---
title: "NG00196- Genotyping short tandem repeats using the ADSP R4 cohort"
id: "9252"
type: "dataset"
slug: "ng00196"
published_at: "2026-09-29T19:12:34+00:00"
modified_at: "2026-10-01T21:11:37+00:00"
url: "https://dss.niagads.org/datasets/ng00196/"
markdown_url: "https://dss.niagads.org/datasets/ng00196.md"
excerpt: "To access this data, please log into DSS and submit an application.Within the application, add this dataset (accession NG00196) 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"
  - "Open and Controlled Access Data"
  - "Short Tandem Repeats"
---

## Overview

To access this data, please log into DSS and submit an application.  
Within the application, add this dataset (accession NG00196) in the “Choose a Dataset” section.  
Once approved, you will be able to log in and access the data within the DARM portal.

#### Description

A two-step pipeline was used to first identify expanded short tandem repeats (STRs) in ADSP samples using ExpansionHunter Denovo and then genotype the identified STRs, along with additional polymorphic STRs identified from population surveys, using ExpansionHunter.

ADSP R4 genomes were profiled using ExpansionHunter Denovo to identify putative STR expansions. Single-sample profiles were merged into multi-sample profiles, and raw read counts were extracted. Since ExpansionHunter Denovo outputs a candidate region and expanded STR motif, a custom pipeline was created to convert these candidate regions/motifs into an ExpansionHunter catalog comprising the best estimate of STR start and end coordinates. In this step, STR regions supported by at least two raw in-repeat reads (IRRs) identified by ExpansionHunter Denovo were retained. These regions were supplemented with additional STRs that were either highly polymorphic or showed evidence of expansion from prior profiling of 22,579 individuals of diverse ancestry, as previously described (PMID: 39627187).

The resulting catalog comprised 165,208 STR loci with motif sizes ranging from 2 to 20 bp. This ExpansionHunter catalog was subsequently used to genotype STRs in the Illumina whole-genome sequencing data from the ADSP R4 data release.

One sample was dropped due to a sex mismatch, five samples were dropped due to being labeled with the incorrect sex, and one sample was dropped due to consent. Phenotypes are not provided directly within this dataset but are available through request of the ADSP Umbrella dataset ([ng00067](https://dss.niagads.org/datasets/ng00067/)
).

#### Sample Summary per Data Type

| Sample Set | Accession | Data Type | Number of Samples |
| --- | --- | --- | --- |
| ADSP R4 Short Tandem Repeats (STRs) | snd10147 | Short Tandem Repeats | 31,681 |

#### Available Filesets

| Name | Accession | Latest Release | Description |
| --- | --- | --- | --- |
| STRs using Expansion Hunter software | fsa000179 | NG00196.v1 | Genotyped STR (Short Tandem Repeats) using Expansion Hunter software. |
| STRs using Expansion HunterDenovo software | fsa000180 | NG00196.v1 | Genotyped STR (Short Tandem Repeats) using Expansion HunterDenovo software. |
| Companion Files | fsa000181 | NG00196.v1 | Sample crosswalk and README |

View the [File Manifest](https://st1.niagads.org/portal/download-public/NG00196.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 |
| --- | --- | --- | --- |
| ADSP R4 Short Tandem Repeats (STRs) | snd10147 | 31,158 | 31,681 |

## Related Studies

- [sa000087 - Genotyping short tandem repeats using ADSP R4](https://dss.niagads.org/studies/sa000087/) Variation in tandem repeats (TRs), particularly large expansions of triplet repeats (e.g., polyCAG), is known to cause a number of late-onset neurological diseases. Due to their repetitive and degenerate nature,… [Learn more](https://dss.niagads.org/studies/sa000087/)

## Cohorts

| Cohort | Number of Participants | Number of Samples |
| --- | --- | --- |
| Adult Changes in Thought (ACT) | 278 | 278 |
| Alzheimer’s Disease Neuroimaging Initiative (ADNI) | 756 | 756 |
| Amish Protective Variant Study | 966 | 966 |
| Case Western Reserve University (CWRU) Autopsy | 96 | 96 |
| Case Western Reserve University (CWRU) Rapid Decline | 159 | 159 |
| Cuban American Alzheimer’s Disease Initiative (CuAADI) | 96 | 96 |
| Erasmus Rucphen Family (ERF) | 92 | 92 |
| Estudio Familiar de Influencia Genetica en Alzheimer (EFIGA) | 1,840 | 1,865 |
| Harmonized Diagnostic Assessment of Dementia for the Longitudinal Aging Study of India (LASI-DAD) | 2,682 | 2,682 |
| Hillblom Aging Network (HAN) | 15 | 15 |
| Indianapolis-Ibadan (IIAA/IIBD) | 1,359 | 1,359 |
| Knight Alzheimer’s Disease Research Center (KGAD) | 577 | 578 |
| LonGenity | 27 | 27 |
| Longevity Genes Project (LGP) | 5 | 5 |
| Mayo Clinic (MAYO) | 169 | 169 |
| Mexican Health and Aging Study (MHAS) | 2,617 | 2,617 |
| Mount Sinai Brain Bank (MSBB) | 340 | 344 |
| National Centralized Repository for Alzheimer’s Disease and Related Dementias Family (NCRAD Family) | 10 | 19 |
| National Institute of Aging Alzheimer’s Disease Family Based Study (NIA AD-FBS) | 62 | 68 |
| NIA Alzheimer's Disease Research Centers (ADRC) | 9,765 | 10,213 |
| Northern Manhattan Study (NOMAS) | 771 | 771 |
| Peru Alzheimer’s Disease Initiative (PeADI) | 247 | 247 |
| Progressive Supranuclear Palsy (PSP) | 679 | 697 |
| Puerto Rican 10/66 Study (PR1066) | 1,517 | 1,517 |
| Puerto Rican Alzheimer’s Disease Initiative (PRADI) | 735 | 735 |
| Religious Orders Study/Memory and Aging Project (ROSMAP) | 729 | 730 |
| Research in African-American Alzheimer’s Disease Initiative (REAAADI) | 679 | 679 |
| Stanford Extreme Phenotypes in AD (StEP AD) | 195 | 195 |
| Texas Alzheimer’s Research and Care Consortium (TARCC) | 758 | 758 |
| University of Miami (MIA) | 969 | 970 |
| University of Miami Brain Bank (MBB) | 309 | 312 |
| University of Pittsburgh (PITT) | 209 | 209 |
| University of Washington Families (RAS) | 7 | 7 |
| Vanderbilt University (VAN) | 72 | 72 |
| Washington Heights and Inwood Community Aging project (WHICAP) | 589 | 589 |
| Wisconsin Registry for Alzheimer’s Prevention (WRAP) | 782 | 789 |

