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Rajabli F, Benchek P, Tosto G, Kushch N, Sha J, Bazemore K, Zhu C, Lee WP, Haut J, Hamilton-Nelson KL, Wheeler NR, Zhao Y, Farrell JJ, Grunin MA, Leung YY, Kuksa PP, Li D, Lucio da Fonseca E, Mez JB, Palmer EL, Pillai J, Sherva RM, Song YE, Zhang X, Iqbal T, Pathak O, Valladares O, Kuzma AB, Abner E, Adams PM, Aguirre A, Albert MS, Albin RL, Allen M, Alvarez L, Apostolova LG, Arnold SE, Asthana S, Atwood CS, Ayres G, Baldwin CT, Barber RC, Barnes LL, Barral S, Beach TG, Becker JT, Beecham GW, Beekly D, Benitez BA, Bennett D, Bertelson J, Bird TD, Blacker D, Boeve BF, Bowen JD, Boxer A, Brewer J, Burke JR, Burns JM, Buxbaum JD, Cairns NJ, Cantwell LB, Cao C, Carlson CS, Carlsson CM, Carney RM, Carrasquillo MM, Chasse S, Chesselet MF, Chin NA, Chui HC, Chung J, Craft S, Crane PK, Cribbs DH, Crocco EA, Cruchaga C, Cuccaro ML, Cullum M, Darby E, Davis B, De Jager PL, DeCarli C, DeToledo J, Dick M, Dickson DW, Dombroski BA, Doody RS, Duara R, Ertekin-Taner NI, Evans DA, Faber KM, Fairchild TJ, Fallon KB, Fardo DW, Farlow MR, Fernandez-Hernandez V, Ferris S, Foroud TM, Frosch MP, Fulton-Howard B, Galasko DR, Gamboa A, Gearing M, Geschwind DH, Ghetti B, Gilbert JR, Goate AM, Grabowski TJ, Graff-Radford NR, Green RC, Growdon JH, Hakonarson H, Hall J, Hamilton RL, Harari O, Hardy J, Harrell LE, Head E, Henderson VW, Hernandez M, Hohman T, Honig LS, Huebinger RM, Huentelman MJ, Hulette CM, Hyman BT, Hynan LS, Ibanez L, Jarvik GP, Jayadev S, Jin LW, Johnson K, Johnson L, Kamboh MI, Karydas AM, Katz MJ, Kauwe JS, Kaye JA, Keene CD, Khaleeq A, Kim R, Knebl J, Kowall NW, Kramer JH, Kukull WA, LaFerla FM, Lah JJ, Larson EB, Lerner A, Leverenz JB, Levey AI, Lieberman AP, Lipton RB, Logue M, Lopez OL, Lunetta KL, Lyketsos CG, Mains D, Margaret FE, Marson DC, Martin ERR, Martiniuk F, Mash DC, Masliah E, Massman P, Masurkar A, McCormick WC, McCurry SM, McDavid AN, McDonough S, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Montine TJ, Monuki ES, Morris JC, Mukherjee S, Myers AJ, Nguyen T, O'Bryant S, Olichney JM, Ory M, Palmer R, Parisi JE, Paulson HL, Pavlik V, Paydarfar D, Perez V, Peskind E, Petersen RC, Pierce A, Polk M, Poon WW, Potter H, Qu L, Quiceno M, Quinn JF, Raj A, Raskind M, Reiman EM, Reisberg B, Reisch JS, Ringman JM, Roberson ED, Rodriguear M, Rogaeva E, Rosen HJ, Rosenberg RN, Royall DR, Sager MA, Sano M, Saykin AJ, Schneider JA, Schneider LS, Seeley WW, Slifer SH, Small S, Smith AG, Smith JP, Sonnen JA, Spina S, St George-Hyslop P, Stern RA, Stevens AB, Strittmatter SM, Sultzer D, Swerdlow RH, Tanzi RE, Tilson JL, Trojanowski JQ, Troncoso JC, Tsuang DW, Van Deerlin VM, van Eldik LJ, Vance JM, Vardarajan BN, Vassar R, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Whitehead PL, Wijsman EM, Wilhelmsen KC, Williams B, Williamson J, Wilms H, Wingo TS, Wisniewski T, Woltjer RL, Woon M, Wright CB, Wu CK, Younkin SG, Yu CE, Yu L, Zhu X, Kunkle BW, Bush WS, Wang LS, Farrer LA, Haines JL, Mayeux R, Pericak-Vance MA, Schellenberg GD, Jun GR, Reitz C, Naj AC. Multi-ancestry genome-wide meta-analysis of 56,241 individuals identifies LRRC4C, LHX5-AS1 and nominates ancestry-specific loci PTPRK , GRB14 , and KIAA0825 as novel risk loci for Alzheimer's disease: the Alzheimer's Disease Genetics Consortium. medRxiv 2023:2023.07.06.23292311. [PMID: 37461624 PMCID: PMC10350126 DOI: 10.1101/2023.07.06.23292311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Limited ancestral diversity has impaired our ability to detect risk variants more prevalent in non-European ancestry groups in genome-wide association studies (GWAS). We constructed and analyzed a multi-ancestry GWAS dataset in the Alzheimer's Disease (AD) Genetics Consortium (ADGC) to test for novel shared and ancestry-specific AD susceptibility loci and evaluate underlying genetic architecture in 37,382 non-Hispanic White (NHW), 6,728 African American, 8,899 Hispanic (HIS), and 3,232 East Asian individuals, performing within-ancestry fixed-effects meta-analysis followed by a cross-ancestry random-effects meta-analysis. We identified 13 loci with cross-ancestry associations including known loci at/near CR1 , BIN1 , TREM2 , CD2AP , PTK2B , CLU , SHARPIN , MS4A6A , PICALM , ABCA7 , APOE and two novel loci not previously reported at 11p12 ( LRRC4C ) and 12q24.13 ( LHX5-AS1 ). Reflecting the power of diverse ancestry in GWAS, we observed the SHARPIN locus using 7.1% the sample size of the original discovering single-ancestry GWAS (n=788,989). We additionally identified three GWS ancestry-specific loci at/near ( PTPRK ( P =2.4×10 -8 ) and GRB14 ( P =1.7×10 -8 ) in HIS), and KIAA0825 ( P =2.9×10 -8 in NHW). Pathway analysis implicated multiple amyloid regulation pathways (strongest with P adjusted =1.6×10 -4 ) and the classical complement pathway ( P adjusted =1.3×10 -3 ). Genes at/near our novel loci have known roles in neuronal development ( LRRC4C, LHX5-AS1 , and PTPRK ) and insulin receptor activity regulation ( GRB14 ). These findings provide compelling support for using traditionally-underrepresented populations for gene discovery, even with smaller sample sizes.
