Data availability. The GWAS summary statistics generated in this study can be accessed through the International Multiple Sclerosis Genetics Consortium website (https://imsgc.net/). Individual-level genetic and phenotype data necessary to replicate the main analysis will be deposited in the European Genome-phenome Archive (EGA) for European centers, and in dbGAP (accession number phs002929.v1.p1) for all other centers. The gene expression profiles of human tissues used in this study can be downloaded from the GTEx Portal v8 (https://gtexportal.org/). The single-cell type expression profiles in human tissues can be downloaded from the Human Protein Atlas (https://www.proteinatlas.org/). We used publicly available data from the eQTL Catalogue release 4 (https://www.ebi.ac.uk/eqtl/), the LDSC GitHub repository (https://github.com/bulik/ldsc/) and the Gonçalo Castelo-Branco Group (https://ki.se/en/mbb/oligointernode/). Detailed information on the GWAS summary statistics used in the Mendelian randomization analysis is provided in Supplementary Table 16.
Code availability. The following software packages were used for data analyses: R version 4.0.5 (https://www.r-project.org/) with additional packages ms.sev version 1.0.4, aberrant version 1.0, survminer version 0.4.9, survival version 3.2-11, metafor version 3.0-2, MASS version 7.3-54, lme4 version 1.1-27.1, lmerTest version 3.1-3, bootpredictlme4 version 0.1, gwasglue version 0.0.0.9000, MendelianRandomization version 0.5.1, TwoSampleMR version 0.5.6, mr.raps version 0.4, MRPRESSO version 1.0, data.table version 1.14.0, tidyverse version 1.3.1, ggplot2 version 3.3.5, ggpubr version 0.4.0, ggvenn version 0.1.9, scattermore version 0.7; GenomeStudio version 2.0 (https://support.illumina.com/downloads/genomestudio-2-0.html), GCTA version 1.93.2beta (https://yanglab.westlake.edu.cn/software/gcta/), EIGENSOFT version 6.1.4 (https://github.com/DreichLab/EIG), PLINK version 1.90beta (https://www.cog-genomics.org/plink/1.9/) and version 2.00 (https://www.cog-genomics.org/plink/2.0/), bcftools version 1.12 (https://samtools.github.io/bcftools/), qctool version 2.0.6 (https://www.well.ox.ac.uk/~gav/qctool_v2/), FINEMAP version 1.4 and LDstore version 2.0 (http://www.christianbenner.com/), EAGLE version 2.4.1 (https://alkesgroup.broadinstitute.org/Eagle/), Minimac4 version 1.0.2 (https://genome.sph.umich.edu/wiki/Minimac4), GWAMA version 2.2.2 (https://manpages.ubuntu.com/manpages/xenial/man1/GWAMA.1.html), LDSC version 1.0.1 (https://github.com/bulik/ldsc), KING version 2.2.5 (https://www.kingrelatedness.com/).
Acknowledgments. We thank all study participants for their support and for making this work possible. This work was supported by funding from the NIH/NINDS (R01NS099240) to S.E.B. and S.J.S., and the European Union’s Horizon 2020 Research and Innovation Funding Programme (EU RIA 733161) to MultipleMS. We acknowledge support from the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre. A.H. is supported by the NMSS-ABF Clinician Scientist Development Award (FAN-1808-32256) funded by the National Multiple Sclerosis Society (NMSS) and the Multiple Sclerosis Society of Canada (MSSC). P.S. is supported by the Magretha af Ugglas foundation and Horizon 2020 EU grant (MultipleMS, 733161). S.E.B holds the Professorship in Neurology I and the Heidrich Family and Friends Endowed Chair in Neurology. The UCSF DNA biorepository is supported by the NMSS (Si-2001-35701). J.L.M. acknowledges funding support from the NIH/NINDS (R01NS096212). L.A. has received academic grant support from the Swedish Research Council, the Swedish Research Council for Health, Working Life and Welfare and the Swedish Brain foundation. S.R.D. has received institutional research grant funding from the NMSS and the NIH/NINDS. T.O. has received academic grant support from the Swedish Research Council, the Swedish Brain foundation, Knut and Alice Wallenberg foundation and Margaretha af Ugglas foundation. M.J.F.