NG00127 - A longitudinal study of Alzheimer Disease and other dementing illnesses

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Description

The search for novel risk factors for Alzheimer disease relies on access to accurate and deeply phenotyped datasets. The Memory and Aging Project at the Knight-ADRC (Knight ADRC-MAP) collects plasma, CSF, fibroblast, neuroimaging clinical and cognition data longitudinally and autopsied brain samples. We are using multi-tissue (brain, CSF and plasma) multi-omic data (genetics, epigenomics, transcriptomics, proteomics and metabolomics) to identify novel risk and protective variants, create new prediction models and identify drug targets. Knight-ADRC participants have to be at least 45 years old and have no memory problems or mild dementia at the time of enrollment. There is no age at onset criteria for this cohort. Cases had to have a CDR >=0.5 whereas controls had to have a CDR=0 at last assessment. AD definition is based on a combination of both clinical and pathological information if available. Pathologic diagnosis will overrule clinical diagnosis. Participants are Non-Hispanic white from North America (82.47%) and African American (13.3%). Autopsy information was provided if available, but it is not a requirement for enrollment. Samples have been obtained from over 5,510 participants, including 2,426 AD cases, 148 FTD, 88 DLB and 2,156 cognitive normal healthy individuals. In addition, there is autopsy material from over 1,182 participants, 474 with fresh frozen parietal tissue.

We have banked more than 8,000 DNA samples form 5,220 unique participants and 1,973 blood RNA from 1,172 unique participants.

Plasma was collected from over 3,798 participants, and 1,650 have longitudinal plasma. We have logged over 8,000 plasma draws during the course of this study. CSF samples was obtained from 1,231 unique participants, and amyloid and tau imaging was obtained from 1,058 unique participants in a longitudinal manner. In addition, we have collected 164 PBMCs and 51 CSF cell pellets from this participant cohort. Fibroblasts were obtained from 207 participants including 16 TREM2 carriers, 27 with different APOE genotypes, 11 African American and 20 with extreme polygenic risk scores. IPSC are available for 22 of these fibroblasts.

Deep molecular profiling has been generated in this study, through the NeuroGenomics and Informatics Center at Washington University (https://neurogenomics.wustl.edu/). GWAS is available for 4,799 participants, and next generation sequence data (NGS) for 2,466 participants, 1,050 whole exome sequencing (WES) and 1,322 whole genome sequence (WGS) data. For 453 brain samples genetics (WGS), methylation (Illumina 880K), transcriptomics (bulk RNA-seq), proteomics (Somalogic 1.3K), metabolomics and lipidomics (Metabolon HD4) has been generated. CSF samples have proteomics (Somalogic 7K) and metabolomics (Metabolon HD4). A total of 3,000 cross-sectional plasma samples have proteomics (Somalogic 7K), metabolomics (Metabolon HD4), RNA-seq and methylation data.

Additional information about Knight ADRC datasets available through NIAGADS/DSS can be found on the Knight ADRC Collection page: https://archive.niagads.org/knight-adrc-collection

Sample Summary per Data Type

Sample Set	Accession	Data Type	Number of Samples
KnightADRC GWAS	snd10036	GWAS	4500

Available Filesets

Fileset	Accession	Latest Release	Description
KnightADRC GWAS	fsa000033	NG00127.v1	GWAS and phenotype data

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

The data being submitted is from participants from the Knight-ADRC MAP study. Genotyping for 4495 participants were generated through 10 different genotyping arrays (Infinium CoreExome-24, Infinium Neuro Consortium Array, Infinium Global Screening Array-24, Infinium OmniExpress-24, Illumina Human660W-Quad, Human610-Quad, Illumina Omni1-Quad, Affy UK Biobank Axiom, Infinium OmniExpressExome-8, and Illumina Human1M-Duo). In particular, 1955 AD cases (57% Females, 56% APOE4+, average age 74), 839 ADRD participants (51% females, 34% APOE4+, average age 63), and 1699 cognitively healthy participants (60% Females, 31% APOE4+, average age 74) individuals are being submitted. Approximately 85% of the samples are self-defined as “White”, and 10% are self-defined as “African-American”.

