Whole-genome sequencing reveals new Alzheimer's disease-associated rare variants in loci related to synaptic function and neuronal development

Abstract

Introduction: Genome-wide association studies have led to numerous genetic loci associated with Alzheimer's disease (AD). Whole-genome sequencing (WGS) now permits genome-wide analyses to identify rare variants contributing to AD risk.

Methods: We performed single-variant and spatial clustering-based testing on rare variants (minor allele frequency [MAF] ≤1%) in a family-based WGS-based association study of 2247 subjects from 605 multiplex AD families, followed by replication in 1669 unrelated individuals.

Results: We identified 13 new AD candidate loci that yielded consistent rare-variant signals in discovery and replication cohorts (4 from single-variant, 9 from spatial-clustering), implicating these genes: FNBP1L, SEL1L, LINC00298, PRKCH, C15ORF41, C2CD3, KIF2A, APC, LHX9, NALCN, CTNNA2, SYTL3, and CLSTN2.

Discussion: Downstream analyses of these novel loci highlight synaptic function, in contrast to common AD-associated variants, which implicate innate immunity and amyloid processing. These loci have not been associated previously with AD, emphasizing the ability of WGS to identify AD-associated rare variants, particularly outside of the exome.

Keywords: Alzheimer's disease; LOAD; RVAS; family-based association study; neuronal development; rare variants; synaptic function; whole-genome sequencing.

FIGURE 1

Data analysis workflow

FIGURE 2

QQ plot of rare (MAF < = 1%) single‐variant association results in the family‐based discovery data set (NIMH and NIA cohorts). The red line corresponds to all statistics, where at least one informative family is observed. The green line corresponds to statistics with at least ten informative families

FIGURE 3

Manhattan plot of rare (MAF < = 1%) single‐variant association results in the family‐based discovery data set (NIMH and NIA cohorts). Genes that correspond to replicated variants as described in the workflow (Figure 1) are highlighted

FIGURE 4

Manhattan plot of spatial clustering association results based on rare (MAF < = 1%) variants in the family‐based discovery data set (NIMH and NIA cohorts). Highlighted are genes, which correspond to replicated regions, described in the workflow (Figure 1)

FIGURE 5

QQ plot of spatial clustering association results based on rare (MAF < = 1%) variants in the family‐based discovery data set (NIMH and NIA cohorts)

FIGURE 6

Network of direct interactions between highly ranked SNV and regional genes and known AD‐associated genes. Direct protein‐protein relationships (blue links) between reference AD genes (red), Table 1 and Table 2 (yellow), Supplementary Table 12 and 15 (blue) protein‐coding genes. LINC00298 co‐regulated expression of directly interacting genes is highlighted (turquoise border). Proteins that are in direct interaction with genes from Tables 1 and 2 have been grouped where possible according to shared GO biological processes (green ellipse). Proteins that may not be directly interacting but are found commonly enriched in immune‐related processes are grouped (pink square). Proteins with dark green–colored borders are enriched in GO:BP nervous system development, whereas a navy blue border is enriched for generation of neurons. Gene‐gene relationships are listed in Supplementary Table 24. The network can be interactively explored via the NDEX project website

FIGURE 7

Cell‐specific enrichment results from the EWCE tool. We compared genes identified in our rare‐variant analysis to common variants published in AD and which cell type each is significantly enriched in. Zero represents the mean expression in each cell based on 10,000 permutations of gene lists of the same size. The data for this figure can be found in Supplementary Table 19