scholarly journals Considering the APOE locus in Alzheimer’s disease polygenic scores in the Health and Retirement Study: a longitudinal panel study

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Erin B. Ware ◽  
Jessica D. Faul ◽  
Colter M. Mitchell ◽  
Kelly M. Bakulski
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Repeated Measures ◽  
Panel Study ◽  
European Ancestry ◽  
Health And Retirement Study ◽  
Carrier Status ◽  
Polygenic Score ◽  
Polygenic Scores ◽  
Retirement Study

Abstract Background Polygenic scores are a strategy to aggregate the small, additive effects of single nucleotide polymorphisms across the genome. With phenotypes like Alzheimer’s disease, which have a strong and well-established genomic locus (APOE), the cumulative effect of genetic variants outside of this area has not been well established in a population-representative sample. Methods Here we examine the association between polygenic scores for Alzheimer’s disease both with and without the APOE region (chr19: 45,384,477 to 45,432,606, build 37/hg 19) at different P value thresholds and dementia. We also investigate the addition of APOE-ε4 carrier status and its effect on the polygenic score—dementia association in the Health and Retirement Study using generalized linear models accounting for repeated measures by individual and use a binomial distribution, logit link, and unstructured correlation structure. Results In a large sample of European ancestry participants of the Health and Retirement Study (n = 9872) with an average of 5.2 (standard deviation 1.8) visit spaced two years apart, we found that including the APOE region through weighted variants in a polygenic score was insufficient to capture the large amount of risk attributed to this region. We also found that a polygenic score with a P value threshold of 0.01 had the strongest association with the odds of dementia in this sample (odds ratio = 1.10 95%CI 1.0 to 1.2). Conclusion We recommend removing the APOE region from polygenic score calculation and treating the APOE locus as an independent covariate when modeling dementia. We also recommend using a moderately conservative P value threshold (e.g. 0.01) when creating polygenic scores for Alzheimer’s disease on dementia. These recommendations may help elucidate relationships between polygenic scores and regions of strong significance for phenotypes similar to Alzheimer’s disease.

scholarly journals Considering the APOE locus in polygenic scores for Alzheimer’s disease

2019 ◽  
Author(s):  
Erin B. Ware ◽  
Jessica D. Faul ◽  
Colter M. Mitchell ◽  
Kelly M. Bakulski
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Cumulative Effect ◽  
Carrier Status ◽  
Nucleotide Polymorphisms ◽  
Genomic Locus ◽  
Single Nucleotide ◽  
Polygenic Score ◽  
Polygenic Scores ◽  
Small Additive

AbstractPolygenic scores are a strategy to aggregate the small, additive effects of single nucleotide polymorphisms across the genome. With phenotypes like Alzheimer’s disease, which have a strong and well established genomic locus (APOE), the cumulative effect of genetic variants outside of this area has not been well established in a population-representative sample. Here we examine the association between polygenic scores both with and without the APOE region at different P value thresholds. We also investigate the addition of APOE-ε4 carrier status and its effect on the polygenic score – dementia association. We found that including the APOE region through weighted variants in a polygenic score was insufficient to capture the large amount of risk attributed to this region. We recommend removing this region from polygenic score calculation and treating the APOE locus as an independent covariate.

scholarly journals Genetic heterogeneity in depressive symptoms following the death of a spouse: Polygenic score analysis of the US Health and Retirement Study

2016 ◽  
Author(s):  
Benjamin W. Domingue ◽  
Hexuan Liu ◽  
Aysu Okbay ◽  
Daniel W. Belsky
Keyword(s):  
Older Adults ◽  
Depressive Symptoms ◽  
Life Stress ◽  
Genome Wide Association Study ◽  
The United States ◽  
Health And Retirement Study ◽  
Polygenic Score ◽  
Polygenic Scores ◽  
Retirement Study

