Description

This dataset includes Compressed Sequence Alignment files (CRAMs) mapped to GRCh38 and GATK-called gVCFs from the ADSP and ADNI studies. These data were called by the Genome Center for Alzheimer’s Disease (GCAD) using VCPA 1.0, a functionally equivalent CCDG/TOPMed pipeline. GCAD processed a total of 4789 whole genomes, including, 876 ADSP Family Discovery and Discovery Extension samples, 3104 ADSP Case Control Extension samples, and 809 ADNI samples. The next data release will include the ADSP quality control checked GATK joint called VCF containing all 4789 whole genomes.

Sample Summary per Data Type

WGS CRAMsWGS gVCFsGATK Called Genotypes
ADSP Discovery
snd10000
n = 580n = 580n = NA
ADSP Extension
snd10001
n = 3400n = 3400n = NA
ADNI-WGS-1
snd10002
n = 809n = 809n = NA

Available Filesets

NameAccessionVersion/DateDescription/What’s New
ADSP Discovery WGS CRAMs/GATK gVCFsnd10000VCPA1.0/2018.07.30Mapped to GRCh38
ADSP Extension WGS CRAMs/ GATK gVCFssnd10001 VCPA1.0/2018.07.30Mapped to GRCh38
ADNI-WGS-1 CRAMs/ GATK gVCFssnd10002 VCPA1.0/2018.07.30Mapped to GRCh38
ADSP/ADNI QC MetricsNA VCPA1.0/2018.07.30Sequencing Data Quality Control Metrics
ADSP/ADNI Phenotypes/Pedigreesdnd000012018.07.30Phenotypes and Pedigree structures for all whole-genome sequenced subjects
Sample SetAccession NumberNumber of Subjects
ADSP Discoverysnd10000574
ADSP Extensionsnd100013367
ADNI-WGS-1snd10002809
Consent LevelNumber of Subjects
DS-ADRDAGE-IRB-PUB214
DS-ADRD-IRB-PUB98
DS-ADRDMEM-IRB-PUB-NPU20
DS-AGEADLT-IRB-PUB173
DS-AGEADLT-IRB-PUB-NPU77
DS-AGEBRMEM-IRB-PUB-GSO7
DS-DEMND-IRB-PUB 186
DS-DEMND-IRB-PUB-NPU91
DS-ND-IRB-PUB61
DS-ND-IRB-PUB-MDS 4
DS-ND-IRB-PUB-NPU64
DS-NEURO-IRB-PUB168
DS-NEURO-IRB-PUB-NPU1
GRU-IRB-PUB3076
GRU-IRB-PUB-NPU36
HMB-IRB-PUB250
HMB-IRB-PUB-GSO102
HMB-IRB-PUB-NPU 122

Visit the Data Use Limitations page for definitions of the consent levels above.

