Description
Data Available
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Description
The APOE and Serotonin Transporter Alleles data product includes data for the APOE isoform, directly genotyped using a TaqMan allelic discrimination SNP assay, where available, or imputed from preexisting genotype array data otherwise. This file also includes human serotonin transporter (5HTTLPR) short and long alleles measured using polymerase chain reaction (PCR). In total, there are 19,193 HRS participants in the data file: 17,237 with directly genotyped data for APOE and 1,956 additional participants with imputed data. There are 17,364 participants with valid values for 5HTTLPR.
Sample Summary per Data Type
Sample Set | Accession | Data Type | Number of Samples |
---|---|---|---|
HRS APOE | snd10040 | Targeted genotyping | 19,193 |
Available Filesets
Name | Accession | Latest Release | Description |
---|---|---|---|
HRS APOE: Targeted genotype data | fsa000040 | NG00132.v1 | Targeted genotype data |
View the File Manifest for a full list of files released in this dataset.
Subject Information
Provided in this dataset is a csv file containing APOE genotypes and HTTLPR calls for 19,193 total subjects. 17,237 subjects’ APOE genotypes were collected directly using a TaqMan allelic discrimination SNP assay at the Center for Inherited Disease Research (CIDR) Genetic Resources Core Facility (GRCF) and Fragment Analysis Facility (FAF) at Johns Hopkins University. 1,956 subjects’ APOE genotypes were imputed from a preexisting genotype array to the 1000G (Phase3 v5) reference panel. 17,364 subjects’ HTTLPR short and long alleles were measured using PCR.
Sample Set | Accession Number | Number of Subjects |
---|---|---|
HRS APOE | snd10040 | 19,193 |
Related Studies
Consent Levels
Consent Level | Number of Subjects |
---|---|
GRU-IRB-PUB-NPU | 19,193 |
Visit the Data Use Limitations page for definitions of the consent levels above.
Approved Users
- Investigator:Cruchaga, CarlosInstitution:Washington University School of MedicineProject Title:The Familial Alzheimer Sequencing (FASe) ProjectDate of Approval:May 9, 2024Request status:ApprovedResearch use statements:Show statementsTechnical Research Use Statement:The goal of this study is to identify new genes and mutations that cause or increase risk for Alzheimer disease (AD), as well as protective factors. Individuals and families were selected from the Knight-ADRC (Washington University) and the NIA-LOAD study. Only families with at least three first-degree affected individuals were included. Families with pathogenic variants in the known AD or FTD genes, or in which APOE4 segregated with disease were excluded. At least two cases and one control were selected per family. Cases had an age at onset (AAO) after 65 yo and controls had a larger age at last assessment than the latest AAO within the family. Whole exome (WES) and whole genome sequencing (WGS) was generated for 1,235 individuals (285 families) that together with data from our collaborators and the ADSP family-based cohort (3,449 individuals and 757 families) will provide enough statistical power to identify new genes for AD. Dr. Tanzi (Harvard Medical School) will provide WGS from 400 families from the NIMH Alzheimer disease genetics initiative study. We will perform single variant and gene-based analyses to identify genes and variants that increase risk for disease in AD families. Single variant analysis will consist of a combination of association and segregation analyses. We will run family-based gene-based methods to identify genes that show and overall enrichment of variants in AD cases. We will also look for protective and modifier variants. To do this we will identify families loaded with AD cases, that also include individuals with a high burden of known risk variants but that do not develop the disease (escapees). We will use the sequence data and the family structure to identify variants that segregate with the escapee phenotype. The most promising variants and genes will be replicated in independent datasets (ADSP case-control, ADNI, Knight-ADRC, NIA-LOAD ). We will perform single variant and gene-based analyses to replicate the initial findings, and survival analysis to replicate the protective variants. We will select the most promising variants/genes for functional studiesNon-Technical Research Use Statement:Family-based approaches led to the identification of disease-causing Alzheimer’s Disease (AD) variants in the genes encoding APP, PSEN1 and PSEN2. The identification of these genes led to the A?-cascade hypothesis and to the development of drugs that target this pathway. Recently, we have identified rare coding variants in TREM2, ABCA7, PLD3 and SORL1 with large effect sizes for risk for AD, confirming that rare coding variants play a role in the etiology of AD. In this proposal, we will identify rare risk and protective alleles using sequence data from families densely affected by AD. We hypothesize that these families are enriched for genetic risk factors. We already have sequence data from 695 families (2,462 individuals), that combined with the ADSP and the NIMH dataset will lead to a dataset of more than 1,042 families (4,684 individuals). Our preliminary results support the flexibility of this approach and strongly suggest that protective and risk variants with large effect size will be found, which will lead to a better understanding of the biology of the disease.