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Naj AC, Reitz C, Rajabli F, Jun GR, Benchek P, Tosto G, Sha J, Zhu C, Kushch NA, Lee W, Haut J, Hamilton‐Nelson KL, Wheeler NR, Zhao Y, Farrell J, Chung J, Grunin M, Leung YY, Li D, da Fonseca EL, Mez JB, Palmer EL, Pillai JA, Sherva R, Song YE, Zhang X, Iqbal T, Pathak O, Valladares O, Kuzma AB, Kunkle BW, Bush WS, Wang L, Farrer LA, Haines JL, Mayeux R, Pericak‐Vance MA, Schellenberg GD. Multi‐Ancestry Genome‐wide Association Analysis of Late‐Onset Alzheimer’s Disease (LOAD) in 60,941 Individuals Identifies a Novel Cross‐Ancestry Association in
LRRC4C. Alzheimers Dement 2022. [DOI: 10.1002/alz.065822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Adam C. Naj
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University New York NY USA
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University New York NY USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Gyungah R Jun
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine Boston MA USA
- Department of Biostatistics, Boston University School of Public Health Boston MA USA
| | - Penelope Benchek
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University New York NY USA
- G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University New York NY USA
| | - Jin Sha
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Congcong Zhu
- Boston University School of Medicine Boston MA USA
| | - Nicholas A. Kushch
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Wan‐Ping Lee
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Jacob Haut
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Kara L. Hamilton‐Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Nicholas R. Wheeler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Yi Zhao
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - John Farrell
- Boston University School of Medicine Boston MA USA
| | | | - Michelle Grunin
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Donghe Li
- Boston University School of Medicine Boston MA USA
| | - Eder Lucio da Fonseca
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Jesse B. Mez
- Boston University School of Medicine Boston MA USA
- Boston University Alzheimer’s Disease Research Center Boston MA USA
| | - Ellen L Palmer
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Jagan A. Pillai
- Cleveland Clinic Neurological Institute Cleveland OH USA
- Cleveland Clinic Lou Ruvo Center for Brain Health Cleveland OH USA
| | - Richard Sherva
- Boston University School of Medicine Boston MA USA
- National Center for PTSD, VA Boston Healthcare System Boston MA USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Xiaoling Zhang
- Boston University School of Medicine Boston MA USA
- Boston University School of Public Health Boston MA USA
| | - Taha Iqbal
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Omkar Pathak
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Otto Valladares
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Amanda B Kuzma
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - William S. Bush
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Li‐San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine Boston MA USA
- Department of Biostatistics, Boston University School of Public Health Boston MA USA
- Department of Ophthalmology, Boston University School of Medicine Boston MA USA
- Department of Neurology, Boston University School of Medicine Boston MA USA
- Department of Epidemiology, Boston University School of Public Health Boston MA USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University New York NY USA
- G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University New York NY USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
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