-P. has received grant support from the Multiple Sclerosis Society of Western Australia (MSWA). M.V. is a PhD fellow (11ZZZ21N) and B.D. is a Clinical Investigator of the Research Foundation-Flanders (FWO-Vlaanderen). B.D. and A.G. have received academic grant support from the Research Fund KU Leuven (C24/16/045) and the Research Foundation Flanders (FWO G.07334.15). S.L. holds research support from the Spanish Government (PI21/010189, PI18/01030, PI15/00587), funded by the Instituto de Salud Carlos III-Subdirección General de Evaluación and co-funded by the European Union, and the Red Española de Esclerosis Múltiple (REEM: RD16/0015/0002, RD16/0015/0003). S.B. and F.Z. have received funding from the German Research Foundation (CRC-TR-128). F.Z. also acknowledges support from the Progressive MS Alliance (BRAVEinMS PA-1604-08492) and the Federal Ministry of Education and Research (VIP+ HaltMS-03VP07030). A.M. is supported by Margaretha af Ugglas foundation. B.H. is associated with DIFUTURE (Data Integration for Future Medicine) [BMBF 01ZZ1804[A-I]]. He received funding for the study by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy within the framework of the Munich Cluster for Systems Neurology [EXC 2145 SyNergy – ID 390857198]. The study was supported by the Italian Foundation of Multiple Sclerosis (FISM, 2011/R/14 2015/R/10, 2019/R-Multi/033, grants), Ricerca finalizzata, Italian Ministry of Health (RF-2016-02361294 grant), the AGING Project for Department of Excellence at the Department of Translational Medicine (DIMET), Università del Piemonte Orientale, Novara, Italy. N.B. is partly supported by the MultipleMS project (Horizon 2020 European, Grant N. 733161). N.A.P. was supported in part by the NMSS (grants JF-1808-32223 and RG-1707-28657). In.K. was partly supported by the MultipleMS project (Horizon 2020 European, Grant N. 733161), the Swedish Research Council (Grant N. 2020-01638) and the Swedish Brain foundation.
This manuscript is dedicated to the memory of Rogier Q. Hintzen, a member of the International Multiple Sclerosis Genetics Consortium, in recognition of his contributions to human genetics.
Competing interests. T.O. has received compensation for advisory boards/lectures from Biogen, Novartis, Merck and Sanofi, as well as unrestricted MS research grants from the same companies, none of which are related to the current article. A.B. and his institution have received compensation for consultancy, lectures and participation in clinical trials from Alexion, Biogen, Celgene, Merck, Novartis, Sandoz/Hexal, Sanofi and Roche, all outside the current work. S.R.D. has received compensation for serving on advisory boards from Novartis, and institutional research grant funding from EMD Serono and Novartis, all outside the current work. M.F. is Editor-in-Chief of the Journal of Neurology, Associate Editor of Human Brain Mapping, Associate Editor of Radiology, and Associate Editor of Neurological Sciences; received compensation for consulting services and/or speaking activities from Alexion, Almirall, Bayer, Biogen, Celgene, Eli Lilly, Genzyme, Merck-Serono, Neopharmed Gentili, Novartis, Roche, Sanofi, Takeda, and Teva Pharmaceutical Industries; and receives research support from Biogen Idec, Merck-Serono, Novartis, Roche, Teva Pharmaceutical Industries, Italian Ministry of Health, Fondazione Italiana Sclerosi Multipla, and ARiSLA (Fondazione Italiana di Ricerca per la SLA). J.L.-S. received travel compensation from Biogen, Merck, Novartis; has been involved in clinical trials with Biogen, Novartis, Roche; her institution has received honoraria for talks and advisory board service from Biogen, Merck, Novartis, Roche, all outside the current work. M.J.F.