Sample Set	Accession Number	Number of Subjects	Number of Samples
KnightADRC GWAS	snd10036	4,496	4,496

Consent Level	Number of Subjects
DS-ADRD-IRB-PUB	4379
DS-ADRD-IRB-PUB-NPU	2
HMB-IRB-PUB	119

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 NG00127.

For investigators using Charles F. and Joanne Knight Alzheimer’s Disease Research Center (sa000008) data:

This work was supported by grants from the National Institutes of Health (R01AG044546, P01AG003991, RF1AG053303, R01AG058501, U01AG058922, RF1AG058501 and R01AG057777). The recruitment and clinical characterization of research participants at Washington University were supported by NIH P50 AG05681, P01 AG03991, and P01 AG026276. This work was supported by access to equipment made possible by the Hope Center for Neurological Disorders, and the Departments of Neurology and Psychiatry at Washington University School of Medicine.

We thank the contributors who collected samples used in this study, as well as patients and their families, whose help and participation made this work possible. This work was supported by access to equipment made possible by the Hope Center for Neurological Disorders, and the Departments of Neurology and Psychiatry at Washington University School of Medicine.

For use of the ADSP-PHC harmonized phenotypes deposited within dataset, ng00067, use the following statement:

The Memory and Aging Project at the Knight-ADRC (Knight-ADRC), supported by NIH grants R01AG064614, R01AG044546, RF1AG053303, RF1AG058501, U01AG058922 and R01AG064877 to Carlos Cruchaga. The recruitment and clinical characterization of research participants at Washington University was supported by NIH grants P30AG066444, P01AG03991, and P01AG026276. Data collection and sharing for this project was supported by NIH grants RF1AG054080, P30AG066462, R01AG064614 and U01AG052410. This work was supported by access to equipment made possible by the Hope Center for Neurological Disorders, the Neurogenomics and Informatics Center (NGI: https://neurogenomics.wustl.edu/) and the Departments of Neurology and Psychiatry at Washington University School of Medicine.

