---
title: "NG00093 – WHICAP GWAS (CHOP)"
id: "7735"
type: "dataset"
slug: "ng00093"
published_at: "2025-01-21T21:41:50+00:00"
modified_at: "2026-07-31T20:35:26+00:00"
url: "https://dss.niagads.org/datasets/ng00093/"
markdown_url: "https://dss.niagads.org/datasets/ng00093.md"
excerpt: "To access this data, please log into DSS and submit an application.Within the application, add this dataset (accession NG00093) in the “Choose a Dataset” section.Once approved, you will be able to log in and access the data within the DARM..."
taxonomy_dataset_categories:
  - "AD"
  - "Controlled Access"
  - "Data Type"
  - "Disease"
  - "Genotyping SNP Array"
  - "Illumina OmniExpress"
  - "Imputation"
  - "Open and Controlled Access Data"
  - "Platform"
  - "TOPMed r2"
---

## Overview

To access this data, please log into DSS and submit an application.  
Within the application, add this dataset (accession NG00093) in the “Choose a Dataset” section.  
Once approved, you will be able to log in and access the data within the DARM portal.

This dataset was originally published on the NIAGADS archive site and was moved to DSS on 07/02/2026.

#### Description

The Washington Heights-Inwood Community Aging Project (WHICAP) is a community-based longitudinal study of aging and dementia among elderly, urban-dwelling residents. Beginning enrolment in 1989, WHICAP has followed more than 5,900 residents over 65 years of age, including white, African American, and Hispanic participants. Detailed clinical assessments were performed at approximately 24-month intervals over the 7 years of the initial study. All interviews were conducted in either English or Spanish. The choice of language was decided by the subject in order to ensure the best performance, and the majority of assessments were performed in the subject’s home, which included medical, neurological, and neuropsychological evaluations. Results of the neurological, psychiatric and neuropsychological assessments were reviewed in a consensus conference comprised of neurologists, psychiatrists, and neuropsychologists. Based on this review all participants were assigned to one of three categories: dementia, cognitive impairment or normal cognitive function. The sample set available in the ADGC for genetic analyses included 73 Alzheimer’s disease cases and 560 subjects with normal cognitive function.

This SNP array dataset, WHICAP, was used by the Alzheimer’s Disease Genetics Consortium (ADGC) to identify genes associated with an increased risk of developing Alzheimer’s disease. Provided here are the PLINK genotype files that have undergone ADGC quality control procedures, covariates formatted by ADGC to be used with the genotype data, and imputation files (.bgen format) generated using the TOPMED-r2 reference panel.

#### Sample Summary per Data Type

| Sample Set | Accession | Data Type | Number of Samples |
| --- | --- | --- | --- |
| WHICAP GWAS | snd10132 | Genotyping SNP Array | 647 |

#### Available Filesets

| Name | Accession | Latest Release | Description |
| --- | --- | --- | --- |
| WHICAP GWAS: Genotype, covariate, and imputation files. | fsa000158 | NG00093.v1 | Genotype, covariate, and imputation files. |

View the [File Manifest](https://st1.niagads.org/portal/download-public/NG00093.v1/fm)
 for a full list of files released in this dataset.

## Participant Information

For a breakdown of the study population characteristics, navigate to the individual sample sets below.

| Sample Set | Accession Number | Number of Participants | Number of Samples |
| --- | --- | --- | --- |
| WHICAP GWAS | snd10132 | 647 | 647 |

## Related Studies

- [sa000007 - Washington Heights and Inwood Community Aging project (WHICAP)](https://dss.niagads.org/studies/sa000007/) Since inception of the study in 1992, over 6,000 participants have enrolled in the Washington Heights and Inwood Community Aging project (WHICAP). The cohort participants were nondemented initially, 65 years… [Learn more](https://dss.niagads.org/studies/sa000007/)

## Cohorts

| Cohort | Number of Participants | Number of Samples |
| --- | --- | --- |
| Washington Heights and Inwood Community Aging project (WHICAP) | 647 | 647 |

## Consent Levels

| Consent Level | Number of Participants | Number of Samples |
| --- | --- | --- |
| GRU-IRB-PUB | 647 | 647 |

Visit the [Data Use Limitations page](/documentation/policies-and-guidelines/data-use-limitations/)
 for definitions of the consent levels above.

