Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

Abstract

We identified rare coding variants associated with Alzheimer's disease in a three-stage case–control study of 85,133 subjects. In stage 1, we genotyped 34,174 samples using a whole-exome microarray. In stage 2, we tested associated variants (P < 1 × 10−4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, we used an additional 14,997 samples to test the most significant stage 2 associations (P < 5 × 10−8) using imputed genotypes. We observed three new genome-wide significant nonsynonymous variants associated with Alzheimer's disease: a protective variant in PLCG2 (rs72824905: p.Pro522Arg, P = 5.38 × 10−10, odds ratio (OR) = 0.68, minor allele frequency (MAF)cases = 0.0059, MAFcontrols = 0.0093), a risk variant in ABI3 (rs616338: p.Ser209Phe, P = 4.56 × 10−10, OR = 1.43, MAFcases = 0.011, MAFcontrols = 0.008), and a new genome-wide significant variant in TREM2 (rs143332484: p.Arg62His, P = 1.55 × 10−14, OR = 1.67, MAFcases = 0.0143, MAFcontrols = 0.0089), a known susceptibility gene for Alzheimer's disease. These protein-altering changes are in genes highly expressed in microglia and highlight an immune-related protein–protein interaction network enriched for previously identified risk genes in Alzheimer's disease. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to the development of Alzheimer's disease.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Association plots of PLCG2, ABI3, and TREM2.
Figure 2: Protein–protein interaction network (using high-confidence human interactions from the STRING database) of 56 genes enriched for both common and rare variants associated with Alzheimer's disease risk.

Similar content being viewed by others

References

  1. Gatz, M. et al. Role of genes and environments for explaining Alzheimer disease. Arch. Gen. Psychiatry 63, 168–174 (2006).

    Article  PubMed  Google Scholar 

  2. Lambert, J.-C. et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat. Genet. 45, 1452–1458 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Harold, D. et al. Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Nat. Genet. 41, 1088–1093 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Lambert, J.-C. et al. Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease. Nat. Genet. 41, 1094–1099 (2009).

    Article  CAS  PubMed  Google Scholar 

  5. Escott-Price, V. et al. Gene-wide analysis detects two new susceptibility genes for Alzheimer's disease. PLoS One 9, e94661 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Hollingworth, P. et al. Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. Nat. Genet. 43, 429–435 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Naj, A.C. et al. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat. Genet. 43, 436–441 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ruiz, A. et al. Toward fine mapping and functional characterization of genome-wide association study–identified locus rs74615166 (TRIP4) for Alzheimer's disease. Alzheimers Dement. 10, 257–P258 (2014).

    Article  Google Scholar 

  9. Jonsson, T. et al. Variant of TREM2 associated with the risk of Alzheimer's disease. N. Engl. J. Med. 368, 107–116 (2013).

    Article  CAS  PubMed  Google Scholar 

  10. Jonsson, T. et al. A mutation in APP protects against Alzheimer's disease and age-related cognitive decline. Nature 488, 96–99 (2012).

    Article  CAS  PubMed  Google Scholar 

  11. Guerreiro, R. et al. TREM2 variants in Alzheimer's disease. N. Engl. J. Med. 368, 117–127 (2013).

    Article  CAS  PubMed  Google Scholar 

  12. Seshadri, S. et al. Genome-wide analysis of genetic loci associated with Alzheimer disease. J. Am. Med. Assoc. 303, 1832–1840 (2010).

    Article  CAS  Google Scholar 

  13. Escott-Price, V. et al. Common polygenic variation enhances risk prediction for Alzheimer's disease. Brain 138, 3673–3684 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  14. Bodmer, W. & Bonilla, C. Common and rare variants in multifactorial susceptibility to common diseases. Nat. Genet. 40, 695–701 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Pritchard, J.K. Are rare variants responsible for susceptibility to complex diseases? Am. J. Hum. Genet. 69, 124–137 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Schork, N.J., Murray, S.S., Frazer, K.A. & Topol, E.J. Common vs. rare allele hypotheses for complex diseases. Curr. Opin. Genet. Dev. 19, 212–219 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Surakka, I. et al. The impact of low-frequency and rare variants on lipid levels. Nat. Genet. 47, 589–597 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Vardarajan, B.N. et al. Coding mutations in SORL1 and Alzheimer disease. Ann. Neurol. 77, 215–227 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Vardarajan, B.N. et al. Rare coding mutations identified by sequencing of Alzheimer disease genome-wide association studies loci. Ann. Neurol. 78, 487–498 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Steinberg, S. et al. Loss-of-function variants in ABCA7 confer risk of Alzheimer's disease. Nat. Genet. 47, 445–447 (2015).

