Research Article: Genetic assessment of age-associated Alzheimer disease risk: Development and validation of a polygenic hazard score

Date Published: March 21, 2017

Publisher: Public Library of Science

Author(s): Rahul S. Desikan, Chun Chieh Fan, Yunpeng Wang, Andrew J. Schork, Howard J. Cabral, L. Adrienne Cupples, Wesley K. Thompson, Lilah Besser, Walter A. Kukull, Dominic Holland, Chi-Hua Chen, James B. Brewer, David S. Karow, Karolina Kauppi, Aree Witoelar, Celeste M. Karch, Luke W. Bonham, Jennifer S. Yokoyama, Howard J. Rosen, Bruce L. Miller, William P. Dillon, David M. Wilson, Christopher P. Hess, Margaret Pericak-Vance, Jonathan L. Haines, Lindsay A. Farrer, Richard Mayeux, John Hardy, Alison M. Goate, Bradley T. Hyman, Gerard D. Schellenberg, Linda K. McEvoy, Ole A. Andreassen, Anders M. Dale, Carol Brayne

Abstract: BackgroundIdentifying individuals at risk for developing Alzheimer disease (AD) is of utmost importance. Although genetic studies have identified AD-associated SNPs in APOE and other genes, genetic information has not been integrated into an epidemiological framework for risk prediction.Methods and findingsUsing genotype data from 17,008 AD cases and 37,154 controls from the International Genomics of Alzheimer’s Project (IGAP Stage 1), we identified AD-associated SNPs (at p < 10−5). We then integrated these AD-associated SNPs into a Cox proportional hazard model using genotype data from a subset of 6,409 AD patients and 9,386 older controls from Phase 1 of the Alzheimer’s Disease Genetics Consortium (ADGC), providing a polygenic hazard score (PHS) for each participant. By combining population-based incidence rates and the genotype-derived PHS for each individual, we derived estimates of instantaneous risk for developing AD, based on genotype and age, and tested replication in multiple independent cohorts (ADGC Phase 2, National Institute on Aging Alzheimer’s Disease Center [NIA ADC], and Alzheimer’s Disease Neuroimaging Initiative [ADNI], total n = 20,680). Within the ADGC Phase 1 cohort, individuals in the highest PHS quartile developed AD at a considerably lower age and had the highest yearly AD incidence rate. Among APOE ε3/3 individuals, the PHS modified expected age of AD onset by more than 10 y between the lowest and highest deciles (hazard ratio 3.34, 95% CI 2.62–4.24, p = 1.0 × 10−22). In independent cohorts, the PHS strongly predicted empirical age of AD onset (ADGC Phase 2, r = 0.90, p = 1.1 × 10−26) and longitudinal progression from normal aging to AD (NIA ADC, Cochran–Armitage trend test, p = 1.5 × 10−10), and was associated with neuropathology (NIA ADC, Braak stage of neurofibrillary tangles, p = 3.9 × 10−6, and Consortium to Establish a Registry for Alzheimer’s Disease score for neuritic plaques, p = 6.8 × 10−6) and in vivo markers of AD neurodegeneration (ADNI, volume loss within the entorhinal cortex, p = 6.3 × 10−6, and hippocampus, p = 7.9 × 10−5). Additional prospective validation of these results in non-US, non-white, and prospective community-based cohorts is necessary before clinical use.ConclusionsWe have developed a PHS for quantifying individual differences in age-specific genetic risk for AD. Within the cohorts studied here, polygenic architecture plays an important role in modifying AD risk beyond APOE. With thorough validation, quantification of inherited genetic variation may prove useful for stratifying AD risk and as an enrichment strategy in therapeutic trials.

Partial Text: Late-onset Alzheimer disease (AD), the most common form of dementia, places a large emotional and economic burden on patients and society. With increasing health care expenditures among cognitively impaired elderly individuals [1], identifying individuals at risk for developing AD is of utmost importance for potential preventative and therapeutic strategies. Inheritance of the ε4 allele of apolipoprotein E (APOE) on Chromosome 19q13 is the most significant risk factor for developing late-onset AD [2]. APOE ε4 has a dose-dependent effect on age of onset, increases AD risk 3-fold in heterozygotes and 15-fold in homozygotes, and is implicated in 20%–25% of AD cases [3].

In this study, by integrating AD-associated SNPs from recent GWASs and disease incidence estimates from the US population into a genetic epidemiology framework, we have developed a novel PHS for quantifying individual differences in risk for developing AD, as a function of genotype and age. The PHS systematically modified age of AD onset, and was associated with known in vivo and pathological markers of AD neurodegeneration. In independent cohorts (including a neuropathologically confirmed dataset), the PHS successfully predicted empirical (actual) age of onset and longitudinal progression from normal aging to AD. Even among individuals who do not carry the ε4 allele of APOE (the majority of the US population), we found that polygenic information was useful for predicting age of AD onset.



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