Carlos Cruchaga - US grants

? DESCRIPTION (provided by applicant): Genome-wide association, whole genome/exome sequencing and gene network studies have already enabled researchers to identify twenty loci influencing Alzheimer's disease (AD) risk and another half dozen genes carrying specific rare variants that influence disease risk. With the new whole-genome sequence (WGS) and whole-exome sequence (WES) data from 10,000+ AD cases and controls from the ADSP, combined with mRNA expression data from 3,500+ individuals from AMP, it is now possible to develop a more comprehensive picture of the genetic architecture of AD and associated risk. Beyond refining AD genetic architecture, our goal is to identify and validate therapeutic targets for AD b identifying genes that functionally drive or protect from AD and interrogating their respective gene networks for therapeutic targets. We will do this using the largest, most comprehensive data set, to date. Genetic and pathway-based analyses have strongly implicated a small number of networks including immune response, phagocytosis, lipid metabolism and endocytosis. We will integrate data from genetic studies and gene expression/regulation studies to identify risk and resilience genes to pinpoint key networks that functionally drive AD development and progression. We will take two complementary approaches to identify risk and resilience AD genes: (1) we will use a family-based approach to identify both risk and protective alleles using publicly available data and our own WGS/WES data from both NIALOAD and Utah families; and (2) we will use publicly available high-dimensional molecular data from AD cases and controls to construct global interaction and causal networks. We will then focus our analysis of ADSP case control sequence data on the most compelling networks, thereby reducing our search space and increasing power. To identify therapeutic targets, we will use network analysis to test known drugs that target networks identified in our sequence analysis of both family-based and case control data. We will then validate our findings by performing in vitro experiments based our in silico observations and determine the functional consequences of risk/resilience alleles identified from the AD sequence data. Together, the findings from this study will pinpoint key networks that functionally drive AD and will provide critical insight into therapeutic intervention

DESCRIPTION (provided by applicant): During the first hours after ischemic stroke onset, neurological deficits can be highly unstable - some patients spontaneously improve while others deteriorate. These early neurological changes are important because they have a large influence on long-term outcome. Potential mechanisms accounting for rapid improvement include fibrinolysis/ reperfusion, recruitment of collateral circulation, or endogenous neuroprotective mechanisms; while mechanisms leading to deterioration include thrombus propagation, peri-infarct spreading depression, or hemorrhagic transformation (HT). Tissue plasminogen activator (tPA), the only FDA-approved drug for the treatment of acute ischemic stroke (AIS), enhances the likelihood of fibrinolysis and reperfusion; but also increases the chances of HT. We hypothesize that genetic variant that affect pathogenic mechanism during acute ischemia may influence early neurological outcomes after AIS, and may also modulate response to IV tPA. In this grant, we propose to identify genetic variants associated with early neurological outcome in AIS patients (untreated or treated with IV tPA). These data will permit us to find novel genes/pathways and potential therapeutic targets that could improve outcome after AIS, and perhaps enhance tPA efficacy. Further, an individual's genetic profile may one day provide personalized risk stratification for treatment with IV tPA, which may guide therapeutic decisions. Currently, we have accumulated 1000 samples from phenotyped AIS patients treated with tPA from both sites (the largest such sample set in the world), which will be used for gene discovery (Discovery Series). During the grant period, we will collect an additional 3000 samples (Replication Series), which will include both tPA-treated and untreated patients so that we can determine which genetic associations are tPA-dependent or independent influences on early neurological outcomes after AIS. We propose 4 aims. Aim 1: To perform genome-wide association studies, examining early neurological improvement or deterioration after AIS. Aim 2: To determine which genetic variants that modulate levels of plasma analytes relevant to AIS pathogenesis influence early neurological outcomes. Aim 3: To replicate genome-wide associations, we will test candidate variants/genes in an independent cohort of AIS patients. And Aim 4: To determine which variants/genes associated with early outcome are tPA-dependent. At the conclusion of this grant, we will identify many variants/genes that influence early neurological outcome after AIS, and will also find variants/genes that influence outcome in a tPA-dependent manner. These findings will have both diagnostic and therapeutic implications.