Total number of approved DARs: 12

Investigator:
Cruchaga, Carlos
Institution:
Washington University School of Medicine
Project Title:
The Familial Alzheimer Sequencing (FASe) Project
Date of Approval:
May 9, 2024
Request status:
Approved
Research use statements:
Show statements
Technical 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 studies
Non-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:
Greicius, Michael
Institution:
Stanford University School of Medicine
Project Title:
Examining Genetic Associations in Neurodegenerative Diseases
Date of Approval:
December 19, 2024
Request status:
Approved
Research use statements:
Show statements
Technical Research Use Statement:
We are studying the effects of rare (minor allele frequency < 5%) genetic variants on the risk of developing late-onset Alzheimer’s Disease (AD). We are interested in variants that have a protective effect in subjects who are at an increased genetic risk, or variants that lead to multiple dementias. Our aim is to identify any genetic variants that are present in the “case” group but not the “AD control” groups for both types of variants. The raw data we receive will be annotated to identify SNP locations and frequencies using existing databases such as 1,000 Genomes. We will filter the data based on genetic models such as compounded heterozygosity, recessive and dominant models to identify different types of variants.
Non-Technical Research Use Statement:
Current genetic understanding of Alzheimer’s Disease (AD) does not fully explain its heritability. The APOE4 allele is a well-established risk factor for the development of Alzheimer’s Disease (AD). However, some individuals who carry APOE4 remain cognitively healthy until advanced ages. Additionally, the cause of mixed dementia pathology development in individuals remains largely unexplained. We aim to identify genetic factors associated with these “protected” and mixed pathology phenotypes.
Investigator:
Hatchwell, Eli
Institution:
Population Bio
Project Title:
Mutational Spectrum of Causal Genes for Neurological/Neurodegenerative Diseases and Endometriosis Identified via High Resolution Genome Wide Copy Number Analysis
Date of Approval:
August 21, 2024
Request status:
Approved
Research use statements:
Show statements
Technical Research Use Statement:
While single gene rare variants have been shown to play a significant role in Early-Onset Alzheimer’s Disease (EOAD), their role in Late-Onset (LOAD) has not been emphasised. The gene discovery methodology we have developed at Population Bio allows for unbiased exploration of highly informative genomic variants in any cohort of interest. Our approach is based on ultra-high resolution copy number variant (CNV) analysis. We have invested heavily in such analysis on normal populations. These are used as comparators for cohorts of interest, such as LOAD. In our LOAD work, this analysis generated a list of CNVs which were either absent in the normal populations we studied or else present at significantly higher frequency in the LOAD cohort. Such CNVs are routinely annotated to determine if they overlie known genes and/or regulatory regions. As an example, we have discovered a deletion in 3% of our LOAD cases, which is present in <= 1% of normals. This deletion disrupts a transcription factor binding site in the intron of a gene, which, via GeneHancer, is known to control exon 1 of the gene. The gene in question is novel to LOAD, and is an important metabolic gene, with known biology. It is vital that we validate this finding by analysis of independent LOAD datasets. In addition, we wish to validate other genes discovered in the same manner We have very deep experience of analyzing WGS/WES datasets. Our focus will be to pull out of the available WGS/WES datasets all the variants for the candidate genes of interest. Such variants, including SNVs, indels and CNVs (called using a variety of tools we have experience with) will be analyzed by reference to databases of normal individuals: i.CNVs, by reference to our own internal database but also gnomad (https://gnomad.broadinstitute.org) CNV data and DGV (http://dgv.tcag.ca) ii.SNVs/indels, by reference to gnomad These analyses will allow us to determine whether there exists a mutational burden for our candidate genes of interest in independent LOAD cohorts, and will serve as validation/refutation. The main phenotype of interest will be definitive diagnoses of LOAD, based on neuropathological and clinical cognitive analyses
Non-Technical Research Use Statement:
Most of the common conditions that affect large numbers of the general population have a genetic basis. While progress has been rapid in the field of cancer, the same cannot be said for common, non-cancer, conditions, such as Late-Onset Alzheimer's Disease (LOAD). It is pretty clear now that not all cases of LOAD represent the same disease, in terms of what is the cause. Our approach has been to consider common diseases as collections of rare subgroups, each of which has a specific cause and which, in due course, will have a specific treatment. We have pioneered and implemented a method to rapidly uncover potentially causal genes in common disorders and will use the data generated from this study to strengthen our discoveries, by validating a set of novel candidate genes we have identified in LOAD Our project will allow us to: 1.Define subsets of disease 2.Work with pharmaceutical companies to develop drugs that will specifically target each subset of disease. In some cases, disease progression may be halted by the therapies developed. In some cases, reversal and/or cure may be possible
Investigator:
Lee, Jonghun
Institution:
TAKEDA PHARMACEUTICAL COMPANY LTD
Project Title:
Identification of genetic risks and potential target for stratified Alzheimer's disease patient groups
Date of Approval:
June 12, 2024
Request status:
Approved
Research use statements:
Show statements
Technical Research Use Statement:
The goal of analyzing ADSP umbrella cohort data is identifying variants, genes and pathways associated to Alzheimer’s disease (AD), and stratifying patients by genetic risks. Following describes procedure.1) Identification and validation of genetic risks The whole genome and whole exome sequencing data will be analyzed to identify genetic variants or genes associated to phenotypes in case-control cohort, such as AD status and Braak stages. Several latest methods will be applied, such as VEP [William McLaren et al, 2016], LOFTEE [Karczewski, 2015] and PEXT scoring [Beryl B.C et al., 2020] for variant annotation and SAIGE-GENE [Wei Zhou et al., 2020] for the association test. The association will be tested for other endophenotypes such as cognitive scores and brain volumes that available in subset of the cohort. Replication and meta-analysis will be conducted on UK biobank and Tohoku medical megabank organization (ToMMo) cohort data. The ToMMo data consists of Japanese cohort so that we can analyze the effect of the variants among multi ethnic groups.2) Patient stratification in ADSP cohort Leveraging the increased sample size, we will stratify the cohort by genetic risks such as ApoE types, or phenotypes such as Braak stages, and compare the effect size of variants or genes among the patient groups. In addition, the genetic risk score (GRS) will be calculated using LDpred2 [Florian Prive, 2020], RapidoPGS [Guillermo Reales, 2020], and PRSice2 [Choi, S.W., 2020], and validated in independent cohorts and compared to available clinical endophenotypes. Last, we will search the effect of the GRS to extensive phenotypes in UK biobank and ToMMo.3) Identification of variants associated with pathologies and disease progression To further characterize patients by genetic risk, we will conduct GWAS and EWAS on pathology measurements, models of co-pathology, comorbidity with other neurological diseases, and disease progression. NG00127 and NG00154 will be used for this purpose.
Non-Technical Research Use Statement:
The aim of our study is identifying variants or genes potentially causal of the Alzheimer’s disease in whole or subset of patients. To be specific, WES and WGS data will be analyzed to investigate common and rare variants associated with disease status and intermediate phenotypes. In addition, the patients will be stratified and sub-grouped by their genetic or phenotypic characteristics. Last, we will incorporate other large biobanks such as UK biobank or ToMMo to investigate the genetic effects to extensive phenotypes potentially linked to symptoms appearing in sub patient groups.
Investigator:
Pendergrass, Rion
Institution:
Genentech
Project Title:
Genetic Analyses Using Data from the Alzheimer’s Disease Sequencing Project (ADSP) and related studies
Date of Approval:
October 3, 2024
Request status:
Approved
Research use statements:
Show statements
Technical Research Use Statement:
The purpose of our study is to identify novel genetic factors associated with Alzheimer’s Disease, corticobasal degeneration (CBD) and progressive supranuclear palsy (PSP). This includes identifying genetic factors associated with the risk of these conditions, as well as genetic risk factors associated with age-at-onset (AAO) for these conditions. We will also evaluate genetic associations with sub-phenotypes individuals have within these broad disease categories, such as their Braak staging results which provide insights into the level of severity of Alzheimer’s. Thus we are requesting access to the set of genomic Whole Exome and Whole Genome Sequences (WES and WGS) have just been released through the National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (DSS NIAGADS). The findings from our genetic association testing have the potential for identification of new therapeutic targets for Alzheimer's Disease, CBD, and PSP. The findings from our studies also have the potential for identification of genetic and phenotypic biomarkers that will be beneficial for subsetting patients in new ways. We will use standard genetic epidemiological methods to handle the WGS and WES data. We will also analyze cell type-specific expression differences in AD to identify biomarkers and disease pathways using standard gene expression analysis methods currently in use. We will also use other multi-omic and other genetic data that has now become available to further understand genetic association results we have found in AD.All data will remain anonymized and securely stored, and only those listed on our application and their staff will have access to these data. We will not share any of the individual level data outside of Genentech nor beyond the researchers on our application. We will adhere to all data use agreement stipulations through the DSS NIAGADS. We have a secure computational environment called Rosalind within Genentech where we will use these data. We have IT security staff that constantly monitor all our research computing, assuring safety and privacy of all of our stored data. We will not collaborate with researchers at other institutions.
Non-Technical Research Use Statement:
Genetic variation and gene expression data allows us to understand more of the genetic contribution to risk and protection from diseases such as Alzheimer’s and dementia. This information also allows us to identify important biological contributors to disease for developing effective treatment strategies, and identifying groups of individuals that would benefit most from new treatments. Our exploration of this relationship between genotype, disease traits, gene expression, and outcomes, through these datasets will allow us to pursue important new findings for disease treatment.
Investigator:
Safo, Sandra
Institution:
University of Minnesota
Project Title:
Innovative Machine and Deep Learning Analyses of Alzheimer's Disease Omics and Phenotypic Data
Date of Approval:
October 27, 2023
Request status:
Expired
Research use statements:
Show statements
Technical Research Use Statement:
AD is the most common cause of dementia and presents a substantial and increasing economic and social burden. Our ability to diagnose and classify AD from cognitive normals (CN), or discriminate among individuals with AD, early mild cognitive impairment [EMCI], or late mild cognitive impairment (LMCI), is essential for the prevention, diagnosis, and treatment of AD. Since individuals with MCI have a high chance of converting to AD, effectively discriminating between those who convert to AD (MCI-C) from those who do not convert (MCINC) is important for early diagnosis of AD. The heterogeneity of AD has motivated attempts to classify distinct subgroups of AD to better inform the underlying physiology. There is evidence to suggest that using data across multiple modalities (e.g. genetics, imaging, metabolomics) has potential to classify AD subgroups better than using single modality. We will apply machine and deep learning methods to gain deeper insight into AD and ADRD pathobiology. We will use datasets that include genomics, genetics, metabolomics, and phenotypic data for this purpose. Data will be divided into discovery and validation sets. On the discovery set, state-of-the-art ML and DL methods for integrative analysis that we and others have developed will be coupled with resampling techniques to determine candidate molecular signatures and pathways discriminating the AD groups considered. Molecular scores will be developed from these candidate biomarkers. The clinical utility of the scores beyond well-known clinical risk factors for AD will be ascertained. We will validate our findings using the validation data. We will visually and quantitatively compare the risk scores across several clinical variables and outcomes. We will use (un)supervised clustering methods to identify molecular clusters, and we will investigate molecular clusters differentiating MCI to AD converters from non-converters. We may explore differences across ethnic subgroups. We will also innovatively apply our multimodal molecular subtyping methods to discover, reproduce, and characterize novel molecular subgroups of AD– this will allow for better risk stratification.
Non-Technical Research Use Statement:
We have been developing novel machine learning (ML) and deep learning (DL) methods that leverage genomics, other omics (including proteomics and metabolomics), clinical and epidemiology data to better understand the pathogenesis of complex diseases. By integrating data from different sources, we have identified molecular signatures contributing to the risk of the development of complex diseases beyond established risk factors. We are proposing to innovatively apply these, and other existing, methods, to data pertaining to Alzheimer’s disease (AD) and Alzheimer’s disease related dementias (ADRD). A deeper understanding of the genes, genetic pathways, and other molecular signatures of AD is essential and could facilitate the identification of potential therapeutic targets for the disease.
Investigator:
Saykin, Andrew
Institution:
Indiana University School of Medicine
Project Title:
Centrally-linked Longitudinal pEripheral biomARkers of AD (CLEAR-AD)
Date of Approval:
November 25, 2024
Request status:
Approved
Research use statements:
Show statements
Technical Research Use Statement:
This U19 aims to bridge these knowledge gaps for discovery and validation of Centrally-linked Longitudinal pEripheral biomARkers of AD (CLEAR-AD) in multi-ethnic populations. CLEAR-AD U19 is based on the premise that AD is a complex disorder in which many biological pathways are disrupted due to multi-omic perturbations, which can be detected in brain and reflected in blood. The specific aims of CLEAR-AD are: 1) To discover CLPMS of the complex and heterogeneous AD pathophysiology and its co-pathologies. 2) To identify longitudinal CLPMS that detect and predict dynamic neuroimaging, fluid biomarker, and clinical changes across AD spectrum. 3) To characterize differences and similarities in CLPMS profiles across NHW, African American (AA) and Latino American (LA) participants to uncover biomarker patterns in multi-ethnic groups. 4) To make these vast resources available to the scientific community to amplify and accelerate its impact. In this U19, we will leverage NIH-funded ADNI, MCSA and ADRC cohorts of >3,700 multi-ethnic participants to generate >20,000 multi-omics measures (Omics Core) that will be processed and integrated with >48,000 harmonized AD cognitive, neuroimaging and fluid endophenotypes (Analytic Core). Using these data, we will identify brain region and cell-type specific CLPMS, which reflect biological subtypes of AD and disease stage (Project 1). We will discover longitudinal changes in CLPMS that predict cognitive and A/T/N/V progression (Project 2). We will define longitudinal cognitive and A/T/N/V changes and CLPMS in URP that are either conserved with NHW or population-specific (Project 3). This U19 will a) Identify the next generation of AD biomarkers with mechanistic insights; b) Establish a precision medicine approach for rigorous multi-omics biomarker discovery and validation in AD; c) Discover molecules that can serve as biomarkers and therapeutic targets; d) Enhance biomarker research in trial-ready multi-ethnic populations; and e) Generate and share a vast and harmonized resource of endophenotype and multi-omics data in NIH-funded cohorts.
Non-Technical Research Use Statement:
There is a clear and immediate need for the discovery of peripheral molecular signatures linked to central disease processes, core and co-pathologies in Alzheimer’s Disease (AD), that will serve as precision medicine blood-based biomarkers for diagnostic, prognostic, theragnostic and therapeutic purposes. AD is a complex disorder in which many biological pathways are disrupted due to multi-omic perturbations, which can be detected in brain and reflected in blood, i.e. centrally-linked peripheral molecular signatures (CLPMS). This U19 will leverage deeply phenotyped, longitudinal NIH-funded multi-ethnic cohorts and cross-disciplinary expertise for multi-omics data generation and its integration with harmonized AD endophenotypes, will share these data and utilize them in integrated U19 projects to discover CLPMS that will serve as the next generation of AD biomarkers.
