Association of Long Runs of Homozygosity With Alzheimer Disease Among African American Individuals
| Autor: | Lee-Way Jin, Rudolph E. Tanzi, Lisa L. Barnes, Neill R. Graff-Radford, Joel H. Kramer, Tatiana Foroud, John R. Gilbert, Wayne W. Poon, Philip L. De Jager, Lei Yu, John M. Ringman, James J. Lah, Marla Gearing, David A. Bennett, Susan M. McCurry, Kenneth B. Fallon, Clinton B. Wright, Deborah Blacker, Bradley T. Hyman, Patricia L. Kramer, Joseph F. Quinn, Alison Goate, Gail P. Jarvik, Allan I. Levey, Jennifer Williamson, Mary Ganguli, Carlos Cruchaga, Julie A. Schneider, Amanda Smith, Eric M. Reiman, Lon S. Schneider, Steven H. Ferris, Richard Mayeux, Randall L. Woltjer, Li-San Wang, Goldie S. Byrd, Malcolm B. Dick, Towfique Raj, Steven L. Carroll, Carol A. Miller, Bradley F. Boeve, John S. K. Kauwe, Elaine R. Peskind, Hugh C. Hendrie, R. C. Kim, Jonathan D. Glass, Helena C. Chui, Guiqing Cai, Deborah C. Mash, Gyungah Jun, James Bowen, Marilyn S. Albert, Kathryn L. Lunetta, Huntington Potter, Walter A. Kukull, Paul K. Crane, Neil W. Kowall, Mark W. Logue, Lindsay A. Farrer, Jean Paul G. Vonsattel, Chang-En Yu, Thomas G. Beach, Gary W. Beecham, Erik D. Roberson, John M Olichney, Gerard D. Schellenberg, Harry V. Vinters, Chiao-Feng Lin, Bruce L. Miller, Duane Beekly, Daniel H. Geschwind, Murray A. Raskind, Kara L. Hamilton-Nelson, Jill R. Murrell, Linda J. Van Eldik, Wendy J. Mack, A. Karydas, Douglas Galasko, Barry Reisberg, Thomas O. Obisesan, Aimee Pierce, Andrew McDavid, Salvatore Spina, M.-Marsel Mesulam, Steven T. DeKosky, Andrew P. Lieberman, Ann C. McKee, Robert Barber, Nigel J. Cairns, Roger L. Albin, Bernardino Ghetti, Nilufer Ertekin-Taner, Kathleen A. Welsh-Bohmer, James B. Leverenz, M. Michael Barmada, F. Yesim Demirci, Hakon Hakonarson, Rodney C.P. Go, Oscar L. Lopez, Joseph D. Buxbaum, Adam C. Naj, Frank Martiniuk, Charles DeCarli, Otto Valladares, Andrew J. Saykin, Kelley Faber, Christine M. Hulette, John C. Morris, M. Ilyas Kamboh, Eliezer Masliah, Christine Sato, Steven E. Arnold, James R. Burke, Daniel C. Marson, Edward H. Koo, Ronald C. Petersen, David G. Clark, William W. Seeley, Robert C. Green, Constantine G. Lyketsos, Rosalyn Lang-Walker, John Q. Trojanowski, Jeffrey Kaye, Eileen H. Bigio, Laura B. Cantwell, Matthew P. Frosch, Jonathan L. Haines, Debby W. Tsuang, Juan C. Troncoso, Joshua W. Miller, Denis A. Evans, Kathleen S. Hall, Frank M. LaFerla, Joseph E. Parisi, Elizabeth Crocco, Mary Sano, Mahdi Ghani, Patrick Griffith, Margaret A. Pericak-Vance, Ashok Raj, Christopher S. Carlson, Jennifer J. Manly, Sid Gilman, Thomas J. Montine, Chuanhai Cao, A. Boxer, Ekaterina Rogaeva, Steven G. Younkin, Ronald L. Hamilton, Rong Cheng, Vahram Haroutunian, Peter St George-Hyslop, Liana G. Apostolova, M. Daniele Fallin, Clinton T. Baldwin, Ruchita Rajbhandary, Robert S. Stern, Sandra Weintraub, David H. Cribbs, Lindy E. Harrell, Wayne C. McCormick, Ge Li, Christiane Reitz, Eric B. Larson, Thomas D. Bird, Gregory A. Jicha, Regina M. Carney, Badri N. Vardarajan, Joshua A. Sonnen, Lawrence S. Honig, Joseph H. Lee, John H. Growdon, Vivianna M. Van Deerlin |
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| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Genetics
