Raw data for the manuscripts published by NGI investigators can be found in NIAGADS, and Synapse.

An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations

Manuscript Full information

Umber Dube, Jorge L Del-Aguila, Zeran Li, John P Budde, Shan Jiang, Simon Hsu Laura Ibanez, Maria Victoria Fernandez, Fabiana Farias, Joanne Norton, Jen Gentsch, Fengxian Wang, the Dominantly Inherited Alzheimer Network (DIAN), Stephen Salloway, Colin L Masters, Jae-Hong Lee, Neill R Graff-Radford, Jasmeer P Chhatwal,  Randall J Bateman, John C Morris, Celeste M Karch, Oscar Harari, and Carlos Cruchaga. An atlas of cortical circular RNA expression demonstrates clinical and pathological associations with Alzheimer disease. Nature Neuroscience. 2019 Oct 3. DOI: 10.1038/s41593-019-0501-5.

https://www.nature.com/articles/s41593-019-0501-5

Summary Statistics

All full summary statistics can be found here and here.

The TMEM106B FTLD-protective variant, rs1990621, is also associated with increased neuronal proportion.

Manuscript Full information

Li Z, Farias FHG, Dube U, Del-Aguila JL, Mihindukulasuriya KA, Fernandez MV, Ibanez L, Budde JP, Wang F, Lake AM, Deming Y, Perez J, Yang C, Bahena JA, Qin W, Bradley JL, Davenport R, Bergmann K, Morris JC, Perrin RJ, Benitez BA, Dougherty JD, Harari O, Cruchaga C. Acta Neuropathol. 2019 Aug 27. doi: 10.1007/s00401-019-02066-0. [Epub ahead of print] PMID: 31456032

https://link.springer.com/article/10.1007%2Fs00401-019-02066-0

Summary Statistics

All full summary statistics can be found here and explore in our Online Neurodegenerative Trait Integrative Multi-Omics Explorer (Ontime)

The MS4A gene cluster is a key modulator of soluble TREM2 and Alzheimer’s disease risk

Manuscript Full information

Yuetiva Deming, Fabia Filipello, Francesca Cignarella, Claudia Cantoni, Simon Hsu, Robert Mikesell, Zeran Li, Jorge L Del-Aguila, Umber Dube, Fabiana Geraldo Farias, Joseph Bradley, John Budde, Laura Ibanez, Maria Victoria Fernandez, Kaj Blennow, Henrik Zetterberg, Amanda Heslegrave, Per M Johansson, Johan Svensson, Bengt Nellgård, Alberto Lleo, Daniel Alcolea, Jordi Clarimon, Lorena Rami, José Luis Molinuevo, Marc Suárez-Calvet, Estrella Morenas-Rodríguez, Gernot Kleinberger, Michael Ewers, Oscar Harari, Christian Haass, Thomas J Brett, Bruno a. Benitez, Celeste m. Karch, Laura Piccio, Carlos Cruchaga. Science Translational Medicine  14 Aug 2019: Vol. 11, Issue 505, eaau2291 DOI: 10.1126/scitranslmed.aau2291

https://stm.sciencemag.org/content/11/505/eaau2291

Free Access to the manuscript:

Reprint: http://stm.sciencemag.org/cgi/rapidpdf/11/505/eaau2291?ijkey=Mkcu6.lXS/QL2&keytype=ref&siteid=scitransmed

Full text: http://stm.sciencemag.org/cgi/content/full/11/505/eaau2291?ijkey=Mkcu6.lXS/QL2&keytype=ref&siteid=scitransmed

Summary Statistics

All full summary statistics can be found here and explore in our Online Neurodegenerative Trait Integrative Multi-Omics Explorer (Ontime)

Genome-wide association study of brain amyloid deposition as measured by Pittsburgh Compound-B (PiB)-PET imaging

Manuscript Full information

Yan Q, Nho K, Del-Aguila JL, Wang X, Risacher SL, Fan KH, Snitz BE, Aizenstein HJ, Mathis CA, Lopez OL, Demirci FY, Feingold E, Klunk WE, Saykin AJ; Alzheimer’s Disease Neuroimaging Initiative (ADNI), Cruchaga C, Kamboh MI. Genome-wide association study of brain amyloid deposition as measured by Pittsburgh Compound-B (PiB)-PET imaging. Mol Psychiatry. 2018; Oct 25. doi: 10.1038/s41380-018-0246-7 PMCID:PMC6219464.