Investigator:
Wainberg, Michael
Institution:
Sinai Health System
Project Title:
Uncovering the causal genetic variants, genes and cell types underlying brain disorders
Date of Approval:
September 5, 2024
Request status:
Approved
Research use statements:
Show statements
Technical Research Use Statement:
We propose a multifaceted approach to elucidate and interpret genetic risk factors for Alzheimer's disease. First, we propose to perform a whole-genome sequencing meta-analysis of the Alzheimer's Disease Sequencing Project with the UK Biobank and All of Us to associate rare coding and non-coding variants with Alzheimer's disease and related dementias. We will explore a variety of case definitions in the UK Biobank and All of Us, including those based on ICD codes from electronic medical records (inpatient, primary care and/or death), self-report of Alzheimer's disease or Alzheimer's disease and related dementias, and/or family history of Alzheimer's disease or Alzheimer's disease and related dementias. We will perform single-variant, coding-variant burden, and non-coding variant burden tests using the REGENIE genome-wide association study toolkit.Second, we propose to develop statistical and machine learning models that can effectively infer (“fine-map”) the causal gene(s), variant(s), and cell type(s) underlying each association we find, as well as associations from existing genome-wide association studies and other Alzheimer's- and aging-related cohorts found in NIAGADS. In particular, we propose to improve causal gene identification by incorporating knowledge of gene function as a complement to functional genomics. For instance, we plan to develop improved methods for inferring biological networks, particularly from single-cell data, and integrate these networks with the results of the non-coding associations from our first aim to fine-map causal genes. To fine-map causal variants and cell types, we plan to integrate the associations from our first aim with single-nucleus chromatin accessibility data from postmortem brain cohorts to simultaneously infer which variant(s) are causal for each discovered locus and which cell type(s) they act through.
Non-Technical Research Use Statement:
We have a comprehensive plan to understand and explain the genetic factors that contribute to Alzheimer's disease. Our approach involves two main steps.First, we'll analyze genetic information from large research databases to identify rare genetic changes associated with Alzheimer's and related memory disorders. We'll look at both specific changes in genes and other parts of the genetic code. We'll use data from different studies and combine them to get a clearer picture.Second, we'll create advanced computer models that can help us figure out which specific genes, genetic changes, and cell types are responsible for these associations. This will help us pinpoint the most important factors contributing to Alzheimer's disease. We'll also analyze data from previous studies to build a more complete understanding of these genetic links.
Investigator:
Xiao, Peng
Institution:
University of Nebrask Medical Center
Project Title:
Uncovering the genetic basis of Alzheimer's Diseases by integrating GWAS with multiomics approaches across different ethnicities
Date of Approval:
August 9, 2024
Request status:
Approved
Research use statements:
Show statements
Technical Research Use Statement:
ObjectivesIn this study we aim to understand the system level understanding of Alzheimer's disease (AD) by integrating GWAS with robust multiomics datasets across diverse ethnic groups and harmonization of the results to include associated genes and pathways to understand underlying disease mechanisms and to inform our understanding of biological continuum of the diseases. Investigating AD associated variants as quantitative trait loci for epigenetic, transcriptomic, and proteomic layers to explore how variants in genes perturb pathways leading to AD.Study designWe will comprehensively examine the genetic architecture of Alzheimer's diseases based on different races (Caucasians, Latinos, Asians and Africans) GWAS data from publicly available datasets. We request access to as many datasets available in NIAGADS and other repositories like EADB-consortium, IGAP and we also have requested access to datasets through our literature search from corresponding authors for Asian cohorts. We will perform meta-analysis at two levels for GWAS datasets and find genome wide significant loci (GWS). Mendelian randomization analyses will be adapted to multi-omics setting through analyzing QTLs and GWS. We will perform correlation and enrichment analysis for significant findings from different omics layers.Analysis PlanGenome wide meta-analysis across different races to identify new loci and functional pathways influencing AD. Find genes most likely to be responsible for association signal with AD at each loci by applying mendelian randomization (MR) method. We plan to use MR method to combine multiomics (GWAS, eqtl, mqtl, aqtl and pqtl).
Non-Technical Research Use Statement:
To our knowledge our findings reveal crosstalk between epigenetic, genomic, and transcriptomic determinants of AD pathogenesis and define catalogues of candidate genes. In addition, rare or population specific common variants can be identified thus genes with underlying genetic support for an association with AD are likely to encode successful drug targets in clinical development. This should further lead to patient stratification.
Investigator:
Zhang, Haiyang
Institution:
Vivid Genomics
Project Title:
Validation and optimization of Alzheimer's Disease phenotypes prediction using machine learning enabled polygenic risk models
Date of Approval:
March 28, 2023
Request status:
Expired
Research use statements:
Show statements
Technical Research Use Statement:
Analyzing postmortem phenotype and genomics data from ~1100 human brain samples with machine learning, Vivid Genomics, Inc., has developed prototype genetic biomarker assays that predict the presence of amyloid plaques, Lewy body pathology, cerebral amyloid angiopathy, and rate of cognitive decline. The objective is to increase subject numbers with similar data available through NIAGADS and NACC, along with datasets from several individual academic centers, to further optimize and validate our assays for neurodegenerative/cerebrovascular lesion types including tau, TDP-43, hippocampal sclerosis and microinfarcts, and for predicting rate of cognitive decline. NIAGADS datasets requested are NG00067 (including the newly released data which is new version 9 for dataset NG00067), NG00119, NG00117 and NG00127; data use limitations from these do not exclude our proposed usage. We are targeting >3000 subjects in total to be used for the validation of our models. We will focus on SNP selection and test the effects of different analysis strategies: 1) changing SNP p-value cutoffs 2) using LD-filtered representative SNPs with full genome coverage 3) testing the value of stratifying by APOE genotype 4) determining if it is better to add other covariates including age and sex. A fraction of the genetic data (~30%) will be withheld for validation. Optimization is defined as an area under the curve (AUC) of 80% and positive predictive value (PPV) of 80%, as well as R2 >0.75 for all assays. Values within 10% of this will be considered a successful validation. Through these assays, this project will benefit those suffering from Alzheimer’s disease and other neurodegenerative disorders by increasing clinical trial efficiency through more precise subject selection and/or stratification.
Non-Technical Research Use Statement:
Vivid Genomics is dedicated to developing genetic tests, typically done from DNA obtained from blood, that will predict, for any given older person, the likelihood that they have, or might develop when they become old, the characteristic brain changes of Alzheimer’s disease as well as other brain changes that affect thinking in older people. These changes include amyloid or senile plaques, tangles or tau, amyloid angiopathy, Lewy bodies, TDP-43 pathology, hippocampal sclerosis and brain infarcts (strokes). The objective of this study is to improve upon initial tests developed by Vivid, and to also develop genetic tests to predict the rate at which older people’s thinking ability decreases over time. To do this, Vivid Genomics requests human subject DNA analysis data stored at NIAGADS. Through these new genetic tests, Vivid hopes to benefit those suffering from Alzheimer’s disease and other brain diseases of aging by allowing better selection of subjects for clinical trials of these diseases, which would increase the chances of clinical trials finding useful new treatments.
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:
November 21, 2023
Request status:
Expired
Research use statements:
Show statements
Technical 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.
Investigator:
Zhou, Weichen
Institution:
University of Michigan
Project Title:
Explore the functional impact of transposable elements in Alzheimer’s disease and related dementias
Date of Approval:
May 9, 2024
Request status:
Approved
Research use statements:
Show statements
Technical Research Use Statement:
Explore somatic transposable elements and their Alzheimer's disease-related patterns using genomic and phenotypic data from large cohorts:In order to explore the impact of the transposable element in Alzheimer's disease, we propose to conduct a systematic survey in the available large cohorts. The ADSP dataset in NIAGAlzheimer's diseaseS (Accession No. NG00067) includes 16,906 whole-genome sequences and 20,504 whole-exome sequences for case-control and family-based studies of Alzheimer's disease from diverse populations, which is a perfect resource to leverage in this project. Under the support of the Michigan Alzheimer's Disease Center, we will request to access NIAGADS. To detect somatic transposable elements in the ADSP dataset, we will employ established computational pipelines to resolve the transposable elements in the sequencing data, MELT and xTEA for WGS and SCRAMble for WES, respectively. Parameters in these tools, for instance, the calling threshold of supporting reads, will be adjusted accordingly to cooperate with the detection of somatic transposable elements in cells at low frequency. To exclude potential germline transposable elements, we will leverage a master set of polymorphic transposable elements from diverse populations, which are based on our previous projects at the Human Genome Structural Variation Consortium, and the case-control information provided by ADSP. We aim to summarize a spectrum of somatic transposable elements that would be Alzheimer's disease-relevant along with various clinical and phenotypic information. To build Alzheimer's disease-related genetic patterns we will implement Mutect2 (GATK) and Strelka2 to discover SNVs from WGS and WES data and link them with transposable elements in the same haplotype. After obtaining this set of patterns, we will collect phenotypic information from the ADSP dataset to conduct family-based associated analysis and gene-burden analysis. RegulomeDB will be used to annotate the effects of non-coding functional impact and regulatory changes for these Alzheimer's disease-related patterns.
Non-Technical Research Use Statement:
It seeks to explore the connection between the somatic transposable elements in the human genome and Alzheimer’s disease and related dementias. It will leverage large-scale datasets to extensively explore the genome-wide transposable elements and then stratify Alzheimer’s disease-relevant ones by using the rich clinical information from the cohorts. Further analysis pipelines will be built based on the results of the proposed project to investigate the functional impact of these transposable elements on Alzheimer’s disease and would improve the understanding of genetic causes of Alzheimer’s disease and related dementias.