    Article  CAS  PubMed  Google Scholar 

  21. Logue, M.W. et al. Two rare AKAP9 variants are associated with Alzheimer's disease in African Americans. Alzheimers Dement. 10, 609–618 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Jun, G. et al. PLXNA4 is associated with Alzheimer disease and modulates tau phosphorylation. Ann. Neurol. 76, 379–392 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Hunkapiller, J. et al. A rare coding variant alters UNC5C function and predisposes to Alzheimer's disease. Alzheimers Dement. 9, 853 (2013).

    Article  Google Scholar 

  24. Wetzel-Smith, M.K. et al. A rare mutation in UNC5C predisposes to late-onset Alzheimer's disease and increases neuronal cell death. Nat. Med. 20, 1452–1457 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Richards, A.L. et al. Exome arrays capture polygenic rare variant contributions to schizophrenia. Hum. Mol. Genet. 25, 1001–1007 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Wessel, J. et al. Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility. Nat. Commun. 6, 5897 (2015).

    Article  CAS  PubMed  Google Scholar 

  27. Igartua, C. et al. Ethnic-specific associations of rare and low-frequency DNA sequence variants with asthma. Nat. Commun. 6, 5965 (2015).

    Article  CAS  PubMed  Google Scholar 

  28. Tachmazidou, I. et al. A rare functional cardioprotective APOC3 variant has risen in frequency in distinct population isolates. Nat. Commun. 4, 2872 (2013).

    Article  CAS  PubMed  Google Scholar 

  29. Huyghe, J.R. et al. Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion. Nat. Genet. 45, 197–201 (2013).

    Article  CAS  PubMed  Google Scholar 

  30. Willer, C.J., Li, Y. & Abecasis, G.R. METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26, 2190–2191 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. R Development Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2014).

  32. Das, S. et al. Next-generation genotype imputation service and methods. Nat. Genet. 48, 1284–1287 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. McCarthy, S. et al. A reference panel of 64,976 haplotypes for genotype imputation. Nat. Genet. 48, 1279–1283 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Jin, S.C. et al. Coding variants in TREM2 increase risk for Alzheimer's disease. Hum. Mol. Genet. 23, 5838–5846 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Lu, Y., Liu, W. & Wang, X. TREM2 variants and risk of Alzheimer's disease: a meta-analysis. Neurol. Sci. 36, 1881–1888 (2015).

    Article  PubMed  Google Scholar 

  36. Cruchaga, C. et al. GWAS of cerebrospinal fluid tau levels identifies risk variants for Alzheimer's disease. Neuron 78, 256–268 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. International Genomics of Alzheimer's Disease Consortium (IGAP).. Convergent genetic and expression data implicate immunity in Alzheimer's disease. Alzheimers Dement. 11, 658–671 (2015).

  38. Zhang, Y. et al. Purification and characterization of progenitor and mature human astrocytes reveals transcriptional and functional differences with mouse. Neuron 89, 37–53 (2016).

    Article  CAS  PubMed  Google Scholar 

  39. Milner, J.D. PLAID: a syndrome of complex patterns of disease and unique phenotypes. J. Clin. Immunol. 35, 527–530 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Fairfax, B.P. et al. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 343, 1246949 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Sekino, S. et al. The NESH/Abi-3-based WAVE2 complex is functionally distinct from the Abi-1-based WAVE2 complex. Cell Commun. Signal. 13, 41 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Nolz, J.C. et al. The WAVE2 complex regulates actin cytoskeletal reorganization and CRAC-mediated calcium entry during T cell activation. Curr. Biol. 16, 24–34 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Xing, J., Titus, A.R. & Humphrey, M.B. The TREM2–DAP12 signaling pathway in Nasu–Hakola disease: a molecular genetics perspective. Res. Rep. Biochem. 5, 89–100 (2015).

    PubMed  PubMed Central  Google Scholar 

  44. Neumann, H. & Takahashi, K. Essential role of the microglial triggering receptor expressed on myeloid cells-2 (TREM2) for central nervous tissue immune homeostasis. J. Neuroimmunol. 184, 92–99 (2007).

