Analysis of Whole-Exome Sequencing Data for Alzheimer Disease Stratified by APOE Genotype

Yiyi Ma, Gyungah R. Jun, Xiaoling Zhang, Jaeyoon Chung, Adam C. Naj, Yuning Chen, Celine Bellenguez, Kara Hamilton-Nelson, Eden R. Martin, Brian W. Kunkle, Joshua C. Bis, Stéphanie Debette, Anita L. Destefano, Myriam Fornage, Gaël Nicolas, Cornelia Van Duijn, David A. Bennett, Philip L. De Jager, Richard Mayeux, Jonathan L. HainesMargaret A. Pericak-Vance, Sudha Seshadri, Jean Charles Lambert, Gerard D. Schellenberg, Kathryn L. Lunetta, Lindsay A. Farrer

Research output: Contribution to journalArticlepeer-review

25 Scopus citations


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 10441 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..

Original languageEnglish (US)
Pages (from-to)1099-1108
Number of pages10
JournalJAMA Neurology
Issue number9
StatePublished - Sep 2019

ASJC Scopus subject areas

  • Clinical Neurology


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