https://www.nature.com/articles/s41380-018-0246-7

Raw Data

Washington University GWAS data: NIAGADS00030; https://www.niagads.org/datasets/ng00030

Summary Statistics

All full summary statistics can be found here and explore in our Online Neurodegenerative Trait Integrative Multi-Omics Explorer (Ontime)

Genome-wide association study for variants that modulate relationships between cerebrospinal fluid amyloid-beta 42, tau, and p-tau levels

Manuscript Full information

Maxwell TJ, Corcoran C, Del-Aguila JL, Budde JP, Deming Y, Cruchaga C, Goate AM, Kauwe JSK; Alzheimer’s Disease Neuroimaging Initiative. Genome-wide association study for variants that modulate relationships between cerebrospinal fluid amyloid-beta 42, tau, and p-tau levels. Alzheimers Res Ther. 2018; 10(1):86.  PMCID: PMC6114488

https://alzres.biomedcentral.com/articles/10.1186/s13195-018-0410-y

Summary Statistics

NIAGADS00055; https://www.niagads.org/datasets/ng00055

Sex-specific genetic predictors of Alzheimer's disease biomarkers.

Manuscript Full information

Deming Y, Dumitrescu L, Barnes LL, Thambisetty M, Kunkle B, Gifford KA, Bush WS, Chibnik LB, Mukherjee S, De Jager PL, Kukull W, Huentelman M, Crane PK, Resnick SM, Keene CD, Montine TJ, Schellenberg GD, Haines JL, Zetterberg H, Blennow K, Larson EB, Johnson SC, Albert M, Moghekar A, Del Aguila JL, Fernandez MV, Budde J, Hassenstab J, Fagan AM, Riemenschneider M, Petersen RC, Minthon L, Chao MJ, Van Deerlin VM, Lee VM, Shaw LM, Trojanowski JQ, Peskind ER, Li G, Davis LK, Sealock JM, Cox NJ; Alzheimer’s Disease Neuroimaging Initiative (ADNI); Alzheimer Disease Genetics Consortium (ADGC), Goate AM, Bennett DA, Schneider JA, Jefferson AL, Cruchaga C, Hohman TJ.  Sex-specific genetic predictors of Alzheimer’s disease biomarkers. Acta Neuropathol. 2018; 136(6) 857-872.  PMCID: PMC6280657

https://link.springer.com/article/10.1007%2Fs00401-018-1881-4

Raw Data

Washington University GWAS data: NIAGADS00030; https://www.niagads.org/datasets/ng00030

Summary Statistics

All full summary statistics can be found here 

Genetic variants associated with Alzheimer's disease confer different cerebral cortex cell-type population structure

Manuscript Full information

Li Z, Del-Aguila JL, Dube U, Budde J, Martinez R, Black K, Xiao Q, Cairns NJ; Dominantly Inherited Alzheimer Network (DIAN), Dougherty JD, Lee JM, Morris JC, Bateman RJ, Karch CM, Cruchaga C, Harari O.  Genetic variants associated with Alzheimer’s disease confer different cerebral cortex cell-type population structure. Genome Med. 2018; 10(1):43.  PMCID: PMC5992755

https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-018-0551-4

Raw Data

The gene expression data can be found in Synapse

Summary Statistics

All full gene-expression matrices can be found here 

Assessment of the Genetic Architecture of Alzheimer’s Disease Risk in Rate of Memory Decline

Manuscript Full information

Del-Aguila JL, Fernández MV, Schindler S, Ibanez L, Deming Y, Ma S, Saef B, Black K, Budde J, Norton J, Chasse R; Alzheimer’s Disease Neuroimaging Initiative (ADNI), Harari O, Goate A, Xiong C, Morris JC, Cruchaga C.  Assessment of the Genetic Architecture of Alzheimer’s Disease Risk in Rate of Memory Decline. J Alzheimers Dis. 2018; 62(2):745-756. PMCID: PMC5989565

https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-018-0551-4

Raw Data

The gene expression data can be found in 

Summary Statistics

All full gene-expression matrices can be found here 

Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease

Manuscript Full information

Fernández MV, Kim JH, Budde JP, Black K, Medvedeva A, Saef B, Deming Y, Del-Aguila J, Ibañez L, Dube U, Harari O, Norton J, Chasse R, Morris JC, Goate A; NIA-LOAD family study group; NCRAD, Cruchaga C. Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease. PLoS Genet. 2017;13(11):e1007045. doi: 0.1371/journal.pgen.1007045. PMCID: PMC5683650