    Article  CAS  PubMed  Google Scholar 

  45. Painter, M.M. et al. TREM2 in CNS homeostasis and neurodegenerative disease. Mol. Neurodegener. 10, 43 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Ulrich, J.D. et al. In vivo measurement of apolipoprotein E from the brain interstitial fluid using microdialysis. Mol. Neurodegener. 8, 13 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Wang, Y. et al. TREM2 lipid sensing sustains the microglial response in an Alzheimer's disease model. Cell 160, 1061–1071 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Rademakers, R. et al. Mutations in the colony stimulating factor 1 receptor (CSF1R) gene cause hereditary diffuse leukoencephalopathy with spheroids. Nat. Genet. 44, 200–205 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Perlmutter, L.S., Barron, E. & Chui, H.C. Morphologic association between microglia and senile plaque amyloid in Alzheimer's disease. Neurosci. Lett. 119, 32–36 (1990).

    Article  CAS  PubMed  Google Scholar 

  50. Wisniewski, H.M., Wegiel, J., Wang, K.C. & Lach, B. Ultrastructural studies of the cells forming amyloid in the cortical vessel wall in Alzheimer's disease. Acta Neuropathol. 84, 117–127 (1992).

    Article  CAS  PubMed  Google Scholar 

  51. Schwab, C., Klegeris, A. & McGeer, P.L. Inflammation in transgenic mouse models of neurodegenerative disorders. Biochim. Biophys. Acta 1802, 889–902 (2010).

    Article  CAS  PubMed  Google Scholar 

  52. Hong, S. et al. Complement and microglia mediate early synapse loss in Alzheimer mouse models. Science 352, 712–716 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Olmos-Alonso, A. et al. Pharmacological targeting of CSF1R inhibits microglial proliferation and prevents the progression of Alzheimer's-like pathology. Brain 139, 891–907 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  54. Paris, D. et al. The spleen tyrosine kinase (Syk) regulates Alzheimer amyloid-β production and tau hyperphosphorylation. J. Biol. Chem. 289, 33927–33944 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Bao, M. et al. CD2AP/SHIP1 complex positively regulates plasmacytoid dendritic cell receptor signaling by inhibiting the E3 ubiquitin ligase Cbl. J. Immunol. 189, 786–792 (2012).

    Article  CAS  PubMed  Google Scholar 

  56. Kurosaki, T. & Tsukada, S. BLNK: connecting Syk and Btk to calcium signals. Immunity 12, 1–5 (2000).

    Article  CAS  PubMed  Google Scholar 

  57. Wang, Y. et al. TREM2-mediated early microglial response limits diffusion and toxicity of amyloid plaques. J. Exp. Med. 213, 667–675 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Yuan, P. et al. TREM2 haplodeficiency in mice and humans impairs the microglia barrier function leading to decreased amyloid compaction and severe axonal dystrophy. Neuron 90, 724–739 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Goldstein, J.I. et al. zCall: a rare variant caller for array-based genotyping: genetics and population analysis. Bioinformatics 28, 2543–2545 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Devlin, B. & Roeder, K. Genomic control for association studies. Biometrics 55, 997–1004 (1999).

    CAS  PubMed  Google Scholar 

  61. Grove, M.L. et al. Best practices and joint calling of the HumanExome BeadChip: the CHARGE Consortium. PLoS One 8, e68095 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Patterson, N., Price, A.L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Howie, B., Fuchsberger, C., Stephens, M., Marchini, J. & Abecasis, G.R. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat. Genet. 44, 955–959 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Fuchsberger, C., Abecasis, G.R. & Hinds, D.A. minimac2: faster genotype imputation. Bioinformatics 31, 782–784 (2015).