Total number of samples: 4,496

Sex

Race

Ethnicity

Diagnosis

APOE

Female 2,597 57.8 %

Male 1,886 41.9 %

2219 (0.4%)
23366 (8.1%)
24136 (3.0%)
331,971 (43.8%)
341,512 (33.6%)
44281 (6.3%)
NA211 (4.7%)

AD
Control	1,783	39.7%
Case	1,958	43.5%

Dementia Lewy Bodies (DLB)
Case	59	1.3%

Fronto Temporal Dementia (FTD)
Case	130	2.9%

Parkinson disease (PD)
Case	20	0.4%

PSP
Case	18	0.4%

Other
Case	1	0.0%
Other	527	11.7%

Not Hispanic or Latino

2,574

57.3%

Hispanic or Latino

0.6%

Not Applicable/Not Available

1,895

42.1%

NG00127 – A longitudinal study of Alzheimer Disease and other dementing illnesses – KnightADRC GWAS

Overview

Description

Sample Summary per Data Type

Available Filesets

Sample information

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Acknowledgement

Acknowledgment statement for any data distributed by NIAGADS:

For investigators using any data from this dataset:

For investigators using Charles F. and Joanne Knight Alzheimer’s Disease Research Center (sa000008) data:

Related Publications

Approved Users

Total number of samples: 4,496