NG00117 – NCRAD Families GWAS

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.

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

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.

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.