    Article  CAS  PubMed  Google Scholar 

  65. Talluri, R. & Shete, S. A linkage disequilibrium–based approach to selecting disease-associated rare variants. PLoS One 8, e69226 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Holmans, P. et al. Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. Am. J. Hum. Genet. 85, 13–24 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Lim, A.S.P. et al. 24-hour rhythms of DNA methylation and their relation with rhythms of RNA expression in the human dorsolateral prefrontal cortex. PLoS Genet. 10, e1004792 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. De Jager, P.L. et al. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat. Neurosci. 17, 1156–1163 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Chan, G. et al. CD33 modulates TREM2: convergence of Alzheimer loci. Nat. Neurosci. 18, 1556–1558 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

GERAD/PERADES. We thank all individuals who participated in this study. Cardiff University was supported by the Alzheimer's Society (AS; grant RF014/164) and the Medical Research Council (MRC; grants G0801418/1, MR/K013041/1, MR/L023784/1) (R. Sims is an AS Research Fellow). Cardiff University was also supported by the European Joint Programme for Neurodegenerative Disease (JPND; grant MR/L501517/1), Alzheimer's Research UK (ARUK; grant ARUK-PG2014-1), the Welsh Assembly Government (grant SGR544:CADR), and a donation from the Moondance Charitable Foundation. Cardiff University acknowledges the support of the UK Dementia Research Institute, of which J. Williams is an associate director. Cambridge University acknowledges support from the MRC. Patient recruitment for the MRC Prion Unit/UCL Department of Neurodegenerative Disease collection was supported by the UCLH/UCL Biomedical Centre and NIHR Queen Square Dementia Biomedical Research Unit. The University of Southampton acknowledges support from the AS. King's College London was supported by the NIHR Biomedical Research Centre for Mental Health and the Biomedical Research Unit for Dementia at the South London and Maudsley NHS Foundation Trust and by King's College London and the MRC. ARUK and the Big Lottery Fund provided support to Nottingham University. Ulster Garden Villages, AS, ARUK, the American Federation for Aging Research, and the Northern Ireland R&D Office provided support for Queen's University, Belfast. The Centro de Biología Molecular Severo Ochoa (CSIS-UAM), CIBERNED, Instituto de Investigación Sanitaria la Paz, University Hospital La Paz, and the Universidad Autónoma de Madrid were supported by grants from the Ministerio de Educación y Ciencia and the Ministerio de Sanidad y Consumo (Instituto de Salud Carlos III) and by an institutional grant of the Fundación Ramón Areces to the CMBSO. We thank I. Sastre and A. Martinez-Garcia for DNA preparation, and P. Gil and P. Coria for their recruitment efforts. The Department of Neurology, University Hospital Mútua de Terrassa, was supported by CIBERNED, Instituto de Salud Carlos III, Madrid, Spain, and acknowledges M.A. Pastor (University of Navarra Medical School and Center for Applied Medical Research), M. Seijo-Martinez (Hospital do Salnes), and R. Rene, J. Gascon, and J. Campdelacreu (Hospital de Bellvitage) for providing DNA samples. The Hospital de la Sant Pau, Universitat Autònoma de Barcelona, acknowledges support from the Spanish Ministry of Economy and Competitiveness (grant PI12/01311) and from the Generalitat de Catalunya (2014SGR-235). The Santa Lucia Foundation and the Fondazione Ca' Granda IRCCS Ospedale Policlinico, Italy, acknowledge the Italian Ministry of Health (grant RC 10.11.12.13/A). The Bonn samples are part of the German Dementia Competence Network (DCN) and the German Research Network on Degenerative Dementia (KNDD), which are funded by the German Federal Ministry of Education and Research (grants KND: 01G10102, 01GI0420, 01GI0422, 01GI0423, 01GI0429, 01GI0431, 01GI0433, 04GI0434; grants KNDD: 01GI1007A, 01GI0710, 01GI0711, 01GI0712, 01GI0713, 01GI0714, 01GI0715, 01GI0716, 01ET1006B). M.M.N. is a member of the German Research Foundation (DFG) cluster of excellence ImmunoSensation. Funding for Saarland University was provided by the German Federal Ministry of Education and Research (BMBF), grant 01GS08125, to M. Riemenschneider. The University of Washington was supported by grants from the US National Institutes of Health (R01-NS085419 and R01-AG044546), the Alzheimer's Association (NIRG-11-200110), and the American Federation for Aging Research (C. Cruchaga was recipient of a New Investigator Award in Alzheimer's disease). Brigham Young University was supported by the Alzheimer's Association (MNIRG-11-205368), the BYU Gerontology Program, and the US National Institutes of Health (R01-AG11380, R01-AG021136, P30-S069329-01, R01-AG042611). We also acknowledge funding from the Institute of Neurology, UCL, London, who was supported in part by ARUK via an anonymous donor, and by a fellowship to R.G. The participation of D.S., M.U., and C. Masullo in the study was completely supported by Ministero della Salute, IRCCS Research Program, Ricerca Corrente 2015–2017, Linea 2 'Malattiecomplesse e Terapie Innovative' and by the '5 × 1000' voluntary contribution. AddNeuromed is supported by InnoMed, an Integrated Project funded by the European Union's Sixth Framework Programme priority FP6-2004-LIFESCIHEALTH-5, Life Sciences, Genomics, and Biotechnology for Health. We are grateful to the Wellcome Trust for awarding a Principal Research Fellowship to D.C.R. (095317/Z/11/Z). M. Riemenschneider was funded by BMBF NGFN grant 01GS08125. B.N. was supported by the Fondazione Cassa di Risparmio di Pistoia e Pescia (grants 2014.0365, 2011.0264, 2013.0347). H. Hampel is supported by the AXA Research Fund, the Fondation Universite Pierre et Marie Curie, and the 'Fondation pour la Recherche sur Alzheimer', Paris, France. The research leading to these results has received funding from the program 'Investissements d'Avenir', ANR-10-IAIHU-06 (Agence Nationale de la Recherche-10-IA Agence Institut Hospitalo-Universitaire-6.

