Exome-wide age-of-onset analysis reveals exonic variants inERN1, TACR3andSPPL2Cassociated with Alzheimer’s disease

Abstract

Despite recent discovery in GWAS of genomic variants associated with Alzheimer's disease (AD), its underlying biological mechanisms are still elusive. Discovery of novel AD-associated genetic variants, particularly in coding regions and from APOE ε 4 non-carriers, may provide more insights into the understanding of the pathology of AD. In this study, we carried out exome-wide association analysis of age-of-onset of AD with ~20,000 subjects, and placed more emphasis on APOE ε 4 non-carriers. Using Cox mixed-effects models, we find that age-of-onset shows a stronger genetic signal than AD case-control status, capturing many known variants with stronger significance, and also revealing three new variants. We identified two novel rare variants, rs56201815, a synonymous variant in ERN1, from the analysis of APOE ε 4 noncarriers, and a missense variant rs144292455 in TACR3. In addition, we detected rs12373123, a common missense variant in SPPL2C in the MAPT region, associated with age-of-onset of AD in APOE ε 4 non-carriers. In an attempt to unravel their regulatory and biological functions, we found that the minor allele of rs56201815 was associated with lower average FDG uptake across five brain regions in ADNI. Our eQTL analyses based on 6198 gene expression samples from ROSMAP and GTEx revealed that the minor allele of rs56201815 was associated with elevated expression of ERN1, a key gene triggering unfolded protein response (UPR), in multiple brain regions, including posterior cingulate cortex and nucleus accumbens. Our cell type-specific eQTL analysis of based on ~80,000 single nuclei in prefrontal cortex revealed that the protective minor allele of rs12373123 significantly increased expression of GRN in microglia, and was associated with MAPT expression in astrocytes. These findings provide novel evidence supporting the hypothesis of the potential involvement of the UPR to ER stress in the pathological pathway of AD, and also provide more insights into underlying regulatory mechanisms behind the pleiotropic effects of rs12373123 in multiple degenerative diseases including AD and Parkinson's disease.In this study, we performed exome-wide association analysis of age-of-onset of AD, in which most genetic variants are rare or low frequency, using an Alzheimer's Disease Sequencing Project (ADSP) sample of 10,216 subjects in the discovery phase. Rare coding variants often show larger effect size and their biological consequences are more explicable, but its association analysis is complicated by insufficient statistical power. Although exome-wide association of AD has recently been explored using AD status (Bis et al., 2018;Cruchaga et al., 2014;Raghavan et al., 2018), our rationale is that more AD-related rare variants can be identified using analysis of age-of-onset of AD with a Cox model given emerging evidence from a previous study showing its advantage in terms of statistical power (He and Kulminski, 2019). We attempted to replicate significant findings in four other studies, with a meta-analysis sample size of a...

A Fast and Robust Strategy to Remove Variant-Level Artifacts in Alzheimer Disease Sequencing Project Data

“…2 In response to this observation, there has been a shift to start using exome sequencing (ES) or genome sequencing (GS) to help capture rare and/or coding variants that contribute to AD risk, which has led to several recent initial successes. 7-15…”

“…2 In response to this observation, there has been a shift to start using exome sequencing (ES) or genome sequencing (GS) to help capture rare and/or coding variants that contribute to AD risk, which has led to several recent initial successes. [7][8][9][10][11][12][13][14][15] In the United States, the Alzheimer Disease Sequencing Project (ADSP) has taken a leading role in the sequencing of AD-related samples at scale, with resultant data being made publicly available to researchers to generate new insights into the genetic etiology of AD. The ADSP has pursued both "whole" ES (WES) and "whole" GS (WGS) approaches (although it should be noted that these for now do not actually provide whole coverage due to technical limitations), where most recently, the focus is increasingly on GS.…”

A fast and robust strategy to remove variant level artifacts in Alzheimer’s Disease Sequencing Project data

“…Despite these important advances, most risk variants identified so far have common allele frequencies and it's estimated that only about half of AD's genetic heritability has been captured, such that much of AD's genetic component remains to be identified 2 . In response to this observation, there has been a shift to start using whole-exome sequencing (WES) or whole-genome sequencing (WGS) to help capture rare and/or coding variants that contribute to AD risk, which has led to several recent initial successes [7][8][9][10][11][12][13][14][15] .…”