Large genetic changes that contribute to dementia risk identified
Discovery provides potential clues for Lewy body and frontotemporal dementias
- Date:
- May 8, 2023
- Source:
- NIH/National Institute of Neurological Disorders and Stroke
- Summary:
- Scientists have identified new genetic risk factors for two types of non-Alzheimer's dementia. These findings detail how researchers identified large-scale DNA changes, known as structural variants, by analyzing thousands of DNA samples. The team discovered several structural variants that could be risk factors Lewy body dementia (LBD) and frontotemporal dementia (FTD).
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Scientists at the National Institutes of Health have identified new genetic risk factors for two types of non-Alzheimer's dementia. These findings were published in Cell Genomics and detail how researchers identified large-scale DNA changes, known as structural variants, by analyzing thousands of DNA samples. The team discovered several structural variants that could be risk factors Lewy body dementia (LBD) and frontotemporal dementia (FTD). The project was a collaborative effort between scientists at the National Institute of Neurological Disorders and Stroke (NINDS) and the National Institute on Aging (NIA) at NIH.
Structural variants have been implicated in a variety of neurological disorders. Unlike more commonly studied mutations, which often affect one or a few DNA building blocks called nucleotides, structural variants represent at least 50 but often hundreds, or even thousands, of nucleotides at once, making them more challenging to study.
"If you imagine that our entire genetic code is a book, a structural variant would be a paragraph, page, or even an entire chapter that has been removed, duplicated, or inserted in the wrong place," said Sonja W. Scholz, M.D., Ph.D., investigator in the neurogenetics branch of NINDS and senior author of this study.
By combining cutting-edge computer algorithms capable of mapping structural variations across the whole genome with machine learning, the research team analyzed whole-genome data from thousands of patient samples and several thousand unaffected controls.
A previously unknown variant in the gene TCPN1 was found in samples from patients with LBD, a disease, that like Parkinson's disease, is associated with abnormal deposits of the protein alpha-synuclein in the brain. This variant, in which more than 300 nucleotides are deleted from the gene, is associated with a higher risk for developing LBD. While this finding is new for LBD, TCPN1 is a known risk factor for Alzheimer's disease, which could mean that this structural variant plays a role in the broader dementia population.
"From a genetics standpoint, this is a very exciting finding," said Dr. Scholz. "It provides a point of reference for cell biology and animal model studies and possibly down the road, a target for intervention."
By looking at a group of 50 genes implicated in inherited neurodegenerative diseases, the investigators were able to identify additional rare structural variants, including several that are known to cause disease. The analyses also identified two well-established risk factors for FTD changes in the C9orf72 and MAPT genes. These proof-of-concept findings bolstered the strength of the study's new findings by demonstrating that the algorithms were properly working.
Because reference maps for currently-available structural variants are limited, the researchers generated a catalog based on the data obtained in these analyses. The analysis code and all the raw data are now available to the scientific community for use in their studies. An interactive app also allows investigators to study their genes of interest and ask which variants are present in controls vs. LBD or FTD cases. The authors assert these resources may make complex genetic data more accessible to non-bioinformatics experts, which will accelerate the pace of discovery.
"Research to unravel the intricate genetic architecture of neurodegenerative diseases is resulting in significant advances in scientific understanding," said Bryan J. Traynor, M.D., Ph.D., senior investigator at NIA. "With each discovery, we shed light on the mechanisms behind neuronal cell death or dysfunction, paving the way for precision medicine to combat these debilitating and fatal disorders."
Researchers expect that the dataset will continue to grow as additional data are analyzed.
This work was supported in part by the Intramural Research Program at NINDS and NIA.
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Materials provided by NIH/National Institute of Neurological Disorders and Stroke. Note: Content may be edited for style and length.
Journal Reference:
- 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, Clifton L. Dalgard, Sandra E. Black, Ziv Gan-Or, Julia Keith, Mario Masellis, Ekaterina Rogaeva, Alexis Brice, Suzanne Lesage, Georgia Xiromerisiou, Andrea Calvo, 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, John A. Hardy, Angela K. Hodges, Seth Love, Ian G. McKeith, Christopher M. Morris, Huw R. Morris, Laura Palmer, Stuart Pickering-Brown, Mina Ryten, Alan J. Thomas, Claire Troakes, Marilyn S. Albert, Matthew J. Barrett, Thomas G. Beach, Lynn M. Bekris, David A. Bennett, Bradley F. Boeve, Clifton L. Dalgard, Ted M. Dawson, Dennis W. Dickson, Kelley Faber, Tanis Ferman, Luigi Ferrucci, Margaret E. Flanagan, Tatiana M. Foroud, Bernardino Ghetti, J. Raphael Gibbs, Alison Goate, David S. Goldstein, Neill R. Graff-Radford, Horacio Kaufmann, Walter A. Kukull, James B. Leverenz, Grisel Lopez, Qinwen Mao, Eliezer Masliah, Edwin Monuki, Kathy L. Newell, Jose-Alberto Palma, Matthew Perkins, Olga Pletnikova, Alan E. Renton, Susan M. Resnick, Liana S. Rosenthal, Owen A. Ross, Clemens R. Scherzer, Geidy E. Serrano, Vikram G. Shakkottai, Ellen Sidransky, Toshiko Tanaka, Nahid Tayebi, Eric Topol, Ali Torkamani, Juan C. Troncoso, Randy Woltjer, Zbigniew K. Wszolek, Sonja W. Scholz, Robert H. Baloh, Robert Bowser, Alexis Brice, James Broach, William Camu, Adriano Chiò, John Cooper-Knock, Carsten Drepper, Vivian E. Drory, Travis L. Dunckley, Eva Feldman, Pietro Fratta, Glenn Gerhard, Summer B. Gibson, Jonathan D. Glass, John A. Hardy, Matthew B. Harms, Terry D. Heiman-Patterson, Lilja Jansson, Janine Kirby, Justin Kwan, Hannu Laaksovirta, John E. Landers, 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, Ekaterina Rogaeva, Jeffrey D. Rothstein, Michael Sendtner, Pamela J. Shaw, Katie C. Sidle, Zachary Simmons, Thor Stein, David J. Stone, Pentti J. Tienari, Bryan J. Traynor, Juan C. Troncoso, Miko Valori, Philip Van Damme, Vivianna M. Van Deerlin, Ludo Van Den Bosch, Lorne Zinman. Genome-wide structural variant analysis identifies risk loci for non-Alzheimer’s dementias. Cell Genomics, 2023; 100316 DOI: 10.1016/j.xgen.2023.100316
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