CHARGE. Infrastructure for the CHARGE Consortium is supported in part by National Heart, Lung, and Blood Institute grant HL105756 and for the neurology working group by AG033193 and AG049505.

Rotterdam (RS). The Rotterdam Study is funded by Erasmus Medical Center and Erasmus University, Rotterdam, the Netherlands Organization for Health Research and Development (ZonMw), the Research Institute for Diseases in the Elderly (RIDE), the Ministry of Education, Culture and Science, the Ministry for Health, Welfare and Sports, the European Commission (DG XII), and the municipality of Rotterdam. The authors are grateful to the study participants, the staff from the Rotterdam Study, and the participating general practitioners and pharmacists. Generation and management of the Illumina exome chip v1.0 array data for the Rotterdam Study (RS-I) was executed by the Human Genotyping Facility of the Genetic Laboratory of the Department of Internal Medicine (http://www.glimdna.org/), Erasmus MC, Rotterdam, the Netherlands. The Exome chip array data set was funded by the Genetic Laboratory of the Department of Internal Medicine, Erasmus MC, from the Netherlands Genomics Initiative (NGI)/Netherlands Organization for Scientific Research (NWO)-sponsored Netherlands Consortium for Healthy Aging (NCHA; project 050-060-810); the Netherlands Organization for Scientific Research (NWO; project 184021007); and by the Rainbow Project (RP10; Netherlands Exome Chip Project) of Biobanking and Biomolecular Research Infrastructure Netherlands (BBMRI-NL; http://www.bbmri.nl). Generation and management of GWAS genotype data for the Rotterdam Study (RS-I, RS-II, RS-III) was executed by the Human Genotyping Facility of the Genetic Laboratory of the Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands. The GWAS data sets are supported by the Netherlands Organization of Scientific Research NWO Investments (175.010.2005.011, 911-03-012), the Genetic Laboratory of the Department of Internal Medicine, Erasmus MC, the Research Institute for Diseases in the Elderly (014-93-015; RIDE2), and the Netherlands Genomics Initiative (NGI)/Netherlands Organization for Scientific Research (NWO) Netherlands Consortium for Healthy Aging (NCHA), project 050-060-810. This study makes use of an extended data set of RS-II and RS-III samples based on Illumina Omni 2.5 and 5.0 GWAS genotype data. This data set was funded by the Genetic Laboratory of the Department of Internal Medicine, the Department of Forensic Molecular Biology, and the Department of Dermatology, Erasmus MC, Rotterdam, the Netherlands. We thank M. Jhamai, S. Higgins, and M. Verkerk for their help in creating the exome chip database; C. Medina-Gomez, L. Karsten, and L. Broer for quality control and variant calling; M. Jhamai, M. Verkerk, L. Herrera, M. Peters, and C. Medina-Gomez for their help in creating the GWAS database; and L. Broer for the creation of the HRC-imputed data. Variants were called using the best practice protocol developed by M.L. Grove and colleagues as part of the CHARGE Consortium Exome Chip central calling effort. The work for this manuscript was further supported by ADAPTED: Alzheimer's Disease Apolipoprotein Pathology for Treatment Elucidation and Development (115975); the CoSTREAM project (http://www.costream.eu/); and funding from the European Union's Horizon 2020 research and innovation programme under grant agreement 667375.