Recent genetic studies identified a variant in TREM2 (R47H) that doubles the risk for Alzheimer's disease (AD), similar to that of APOE?4, the strongest known genetic risk factor for late-onset AD. We performed deep resequencing of TREM2 in a large European-American (EA) and African-American (AA) population and found an enrichment of TREM2 coding variants in AD cases compared to controls, indicating that additional TREM2 variants affect AD risk. Additionally, recent studies in small datasets found that soluble TREM2 (sTREM2) levels in the cerebrospinal (CSF) are increased in AD cases compared to controls. Furthermore, CSF sTREM2 levels strongly correlate with CSF tau levels. These studies suggest that CSF sTREM2 levels may reflect biological events that link amyloid deposition and neurofibrillary tangle formation to cognitive decline. Studies from our group indicate that CSF sTREM2 levels are an informative phenotype for genetic studies. While these preliminary studies are promising, based on past successes of this approach, larger datasets will provide us with the power to identify novel genetic modifiers of CSF sTREM2. In this proposal, we will analyze a very large (n=3,476) and well-characterized dataset with extensive pre-existing CSF biomarker (A?, Tau, ptau and sTREM2), clinical and genetic data. The aims of the project are: 1) to identify single (common and rare) variants, genes and pathways associated with CSF sTREM2 levels; 2) to determine the role of those variants and genes on AD risk, onset and progression and 3) to perform functional analyses in iPSC-derived human microglia to determine the mechanisms by which the genetic variants identified in the genetic analyses affect sTREM2 levels and microglia function.

Project 3 Project Summary Alzheimer's disease (AD) is the most common neurodegenerative disease with no effective means of prevention or treatment. Most of the recent published genetic studies for AD have focused on the identification of genetic variants associated with risk for disease. Other aspects of AD, such as age at onset, disease duration or rate of disease progression are less well studied. It is very likely that different genetic variants and genes will influence these different aspects of disease. The goal of this study is to identify novel genetic variants and genes associated with rate of disease progression and other informative endophenotypes for AD, such as amyloid imaging (Pittsburgh compound B or florbetapir) and hippocampal volume. We will use innovative genomic and statistical methods, to analyze not only the effect of common variants but also rare coding variants on endophenotype levels by incorporating genome-wide association data, whole-genome sequencing and exome-chip data into our analyses. We will also test whether the variants associated with rate of progression, amyloid imaging and hippocampal volume are also associated with risk for disease, cerebrospinal fluid tau and A? levels and other AD phenotypes. The broad, long-term goal of this research is to dissect the complex genetic architecture of Alzheimer's disease, which will lead to better prediction and treatment of this devastating disease. By studying several AD endophenotypes we expect to identify genetic variants, genes and pathways affecting different aspects of the disease. These findings will help to identify novel and key proteins involved in disease pathogenesis and potential therapeutic targets.

Abstract Family-based approaches led to the identification of disease-causing Alzheimer?s Disease (AD) variants in the genes encoding amyloid-beta precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2). Subsequently, the identification of these genes led to the A?-cascade hypothesis and recently to the development of drugs that target that pathway. In this proposal, we will identify rare risk and protective alleles. In a recent study, we identified a rare coding variant in TREM2 with large effect size for risk for AD, confirming that rare coding variants play a role in the etiology of AD. We will use sequence data from families densely affected by AD, because we hypothesize that these families are enriched for genetic risk factors. We already have access to sequence data from 695 families (2,462 individuals), that combined with the ADSP data will lead to a very large family-based dataset: more than 805 families and 4,512 participants. Our preliminary results support the flexibility of this approach and strongly suggest that protective and risk variants with large effect size will be found. The identification of those variants and genes will lead to a better understanding of the biology of the disease.

Recent genetic studies of complex traits and diseases have focused on the identification of common variants associated with risk through genome-wide association studies (GWAS). Other aspects such as rate of progression, age at onset and the effect of rare variants are generally not investigated. These studies have been very successful in identifying novel loci associated with many complex diseases. The current proposal focuses on these understudied aspects of disease etiology, namely the role of common and rare genetic variation on quantitative diagnostic and prognostic endophenotypes of Alzheimer's disease (AD). We will use GWAS and exome-chip data to identify single variants, genes and pathways associated with cerebrospinal fluid (CSF) levels of known AD biomarkers (tau, ptau, A?, YKL40, VILIP1) and other AD-related proteins (CLU, APOE, TREM2). The integration of these endophenotypes will enable us to disentangle the genetic architecture of AD. With this insight, we will then determine whether those SNPs, genes or pathways are also associated with other AD phenotypes (risk, age at onset or progression), and whether we can use genetic information to increase the diagnostic or prognostic ability of these CSF biomarkers. Further, we will utilize Mendelian Randomization and a novel network-based approach to identify causal plasma and CSF proteins involved in AD and other complex traits. We will have access to a unique resource ? a large number of CSF and plasma protein levels ? allowing us to leverage unbiased approaches to reveal novel biomarkers and endophenotypes associated with AD and complex traits.