  • Investigator:
    Adanve, Bertrand
    Institution:
    Genetic Intelligence, Inc
    Project Title:
    AI-based platform to identify causal, genetically-defined therapeutic targets for Alzheimer's disease
    Date of Approval:
    November 8, 2019
    Request status:
    Approved
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  • Investigator:
    Boerwinkle, Eric
    Institution:
    University of Texas Health Science Center at Houston
    Project Title:
    ADSP Data Analysis
    Date of Approval:
    March 5, 2019
    Request status:
    Approved
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  • Investigator:
    Bras, Jose
    Institution:
    Van Andel Research Institute
    Project Title:
    Rare Variants in Alzheimer’s Disease and Other Dementias
    Date of Approval:
    May 13, 2019
    Request status:
    Approved
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  • Investigator:
    Carter, Gregory
    Institution:
    The Jackson Laboratory
    Project Title:
    Prioritization of Genetic Variants Contributing to Late-Onset Alzheimer’s Disease
    Date of Approval:
    December 17, 2019
    Request status:
    Approved
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  • Investigator:
    Cruchaga, Carlos
    Institution:
    Washington University School of Medicine
    Project Title:
    The Familial Alzheimer Sequencing (FASe) Project
    Date of Approval:
    January 23, 2019
    Request status:
    Expired
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  • Investigator:
    Curtis, David
    Institution:
    University College London
    Project Title:
    Developing improved methods to analyse next generation sequence data
    Date of Approval:
    September 13, 2019
    Request status:
    Approved
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  • Investigator:
    DeStefano, Anita
    Institution:
    Boston University
    Project Title:
    Therapeutic target discovery in ADSP data via comprehensive whole-genome analysis incorporating ethnic diversity and systems approaches
    Date of Approval:
    March 4, 2019
    Request status:
    Approved
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  • Investigator:
    Ebbert, Mark
    Institution:
    Mayo Clinic
    Project Title:
    Resolving mutations in challenging genomic regions to test association with disease phenotypes
    Date of Approval:
    January 22, 2020
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    Approved
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  • Investigator:
    Farrer, Lindsay
    Institution:
    Boston University
    Project Title:
    ADSP Data Analysis
    Date of Approval:
    January 9, 2020
    Request status:
    Approved
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  • Investigator:
    Goate, Alison
    Institution:
    Icahn School of Medicine at Mount Sinai
    Project Title:
    Study of Alzheimer's disease and other dementias (e.g. frontotemporal dementia) and related phenotypes
    Date of Approval:
    December 2, 2019
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    Approved
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  • Investigator:
    Greicius, Michael
    Institution:
    Stanford University School of Medicine
    Project Title:
    Examining Genetic Associations in Neurodegenerative Diseases
    Date of Approval:
    February 10, 2020
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    Approved
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  • Investigator:
    Haines, Jonathan
    Institution:
    Case Western Reserve University
    Project Title:
    Alzheimer Disease Sequence Analysis Collaborative (a.k.a. Collaborative Alzheimer Disease REsearch; CADRE)
    Date of Approval:
    October 22, 2018
    Request status:
    Expired
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  • Investigator:
    Hohman, Timothy
    Institution:
    Vanderbilt University Medical Center
    Project Title:
    Genetic Drivers of Resilience to Alzheimer's Disease
    Date of Approval:
    November 8, 2019
    Request status:
    Approved
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  • Investigator:
    Holstege, Henne
    Institution:
    Amsterdam UMC
    Project Title:
    Searching for Alzheimer-related genetic variants and genes
    Date of Approval:
    May 7, 2019
    Request status:
    Approved
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  • Investigator:
    Jinwal, Umesh
    Institution:
    University of South Florida, College of Pharmacy
    Project Title:
    Characterize the Role of Shroom-3 in Alzheimer's Disease
    Date of Approval:
    February 5, 2020
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    Approved
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  • Investigator:
    Kulminski, Alexander
    Institution:
    Duke University
    Project Title:
    ApoE2 and protective molecular signatures in Alzheimer’s disease and aging
    Date of Approval:
    July 10, 2019
    Request status:
    Approved
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  • Investigator:
    Lichtarge, Olivier
    Institution:
    Baylor College of Medicine
    Project Title:
    Integrating the impact of exome variations
    Date of Approval:
    July 10, 2019
    Request status:
    Approved
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  • Investigator:
    Lo, Cecilia
    Institution:
    University of Pittsburgh
    Project Title:
    Exploring the shared genetic etiologies of CHD and Alzheimer’s disease
    Date of Approval:
    October 11, 2019
    Request status:
    Approved
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  • Investigator:
    Mayeux, Richard
    Institution:
    Columbia University
    Project Title:
    Alzheimer's Disease Sequencing Project
    Date of Approval:
    November 16, 2018
    Request status:
    Expired
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  • Investigator:
    Michaelis, Elias
    Institution:
    University of Kansas
    Project Title:
    Analysis of genome-wide sequencing data from NIAGADS: Searching for gene variants related to gender-Alzheimer's disease (AD) association
    Date of Approval:
    July 5, 2019
    Request status:
    Approved
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  • Investigator:
    Nicolas, Gael
    Institution:
    University of Rouen
    Project Title:
    Searching for Alzheimer-related genetic variants and genes
    Date of Approval:
    November 21, 2019
    Request status:
    Approved
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  • Investigator:
    Pan, Wei
    Institution:
    University of Minnesota
    Project Title:
    Powerful and novel statistical methods to detect genetic variants associated with or putative causal to Alzheimer’s disease
    Date of Approval:
    December 18, 2019
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    Approved
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  • Investigator:
    PARIDA, LAXMI
    Institution:
    IBM Thomas J Watson Research Center
    Project Title:
    WAGE ADSP Data Analysis
    Date of Approval:
    January 17, 2020
    Request status:
    Approved
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  • Investigator:
    Park, Peter
    Institution:
    Harvard Medical School
    Project Title:
    Examining the association between clonal hematoposiesis and Alzheimer's Disease
    Date of Approval:
    December 3, 2019
    Request status:
    Approved
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  • Investigator:
    Pericak-Vance, Margaret
    Institution:
    University of Miami
    Project Title:
    Collaboration on Alzheimer Disease Research
    Date of Approval:
    November 5, 2018
    Request status:
    Expired
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  • Investigator:
    Ridge, Perry
    Institution:
    Brigham Young University
    Project Title:
    Mitochondrial Genetics of Alzheimer's Disease
    Date of Approval:
    January 2, 2019
    Request status:
    Expired
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  • Investigator:
    Saykin, Andrew
    Institution:
    Indiana University School of Medicine
    Project Title:
    Alzheimer's Disease Genomics: Systems Biology and Endophenotypes
    Date of Approval:
    November 15, 2018
    Request status:
    Expired
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  • Investigator:
    Schellenberg, Gerard
    Institution:
    University of Pennsylvania
    Project Title:
    ADSP Data Analysis
    Date of Approval:
    February 13, 2020
    Request status:
    Approved
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  • Investigator:
    Sul, Jae Hoon
    Institution:
    University of California, Los Angeles
    Project Title:
    Impact of common and rare genetic variants in Alzheimer's Disease using whole-genome and whole-exome sequencing data
    Date of Approval:
    January 9, 2020
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    Approved
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  • Investigator:
    Tanzi, Rudolph
    Institution:
    Massachusetts General Hospital
    Project Title:
    ADSP extension
    Date of Approval:
    December 3, 2019
    Request status:
    Approved
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  • Investigator:
    Valdmanis, Paul
    Institution:
    University of Washington
    Project Title:
    Quantification of Noncoding Variant Burden in DNA De-Identified Samples and Data from Patients with Alzheimer's Disease Versus Controls.
    Date of Approval:
    June 10, 2019
    Request status:
    Approved
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  • Investigator:
    Wang, Li-San
    Institution:
    University of Pennsylvania
    Project Title:
    ADSP Data Processing
    Date of Approval:
    August 23, 2018
    Request status:
    Approved
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  • Investigator:
    Wijsman, Ellen
    Institution:
    University of Washington
    Project Title:
    Therapeutic target discovery in ADSP data via comprehensive whole-genome analysis incorporating ethnic diversity and systems approaches
    Date of Approval:
    July 22, 2019
    Request status:
    Approved
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  • Investigator:
    Wingo, Thomas
    Institution:
    Emory University
    Project Title:
    Identifying Alzheimer's Disease Genetic Risk Factors By Integrated Genomic and Proteomic Analysis
    Date of Approval:
    September 17, 2019
    Request status:
    Approved
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  • Investigator:
    Yang, Jingjing
    Institution:
    Emory University
    Project Title:
    Novel Bayesian methods for integrating transcriptomic data in GWAS
    Date of Approval:
    November 8, 2019
    Request status:
    Approved
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  • Investigator:
    Yesavage, Jerome
    Institution:
    Stanford University
    Project Title:
    Identifying Variable Number Tandem Repeats Associated with Alzheimer Disease in Diverse Populations
    Date of Approval:
    December 18, 2019
    Request status:
    Approved
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  • Investigator:
    Yokoyama, Jennifer
    Institution:
    University of California, San Francisco
    Project Title:
    Rare variation contributing to Alzheimer's disease risk
    Date of Approval:
    February 19, 2019
    Request status:
    Expired
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  • Investigator:
    Zhao, Jinying
    Institution:
    University of Florida
    Project Title:
    Identifying novel biomarkers for human complex diseases using an integrated multi-omics approach
    Date of Approval:
    March 19, 2019
    Request status:
    Approved
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Acknowledgment statement for any data distributed by NIAGADS:

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), funded by the National Institute on Aging.

Use the study-specific acknowledgement statements below (as applicable):

For investigators using ADSP data:

Please cite/reference the use of NIAGADS data by including the accession NG00067. The acknowledgment statement to use from the ADSP can be found here.

For investigators using ADNI data:

Please cite/reference the use of NIAGADS data by including the accession NG00066. The acknowledgement statement to use from ADNI can be found here.

  1. Nafikov RA. Analysis of pedigree data in populations with multiple ancestries: Strategies for dealing with admixture in Caribbean Hispanic families from the ADSP. Genet Epidemiol. 2018 Jun. doi: 10.1002/gepi.22133. PubMed link
  2. Naj AC. Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer’s disease sequencing project. Genomics. 2018 May. pii: S0888-7543(18)30281-7. PubMed link
  3. Butkiewicz M. Functional Annotation of genomic variants in studies of Late-Onset Alzheimer’s Disease. Bioinformatics. 2018 Mar; doi: 10.1093/bioinformatics/bty177. PubMed link
  4. Vardarajan BN. Whole genome sequencing of Caribbean Hispanic families with late-onset Alzheimer’s disease. Ann Clin Transl Neurol. 2018 Mar; 5(4): 406-417. PubMed link
  5. Blue EE. Genetic Variation in Genes Underlying Diverse Dementias May Explain a Small Proportion of Cases in the Alzheimer’s Disease Sequencing Project. Dement Geriatr Cogn Disord. 2018 Feb; 45(1-2): 1-17. PubMed link
  6. Beecham GW. The Alzheimer’s Disease Sequencing Project: Study design and sample selection. Neurol Genet. 2017 Oct; 3(5): e194. PubMed link