AGES. The AGES study has been funded by NIA contracts N01-AG-12100 and HHSN271201200022C with contributions from NEI, NIDCD, and NHLBI, the NIA Intramural Research Program, Hjartavernd (the Icelandic Heart Association), and the Althingi (the Icelandic Parliament).

Cardiovascular Health Study (CHS). This research was supported by contracts HHSN268201200036C, HHSN268200800007C, N01HC55222, N01HC85079, N01HC85080, N01HC85081, N01HC85082, N01HC85083, and N01HC85086 and grant U01HL080295 from the National Heart, Lung, and Blood Institute (NHLBI), with additional contribution from the National Institute of Neurological Disorders and Stroke (NINDS). Additional support was provided by R01AG033193, R01AG023629, R01AG15928, and R01AG20098 and by U01AG049505 from the National Institute on Aging (NIA). The provision of genotyping data was supported in part by the National Center for Advancing Translational Sciences, CTSI grant UL1TR000124, and National Institute of Diabetes and Digestive and Kidney Disease Diabetes Research Center (DRC) grant DK063491 to the Southern California Diabetes Endocrinology Research Center. A full list of CHS principal investigators and institutions can be found at https://chs-nhlbi.org/. The content is solely the responsibility of the authors and does not necessarily represent the official views of the US National Institutes of Health.

Framingham Heart Study. This work was supported by the National Heart, Lung, and Blood Institute's Framingham Heart Study (contracts N01-HC-25195 and HHSN268201500001I). This study was also supported by grants from the National Institute on Aging: AG033193, U01-AG049505, and AG008122 (S. Seshadri). S. Seshadri and A.L.D. were also supported by additional grants from the National Institute on Aging (R01AG049607) and the National Institute of Neurological Disorders and Stroke (R01-NS017950).

Fundació ACE. We sincerely acknowledge the collaboration of S. Ruiz, M. Rosende-Roca, A. Mauleon, L. Vargas, O. Rodriguez-Gomez, M. Alegret, A. Espinosa, G. Ortega, M. Tarragona, C. Abdelnour, and D. Sanchez. We thank all patients for their participation in this project. We are obliged to T. Port-Carbo and her family for their support of the Fundació ACE research programs. Fundació ACE collaborates with CIBERNED and is one of the participating centers of Dementia Genetics Spanish Consortium 430 (DEGESCO). CIBERNED is an Instituto de Salud Carlos III Project. A. Ruiz is supported by grant PI13/02434 (Acción Estratégica en Salud, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain) and Obra Social 'La Caixa' (Barcelona, Spain).