Core G: Genetics Project Summary/Abstract One hundred years ago, dementing illnesses were classified based upon their clinical presentation and neuropathology. The promise of the twenty-first century is that we will be able to classify these same diseases by the genetic cause or genetic risk factors, a classification based upon etiology not symptomatology. During the last two decades many genes have been shown to cause autosomal dominant forms of early onset dementing illnesses. These rare disorders have provided enormous insight into the pathogenesis of more common variants of the same diseases. In 1993, a polymorphism in the apolipoprotein E (APOE) gene was identified as the first genetic risk factor for AD. A dose-dependent effect of the APOE4 allele has now become an important variable in all studies of AD. During the last five years genome-wide association studies and next generation sequencing studies have begun to identify many novel risk factors for AD. The goal of the Genetics Core of the Knight ADRC is to provide genetic information and useful biological materials on all ADRC participants. We will obtain family history data, plasma, serum, DNA, RNA, and APOE genotypes on all ADRC participants. Blood samples on all participants will be sent to NCRAD. Many participants will also have GWAS, exome array and whole exome/genome sequence data through national and international initiatives and ADRC affiliated projects held by Drs. Goate and Cruchaga. These data will be stored in the master ADRC database and provided to investigators upon request. We will identify and assess novel multiplex kindreds. Families that meet criteria for other funded projects such as DIAN, NIA-LOAD and LEFFTDS will be invited to participate in these studies. The Core will support Projects 1, 2 and 3 of the Knight ADRC and will continue to support the Health Aging and Senile Dementia and Adult Children Study Program Project Grants (JC Morris, PI) during the next five years. New in this application we will collect skin biopsies from targeted individuals carrying specific genetic risk factors for AD and we will begin to collect blood annually for RNA expression and DNA methylation studies to enable novel biomarker programs in peripheral tissues.

Project 3 Project Summary Aging populations worldwide, particularly in developed countries, face an increasing burden of neurodegenerative diseases. The most common neurodegenerative disease is Alzheimer disease (AD), which is characterized by protein misfolding and aggregation. One intriguing characteristic is the broad spectrum of age at onset, even within specific risk groups (i.e, mutation carriers). Furthermore, the existence of resilient individuals (individuals who are positive for known biomarkers or have a high burden of genetic risk variants but do not exhibit symptoms), suggests that there are protective and disease-modifying genetic factors. The goal of this Project is to identify variants and genes that confer resilience as well as novel protective and modifying factors. We will use genetic data (GWAS, Exome-chip, Whole Exome Sequencing and Whole Genome Sequencing) from resilient individuals and compare them with matched affected individuals to identify protective and modifying genetic factors. The multi-factorial etiology and heterogeneity of AD may reveal itself in racial or ethnic differences in overall AD risk and in putative risk or protective factors or in the progression of neuropathology. For this reason, we will also determine if the modifier and protective variants, genes and pathways also play a role in other races, especially in African Americans.