- Investigator:Ware, ErinInstitution:University of MichiganProject Title:DNA Methylation,Genetics, and Modifiable Risk Factors of Dementia in a Nationally Representative, Multi-Ethnic CohortDate of Approval:July 2, 2024Request status:ApprovedResearch use statements:Show statementsTechnical Research Use Statement:Our goal is to determine the joint epigenetic and environmental contributions to ADRD risk that underlie these health disparities. Using existing epigenetic and genetic data, well-characterized dementia phenotypes, and diverse risk factor data, we will analyze a population representative, multi-ethnic aging sample from the Health and Retirement Study (HRS). We aim to (1) test the associations between DNA methylation and dementia phenotypes (prevalent, 8-year incident), stratified by race/ethnicity and test for effect modification by ADRD disparity-related factors (educational attainment, sex, urban/rural); (2) identify associations between longitudinal measures of modifiable risk factors for ADRD and DNA methylation, stratified by race/ethnicity and test for effect modification or mediation by ADRD disparity-related factors; and finally, (3) identify genetic polymorphisms controlling DNA methylation and whether these are enriched in dementia outcomes to evaluate the role of DNA methylation in disease development. This study will likely impact the field of Alzheimer’s research and contribute to public health because it will a) establish the relevance of DNA methylation on ADRD in multiple race/ethnicities; b) elucidate important biological epigenetic mechanisms; c) determine the combined and individual epigenetic-environment interplay contributions to ADRD; and d) consider the effects of sex, educational attainment, race/ethnicity, younger age groups, and urban/rural status in the same study where comparisons of relative contribution to risk can be made. Here, we have the opportunity to simultaneously and substantially improve our understanding of the genetic and environmental etiologic contributions to health disparities in ADRD.Non-Technical Research Use Statement:The overall purpose of this proposal is to identify modifiable risk factors for Alzheimer’s disease and related dementias that influence DNA methylation and dementia status among groups at increased risk for dementia including women, minorities, rural inhabitants, and those with low educational attainment. Results from this proposal may provide an opportunity to identify epigenetic components that contribute to the prevalence and risk of dementia that could lead to a mechanistic understanding or targeted interventions that may substantially decrease the burden of Alzheimer’s disease and related dementias in the US population
- Investigator:Zhao, JinyingInstitution:University of FloridaProject Title:Identifying novel biomarkers for human complex diseases using an integrated multi-omics approachDate of Approval:November 21, 2023Request status:ApprovedResearch use statements:Show statementsTechnical Research Use Statement:GWAS, WES and WGS have identified many genes associated with Alzheimer’s Dementia (AD) and its related traits. However, the identified genes thus far collectively explain only a small proportion of disease heritability, suggesting that more genes remained to be identified. Moreover, there is a clear gender and ethnic disparity for AD susceptibility, but little research has been done to identify gender- and ethnic-specific variants associated with AD. Of the many challenges for deciphering AD pathology, lacking of efficient and power statistical methods for genetic association mapping and causal inference represents a major bottleneck. To tackle this challenge, we have developed a set of novel statistical and bioinformatics approaches for genetic association mapping and multi-omics causation inference in large-scale ethnicity-specific epidemiological studies. The goal of this project is to leverage the multi-omics and clinical data archived by the ADSP, ADNI, ADGC as well as other AD-related data repositories to identify novel genes and molecular markers for AD. Specifically, we will (1) validate our novel methods for identifying novel risk and protective genomic variants and multi-omics causal pathways of AD; (2) identify novel ethnicity- and gender-specific genes and molecular causal pathways of AD. We will share our results, statistical methods and computational software with the scientific community.Non-Technical Research Use Statement:Although many genes have been associated with Alzheimer’s Dementia (AD), these genes altogether explain only a small fraction of disease etiology, suggesting more genes remained to be identified. Of the many challenges for deciphering AD pathology, lacking of power statistical methods represents a major bottleneck. To tackle this challenge, we have developed a set of novel statistical and bioinformatics approaches for genetic association mapping and multi-omics causation inference in large-scale ethnicity-specific epidemiological studies. The goal of this project is to leverage the rich genetic and other omic data along with clinical data archived by the ADSP, ADNI, ADGC as well as other AD-related data repositories to identify novel genes and molecular markers for AD. Such results will enhance our understanding of AD pathogenesis and may also serve as biomarkers for early diagnosis and therapeutic targets.
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 NG00132.
For investigators using Health and Retirement Study (sa000021) data:
HRS is supported by the National Institute on Aging (NIA U01AG009740). The genotyping was partially funded by separate awards from NIA (RC2 AG036495 and RC4 AG039029). Our genotyping was conducted by the NIH Center for Inherited Disease Research (CIDR) at Johns Hopkins University. Genotyping quality control and final preparation were performed by the Genetics Coordinating Center at University of Washington (Phases 1-3) and the University of Michigan (Phase 4).