ADGC. The US National Institutes of Health, National Institute on Aging (NIH-NIA) supported this work through the following grants: ADGC, U01 AG032984, and RC2 AG036528. Samples from the National Cell Repository for Alzheimer's Disease (NCRAD), which receives government support under a cooperative agreement grant (U24 AG21886) awarded by the National Institute on Aging (NIA), were used in this study. We thank the contributors who collected samples used in this study, as well as the patients and their families, whose help and participation made this work possible. Data for this study were prepared, archived, and distributed by the National Institute on Aging Alzheimer's Disease Data Storage Site (NIAGADS) at the University of Pennsylvania (U24-AG041689-01), NACC (U01 AG016976), NIA LOAD (Columbia University) (U24 AG026395, R01AG041797), Banner Sun Health Research Institute (P30 AG019610), Boston University (P30 AG013846, U01 AG10483, R01 CA129769, R01 MH080295, R01 AG017173, R01 AG025259, R01 AG048927, R01AG33193), Columbia University (P50 AG008702, R37 AG015473), Duke University (P30 AG028377, AG05128), Emory University (AG025688), Group Health Research Institute (UO1 AG006781, UO1 HG004610, UO1 HG006375), Indiana University (P30 AG10133), Johns Hopkins University (P50 AG005146, R01 AG020688), Massachusetts General Hospital (P50 AG005134), Mayo Clinic (P50 AG016574), Mount Sinai School of Medicine (P50 AG005138, P01 AG002219), New York University (P30 AG08051, UL1 RR029893, 5R01AG012101, 5R01AG022374, 5R01AG013616, 1RC2AG036502, 1R01AG035137), Northwestern University (P30 AG013854), Oregon Health & Science University (P30 AG008017, R01 AG026916), Rush University (P30 AG010161, R01 AG019085, R01 AG15819, R01 AG17917, R01 AG30146), TGen (R01 NS059873), University of Alabama at Birmingham (P50 AG016582), University of Arizona (R01 AG031581), University of California, Davis (P30 AG010129), University of California, Irvine (P50 AG016573), University of California, Los Angeles (P50 AG016570), University of California, San Diego (P50 AG005131), University of California, San Francisco (P50 AG023501, P01 AG019724), University of Kentucky (P30 AG028383, AG05144), University of Michigan (P50 AG008671), University of Pennsylvania (P30 AG010124), University of Pittsburgh (P50 AG005133, AG030653, AG041718, AG07562, AG02365), University of Southern California (P50 AG005142), University of Texas Southwestern (P30 AG012300), University of Miami (R01 AG027944, AG010491, AG027944, AG021547, AG019757), University of Washington (P50 AG005136), University of Wisconsin (P50 AG033514), Vanderbilt University (R01 AG019085), and Washington University (P50 AG005681, P01 AG03991). The Kathleen Price Bryan Brain Bank at Duke University Medical Center is funded by NINDS grant NS39764, NIMH MH60451, and by GlaxoSmithKline. Support was also provided by the Alzheimer's Association (L.A.F., IIRG-08-89720; M.P.-V., IIRG-05-14147), the US Department of Veterans Affairs Administration, the Office of Research and Development, the Biomedical Laboratory Research Program, and the BrightFocus Foundation (M.P.-V., A2111048). P.S.G.-H. is supported by the Wellcome Trust, the Howard Hughes Medical Institute, and the Canadian Institutes of Health Research. Genotyping of the TGEN2 cohort was supported by Kronos Science. The TGen series was also funded by NIA grant AG041232 to A.J.M. and M.J.H., the Banner Alzheimer's Foundation, the Johnnie B. Byrd Sr. Alzheimer's Institute, the Medical Research Council, and the state of Arizona and also includes samples from the following sites: the Newcastle Brain Tissue Resource (funding via the Medical Research Council, local NHS trusts, and Newcastle University), the MRC London Brain Bank for Neurodegenerative Diseases (funding via the Medical Research Council), the South West Dementia Brain Bank (funding via numerous sources including the Higher Education Funding Council for England (HEFCE), Alzheimer's Research UK (ARUK), and BRACE as well as the North Bristol NHS Trust Research and Innovation Department and DeNDRoN), the Netherlands Brain Bank (funding via numerous sources including Stichting MS Research, Brain Net Europe, Hersenstichting Nederland Breinbrekend Werk, International Parkinson Fonds, Internationale Stiching Alzheimer Onderzoek), and the Institut de Neuropatologia, Servei Anatomia Patologica, Universitat de Barcelona. ADNI data collection and sharing were funded by US National Institutes of Health grant U01 AG024904 and Department of Defense award W81XWH-12-2-0012. ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: AbbVie, Alzheimer's Association; the Alzheimer's Drug Discovery Foundation; Araclon Biotech; BioClinica, Inc.; Biogen; Bristol-Myers Squibb Company; CereSpir, Inc.; Eisai, Inc.; Elan Pharmaceuticals, Inc.; Eli Lilly and Company; EuroImmun; F. Hoffmann-La Roche, Ltd., and its affiliated company Genentech, Inc.; Fujirebio; GE Healthcare; IXICO, Ltd.; Janssen Alzheimer Immunotherapy Research & Development, LLC.; Johnson & Johnson Pharmaceutical Research & Development, LLC.; Lumosity; Lundbeck; Merck & Co., Inc.; Meso Scale Diagnostics, LLC.; NeuroRx Research; Neurotrack Technologies; Novartis Pharmaceuticals Corporation; Pfizer, Inc.; Piramal Imaging; Servier; Takeda Pharmaceutical Company; and Transition Therapeutics. The Canadian Institutes of Health Research provide funds to support ADNI clinical sites in Canada. Private sector contributions are facilitated by the Foundation for the National Institutes of Health (http://www.fnih.org/). The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer's Disease Cooperative Study at the University of California, San Diego. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of Southern California. We thank D.S. Snyder and M. Miller from the NIA who are ex-officio ADGC members.