-P. has received travel compensation from Merck outside the current work. A.G.K. has received speaker honoraria and Scientific Advisory Board fees from Bayer, BioCSL, Biogen-Idec, Lgpharma, Merck, Novartis, Roche, Sanofi-Aventis, Sanofi-Genzyme, Teva, NeuroScientific Biopharmaceuticals, Innate Immunotherapeutics, and Mitsubishi Tanabe Pharma, all outside of the current work. F.Z. has recently received research grants and/or consultation funds from Biogen, Ministry of Education and Research (BMBF), Bristol-Meyers-Squibb, Celgene, German Research Foundation (DFG), Janssen, Max-Planck-Society (MPG), Merck Serono, Novartis, Progressive MS Alliance (PMSA), Roche, Sanofi Genzyme, and Sandoz, all outside of the current work. B.D. has received consulting fees and/or funding from Biogen Idec, BMS, Sanofi-Aventis and Teva. B.D. and A.G. have received consulting/travel fees and/or research funding from Novartis, Roche and Merck, all outside the current work. SL received compensation for consulting services and speaker honoraria from Biogen Idec, Novartis, TEVA, Genzyme, Sanofi and Merck, all outside the current work. S.B. has received honoraria from Biogen Idec, Bristol Meyer Squibbs, Merck Healthcare, Novartis, Roche, Sanofi Genzyme and TEVA; his research is funded by the German Research Foundation (DFG), Hertie Foundation and the Hermann and Lilly-Schilling Foundation. F.E. received compensation for consulting services and speaker honoraria from Novartis, Sanofi Genzyme, Almirall, Teva, and Merck-Serono. Jo.S. received consultancy and/or lecture fee from Biogen, Merck, Novartis and Sanofi Genzyme, his institution received research funding by Biogen, GSK, Idorsia, and Merck, all outside the current work. B.H. has served on scientific advisory boards for Novartis; he has served as DMSC member for AllergyCare, Polpharma and TG therapeutics; he or his institution have received speaker honoraria from Desitin; his institution received research grants from Regeneron for multiple sclerosis research. He holds part of two patents; one for the detection of antibodies against KIR4.1 in a subpopulation of patients with multiple sclerosis and one for genetic determinants of neutralizing antibodies to interferon. Ja.S. received speaker honoraria and a research grant for rare diseases from Sanofi Genzyme, and is a founder and minority shareholder of the University of Helsinki spin-off company VEIL.AI. J.L.M. has participated in advisory board meetings for Sanofi-Genzyme and received research funding from Genentech, Biogen Idec, and the Bristol-Myers Squibb Foundation. N.A.P. is currently an employee of Novartis Institutes for BioMedical Research (NIBR).
The remaining authors declare no competing interests related to this work.
The International Multiple Sclerosis Genetics Consortium and MultipleMS Consortium
Adil Harroud1, Pernilla Stridh2, Jacob L. McCauley3,4, Janna Saarela5,6, Ingileif Jónsdóttir7,8, Lars Alfredsson2, Katayoun Alikhani9, Till F. M. Andlauer10, Maria Ban11, Lisa F. Barcellos12, Nadia Barizzone13, Ashley H. Beecham3, Tone Berge14,15, Achim Berthele10, Stefan Bittner16, Yolanda Blanco17, Steffan D. Bos18,19, Farren B. S. Briggs20, Stacy J. Caillier1, Domenico Caputo21, Paola Cavalla22, Elisabeth G. Celius18,19, Tanuja Chitnis23,24, Ferdinando Clarelli25, Manuel Comabella26, Giancarlo Comi27,28, Chris Cotsapas29,30, Bruce C. A. Cree1, Sandra D’Alfonso13, Efthimios Dardiotis31, Philip L. De Jager32, Silvia R. Delgado33, Bénédicte Dubois34,35, Sinah Engel16, Federica Esposito36, Marzena J. Fabis-Pedrini37,38, Massimo Filippi39,28, Christiane Gasperi10, Lissette Gomez3, Refujia Gomez1, Georgios Hadjigeorgiou40, Friederike Held10, Roland G. Henry1, Jan Hillert2, Noriko Isobe41, Maja Jagodic2, Allan G. Kermode42,38, Michael Khalil43, Trevor J. Kilpatrick44,45,46, Ioanna Konidari3, Karim L. Kreft47, Jeannette Lechner-Scott48,49, Maurizio Leone50, Sara Llufriu17, Felix Luessi16, Lohith Madireddy1, Sunny Malhotra26, Ali Manouchehrinia2, Clara P. Manrique3, Filippo Martinelli-Boneschi51,52, Elisabetta Mascia25, Luanne M. Metz9, Luciana Midaglia26, Xavier Montalban26, Jorge R. Oksenberg1, Tomas Olsson2, Annette Oturai53, Kimmo Pääkkönen6, Grant P. Parnell54,55, Nikolaos A. Patsopoulos56,57,58, Margaret A. Pericak-Vance3,4, Fredrik Piehl2, Justin P. Rubio45,46, Albert