AbstractExperience of stressful life events is associated with risk of depression. Yet many exposed individuals do not become depressed. A controversial hypothesis is that genetic factors influence vulnerability to depression following stress. This hypothesis is most commonly tested with a “diathesis-stress” model, in which genes confer excess vulnerability. We tested an alternative model, in which genes may buffer against the depressogenic effects of life stress. We measured the hypothesized genetic buffer using a polygenic score derived from a published genome-wide association study (GWAS) of subjective wellbeing. We tested if married older adults who had higher polygenic scores were less vulnerable to depressive symptoms following the death of their spouse as compared to age-peers who had also lost their spouse and who had lower polygenic scores. We analyzed data from N=9,453 non-Hispanic white adults in the Health and Retirement Study (HRS), a population-representative longitudinal study of older adults in the United States. HRS adults with higher wellbeing polygenic scores experienced fewer depressive symptoms during follow-up. Those who survived death of their spouses during follow-up (n=1,829) experienced a sharp increase in depressive symptoms following the death and returned toward baseline over the following two years. Having a higher polygenic score buffered against increased depressive symptoms following a spouse's death. Effects were small and clinical relevance is uncertain, although polygenic score analyses may provide clues to behavioral pathways that can serve as therapeutic targets. Future studies of gene-environment interplay in depression may benefit from focus on genetics discovered for putative protective factors.

scholarly journals A non-APOE Polygenic score for Alzheimer’s disease and APOE-ε4 have independent associations with dementia in the Health and Retirement Study

2020 ◽  
Author(s):  
Kelly M. Bakulski ◽  
Harita S. Vadari ◽  
Jessica D. Faul ◽  
Steven G. Heeringa ◽  
Sharon LR Kardia ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Cognitive Impairment ◽  
Genetic Risk ◽  
Population Based ◽  
Health And Retirement Study ◽  
Polygenic Score ◽  
Genetic Region ◽  
Apoe Ε4 ◽  
Normal Cognition ◽  
Retirement Study

AbstractINTRODUCTIONAlzheimer’s disease (AD) is a common and costly neurodegenerative disorder. A large proportion of risk is heritable and many genetic risk factors for AD have been identified. The cumulative genetic risk of known markers has not been benchmarked for dementia in a population-based sample.METHODSIn the United States population-based Health and Retirement Study (HRS) (waves 1995-2014), we evaluated the role of cumulative genetic risk for AD, with and without the APOE-ε4 alleles, on dementia status (dementia, cognitive impairment without dementia, borderline cognitive impairment without dementia, cognitively normal). We used logistic regression, accounting for demographic covariates and genetic principal components, and analyses were stratified by European and African genetic ancestry.RESULTSIn the European ancestry sample (n=8399), both AD polygenic score excluding the APOE genetic region (odds ratio (OR)=1.10; 95% confidence interval (CI): 1.00, 1.20) and the presence of any APOE-ε4 alleles (OR=2.42; 95% CI: 1.99, 2.95) were associated with the odds of dementia relative to normal cognition in a mutually-adjusted model. In the African ancestry sample (n=1605), the presence of any APOE-ε4 alleles was associated with 1.77 (95% CI: 1.20, 2.61) times higher odds of dementia, while the AD polygenic score excluding the APOE genetic region was not significantly associated with the odds of dementia relative to normal cognition 1.06 (95% CI: 0.97, 1.30).DISCUSSIONCumulative genetic risk for AD and APOE-ε4 are both independent predictors of dementia. This study provides important insight into the polygenic nature of dementia and demonstrates the utility of polygenic scores in dementia research.

scholarly journals Applications of Stochastic Process Models to Constructing Predictive Models of Alzheimer’s Disease

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 263-263
Author(s):  
Konstantin Arbeev ◽  
Olivia Bagley ◽  
Arseniy Yashkin ◽  
Hongzhe Duan ◽  
Igor Akushevich ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Stochastic Process ◽  
Repeated Measures ◽  
Process Model ◽  
Large Scale ◽  
Disease Onset ◽  
Building Blocks ◽  
Process Models ◽  
Polygenic Scores