EADI. This work was supported by INSERM, the National Foundation for Alzheimer's Disease and Related Disorders, the Institut Pasteur de Lille, and the Centre National de Génotypage. This work has been developed and supported by the LABEX (Laboratory of Excellence Program Investment for the Future) DISTALZ grant (Development of Innovative Strategies for a Transdisciplinary Approach to Alzheimer's Disease) including funding from MEL (Métropole Européenne de Lille), ERDF (European Regional Development Fund), and the Conseil Régional du Nord-Pas-de-Calais. The Three-City Study was performed as part of collaboration between INSERM, Victor Segalen Bordeaux II University, and Sanofi-Synthelabo. The Fondation pour la Recherche Médicale funded the preparation and initiation of the study. The 3C Study was also funded by the Caisse Nationale Maladie des Travailleurs Salaries, Direction Générale de la Santé, MGEN, Institut de la Longévité, Agence Française de Sécurité Sanitaire des Produits de Santé, the Aquitaine and Bourgogne regional councils, Agence Nationale de la Recherche (ANR supported the COGINUT and COVADIS projects), Fondation de France, and the joint French Ministry of Research/INSERM 'Cohortes et Collections de Données Biologiques' program. The Lille Genopole received an unconditional grant from Eisai and was supported by the European Joint Programme for Neurodegenerative Disease (JPND: grant MR/L501517/1). The Three-City Biological Bank was developed and maintained by the Laboratory for Genomic Analysis LAG-BRC, Institut Pasteur de Lille.

Belgium sample collection. Research at the Antwerp site is funded in part by the Interuniversity Attraction Poles program of the Belgian Science Policy Office, the Foundation for Alzheimer Research (SAO-FRA), a Methusalem Excellence Grant of the Flemish Government, the Research Foundation Flanders (FWO), and the Special Research Fund of the University of Antwerp, Belgium. Authors from the Antwerp site thank the personnel of the VIB Genetic Service Facility, the Biobank of the Institute Born-Bunge, and the Departments of Neurology and Memory Clinics at the Hospital Network Antwerp and University Hospitals Leuven.

Finnish sample collection. Financial support for this project was provided by the Health Research Council of the Academy of Finland, EVO grant 5772708 of Kuopio University Hospital, and the Nordic Center of Excellence in Neurodegeneration.

Swedish sample collection. Sample collection was financially supported in part by the Swedish Brain Power network, the Marianne and Marcus Wallenberg Foundation, the Swedish Research Council (521-2010-3134), King Gustaf V and Queen Victoria's Foundation of Freemasons, the Regional Agreement on Medical Training and Clinical Research (ALF) between the Stockholm County Council and the Karolinska Institutet, the Swedish Brain Foundation, and the Swedish Alzheimer Foundation.

AMP AD University of Florida/Mayo Clinic/Institutes of Systems Biology. For human brain donations, we thank all patients and their families, without whom this work would not have been possible. This work was supported by NIH/NIA AG046139-01 (T.E.G., N.E.-T., N.P., S.G.Y.). We thank T.G. Beach (Banner Sun Health Institute) for sharing human tissue.

The Mayo Clinic Brain Bank. Data collection was supported through funding by NIA grants P50 AG016574, R01 AG032990, U01 AG046139, R01 AG018023, U01 AG006576, U01 AG006786, R01 AG025711, R01 AG017216, and R01 AG003949, NINDS grant R01 NS080820, the CurePSP Foundation, and support from the Mayo Foundation.

Sun Health Research Institute Brain and Body Donation Program of Sun City, Arizona. The Brain and Body Donation Program is supported by the National Institute of Neurological Disorders and Stroke (U24 NS072026 National Brain and Tissue Resource for Parkinson's Disease and Related Disorders), the National Institute on Aging (P30 AG19610 Arizona Alzheimer's Disease Core Center), the Arizona Department of Health Services (contract 211002, Arizona Alzheimer's Research Center), the Arizona Biomedical Research Commission (contracts 4001, 0011, 05-901, and 1001 to the Arizona Parkinson's Disease Consortium), and the Michael J. Fox Foundation for Parkinson's Research.

Author information

Authors and Affiliations

Authors