PROJECT SUMMARY Genomic studies of Alzheimer's disease (AD) have primarily focused on non-Hispanic White (NHW) participants affected by the late-onset form of the disease (LOAD; onset age: >65), or the study of early onset AD (EOAD; onset age <=65) cases from families showing Mendelian inheritance patterns associated with mutations in the APP, PSEN1 and PSEN2 genes. However, mutations in these three genes explain ~10% of EOAD cases. There are no large-scale efforts to collect and study EOAD cases not explained by these genes, despite the fact that this unexplained EOAD category accounts for ~90% of cases. The few smaller studies that have been conducted suggest that the genetic architecture of EOAD overlaps with the late-onset form only partially. Thus, studying EOAD in subjects without APP, PSEN1 and PSEN2 mutations is a critical gap that provides a unique opportunity for discovering novel therapeutic targets and molecular pathways. To address this issue we aim to identify additional EOAD-associated variants through a large-scale whole- genome sequencing (WGS) study of unexplained EOAD. We will include cases from several well-established AD cohorts including the Resource for Early-onset Alzheimer Disease Research (READR), the Knight-ADRC at Washington University, the Alzheimer's Disease Genetics Consortium (ADGC), and others. Generating and harmonizing a dataset of 200 non-Hispanic White (NHW) and Caribbean Hispanic (CH) multiplex EOAD families, over 4,000 EOAD singletons and over 13,000 unrelated, cognitive controls, all with WGS, this project will yield the largest EOAD genomics dataset to-date, improving statistical power for variant identification and allowing us to assess the impact of specific factors such as APOE genotype, vascular risk factors, and neuropsychiatric comorbidities. The inclusion of a large set of CH families and singletons will allow the examination of EOAD risk in a significantly understudied but fast-growing minority population. Analyses will comprise both linkage and association-based approaches, analyses of polygenic and ancestry effects, and a thorough examination of neurocognitive, neuropsychiatric and cardiovascular endophenotypes. We expect that when successfully completed, this study will point to novel genetic contributors to EOAD, shed light on the mechanisms of AD and facilitate the development of novel therapeutics. Sampling, phenotyping and sequencing analysis protocols will be complementary to and compatible with the existing LOAD genomics resources, such as the Alzheimer Disease Sequencing Project (ADSP) and related studies. This phenotypic and genomic consistency, together with the use of existing AD infrastructure (NIAGADS), allows for immediate integration with the leading efforts on LOAD, enabling rapid large-scale investigation of a variety of additional critical AD genomics hypotheses.

Core F: Genetics SUMMARY During the last two decades three genes have been shown to cause autosomal dominant forms of early onset dementing illnesses. These rare disorders have provided enormous insight into the pathogenesis of more common variants of the same diseases. Several of the most promising new therapeutics are based on the Aß hypothesis, a hypothesis strongly supported by the causative mechanisms of disease mutations in autosomal dominant families. As these putative therapeutics are tested in clinical trials there is a growing need to use the ADAD kindreds both to understand the natural history of the earliest clinical and preclinical phases of the disease and to test the efficacy of the therapeutics in a setting, where if the A? hypothesis is correct, they should have a dramatic effect on prognosis. During the last funding cycle, we have expanded our network of centers and have begun longitudinal characterization of a large series of ADAD kindreds with known disease-causing mutations. The goal of the next funding period will be to continue longitudinal follow up of these kindreds to identify the earliest detectable changes associated with development of disease and to characterize the temporal series of events that occurs up to and including the diagnosis of symptomatic AD. The goal of the Genetics Core of the DIAN initiative is to provide genetic information and useful biological and genomic materials to the research community for the study of AD. We have already collected genomic samples from 531 individuals and generated fibroblasts from 99 individuals. We anticipate collection of an additional 125 new individuals during the next funding cycle, including participants from NIH and self-funded sites. We will expand the fibroblast and induced pluripotent stem cell collection. The Core will maintain and curate a list of pathogenic mutations and confirm that new DIAN families carry an ADAD mutation. The Core will also generate GWAS and APOE genotype data on all individuals and obtain biological materials (fibroblasts, induced pluripotent stem cells, white blood cells) to perform cell-based functional studies. All data will be placed in the DIAN database. We will support all projects in DIAN and perform analyses with other Cores to identify novel factors modulating age at onset in these families.

