Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

SLALOM Consortium, PARALS Consortium, SLAGEN Consortium, SLAP Consortium, 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 DolzhenkoAnnelot 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, Lude Franke, Jan H. Veldink*

*Corresponding author for this work

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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.

Original languageEnglish
Pages (from-to)1636-1648
Number of pages13
JournalNature genetics
Volume53
Issue number12
DOIs
Publication statusPublished - 1-Dec-2021

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