Description

This dataset includes sequencing data from samples sequenced by the Alzhiemer’s Disease Sequencing Project and other AD and Related Dementia’s studies. Samples are processed using a common workflow called VCPA (Variant Calling Pipeline and data management tool), a functionally equivalent CCDG/TOPMed pipeline.

Data Releases:

  1. The first release (July 30, 2018) included CRAMs, gVCFs, and phenotypes for 4,789 whole genomes. These data were called by GCAD using the VCPA1.0 pipeline.
  2. The second release (October 30, 2018) included an ADSP quality controlled project level VCF for the 4,789 whole genomes previously released.
  3. The third release (February 18, 2020) includes CRAMs, gVCFs, and phenotypes for 19,922 whole exomes. These data were called by GCAD using the VCPA1.1 pipeline.

Sample Summary per Data Type

Sample SetAccessionCRAMsgVCFsGATK Called Genotypes
ADSP Discovery - WGSsnd10000n = 580n = 580n = 580
ADSP Discovery - WESsnd10000n = 10088n = 10088NA
ADSP Extension - WGSsnd10001n = 3400n = 3400n = 3400
ADNI-WGS-1snd10002n = 809n = 809n = 809
ADGC AA - WES snd10003n = 3144 n = 3144NA
FASe Families - WESsnd10004n = 1100n = 1100NA
Brkanac Families - WESsnd10005n = 75n = 75NA
Miami Families - WESsnd10006n = 108n = 108NA
Columbia WHICAP - WESsnd10007n = 3861n = 3861NA
Knight ADRC - WESsnd10008n = 650n - 650NA
CBD - WESsnd10009n = 346n = 346NA
PSP - WESsnd10010n = 550n = 550NA

Available Filesets

NameAccessionVersion/DateDescription/What’s New
WGS CRAMs/GATK gVCFsfsa000001VCPA1.0/2018.07.30Mapped to GRCh38
WGS QC Metricsfsa000001VCPA1.0/2018.07.30Sequencing Data Quality Control Metrics
Phenotypes/Pedigreesfsa0000022020.01.15Phenotypes and Pedigree structures for all sequenced subjects
WGS Project Level VCFfsa0000032018.09.17ADSP quality control checked GATK joint called VCF containing 4789 whole-genomes.
WES CRAMs/GATK gVCFsfsa000004VCPA1.1/2020.01.15Mapped to GRCh38

View the File Manifest for a full list of files released in this dataset.

For more demographic information about the subjects, navigate to the sample sets below.

Sample SetAccession NumberNumber of Subjects
ADSP Discoverysnd1000010634
ADSP Extensionsnd100013370
ADNI-WGS-1snd10002809
ADGC AAsnd100032763
FASe Familiessnd100041041
Brkanac Familiessnd1000565
Miami Familiessnd1000659
Columbia WHICAP snd100073170
Knight ADRCsnd10008650
CBDsnd10009335
PSPsnd10010549
Consent LevelNumber of Subjects
DS-ADRDAGE-IRB-PUB1046
DS-ADRD-IRB-PUB1180
DS-ADRD-IRB-PUB-NPU2710
DS-ADRDMEM-IRB-PUB-NPU134
DS-AGEADLT-IRB-PUB647
DS-ND-IRB-PUB343
DS-ND-IRB-PUB-MDS 18
DS-ND-IRB-PUB-NPU1091
DS-NEURO-IRB-PUB675
GRU-IRB-PUB20070
HMB-IRB-PUB1375
HMB-IRB-PUB-GSO745
HMB-IRB-PUB-MDS1315
HMB-IRB-PUB-NPU 1787
HMB-IRB-PUB-NPU-MDS274

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:
    Expired
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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:
    March 10, 2020
    Request status:
    Approved
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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:
    Expired
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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
    Request status:
    Approved
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  • Investigator:
    Farrer, Lindsay
    Institution:
    Boston University
    Project Title:
    ADSP Data Analysis
    Date of Approval:
    March 10, 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
    Request status:
    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:
    January 10, 2019
    Request status:
    Expired
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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
    Request status:
    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
    Request status:
    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:
    February 24, 2020
    Request status:
    Approved
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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
    Request status:
    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
    Request status:
    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:
    February 26, 2020
    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:
    Expired
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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 any data from this dataset:

Please cite/reference the use of NIAGADS data by including the accession NG00067.

For investigators using ADSP (sa000001) data:

The acknowledgment statement to use can be found on the sa000001 study page here.

For investigators using ADNI (sa000002) data:

The acknowledgment statement to use can be found on the sa000002 study page here.

For investigators using ADGC AA (sa000003) data:

The acknowledgment statement to use can be found on the sa000003 study page here.

For investigators using FASe Families (sa000004) data:

The acknowledgment statement to use can be found on the sa000004 study page here.

For investigators using Brkanac Families (sa000005) data:

The acknowledgment statement to use can be found on the sa000005 study page here.

For investigators using Miami Families (sa000006) data:

The acknowledgment statement to use can be found on the sa000006 study page here.

For investigators using Columbia WHICAP (sa000007) data:

The acknowledgment statement to use can be found on the sa000007 study page here.

For investigators using Knight ADRC (sa000008) data:

The acknowledgment statement to use can be found on the sa000008 study page here.

For investigators using CBD (sa000009) data:

The acknowledgment statement to use can be found on the sa000009 study page here.

For investigators using PSP (sa000010) data:

The acknowledgment statement to use can be found on the sa000010 study page here.

  • Leung YY. VCPA: genomic Variant Calling pipeline and data management tool for Alzheimer’s Disease Sequencing Project. Bioinformatics. 2018 Oct. doi: 10.1093/bioinformatics/bty894.  PubMed link
  • 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
  • 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
  • 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
  • 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
  • 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
  • Beecham GW. The Alzheimer’s Disease Sequencing Project: Study design and sample selection. Neurol Genet. 2017 Oct; 3(5): e194. PubMed link