NG00121 – Alzheimer’s disease single-neuron whole-genome sequencing – Miller 2022

Alzheimer's disease(AD) is the most common cause of dementia, accounting for 60% to 80% of cases that affect over six million people in the United States. The disease gradually progresses from mild cognitive impairment(MCI) to dementia, which takes more than a decade. Identifying individuals who have a high risk of AD earlier is essential for AD prevention and intervention. As the heritability of AD is high(up to 79%), genetic data should be powerful to identify individuals at high risk. Indeed, polygenic risk score (PRS), designed to estimate individual genetic liability by integrating large GWAS summary statistics and individual genotype data, has been shown to be promising for AD risk prediction(AUCs up to 84%). However, the prediction accuracy using a single PRS is still not sufficient for MCI and AD classification in clinical practice. We hypothesize that convolution neural network(CNN) models can improve the classification of AD and MCI by multiple integrating PRSs from multiple traits, multi-omics data (genotyping data, scRNA-seq), clinical data, and imaging data. The objective is to develop advanced AI algorithms and build data-driven models for disease risk assessment, earlier identifying individuals with high risk for MCI and AD. Our long-term goal is to develop and validate a prediction model that can be translated into clinical practice. Our CNN model has recently shown an improved performance for AD with PRSs from multiple traits(AUC 92.4%). We want to extend our approach to predicting AD and MCI in different ethnic groups and validate the results with independent datasets. To this end, we would like to apply for multi-omics data in NG00067.v9 from https://dss.niagads.org/datasets/ng00067/. With an extensive experience in genetic studies on complex disorders and disease modeling, we are confident that we will achieve the specified goals and promote the integration of genetic data with AI algorithms, facilitating data-driven, personalized care of AD. We expect to finish this study within 2 years with publication and grant application. We have IRB approval and will follow the rules for data sharing and acknowledgment.

Alzheimer’s disease (AD), the most common form of dementia, that usually develops from mild cognitive impairment to dementia. There is currently no treatment to slow the progression of this disorder. But earlier identification of the individuals with higher risk maybe critical to prevent the disease. We propose a new approach to create models for classification of AD and MCI with artificial intelligence and genetic data. This study will have a significant value in personalized medicine for AD risk assessment, classification, and earlier intervention.We don’t have the planned collaboration with researchers outside Cleveland Clinic in the current analytic plans.

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

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.

As part of the Collaborative for Alzheimer's Disease genetics REsearch (CADRE: NIA grant U01-AG058654), we plan to analyze whole exome and whole genome sequence data generated from subjects with Alzheimer's disease (AD) and elderly normal controls. These data will be generated by the National Human Genome Institute Large-Scale Sequence Program. The goal of the planned analyses is to identify genes that have alleles that protect against or increase susceptibility to AD. We will evaluate variants detected in the sequence data for association with AD to identify protective and susceptibility alleles using the whole exome case-control data. We will also evaluate sequence data from multiplex AD families to identify variants associated with AD risk and protection, and evaluate variant co-segregation with AD. The family data will be whole genome data. The family-based data will be used to inform the cases control analysis and visa versa. We also will focus on structural variants (insertion-deletions, copy number variants, and chromosomal rearrangements). Evaluation of structural variants will involve both whole genome and whole exome data. Structural variants will be analyzed with single nucelotide variants detected and analyzed in the case-control and family-based data.

We are attempting to identify all the inherited elements that contribute to Alzheimer's disease risk. To do this we will analyze DNA sequence data from subjects with Alzheimer's disease and elderly subjects who are cognitively normal. The sequence data from these 2 groups will be compared to identify differences that contribute to the risk of developing Alzheimer's disease of that protect against Alzheimer's disease. These DNA differences can be at a single site in the genetic code, or can span multiple sites, changing the copy number of DNA sequences. Both types of genetic variants will be examined.

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

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

Our objective is to study somatic mutations in the genome of human neurons in Alzheimer's disease (AD). Our study design is as follows. We will identify somatic mutations present in the single-cell whole-genome sequencing datasets in this dataset using established algorithms. We will then characterize those mutations in various ways, including 1) location of mutations (exons, introns, intergenic regions), 2) mutation types (substitutions, indels, aneuploidy), and 3) mutation signatures (exact nature of base changes, for example C>T vs. C>A mutations, small vs. large deletions). Our analysis plan is to compare patterns of mutation in advanced AD neurons to neurotypical controls. AD stage was determined by the authors using the Braak staging system. The Braak staging system uses the intensity and brain region distribution of staining of Tau neurofibrillary tangles in the brain to assign the severity of AD pathology. Donors with significant staining in the prefrontal cortex are considered late-stage. We will not analyze germline genetic markers in this study.

