Cumulative genetic risk and C9orf72 repeat status independently associate with ALS status in two case-control studies

Background Most amyotrophic lateral sclerosis (ALS) patients lack a monogenic mutation. This study evaluates ALS cumulative genetic risk in an independent Michigan and Spanish replication cohort using polygenic scores. Methods ALS (n=219) and healthy control (n=223) participant samples from University of Michigan were genotyped and assayed for the C9orf72 hexanucleotide expansion. Polygenic scores excluding the C9 region were generated using an independent ALS genome-wide association study (20,806 cases, 59,804 controls). Adjusted logistic regression and receiver operating characteristic curves evaluated the association and classification between polygenic scores and ALS status, respectively. Population attributable fractions and pathway analyses were conducted. An independent Spanish study sample (548 cases, 2,756 controls) was used for replication. Results Polygenic scores constructed from 275 single nucleotide polymorphisms had the best model fit in the Michigan cohort. A standard deviation increase in ALS polygenic score associated with 1.28 (95%CI 1.04-1.57) times higher odds of ALS with area under the curve of 0.663 versus a model without the ALS polygenic score (p-value=1×10−6). The population attributable fraction of the highest 20th percentile of ALS polygenic scores, relative to the lowest 80th percentile, was 4.1% of ALS cases. Genes annotated to this polygenic score enriched for important ALS pathomechanisms. Meta-analysis with the Spanish study, using a harmonized 132 single nucleotide polymorphism polygenic score, yielded similar logistic regression findings (odds ratio: 1.13, 95%CI 1.04-1.23). Conclusion ALS polygenic scores can account for cumulative genetic risk in populations and reflect disease-relevant pathways. If further validated, this polygenic score will inform future ALS risk models. What is already known on this topic Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disease caused in part by genetic factors, and methods to account for ALS polygenic disease risk are needed. What this study adds An ALS polygenic score reflects disease risk in the population and helps ascribe the magnitude of the risk. How this study might affect research, practice or policy ALS polygenic scores can assign the overall distribution of genetic risk in a population and can be used to screen individuals at higher risk. ### Competing Interest Statement JFV-C receives payment for lectures and presentations from Biogen. PM receives payments for honoraria or lectures from Abbvie, Abbott, and Zambon. LG-D receives consulting fees, payment, or honoraria from Akcea, Alnylan, Genzyme, Sobi, Pfizer and equipment donation from Pfizer. JIC receives payment for lectures and presentations from Abbvie, Bial, and Zambon. BJT holds a patent for Diagnostic and therapeutic implications for the C9orf72 repeat expansion and has collaborative research agreements with Ionis Pharmaceuticals, Roche, and Optimeos. ELF receives consulting fees from Novartis and is an inventor on a patent held by University of Michigan titled, Methods for Treating Amyotrophic Lateral Sclerosis. JFD, KMB, KG, JH, LZ, SS-A, ARS, RC, AG-R, RR-G, RFS, SB-C, PG-C, MTP, JP-T, FC, MM-G, JR, and DB-H declare no competing interests. SAG is an inventor on a patent held by University of Michigan titled, Methods for Treating Amyotrophic Lateral Sclerosis. ### Funding Statement National ALS Registry/CDC/ATSDR (1R01TS000289); National ALS Registry/CDC/ATSDR CDCP-DHHS-US (CDC/ATSDR 200-2013-56856); NIEHS K23ES027221; NIEHS R01ES030049; NINDS R01NS127188, ALS Association (20-IIA-532), the Dr. Randall W. Whitcomb Fund for ALS Genetics, the Peter R. Clark Fund for ALS Research, the Scott L. Pranger ALS Clinic Fund, and the NeuroNetwork for Emerging Therapies at the University of Michigan. This work was supported in part by the Intramural Research Program of the NIH, National Institute on Aging (Z01-AG000949-02). Project ALS Genetic study in Madrid Autonomous Community funded by ESTRATEGIAS FRENTE A ENFERMEDADES NEURODEGENERATIVAS from Spanish Ministry of Health ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: For the Michigan cohort, the study was approved by the University of Michigan Institutional Review Board (protocol HUM28826). For all Spanish Neurological Consortium samples, coordination and analysis of samples was approved by the institutional review board of the National Institute on Aging (protocol number 03-AG-N329). For Spanish Neurological Consortium healthy control samples, written consent was obtained from all individuals enrolled. The participants were recruited through several centers in Spain, where ethics approval of samples was obtained from each participating institution: Universidad de Sevilla, University Hospital Mutua de Terrassa, Hospital Universitario Central de Asturias, Universidad de Granada, Instituto de Investigacion Sanitaria Biodonostia, Universidad de Murcia, Hospital Clinic de Barcelona, Hospital General de Segovia, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona and Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Hospital Gregorio Maranon, Instituto de Investigacion Biosanitaria de Granada, Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz, Hospital Universitario Virgen de la Victoria, Hospital Universitario Marques de Valdecilla-IDIVAL, Instituto de Investigacion Sanitaria Biodonostia, Institut de Recerca Sant Joan de Deu, Hospital Universitario Ramon y Cajal, Hospital Universitario y Politecnico La Fe, Hospital Clinic Barcelona, Hospital Universitario Infanta Sofia, Hospital Sant Pau, Hospital Universitario Virgen de la Victoria, Hospital Universitario Donostia, Instituto de Investigacion Sanitaria Biodonostia, Hospital Universitario Marques de Valdecilla-IDIVAL, Hospital Universitario Marques de Valdecilla-IDIVAL, Hospital General de Segovia, and Hospital Universitario Fundacion Alcorcon. Spanish Neurological Consortium ALS samples were obtained from the ALS Genetic Spanish Consortium. Written consent was obtained from all individuals enrolled. The participants of the ALS Genetic Spanish Consortium were recruited through several motor neuron disease centers in Spain, where ethics approval of samples was obtained from each participating institution: Instituto de Investigacion Biomedica Hospital 12 de Octubre, Hospital Universitario Gregorio Maranon, Hospital Carlos III, Hospital Universitario Basurto, Hospital de la Fe, Hospital Clinico Universitario San Carlos, Institut de Biomedicina de Valencia-CSIC, Hospital Universitario Donostia, Hospital Universitario Virgen del Rocio, Hospital Clinic of Barcelona, Hospital Clinico Universitario Lozano Blesa, Hospital Miguel Servet, Hospital del Mar, Hospital General Yague, Hospital Nuestra Senora de Valme, Hospital Virgen del Camino, Hospital de Getafe, Hospital General Universitario de Alicante, Hospital Severo Ochoa, Hospital de la Santa Creu i Sant Pau. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Data may be shared by qualified investigators by reasonable request to the corresponding author. A data request proposal is reviewed and approved by a review panel, and a signed data-sharing agreement will then be approved. Code to perform preprocessing and analyses is available ().