Saiz17, Adam Santaniello1, Silvia Santoro25, Catherine Schaefer59, Finn Sellebjerg53,60, Hengameh Shams1, Klementy Shchetynsky2,61, Claudia Silva9, Vasileios Siokas31, Joost Smolders62,63, Helle B. Søndergaard53, Melissa Sorosina25, Bruce Taylor64, Marijne Vandebergh35, Domizia Vecchio65, Pablo Villoslada17,66, Margarete M. Voortman43, Howard L. Weiner23,24, V. Wee Yong9, Kári Stefánsson7,8, David A. Hafler56,67, Graeme J. Stewart68,69, Alastair Compston11, Frauke Zipp16, Hanne F. Harbo18,19, Bernhard Hemmer10,70, An Goris35, Stephen L. Hauser1, Ingrid Kockum2, Stephen J. Sawcer11,71, Sergio E. Baranzini1,71.
1UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA. 2Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden. 3John P Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA. 4The Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA. 5Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway. 6Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Helsinki, Finland. 7deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. 8Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.. 9Department of Clinical Neurosciences and the Hotchkiss Brain Institute, University of Calgary, Calgary, Canada. 10Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany. 11Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. 12Genetic Epidemiology and Genomics Laboratory, Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA. 13Department of Health Sciences and Center on Auto-immune and Allergic Diseases (CAAD), University of Eastern Piedmont, Novara, Italy. 14Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway. 15Institute of Mechanical, Electronics and Chemical Engineering, Faculty of Technology, Art and Design, Oslo Metropolitan University, Oslo, Norway.16Department of Neurology, Focus Program Translational Neuroscience (FTN) and Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany. 17Department of Neurology, Hospital Clinic Barcelona, Institut d’Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Universitat de Barcelona, Barcelona, Spain. 18Department of Neurology, Oslo University Hospital, Oslo, Norway. 19Institute of Clinical Medicine, University of Oslo, Oslo, Norway. 20Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA. 21IRCCS Fondazione Don Gnocchi ONLUS, Milano, Italy. 22Department Neuroscience and Mental Health, City of Health and Science University Hospital of Turín, Turín, Italy. 23Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Boston, MA, USA. 24Brigham Multiple Sclerosis Center, Brigham and Women’s Hospital, Boston, MA, USA. 25Laboratory of Human Genetics of Neurological Disorders, IRCCS San Raffaele Scientific Institute, Milan, Italy. 26Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Vall d’Hebron Institut de Recerca, Vall d’Hebron Hospital Universitari, Barcelona, Spain. 27Casa di Cura Privata del Policlinico, Milan, Italy. 28Vita-Salute San Raffaele University, Milan, Italy. 29Departments of Neurology and Genetics, Yale School of Medicine, New Haven, CT, USA. 30Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. 31Department of Neurology, University General Hospital of Larissa, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece. 32Center For Translational & Computational Neuroimmunology and the Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA. 33Multiple Sclerosis Division, Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA. 34Department of Neurology, University Hospitals Leuven, Leuven, Belgium. 35KU Leuven, Leuven Brain Institute, Department of Neurosciences, Leuven, Belgium. 36Neurology Unit and Laboratory of Human Genetics of Neurological Disorders, IRCCS San Raffaele Scientific Institute, Milan, Italy. 37Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia. 38Perron Institute for Neurological and Translational Science, University of Western Australia, Perth, Australia. 39Neurology Unit, Neurorehabilitation Unit, Neurophysiology Service and Neuroimaging Research Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy. 40Medical School, University of Cyprus, Nicosia, Cyprus. 41Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan. 42Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia. 43Department of Neurology, Medical University of Graz, Graz, Austria. 44Department of Neurology, Royal Melbourne Hospital, Melbourne, Australia. 45Florey Department of Neuroscience and Mental Health, University of Melbourne, Melbourne, Australia. 46Florey institute of Neuroscience and Mental Health, Melbourne, Australia. 47Department of Neurology, MS center ErasMS, Erasmus University Medical Center, Rotterdam, Netherlands. 48Department of Neurology, John Hunter Hospital, Hunter New England Health District, Newcastle, Australia. 49Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia. 50SC Neurologia, Dipartimento di Scienze Mediche, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy. 51Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy. 52IRCCS Fondazione Ca’ Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy. 53Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark. 54Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Westmead, Australia. 55School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia. 56Broad Institute of MIT and Harvard University, Cambridge, MA, USA. 57Division of Genetics, Department of Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA. 58Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham & Women’s Hospital, Boston, MA, USA. 59Kaiser Permanente Division of Research, Oakland, CA, USA. 60Department of Clinical Medicine, Faculty of Healthy and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. 61Department of Neurology, Yale School of Medicine, New Haven, CT, USA. 62Departments of Neurology and Immunology, MS center ErasMS, Erasmus University Medical Center, Rotterdam, Netherlands. 63Neuroimmunology Research group, Netherlands Institute for Neuroscience, Amsterdam, Netherlands. 64Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia. 65Department of Translational Medicine and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Eastern Piedmont, Novara, Italy. 66Stanford University, Stanford, CA, USA. 67Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA. 68University of Sydney, Sydney, Australia. 69Westmead Institute for Medical Research, Sydney, Australia. 70Munich Cluster for Systems Neurology (SyNergy), Munich, Germany. 71These authors jointly supervised this work: Stephen J. Sawcer and Sergio E. Baranzini.
Author contributions. Conceived and designed the study: A.H., Ja.S., D.A.H., G.J.S., A.C., F.Z., H.F.H., A.G., S.L.H., In.K., S.J.S., S.E.B. Collected the data: A.H., J.L.M., L.A., K.A., T.F.M.A., M.B., L.F.B., N.B., T.B., A.B., S.B., Y.B., S.D.B., S.J.C., D.C., P.C., E.G.C., T.C., F.C., M.C., G.C., C.C., B.C.A.C., S.D., E.D., P.L.D., S.R.D., B.D., S.E., F.E., M.F.-P., M.F., C.G., R.G., G.H., F.H., J.H., N.I., A.G.K., M.K., T.J.K., Io.K., K.L.K., J.L.-S., M.L., S.L., F.L., L.M., S.M., C.P.M., F.M.-B., E.M., L.M.M., Lu.M., X.M., J.R.O., T.O., A.O., K.P., G.P.P., N.A.P., M.P.-V., F.P., J.P.R., Al.S., Ad.S., S.S., Ca.S., F.S., H.S., Kl.S., Cl.S., V.S., Jo.S., H.B.S., M.S., B.T., M.V., D.V., P.V., M.M.V., H.L.W., V.Y., D.A.H., G.J.S., A.C., F.Z., H.F.H., B.H., A.G., S.L.H., In.K., S.J.S., S.E.B. Performed genotyping and/or quality control: A.H., J.L.M., Ja.S., I.J., A.H.B., L.G., Io.K., K.P., Kl.S., Ká.S. Analyzed the data: A.H., P.S., S.J.S., S.E.B. Supervised the study: In.K., S.J.S., S.E.B. Drafted the manuscript: A.H., S.J.S., S.E.B. Revised and edited the manuscript: A.H., P.S., J.L.M., Ja.S., I.J., K.A., T.F.M.A., M.B., L.F.B., A.H.B., T.B., S.B., S.D.B., F.B.S.B., E.G.C., F.C., C.C., B.C.A.C., S.D., P.L.D., B.D., S.E., F.E., M.F.-P., M.F., C.G., R.G.H., N.I., M.J., A.G.K., M.K., T.J.K., K.L.K., J.L.-S., F.L., A.M., F.M.-B., L.M.M., J.R.O., G.P.P., J.P.R., H.S., Cl.S., Jo.S., M.S., B.T., M.V., M.M.V., V.Y., Ká.S., D.A.H., G.J.S., A.C., F.Z., H.F.H., B.H., A.G., S.L.H., In.K., S.J.S., S.E.B.