Chicago Indiana business.industry Haplotype Homozygote Case-control study Single-nucleotide polymorphism Genome-wide association study Genes Recessive Runs of Homozygosity Polymorphism Single Nucleotide Article Black or African American Alzheimer Disease Case-Control Studies SNP Medicine Humans Neurology (clinical) business Imputation (genetics) SNP array Aged Genome-Wide Association Study |
| Popis: | Importance Mutations in known causal Alzheimer disease (AD) genes account for only 1% to 3% of patients and almost all are dominantly inherited. Recessive inheritance of complex phenotypes can be linked to long (>1-megabase [Mb]) runs of homozygosity (ROHs) detectable by single-nucleotide polymorphism (SNP) arrays. Objective To evaluate the association between ROHs and AD in an African American population known to have a risk for AD up to 3 times higher than white individuals. Design, Setting, and Participants Case-control study of a large African American data set previously genotyped on different genome-wide SNP arrays conducted from December 2013 to January 2015. Global and locus-based ROH measurements were analyzed using raw or imputed genotype data. We studied the raw genotypes from 2 case-control subsets grouped based on SNP array: Alzheimer’s Disease Genetics Consortium data set (871 cases and 1620 control individuals) and Chicago Health and Aging Project–Indianapolis Ibadan Dementia Study data set (279 cases and 1367 control individuals). We then examined the entire data set using imputed genotypes from 1917 cases and 3858 control individuals. Main Outcomes and Measures The ROHs larger than 1 Mb, 2 Mb, or 3 Mb were investigated separately for global burden evaluation, consensus regions, and gene-based analyses. Results The African American cohort had a low degree of inbreeding ( F ~ 0.006). In the Alzheimer’s Disease Genetics Consortium data set, we detected a significantly higher proportion of cases with ROHs greater than 2 Mb ( P = .004) or greater than 3 Mb ( P = .02), as well as a significant 114-kilobase consensus region on chr4q31.3 (empirical P value 2 = .04; ROHs >2 Mb). In the Chicago Health and Aging Project–Indianapolis Ibadan Dementia Study data set, we identified a significant 202-kilobase consensus region on Chr15q24.1 (empirical P value 2 = .02; ROHs >1 Mb) and a cluster of 13 significant genes on Chr3p21.31 (empirical P value 2 = .03; ROHs >3 Mb). A total of 43 of 49 nominally significant genes common for both data sets also mapped to Chr3p21.31. Analyses of imputed SNP data from the entire data set confirmed the association of AD with global ROH measurements (12.38 ROHs >1 Mb in cases vs 12.11 in controls; 2.986 Mb average size of ROHs >2 Mb in cases vs 2.889 Mb in controls; and 22% of cases with ROHs >3 Mb vs 19% of controls) and a gene-cluster on Chr3p21.31 (empirical P value 2 = .006-.04; ROHs >3 Mb). Also, we detected a significant association between AD and CLDN17 (empirical P value 2 = .01; ROHs >1 Mb), encoding a protein from the Claudin family, members of which were previously suggested as AD biomarkers. Conclusions and Relevance To our knowledge, we discovered the first evidence of increased burden of ROHs among patients with AD from an outbred African American population, which could reflect either the cumulative effect of multiple ROHs to AD or the contribution of specific loci harboring recessive mutations and risk haplotypes in a subset of patients. Sequencing is required to uncover AD variants in these individuals. |
| Databáze: | OpenAIRE |
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