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007045

 

Raw Data

The Washington Univeristy sequencing data can be found at NIAGADS00060: https://www.niagads.org/datasets/ng00060

 

 

 

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

Manuscript Full information

Sims R, van der Lee SJ, Naj AC, Bellenguez C, …., Cruchaga C, .., Lambert JC, Seshadri S, Williams J, Schellenberg GD, Etal.  Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer’s disease.  Nat Genet. 2017; 49(9):1373-1384. PMCID: PMC5669039

https://www.nature.com/articles/ng.3916

 

Raw Data

Washington University GWAS data: NIAGADS00085; https://www.niagads.org/datasets/ng00085

 

Summary Statistics

All full summary statistics can be found at NIAGADS00075 https://www.niagads.org/datasets/ng00075

A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease

Manuscript Full information

Huang KL, Marcora E, Pimenova AA, DiNarzo AF, Kapoor M, Jin SC, Harari O, Bertelsen S, Fairfax BP, Czajkowski J, Chouraki V, Grenier-Boley B, Bellenguez C, Deming Y, McKenzie A, Raj T, Renton AE, Budde J, Smith A, Fitzpatrick A, Bis JC, DeStefano A, Adams HHH, Ikram MA, VanDerLee S, Del-Aguila JL, Fernandez MV, Ibanez L, The international Genomics of Alzheimer’s Project, The Alzheimer’s Disease Neuroimaging Initiative, Sims, R, Escott-Price V, Mayeux R, Haines JL, Farrer LA, Pericak-Vance MA, Lambert JC, van Duijn C, Launer L, Seshadri S, Williams J, Amouyel P, Schellenberg GD, Zhang B, Borecki I, Kauwe JSK, Cruchaga C, Hao K, Goate AM. A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer’s disease.  Nat Neuroscience 2017. 20(8):1052-1061. PMCID: PMC5759334

https://www.nature.com/articles/nn.4587

 

Summary Statistics

All full summary statistics can be found here and explore in our Online Neurodegenerative Trait Integrative Multi-Omics Explorer (Ontime)

Genome-wide association study identifies four novel loci associated with Alzheimer’s endophenotypes and disease modifiers

Manuscript Full information

Deming Y, Li Z, Kapoor M, Harari O, Del-Aguila JL, Black K, Carrell D, Cai Y, Fernandez MV, Budde J, Ma S, Saef B, Howells B, Huang KL, Bertelsen S, Fagan AM, Holtzman DM, Morris JC, Kim S, Saykin AJ, De Jager PL, Albert M, Moghekar A, O’Brien R, Riemenschneider M, Petersen RC, Blennow K, Zetterberg H, Minthon L, Van Deerlin VM, Lee VM, Shaw LM, Trojanowski JQ, Schellenberg G, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Peskind ER, Li G, Di Narzo AF; Alzheimer’s Disease Neuroimaging Initiative (ADNI).; Alzheimer Disease Genetic Consortium (ADGC)., Kauwe JS, Goate AM, Cruchaga C.  Genome-wide association study identifies four novel loci associated with Alzheimer’s endophenotypes and disease modifiers. Acta Neuropathol. 2017; 133(5):839-856. PMCID: PMC5613285

https://link.springer.com/article/10.1007%2Fs00401-017-1685-y

Raw Data

Washington University GWAS data: NIAGADS00030; https://www.niagads.org/datasets/ng00030

Summary Statistics

All full summary statistics can be found here, in NIAGADS0055: https://www.niagads.org/datasets/ng00055, and explore in our Online Neurodegenerative Trait Integrative Multi-Omics Explorer (Ontime)

Chitinase-3-like 1 protein (CHI3L1) locus influences cerebrospinal fluid levels of YKL-40