## Acknowledgement

### 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 [NG00093](https://archive.niagads.org/datasets/NG00093)
.

### For investigators using Washington Heights and Inwood Community Aging project (WHICAP) (sa000007) data:

Data collection and sharing for this project was supported by the Washington Heights-Inwood Columbia Aging Project (WHICAP R01AG072474, PO1AG07232, R01AG037212, RF1AG054023) funded by the National Institute on Aging (NIA). This manuscript has been reviewed by WHICAP investigators for scientific content and consistency of data interpretation with previous WHICAP Study publications. We acknowledge the WHICAP study participants and the WHICAP research and support staff for their contributions to this study**.**

## Publications

- Kunkle BW. **Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing.***Nature genetics. 2019 Mar.*[PubMed link](https://pubmed.ncbi.nlm.nih.gov/30820047/)

## Approved Users

**Total number of approved DARs:** 1

[JSON Export](https://st1.niagads.org/portal/v1/adars/NG00093)
|[CSV Export](https://dss.niagads.org/wp-admin/admin-post.php?action=niagads_export_dars_csv&accession=NG00093)

- Investigator: Blue, Elizabeth Institution: University of Washington Project Title: Genetic modifiers of Alzheimer's disease Date of Initial Approval: July 15, 2025 Current Status: Approved Publications: None Reported Research Use Statements: Show statements Technical Research Use Statement: The objective of the proposed research is to identify and characterize genetic variants involved in Alzheimer's disease (AD) risk and AD-related phenotypes to ultimately identify potential avenues for therapeutic approaches and prevention of the disease. Our study design will use phenotypic (ex., AD diagnosis, age-at-onset, APOE genotype) and genomic data (ex., WGS, array, imputed genotypes) from NIAGADS studies to investigate genotype-phenotype associations. Strategies include association testing and haplotype- and family-based approaches, including estimates of relatedness and population genetics analyses as needed to perform the association testing (ex. control for population structure). NIAGADS data will not be used to investigate individual identity. Consent type and other Data Use Limitations (DUL) for each study will be respected in all analyses. Data from an individual with disease-specific consent will not be used in analyses outside of that restriction, including indirect uses such as imputation reference panels or variant summary statistics. When an individual’s DUL prohibits investigation of population genetics, population history or related issues, their data will be excluded from studies that address those issues. We intend to publish or otherwise broadly share any findings from this study with the scientific community. As such, genomic summary results from datasets with a “sensitive” designation will only be shared through publications to support study’s conclusions and through NIH-funded data repositories which maintain restricted access (ex. NIAGADS). Data from NIAGADS may be combined with non-NIAGADS data from the same or other studies (obtained from dbGaP or other sources), to improve the power for novel genetic discoveries, while respecting the consent of all participants. We expect that this activity creates no additional risks to participants. Data will be shared only among Internal Collaborators at the University of Washington. We do not plan to collaborate with External Collaborators at other institutions. Non-Technical Research Use Statement: We propose to identify and characterize genetic variation involved in Alzheimer's disease (AD), providing insight as to why some individuals develop or avoid AD, and ultimately identifying potential avenues for therapeutic approaches and prevention of the disease. We will combine phenotype and genotype data using association testing and haplotype- and family-based approaches to identify and characterize associations and refine those signals with fine-mapping tools and external data.

### Total number of participants: 647

SexRaceEthnicityDiagnosisAPOE

Female39160.4 %

Male24237.4 %

Sex not reported: 14 (2.2%)

| White | 633 |
| --- | --- |
| NA | 14 |

- 221 (0.2%)
- 2375 (11.6%)
- 248 (1.2%)
- 33423 (65.4%)
- 34117 (18.1%)
- 448 (1.2%)
- NA15 (2.3%)

| AD |  |  |
| --- | --- | --- |
| Control | 560 | 86.6% |
| Case | 73 | 11.3% |
| Unknown | 14 | 2.2% |

Not Hispanic or Latino

633

97.8%

Not Applicable/Not Available

14

2.2%