Abstract Large-scale population-based data collecting repeated measures of biomarkers, follow-up data on events (incidence of diseases and mortality), and extensive genetic data provide excellent opportunities for applying statistical models for joint analyses of longitudinal dynamics of biomarkers and time-to-event outcomes that allow investigating dynamics of biomarkers and other relevant factors (including genetic) in relation to risks of diseases and death and how this may propagate to the future. Here we applied one such model, the stochastic process model (SPM), to data on longitudinal trajectories of different variables (comorbidity index, body mass index, cognitive scores), other relevant covariates (including genetic factors such as APOE polymorphisms and polygenic scores, PGS), and data on onset of Alzheimer’s disease (AD) in the Health and Retirement Study. We observed that different aging-related characteristics estimated from trajectories of respective variables in SPM are strongly associated with risks of onset of AD and found that these associations differ by sex, APOE status (carriers vs. non-carriers of APOE e4) and by PGS groups. The approach allows modeling and estimating time trends (e.g., by birth cohorts) in relevant dynamic characteristics in relation to the disease onset. These results provide building blocks for constructing the models for forecasting future trends and burden of AD that take into account dynamic relationships between individual trajectories of relevant repeatedly measured characteristics and the risk of the disease. Such models also provide the analytic framework for understanding AD in the context of aging and for finding genetic underpinnings of such links between AD and aging.

scholarly journals Circulating biomarkers of immunity and inflammation, risk of Alzheimer’s disease, and hippocampal volume: a Mendelian randomization study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lana Fani ◽  
Marios K. Georgakis ◽  
M. Arfan Ikram ◽  
M. Kamran Ikram ◽  
Rainer Malik ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Mendelian Randomization ◽  
Hippocampal Volume ◽  
Cd4 Count ◽  
European Ancestry ◽  
Monocyte Count ◽  
Circulating Biomarkers ◽  
Lymphocyte Ratio ◽  
Immune Biomarkers

AbstractThe aim of this study was to explore the association between genetically predicted circulating levels of immunity and inflammation, and the risk of Alzheimer’s disease (AD) and hippocampal volume, by conducting a two-sample Mendelian Randomization Study. We identified 12 markers of immune cells and derived ratios (platelet count, eosinophil count, neutrophil count, basophil count, monocyte count, lymphocyte count, platelet-to-lymphocyte ratio, monocyte-to-lymphocyte ratio, CD4 count, CD8 count, CD4-to-CD8 ratio, and CD56) and 5 signaling molecules (IL-6, fibrinogen, CRP, and Lp-PLA2 activity and mass) as primary exposures of interest. Other genetically available immune biomarkers with a weaker a priori link to AD were considered secondary exposures. Associations with AD were evaluated in The International Genomics of Alzheimer’s Project (IGAP) GWAS dataset (21,982 cases; 41,944 controls of European ancestry). For hippocampal volume, we extracted data from a GWAS meta-analysis on 33,536 participants of European ancestry. None of the primary or secondary exposures showed statistically significant associations with AD or with hippocampal volume following P-value correction for multiple comparisons using false discovery rate < 5% (Q-value < 0.05). CD4 count showed the strongest suggestive association with AD (odds ratio 1.32, P < 0.01, Q > 0.05). There was evidence for heterogeneity in the MR inverse variance-weighted meta-analyses as measured by Cochran Q, and weighted median and weighted mode for multiple exposures. Further cluster analyses did not reveal clusters of variants that could influence the risk factor in distinct ways. This study suggests that genetically predicted circulating biomarkers of immunity and inflammation are not associated with AD risk or hippocampal volume. Future studies should assess competing risk, explore in more depth the role of adaptive immunity in AD, in particular T cells and the CD4 subtype, and confirm these findings in other ethnicities.

scholarly journals Long runs of homozygosity are associated with Alzheimer’s disease

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sonia Moreno-Grau ◽  
◽  
Maria Victoria Fernández ◽  
Itziar de Rojas ◽  
Pablo Garcia-González ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
European Ancestry ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Outbred Population ◽  
Whole Exome ◽  
Whole Exome Sequencing Data ◽  
Outbred Populations ◽  
Recessive Effects