## Consent Levels

| Consent Level | Number of Participants | Number of Samples |
| --- | --- | --- |
| DS-ADRD-IRB-PUB | 2,275 | 2,305 |
| DS-ADRD-IRB-PUB-NPU | 3,284 | 3,285 |
| DS-ADRDAGE-IRB-PUB | 1,269 | 1,297 |
| DS-ADRDMEM-IRB-PUB-NPU | 182 | 186 |
| DS-AGEADLT-IRB-PUB | 176 | 176 |
| DS-AGEBRMEM-IRB-PUB-GSO | 2,617 | 2,617 |
| DS-ND-IRB-PUB | 854 | 945 |
| DS-ND-IRB-PUB-MDS | 80 | 83 |
| DS-ND-IRB-PUB-NPU | 907 | 914 |
| DS-NEURO-IRB-PUB | 7 | 7 |
| DS-NEURO-IRB-PUB-NPU | 292 | 303 |
| GRU-IRB-PUB | 15,024 | 15,257 |
| GRU-IRB-PUB-NPU | 160 | 164 |
| HMB-IRB-PUB | 2,890 | 2,990 |
| HMB-IRB-PUB-GSO | 102 | 102 |
| HMB-IRB-PUB-MDS | 528 | 539 |
| HMB-IRB-PUB-NPU | 92 | 92 |
| HMB-IRB-PUB-NPU-MDS-GSO | 419 | 419 |

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 [NG00196](https://archive.niagads.org/datasets/NG00196)
.

### For investigators using Genotyping short tandem repeats using ADSP R4 (sa000087) data:

This work was supported by NIA grant 1RF1AG075051-01A1 to AJS. The Alzheimer’s Disease Sequencing Project (ADSP) is comprised of two Alzheimer’s Disease (AD) genetics consortia and three National Human Genome Research Institute (NHGRI) funded Large Scale Sequencing and Analysis Centers (LSAC). The full acknowledgment for the ADSP dataset can be found here: [ADSP Acknowledgement](https://dss.niagads.org/datasets/ng00067/#acknowledgement)
.

## Publications

- Dolzhenko E. **ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions.***Bioinformatics (Oxford, England). 2019 Nov 1.*[PubMed link](https://pubmed.ncbi.nlm.nih.gov/31134279/)
- Dolzhenko E. **ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data.***Genome biology. 2020 Apr 28.*[PubMed link](https://pubmed.ncbi.nlm.nih.gov/32345345/)

### Total number of participants: 31,158

SexRaceEthnicityDiagnosisAPOE

Female19,33862.1 %

Male11,82037.9 %

| American Indian/Alaska Native | 110 |
| --- | --- |
| Asian | 2,822 |
| Native Hawaiian or Other Pacific Islander | 2 |
| Black or African American | 5,469 |
| White | 15,462 |
| Other | 4,654 |
| NA | 2,639 |

- 2290 (0.3%)
- 231,871 (6.0%)
- 24536 (1.7%)
- 3313,000 (41.7%)
- 347,745 (24.9%)
- 441,499 (4.8%)
- NA6,417 (20.6%)

| AD |  |  |
| --- | --- | --- |
| Control | 16,138 | 51.8% |
| Case | 9,265 | 29.7% |
| Other | 213 | 0.7% |
| Unknown | 4,863 | 15.6% |

| PSP |  |  |
| --- | --- | --- |
| Case | 679 | 2.2% |

Not Hispanic or Latino

19,648

63.1%

Hispanic or Latino

10,175

32.7%

Not Applicable/Not Available

1,335

4.3%

## Source Datasets

This dataset was generated using the following source dataset(s):

- [NG00067 - Alzheimer's Disease Sequencing Project Umbrella Study](/datasets/ng00067)