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.

Neuroinflammation in Alzheimer’s Disease

“…LOAD, however, comprises most AD cases (>95%) where the greatest risk factor is advanced age [ 51 ], while the common genetic risk factor is an allelic variation in apolipoprotein E (Apo E) [ 52 ]. Recent large scale studies of AD genetics, employing genome-wide association studies (GWAS), whole exome sequencing (WES), and whole genome sequencing (WGS), have defined additional genes whose variants contribute to increased risk [ 53 , 54 ]. These include Clusterin (CLU), Sortilin-related receptor-1 (SORL1), ATP-binding cassette subfamily A member 7 (ABCA7), Bridging integrator 1 (BIN1), phosphatidylinositol binding clathrin assembly protein (PICALM), CD2 associated protein (CD2AP), Complement component (3b/4b) receptor 1 (CR1), CD33, triggering receptor expressed on myeloid cells 2 (TREM2), and phospholipase D3 (PLD3) [ 55 , 56 , 57 ].…”

Region-based analysis of rare genomic variants in whole-genome sequencing datasets reveal two novel Alzheimer’s disease-associated genes: DTNB and DLG2

“…The most enriched part of the network was for proteins interacting with DLG2 that are connected to neurexins and neuroligins, as well as trafficking of AMPA receptors. DLG2 also interacted with 4 proteins (NOS1, ERBB4, DLGAP2, NRXN3) previously associated with AD risk 20 , and 4 proteins (GRIN1, GRIN2A, GRIN2B, GAPDH) associated with AD in the KEGG Alzheimer’s pathway. DLG2 and DTNB also share protein-protein or co-expression interactions through KIF1B, MLC1, and SH3D19.…”

“…Our approach utilized two region-based tests (burden and SKAT) in a family-based design, in which the joint distribution of rare variants is not estimated, but rather obtained by the haplotype algorithm for FBAT, which is robust against population structure and admixture, and allows for construction of exact or simulation-based p-values. Previously, we performed region-based rare variant testing, but with different region definitions, and using only burden tests with empirical estimation of the variant correlations and asymptotic p-values 20 . While this is the largest combined family-based AD-specific WGS dataset available, larger datasets will be needed to confirm our findings in future studies.…”

ZCWPW1loss-of-function variants in Alzheimer’s Disease

“…First, a UK whole exome sequencing (WES) project observed an increased burden of PILRA variants in AD patients as their top-associated hit, suggesting a direct role of PILRA in AD pathogenesis 11 . In contrast, one of the largest WES studies on AD reported to date pinpointed significant enrichment of ultra-rare (allele frequency < 0.01%) ZCWPW1 predicted loss-offunction (LoF) variants in AD patients 12 , and additionally, a nominally significant association of genic rare (allele frequency < 1%) variants within ZCWPW1 was reported in a recent large-scale WGS study on AD 13 . Second, the discovery lead SNP in the locus, rs1476679, has strong regulatory potential, with the top RegulomeDB 14 rank score among the lead SNPs of the significant loci from all published AD GWAS, and two independent studies observed that rs1476679 is an eQTL for PILRB 15,16 .…”