AbstractLong runs of homozygosity (ROH) are contiguous stretches of homozygous genotypes, which are a footprint of inbreeding and recessive inheritance. The presence of recessive loci is suggested for Alzheimer’s disease (AD); however, their search has been poorly assessed to date. To investigate homozygosity in AD, here we performed a fine-scale ROH analysis using 10 independent cohorts of European ancestry (11,919 AD cases and 9181 controls.) We detected an increase of homozygosity in AD cases compared to controls [βAVROH (CI 95%) = 0.070 (0.037–0.104); P = 3.91 × 10−5; βFROH (CI95%) = 0.043 (0.009–0.076); P = 0.013]. ROHs increasing the risk of AD (OR > 1) were significantly overrepresented compared to ROHs increasing protection (p < 2.20 × 10−16). A significant ROH association with AD risk was detected upstream the HS3ST1 locus (chr4:11,189,482‒11,305,456), (β (CI 95%) = 1.09 (0.48 ‒ 1.48), p value = 9.03 × 10−4), previously related to AD. Next, to search for recessive candidate variants in ROHs, we constructed a homozygosity map of inbred AD cases extracted from an outbred population and explored ROH regions in whole-exome sequencing data (N = 1449). We detected a candidate marker, rs117458494, mapped in the SPON1 locus, which has been previously associated with amyloid metabolism. Here, we provide a research framework to look for recessive variants in AD using outbred populations. Our results showed that AD cases have enriched homozygosity, suggesting that recessive effects may explain a proportion of AD heritability.

Abstract 44: Associations of Atrial Fibrillation, Neuroimaging Measures of Cerebrovascular Disease and Alzheimer’S Disease-related Pathology, and Cognitive Impairment

Stroke ◽  
2015 ◽  
Vol 46 (suppl_1) ◽  
Author(s):  
Jonathan Graff-Radford ◽  
Rosebud Roberts ◽  
Malini Madhavan ◽  
Alejandro Rabinstein ◽  
Ruth Cha ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Cognitive Impairment ◽  
White Matter ◽  
Cerebrovascular Disease ◽  
Regression Models ◽  
Grey Matter ◽  
White Matter Hyperintensity ◽  
Carrier Status

The objective of this study was to investigate the cross-sectional associations of atrial fibrillation with neuroimaging measures of cerebrovascular disease and Alzheimer’s disease-related pathology, and their interaction with cognitive impairment. MRI scans of non-demented individuals (n=1044) from the population-based Mayo Clinic Study of Aging were analyzed for infarctions, total grey matter, hippocampal and white matter hyperintensity volumes. A subset of 496 individuals underwent FDG and C-11 Pittsburgh compound B (PiB) PET scans. We assessed the associations of atrial fibrillation with i) categorical MRI measures (cortical and subcortical infarctions) using multivariable logistic regression models, and with ii) continuous MRI measures ( hippocampal, total grey matter, and white matter hyperintensity volumes) and FDG-PET and PiB-PET measures using multivariable linear regression models, and adjusting for confounders. Among participants who underwent MRI (median age, 77.8, 51.6% male), 13.5% had atrial fibrillation. Presence of atrial fibrillation was associated with subcortical infarctions (odds ratio [OR], 1.83; p=0.002), cortical infarctions (OR, 1.91; p=0.03), total grey matter volume (Beta [β], -.025, p<.0001) after controlling for age, education, gender, APOE e4 carrier status, coronary artery disease, diabetes, history of clinical stroke, and hypertension. However, atrial fibrillation was not associated with white matter hyperintensity volume, hippocampal volume, Alzheimer’s pattern of FDG hypometabolism or PiB uptake. There was a significant interaction of cortical infarction (p for interaction=0.004) and subcortical infarction (p for interaction =0.015) with atrial fibrillation with regards to odds of mild cognitive impairment (MCI). Using subjects with no atrial fibrillation and no infarction as the reference, the OR (95% confidence intervals [CI]) for MCI was 2.98 (1.66, 5.35;p = 0.0002) among participants with atrial fibrillation and any infarction, 0.69 (0.36, 1.33;p= 0.27) for atrial fibrillation and no infarction, and 1.50 (0.96, 2.32;p = 0.07) for no atrial fibrillation and any infarction. These data highlight that atrial fibrillation is associated with MCI in the presence of infarctions.