Manuscript Full information

Deming Y, Black K, Carrell D, Cai Y, Del-Aguila JL, Fernandez MV, Budde J, Ma S, Saef B, Howells B, Bertelsen S, Huang KL, Sutphen CL, Tarawneh R, Fagan AM, Holtzman DM, MorrisJC, Goate AM, Dougherty JD, Cruchaga C.  Chitinase-3-like 1 protein (CHI3L1) locus Influences cerebrospinal fluid levels of YKL-40.  BMC Neurol 2016; 16(1):217. PMCID:  PMC5105244.

https://bmcneurol.biomedcentral.com/articles/10.1186/s12883-016-0742-9

 

Raw Data

Washington University GWAS data: NIAGADS00030; https://www.niagads.org/datasets/ng00030

 

Summary Statistics

All full summary statistics can be found here, and explore in our Online Neurodegenerative Trait Integrative Multi-Omics Explorer (Ontime)

SORL1 variants across Alzheimer's disease European American cohorts

Manuscript Full information

Fernández MV, Black K, Carrell D, Saef B, Budde J, Deming Y, Howells B, Del-Aguila JL, Ma S, Bi C, Norton J, Chasse R, Morris J, Goate A, Cruchaga C; NIA-LOAD family study group, NCRAD.  SORL1 variants across Alzheimer’s disease European American cohorts.  Eur J Hum Genet 2016; 24(12):1828-1830. PMCID: PMC5117924

https://www.nature.com/articles/ejhg2016122

 

Raw Data

Washington University GWAS data: NIAGADS00051; https://www.niagads.org/datasets/ng00051

 

A potential endophenotype for Alzheimer's disease: cerebrospinal fluid clusterin

Manuscript Full information

Deming Y, Xia J, Cai Y, Lord J, Holmans P, Bertelsen S, Holtzman D, Morris JC, Bales K, Pickering EH, Kauwe J, Goate A, Cruchaga C; Alzheimer’s Disease Neuroimaging Initiative (ADNI).  A potential endophenotype for Alzheimer’s disease: cerebrospinal fluid clusterin. Neurobiol Aging 2016; 37:208.  PMCID:  PMC5118651

https://linkinghub.elsevier.com/retrieve/pii/S0197-4580(15)00466-2

 

Raw Data

Washington University GWAS data: NIAGADS00050; https://www.niagads.org/datasets/ng00050

 

Summary Statistics

All full summary statistics can be found here, the NIAGADS0050, and explore in our Online Neurodegenerative Trait Integrative Multi-Omics Explorer (Ontime)

Genome-wide association study of CSF levels of 59 alzheimer's disease candidate proteins: significant associations with proteins involved in amyloid processing and inflammation

Manuscript Full information

Kauwe JS, Bailey MH, Ridge PG, Perry R, Wadsworth ME, Hoyt KL, Staley LA, Karch CM, Harari O, Cruchaga C, Ainscough BJ, Bales K, Pickering EH, Bertelsen S; the Alzheimer’s Disease Neuroimaging Initiative, Fagan AM, Holtzman DM, Morris JC, Goate AM. Genome-Wide Association Study of CSF Levels of 59 Alzheimer’s Disease Candidate Proteins: Significant Associations with Proteins Involved in Amyloid Processing and Inflammation. PloS Genet 2014; 10(10):e1004758. PMCID: PMC4207667.

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004758

Summary Statistics

All full summary statistics can be found here,  and explore in our Online Neurodegenerative Trait Integrative Multi-Omics Explorer (Ontime)

Genetic studies of plasma analytes identify novel potential biomarkers for several complex traits

Manuscript Full information

Deming Y, Xia J, Cai Y, Lord J, Del-Aguila JL, Fernandez MV, Carrell D, Black K, Budde J, Ma S, Saef B, Howells B, Bertelsen S, Bailey M, Ridge PG, Alzheimer’s Disease Neuroimaging Initiative (ADNI), Holtzman D, Morris JC, Bales K, Pickering EH, Lee JM, Heitsch L, Kauwe J, Goate A, Piccio L, Cruchaga C. Genetic studies of plasma analytes identify novel potential biomarkers for several complex traits. Sci Rep. 2016; 6: 18092. PMCID: PMC4698720

https://www.nature.com/articles/srep18092

 

Summary Statistics

All full summary statistics can be found here, and explore in our Online Neurodegenerative Trait Integrative Multi-Omics Explorer (Ontime)