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1. Genome-wide structural variant analysis identifies risk loci for non-Alzheimer's dementias

Author

Karri Kaivola, Ruth Chia, Jinhui Ding, Memoona Rasheed, Masashi Fujita, Vilas Menon, Ronald L. Walton, Ryan L. Collins, Kimberley Billingsley, Harrison Brand, Michael Talkowski, Xuefang Zhao, Ramita Dewan, Ali Stark, Anindita Ray, Sultana Solaiman, Pilar Alvarez Jerez, Laksh Malik, Ted M. Dawson, Liana S. Rosenthal, Marilyn S. Albert, Olga Pletnikova, Juan C. Troncoso, Mario Masellis, Julia Keith, Sandra E. Black, Luigi Ferrucci, Susan M. Resnick, Toshiko Tanaka, Eric Topol, Ali Torkamani, Pentti Tienari, Tatiana M. Foroud, Bernardino Ghetti, John E. Landers, Mina Ryten, Huw R. Morris, John A. Hardy, Letizia Mazzini, Sandra D'Alfonso, Cristina Moglia, Andrea Calvo, Geidy E. Serrano, Thomas G. Beach, Tanis Ferman, Neill R. Graff-Radford, Bradley F. Boeve, Zbigniew K. Wszolek, Dennis W. Dickson, Adriano Chiò, David A. Bennett, Philip L. De Jager, Owen A. Ross, Clifton L. Dalgard, J. Raphael Gibbs, Bryan J. Traynor, Sonja W. Scholz, Anthony R. Soltis, Coralie Viollet, Gauthaman Sukumar, Camille Alba, Nathaniel Lott, Elisa McGrath Martinez, Meila Tuck, Jatinder Singh, Dagmar Bacikova, Xijun Zhang, Daniel N. Hupalo, Adelani Adeleye, Matthew D. Wilkerson, Harvey B. Pollard, Ziv Gan-Or, Ekaterina Rogaeva, Alexis Brice, Suzanne Lesage, Georgia Xiromerisiou, Antonio Canosa, Adriano Chio, Giancarlo Logroscino, Gabriele Mora, Reijko Krüger, Patrick May, Daniel Alcolea, Jordi Clarimon, Juan Fortea, Isabel Gonzalez-Aramburu, Jon Infante, Carmen Lage, Alberto Lleó, Pau Pastor, Pascual Sanchez-Juan, Francesca Brett, Dag Aarsland, Safa Al-Sarraj, Johannes Attems, Steve Gentleman, Angela K. Hodges, Seth Love, Ian G. McKeith, Christopher M. Morris, Laura Palmer, Stuart Pickering-Brown, Alan J. Thomas, Claire Troakes, Matthew J. Barrett, Lynn M. Bekris, Kelley Faber, Margaret E. Flanagan, Alison Goate, David S. Goldstein, Horacio Kaufmann, Walter A. Kukull, James B. Leverenz, Grisel Lopez, Qinwen Mao, Eliezer Masliah, Edwin Monuki, Kathy L. Newell, Jose-Alberto Palma, Matthew Perkins, Alan E. Renton, Clemens R. Scherzer, Vikram G. Shakkottai, Ellen Sidransky, Nahid Tayebi, Randy Woltjer, Robert H. Baloh, Robert Bowser, James Broach, William Camu, John Cooper-Knock, Carsten Drepper, Vivian E. Drory, Travis L. Dunckley, Eva Feldman, Pietro Fratta, Glenn Gerhard, Summer B. Gibson, Jonathan D. Glass, Matthew B. Harms, Terry D. Heiman-Patterson, Lilja Jansson, Janine Kirby, Justin Kwan, Hannu Laaksovirta, Francesco Landi, Isabelle Le Ber, Serge Lumbroso, Daniel J.L. MacGowan, Nicholas J. Maragakis, Kevin Mouzat, Liisa Myllykangas, Richard W. Orrell, Lyle W. Ostrow, Roger Pamphlett, Erik Pioro, Stefan M. Pulst, John M. Ravits, Wim Robberecht, Jeffrey D. Rothstein, Michael Sendtner, Pamela J. Shaw, Katie C. Sidle, Zachary Simmons, Thor Stein, David J. Stone, Pentti J. Tienari, Miko Valori, Philip Van Damme, Vivianna M. Van Deerlin, Ludo Van Den Bosch, Lorne Zinman, Fonds National de la Recherche - FnR [sponsor], Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Clinical & Experimental Neuroscience (Krüger Group) [research center], and Luxembourg Institute of Health - LIH [research center]

Subjects
amyotrophic lateral sclerosis, Neurologie [D14] [Sciences de la santé humaine], genome-wide association study, Neurology [D14] [Human health sciences], case-control study, Non-Alzheimer dementia, resource, Biochemistry, Genetics and Molecular Biology (miscellaneous), frontotemporal dementia, structural variant, Genetics, non–Alzheimer's dementia, Genetics & genetic processes [F10] [Life sciences], Lewy body dementia, Structural variants, Génétique & processus génétiques [F10] [Sciences du vivant]
Abstract

We characterized the role of structural variants, a largely unexplored type of genetic variation, in two non-Alzheimer’s dementias, namely Lewy body dementia (LBD) and frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS). To do this, we applied an advanced structural variant calling pipeline (GATK-SV) to short-read whole-genome sequence data from 5,213 European-ancestry cases and 4,132 controls. We discovered, replicated, and validated a deletion in TPCN1 as a novel risk locus for LBD and detected the known structural variants at the C9orf72 and MAPT loci as associated with FTD/ALS. We also identified rare pathogenic structural variants in both LBD and FTD/ALS. Finally, we assembled a catalog of structural variants that can be mined for new insights into the pathogenesis of these understudied forms of dementia.

Published
2023

2. Cumulative genetic risk andC9orf72repeat status independently associate with ALS status in two case-control studies

Author

Kai Guo, Pau Pastor, Ruth Chia, John Dou, Junguk Hur, Manuel Menéndez González, Kelly Bakulski, and Ali Stark

Abstract

BackgroundMost 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.MethodsALS (n=219) and healthy control (n=223) participant samples from University of Michigan were genotyped and assayed for theC9orf72hexanucleotide 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.ResultsPolygenic 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 20thpercentile of ALS polygenic scores, relative to the lowest 80thpercentile, 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).ConclusionALS 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 topicAmyotrophic 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 addsAn 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 policyALS polygenic scores can assign the overall distribution of genetic risk in a population and can be used to screen individuals at higher risk.

Published
2022
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