Project Summary/Abstract In order to enhance and focus research on Alzheimer's disease (AD)-specific proteinopathies, the 2018 research framework proposed by the National Institute on Aging and Alzheimer's Association (NIA-AA) recommends that AD be defined by its specific biological signatures that can be documented at autopsy or in living people by biomarkers rather than by its non-specific neurodegenerative and clinical syndromic features. Of the three proposed biomarkers by the NIA-AA research framework in living people (amyloid A-beta (A?), pathologic tau and neurodegeneration), only the two AD-specific proteinopathies (A? and pathologic tau) are considered obligatory for the biological definition of AD, while neurodegeneration, although contribute to cognitive impairment and is part of the fully manifested disease, can also occur in other brain disorders and thus is not specific to AD. The purpose of this harmonized biological definition of AD in living people that includes the preclinical phase is to distinguish AD from other types of brain disorders and dementia, to accelerate and focus research on AD-specific proteinopathies that manifest decades before the clinical manifestation of first symptoms of AD, to enhance better understanding in the underlying mechanisms of AD clinical expression, and to use (and discover) targeted disease modifying interventions that can prevent or delay the onset of AD symptoms. Our ongoing and long-term research interest coincides well with the NIA-AA research framework in living people where we have already performed genome-wide association studies (GWAS) on CSF A?42/tau levels and A? deposition in the brain measured by amyloid-PET and identified known and novel associations in the APOE and non-APOE regions. However, the identified signals do not explain all of the phenotypic variation in the two AD-specific proteinopathies or endophenotypes. Here we propose a collaborative study between leading experts in the field to extend our ongoing efforts to delineate the complete genetic basis of the two AD- specific proteinopathies (A? and pathologic tau) by whole genome sequencing (WGS) using well-characterized and large amyloid-PET and CSF A?42/tau datasets with clinical outcomes of dementia followed by testing the effects of identified significant variants on downstream neurodegeneration markers, and performing extensive bioinformatics and functional studies. The primary objective of this application is to perform and analyze WGS in adequately powered large discovery samples with well-characterized A? and tau data along with clinical outcomes of dementia to identify putative functional variants associated with A? and tau pathologies followed by replications in independent and large samples with A? and tau data (Aims 1-2). We will integrate genetic information to create polygenic risk scores in order to predict A? and tau pathologies and will also examine the role of AD pathology-associated variants with downstream neurodegeneration, neuropathologies that coexist with AD and the risk and age-at-onset of AD (Aim3). Finally, we will functionally characterize genetic association using bioinformatics and in vitro experiments to understand their roles in affecting gene expression as being expression quantitative traits loci, and affecting intracellular and extracellular APP/A? and tau levels. The successful completion of this study will help to identify novel AD-related genes and pathways, and to uncover underlying possible mechanisms for AD.

Abstract Family-based approaches led to the identification of disease-causing Alzheimer?s Disease (AD) variants in the genes encoding Amyloid-beta Precursor Protein (APP), Presenilin 1 (PSEN1) and Presenilin 2 (PSEN2). Subsequently, the identification of these genes led to the A?-cascade hypothesis and recently to the development of drugs that target that pathway. In this proposal, we will identify rare risk and protective alleles. In recent studies, we have identified a rare coding variant 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. We will use sequence data from families densely affected by AD, because we hypothesize that these families are enriched for genetic risk factors. We have generated to sequence data from 285 families (1,235 individuals), that combined with the Alzheimer's Disease Sequencing Project (ADSP) data and the families form the National Institute of Mental Health (NIMH) will lead to a very large family-based dataset, totalizing more than 1,042 families and 4,684 participants. Our preliminary results support the flexibility of this approach and strongly suggest that protective and risk variants with large effect size will be found. The identification of those variants and genes will lead to a better understanding of the biology of the disease.

Core G: Genetics and High Throughput -Omics Project Summary Aging populations worldwide, particularly in developed countries, face an increasing burden of neurodegenerative diseases, particularly Alzheimer disease (AD), Frontotemporal dementia (FTD), and other AD-related dementias (ADRDs). Genetic studies have greatly contributed to our understanding of these complex diseases. Initial studies of a Mendelian form of AD resulted in the identification of mutations in the genes encoding ?-amyloid precursor protein (APP), Presenilin 1 (PSEN1), and Presenilin 2 (PSEN2). Mutations in Granulin (GRN), Microtubule-Associated Protein Tau (MAPT), and C9orf72 have been identified as causes of FTD. These diseases are characterized by protein misfolding and aggregation, and also share some clinical and neuropathological characteristics. The promise of the twenty-first century is that we will be able to classify these diseases by the genetic cause or genetic risk factors. Furthermore, it is clear that studies beyond genetics, such as transcriptomics, proteomics, or epigegomics, are needed to fully understand the biology of AD and ADRDs, with the intention of identifying novel biomarkers and therapeutic targets. The goal of the Genetics and High Throughput -Omics Core at the Knight ADRC is to obtain, bank and QC biospecimens (DNA, RNA and plasma) from Knight ADRC participants. The Core shares these biospecimens with qualified investigators that will generate genetic or other -omic data for these samples. The Core also stores and harmonizes all genome-wide association study (GWAS), whole exome sequencing (WES), whole genome sequencing (WGS), transcriptomic, and proteomic data generated for Knight ADRC participants in order to guarantee the integrity and compatibility of the data so that these data can be shared with the scientific community.