Alzheimer’s disease (AD) and other neurodegenerative diseases are characterized by age-related loss of neurons in the brain, and afflict about half of individuals over the age 85. Scientists currently have a poor understanding of the causes of these disorders. This study will examine how DNA damage and somatic mutation changes during healthy aging relates to AD, with the goal of better understanding the causes of these diseases so that treatments and cures can be developed.

The objective of our research is to characterize genomic rearrangements associated with various human disease including Alzheimer’s. The overarching hypothesis guiding our research is that repair of DNA double-strand breaks (DSBs) by using ‘risky’ inaccurate pathways can lead to genomic destabilization. Our focus is on two DSB repair pathways: break-induced replication (BIR) and microhomology-mediated BIR (MMBIR). BIR is initiated by a broken DNA end invading into a homologous template followed by extensive DNA synthesis that is highly mutagenic. Interruptions of BIR leads to initiation of MMBIR, a template-switching event that often leads to complex genomic rearrangements and has been linked to neurological conditions and to cancer. The overall goal of our proposed research is to define the molecular mechanisms of MMBIR, and to identify factors that inhibit or promote cells entering into MMBIR.We aim to achieve this using our MMBSearch tool to detect MMBIR events that are often missed by other methods in human WGS analyses. Using MMBSearch we will analyze data from NIAGADS, specifically data on neurological disease associated whole genome sequencing (WGS) and whole exome sequencing (WES) to detect MMBIR events associated with neurodegenerative disorders.The results of this analyses will be used to determine the frequency of MMBIR in various types of human cells and their association with neurodegenerative disorders. In addition, we will identify chromosomal locations where MMBIR events are especially abundant and specific features in humans that predispose them to MMBIR. We will identify genetic variations predisposing cells to MMBIR, which may uncover that specific SNPs, structural variations, certain gene mutations, etc. are associated with MMBIR events. We specifically hypothesize that mutations in DNA repair, DNA replication, chromatin maintenance, and DNA damage checkpoint genes could promote MMBIR. These studies will shed light on the etiology and mechanism of MMBIR to potentially develop biomarkers for early detection and design targeted therapies to treat human disorders.

The goal of our research is to understand the underlying mechanisms of genomic instability that lead to human disease. In particular, we are interested to investigate the molecular mechanism of an essentially uncharacterized DNA repair pathway, microhomology-mediated break-induced replication (MMBIR) that has been implicated in DNA mutations and found in a variety of human cancers and in association with neurological diseases. We have recently described a diagnostic pattern of mutations associated with MMBIR using a yeast model, which has allowed us to develop a novel algorithm to search for MMBIR events in sequenced human genomes. We are planning to apply this new algorithm to identify MMBIR events in analyzing human genome databases. The proposed research will allow us to further understand mechanisms of leading to various human diseases including cancer and neurological human diseases and to refine our software that is aimed to detect MMBIR in human genomes. The proposed research will be focused on analyzing the data from NIAGADS database.

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.

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.

Alzheimer's disease (AD) is the most common form of dementia and is characterized by cognitive impairment and progressive neurodegeneration. Genome-wide association studies of AD have identified more than 70 risk loci; however, a major challenge in the field is that the majority of these risk factors are harbored within non-coding regions where their impact on AD pathogenesis has been difficult to establish. Therefore, the molecular basis of AD development and progression remains elusive and, so far, reliable treatments have not been found. The overarching goal of this proposal is to examine and validate AD-related changes on chromatin accessibility and the 3D genome at the single cell level. Based on recent data from our group and others, we hypothesize that genotype-phenotype associations in AD are causally mediated by cell type-specific alterations in the regulatory mechanisms of gene expression. To test our hypothesis, we propose the following Specific Aims: (1) perform multimodal (i.e., within cell) profiling of the chromatin accessibility and transcriptome at the single cell level to identify cell type-specific AD-related changes on the 3D genome; (2) fine-map AD risk loci to identify causal variants, regulatory regions and genes; (3) functionally validate putative causal variants and regulatory sequences using novel approaches that combine massively parallel reporter assays, CRISPR and single cell assays in neurons and microglia derived from induced pluripotent stem cells; and (4) develop and maintain a community workspace that provides for the rapid dissemination and open evaluation of data, analyses, and outcomes. Overall, our multidisciplinary computational and experimental approach will provide a compendium of functionally and causally validated AD risk loci that has the potential to lead to new insights and avenues for therapeutic development.

Alzheimer’s disease (AD) affects half the US population over the age of 85 and despite decades of research, reliable treatments for AD have not been found. The overarching goal of our proposal is to generate multiscale genomics (gene expression and epigenome regulation) data at the single cell level and perform fine mapping to detect and validate causal variants, transcripts and regulatory sequences in AD. The proposed work will bridge the gap in understanding the link among the effects of risk variants on enhancer activity and transcript expression, thus illuminating AD molecular mechanisms and providing new targets for future therapeutic development.

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.

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.

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.

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.

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.

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.