|Title||Analysis of Whole-Exome Sequencing Data for Alzheimer Disease Stratified by APOE Genotype.|
|Publication Type||Journal Article|
|Year of Publication||2019|
|Authors||Ma Y, Jun GR, Zhang X, Chung J, Naj AC, Chen Y, Bellenguez C, Hamilton-Nelson K, Martin ER, Kunkle BW, Bis JC, Debette S, DeStefano AL, Fornage M, Nicolas G, van Duijn C, Bennett DA, De Jager PL, Mayeux R, Haines JL, Pericak-Vance MA, Seshadri S, Lambert J-C, Schellenberg GD, Lunetta KL|
|Secondary Authors||Farrer LA|
|Corporate Authors||Alzheimer’s Disease Sequencing Project and Alzheimer’s Disease Exome Sequencing–France Project|
|Date Published||2019 Jun 10|
Importance: Previous genome-wide association studies of common variants identified associations for Alzheimer disease (AD) loci evident only among individuals with particular APOE alleles.
Objective: To identify APOE genotype-dependent associations with infrequent and rare variants using whole-exome sequencing.
Design, Setting, and Participants: The discovery stage included 10 441 non-Hispanic white participants in the Alzheimer Disease Sequencing Project. Replication was sought in 2 independent, whole-exome sequencing data sets (1766 patients with AD, 2906 without AD [controls]) and a chip-based genotype imputation data set (8728 patients with AD, 9808 controls). Bioinformatics and functional analyses were conducted using clinical, cognitive, neuropathologic, whole-exome sequencing, and gene expression data obtained from a longitudinal cohort sample including 402 patients with AD and 647 controls. Data were analyzed between March 2017 and September 2018.
Main Outcomes and Measures: Score, Firth, and sequence kernel association tests were used to test the association of AD risk with individual variants and genes in subgroups of APOE ε4 carriers and noncarriers. Results with P ≤ 1 × 10-5 were further evaluated in the replication data sets and combined by meta-analysis.
Results: Among 3145 patients with AD and 4213 controls lacking ε4 (mean [SD] age, 83.4 [7.6] years; 4363 [59.3.%] women), novel genome-wide significant associations were obtained in the discovery sample with rs536940594 in AC099552 (odds ratio [OR], 88.0; 95% CI, 9.08-852.0; P = 2.22 × 10-7) and rs138412600 in GPAA1 (OR, 1.78; 95% CI, 1.44-2.2; meta-P = 7.81 × 10-8). GPAA1 was also associated with expression in the brain of GPAA1 (β = -0.08; P = .03) and its repressive transcription factor, FOXG1 (β = 0.13; P = .003), and global cognition function (β = -0.53; P = .009). Significant gene-wide associations (threshold P ≤ 6.35 × 10-7) were observed for OR8G5 (P = 4.67 × 10-7), IGHV3-7 (P = 9.75 × 10-16), and SLC24A3 (P = 2.67 × 10-12) in 2377 patients with AD and 706 controls with ε4 (mean [SD] age, 75.2 [9.6] years; 1668 [54.1%] women).
Conclusions and Relevance: The study identified multiple possible novel associations for AD with individual and aggregated rare variants in groups of individuals with and without APOE ε4 alleles that reinforce known and suggest additional pathways leading to AD.
|Alternate Journal||JAMA Neurol|
|PubMed Central ID||PMC6563544|
|Grant List||R01 AG054076 / AG / NIA NIH HHS / United States |
U24 AG021886 / AG / NIA NIH HHS / United States
U01 AG049507 / AG / NIA NIH HHS / United States
U24 AG056270 / AG / NIA NIH HHS / United States
UF1 AG047133 / AG / NIA NIH HHS / United States
R01 AG041797 / AG / NIA NIH HHS / United States
U01 AG052409 / AG / NIA NIH HHS / United States
U01 AG049505 / AG / NIA NIH HHS / United States
U01 AG058654 / AG / NIA NIH HHS / United States
R01 NS017950 / NS / NINDS NIH HHS / United States
RF1 AG054023 / AG / NIA NIH HHS / United States
P50 AG005136 / AG / NIA NIH HHS / United States
RF1 AG057519 / AG / NIA NIH HHS / United States
RF1 AG015473 / AG / NIA NIH HHS / United States
P30 AG010129 / AG / NIA NIH HHS / United States