva, Christian Lunetta, Francesca Gerardi, Maria Sofia Cotelli, Fabrizio Rinaldi, Luca Chiveri, Maria Cristina Guaita, Patrizia Perrone, Mauro Ceroni, Luca Diamanti, Carlo Ferrarese, Lucio Tremolizzo, Maria Luisa Delodovici, Giorgio Bono, Antonio Canosa, Umberto Manera, Rosario Vasta, Alessandro Bombaci, Federico Casale, Giuseppe Fuda, Paolina Salamone, Barbara Iazzolino, Laura Peotta, Paolo Cugnasco, Giovanni De Marco, Maria Claudia Torrieri, Francesca Palumbo, Salvatore Gallone, Marco Barberis, Luca Sbaiz, Salvatore Gentile, Alessandro Mauro, Letizia Mazzini, Fabiola De Marchi, Lucia Corrado, Sandra D’Alfonso, Antonio Bertolotto, Maurizio Gionco, Daniela Leotta, Enrico Odddenino, Daniele Imperiale, Roberto Cavallo, Pietro Pignatta, Marco De Mattei, Claudio Geda, Diego Maria Papurello, Graziano Gusmaroli, Cristoforo Comi, Carmelo Labate, Luigi Ruiz, Delfina Ferrandi, Eugenia Rota, Marco Aguggia, Nicoletta Di Vito, Piero Meineri, Paolo Ghiglione, Nicola Launaro, Michele Dotta, Alessia Di Sapio, Guido Giardini, Cinzia Tiloca, Silvia Peverelli, Franco Taroni, Viviana Pensato, Barbara Castellotti, Giacomo P. Comi, Roberto Del Bo, Mauro Ceroni, Stella Gagliardi, Lucia Corrado, Letizia Mazzini, Flavia Raggi, Costanza Simoncini, Annalisa Lo Gerfo, Maurizio Inghilleri, Alessandra Ferlini, Isabella L. Simone, Bruno Passarella, Vito Guerra, Stefano Zoccolella, Cecilia Nozzoli, Ciro Mundi, Maurizio Leone, Michele Zarrelli, Filippo Tamma, Francesco Valluzzi, Gianluigi Calabrese, Giovanni Boero, Augusto Rini, Bryan J. Traynor, Andrew B. Singleton, Miguel Mitne Neto, Ruben J. Cauchi, Roel A. Ophoff, Martina Wiedau-Pazos, Catherine Lomen-Hoerth, Vivianna M. van Deerlin, Julian Grosskreutz, Annekathrin Roediger, Nayana Gaur, Alexander Jörk, Tabea Barthel, Erik Theele, Benjamin Ilse, Beatrice Stubendorff, Otto W. Witte, Robert Steinbach, Christian A. Hübner, Caroline Graff, Lev Brylev, Vera Fominykh, Vera Demeshonok, Anastasia Ataulina, Boris Rogelj, Blaž Koritnik, Janez Zidar, Metka Ravnik-Glavač, Damjan Glavač, Zorica Stević, Vivian Drory, Monica Povedano, Ian P. Blair, Matthew C. Kiernan, Beben Benyamin, Robert D. Henderson, Sarah Furlong, Susan Mathers, Pamela A. McCombe, Merrilee Needham, Shyuan T. Ngo, Garth A. Nicholson, Roger Pamphlett, Dominic B. Rowe, Frederik J. Steyn, Kelly L. Williams, Karen A. Mather, Perminder S. Sachdev, Anjali K. Henders, Leanne Wallace, Mamede de Carvalho, Susana Pinto, Susanne Petri, Markus Weber, Guy A. Rouleau, Vincenzo Silani, Charles J. Curtis, Gerome Breen, Jonathan D. Glass, Robert H. Brown, John E. Landers, Christopher E. Shaw, Peter M. Andersen, Ewout J. N. Groen, Michael A. van Es, R. Jeroen Pasterkamp, Dongsheng Fan, Fleur C. Garton, Allan F. McRae, George Davey Smith, Tom R. Gaunt, Michael A. Eberle, Jonathan Mill, Russell L. McLaughlin, Orla Hardiman, Kevin P. Kenna, Naomi R. Wray, Ellen Tsai, Heiko Runz, Lude Franke, Ammar Al-Chalabi, Philip Van Damme, Leonard H. van den Berg, Jan H. Veldink
Journal: Nature Genetics (2021)

Abstract Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a lifetime risk of one in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry genome-wide association study (GWAS) including 29,612 patients with ALS and 122,656 controls, which identified 15 risk loci. When combined with 8,953 individuals with whole-genome sequencing (6,538 patients, 2,415 controls) and a large cortex-derived expression quantitative trait locus (eQTL) dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, short tandem repeats or regulatory effects. ALS-associated risk loci were shared with multiple traits within the neurodegenerative spectrum but with distinct enrichment patterns across brain regions and cell types. Of the environmental and lifestyle risk factors obtained from the literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. The combination of all ALS-associated signals reveals a role for perturbations in vesicle-mediated transport and autophagy and provides evidence for cell-autonomous disease initiation in glutamatergic neurons.