scholarly journals P-tau and neurodegeneration mediate the effect of β-amyloid on cognition in non-demented elders

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Ling-Zhi Ma ◽  
Hao Hu ◽  
Zuo-Teng Wang ◽  
Ya-Nan Ou ◽  
Qiang Dong ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Cognitive Decline ◽  
Mediating Effect ◽  
Total Effect ◽  
Independent Effect ◽  
Carrier Status ◽  
Mediation Effects ◽  
Β Amyloid ◽  
The Impact

Abstract Background There are many pathological changes in the brains of Alzheimer’s disease (AD) patients. For many years, the mainstream view on the pathogenesis of AD believes that β-amyloid (Aβ) usually acts independently in addition to triggering functions. However, the evidence now accumulating indicates another case that these pathological types have synergies. The objective of this study was to investigate whether effects of Aβ pathology on cognition were mediated by AD pathologies, including tau-related pathology (p-tau), neurodegeneration (t-tau, MRI measurements), axonal injury (NFL), synaptic dysfunction (neurogranin), and neuroinflammation (sTREM2, YKL-40). Methods Three hundred seventy normal controls (CN) and 623 MCI patients from the ADNI (Alzheimer’s Disease Neuroimaging Initiative) database were recruited in this research. Linear mixed-effects models were used to evaluate the associations of baseline Aβ with cognitive decline and biomarkers of several pathophysiological pathways. Causal mediation analyses with 10,000 bootstrapped iterations were conducted to explore the mediation effects of AD pathologies on cognition. Results Tau-related pathology, neurodegeneration, neuroinflammation are correlated with the concentration of Aβ, even in CN participants. The results show that age, gender, and APOE ε4 carrier status have a moderating influence on some of these relationships. There is a stronger association of Aβ with biomarkers and cognitive changes in the elderly and females. In CN group, Aβ pathology is directly related to poor cognition and has no mediating effect (p < 0.05). In mild cognitive impairment, tau-related pathology (26.15% of total effect) and neurodegeneration (14.8% to 47.0% of total effect) mediate the impact of Aβ on cognition. Conclusions In conclusion, early Aβ accumulation has an independent effect on cognitive decline in CN and a tau, neurodegeneration-dependent effect in the subsequent cognitive decline in MCI patients.

ABCA7, a Genetic Risk Factor Associated with Alzheimer’s Disease Risk in African Americans

2022 ◽  
pp. 1-15
Author(s):  
Kaitlyn E. Stepler ◽  
Taneisha R. Gillyard ◽  
Calla B. Reed ◽  
Tyra M. Avery ◽  
Jamaine S. Davis ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
African American ◽  
Amyloid Beta ◽  
Disease Risk ◽  
African Ancestry ◽  
European Ancestry ◽  
Black Adults ◽  
American Black ◽  
The Impact

African American/Black adults are twice as likely to have Alzheimer’s disease (AD) compared to non-Hispanic White adults. Genetics partially contributes to this disparity in AD risk, among other factors, as there are several genetic variants associated with AD that are more prevalent in individuals of African or European ancestry. The phospholipid-transporting ATPase ABCA7 (ABCA7) gene has stronger associations with AD risk in individuals with African ancestry than in individuals with European ancestry. In fact, ABCA7 has been shown to have a stronger effect size than the apolipoprotein E (APOE) ɛ4 allele in African American/Black adults. ABCA7 is a transmembrane protein involved in lipid homeostasis and phagocytosis. ABCA7 dysfunction is associated with increased amyloid-beta production, reduced amyloid-beta clearance, impaired microglial response to inflammation, and endoplasmic reticulum stress. This review explores the impact of ABCA7 mutations that increase AD risk in African American/Black adults on ABCA7 structure and function and their contributions to AD pathogenesis. The combination of biochemical/biophysical and ‘omics-based studies of these variants needed to elucidate their downstream impact and molecular contributions to AD pathogenesis is highlighted.

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