Abstract Alzheimer?s disease (AD) is a complex and heterogenous condition in which multiple molecular pathways are disrupted in different cell-types and lead to disease. Genetic findings indicate that amyloid-beta protein clearance and degradation pathways, cholesterol metabolism and the immune system are associated with AD etiology. However, the specific mechanism, genes and molecular networks have not yet been completely identified. Single-nuclei transcriptomic (snRNA-seq) data from human brains provides a detailed molecular atlas to study the pathways dysregulated in AD. We propose to deepen our understanding of the genes, network and molecular pathways associated with AD by sequencing a high-number of neuronal and glial cells (approximately 3.3 million cells) from human brain carriers of key genetic mutations and high risk variants, non-carrier sporadic AD cases and neuropath-free controls. We will leverage a unique collection of human tissue from the Dominantly Inherited Alzheimer Network and Knight-ADRC brain banks, and select +220 brains to perform systematic cell- type specific transcriptomic analyses. This is a unique and innovative study designed to analyze cell-specific transcriptomic dysregulation in carriers of high effect risk variants (TREM2 and APOE) and fully penetrant pathogenic mutations in APP/PSEN1/PSEN2 and by comparing them to sporadic AD cases and neuropath-free controls. This is a powerful approach to address disease heterogeneity, and will provide highly informative insights into the biology and pathology of neurodegeneration. Replication of these findings will be performed in snRNA-seq data from induced pluripotent stem cell derived neurons, astrocytes, and microglia-like cells that will be genome edited to add/remove genetic variants, as well as datasets that are being publicly released. Finally, we will create a knowledge portal in which all of the processed snRNA-seq data from our study will be harmonized with that of other research groups to provide a comprehensive molecular atlas that will provide additional insights into the biology and pathology of AD for the entire research community.

Project Summary/Abstract In order to enhance and focus research on Alzheimer's disease (AD)-specific proteinopathies, the 2018 research framework proposed by the National Institute on Aging and Alzheimer's Association (NIA-AA) recommends that AD be defined by its specific biological signatures that can be documented at autopsy or in living people by biomarkers rather than by its non-specific neurodegenerative and clinical syndromic features. Of the three proposed biomarkers by the NIA-AA research framework in living people (amyloid-beta (A?), pathologic tau and neurodegeneration), only the two AD-specific proteinopathies (A? and pathologic tau) are considered obligatory for the biological definition of AD, while neurodegeneration, although contribute to cognitive impairment and is part of the fully manifested disease, can also occur in other brain disorders and thus is not specific to AD. The purpose of this harmonized biological definition of AD in living people that includes the preclinical phase is to distinguish AD from other types of brain disorders and dementia, to accelerate and focus research on AD-specific proteinopathies that manifest decades before the clinical manifestation of first symptoms of AD, to enhance better understanding in the underlying mechanisms of AD clinical expression, and to use (and discover) targeted disease modifying interventions that can prevent or delay the onset of AD symptoms. Our ongoing and long-term research interest coincides well with the NIA-AA research framework in living people where we have already performed genome-wide association studies (GWAS) on CSF A?42/tau levels and A? deposition in the brain measured by amyloid-PET and identified known and novel associations in the APOE and non-APOE regions. However, the identified signals do not explain all of the phenotypic variation in the two AD-specific proteinopathies or endophenotypes. Here we propose a collaborative study between leading experts in the field to extend our ongoing efforts to delineate the complete genetic basis of the two AD- specific proteinopathies (A? and pathologic tau) by whole genome sequencing (WGS) using well-characterized and large amyloid-PET and CSF A?42/tau datasets with clinical outcomes of dementia followed by testing the effects of identified significant variants on downstream neurodegeneration markers, and performing extensive bioinformatics and functional studies. The primary objective of this application is to perform and analyze WGS in adequately powered large discovery samples with well-characterized A? and tau data along with clinical outcomes of dementia to identify putative functional variants associated with A? and tau pathologies followed by replications in independent and large samples with A? and tau data (Aims 1-2). We will integrate genetic information to create polygenic risk scores in order to predict A? and tau pathologies and will also examine the role of AD pathology-associated variants with downstream neurodegeneration, neuropathologies that coexist with AD and the risk and age-at-onset of AD (Aim3). Finally, we will functionally characterize genetic association using bioinformatics, causality tests and in vitro experiments to understand their roles in affecting gene expression as being expression quantitative traits loci, affecting intracellular and extracellular APP/A? and tau levels, and in myeloid cell function. The successful completion of this study will help to identify novel AD-related genes and pathways, and to uncover underlying possible mechanisms for AD.