Department of Psychiatry
Genetic Phenomena | Nervous System Diseases | Neurology | Neuroscience and Neurobiology | Population Biology
BACKGROUND: APOE epsilon4 allele is most common genetic risk factor for Alzheimer's disease (AD) and cognitive decline. However, it remains poorly understood why only some carriers of APOE epsilon4 develop AD and how ethnic variabilities in APOE locus contribute to AD risk. Here, to address the role of APOE haplotypes, we reassessed the diversity of APOE locus in major ethnic groups and in Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset on patients with AD, and subjects with mild cognitive impairment (MCI), and control non-demented individuals.
RESULTS: We performed APOE gene haplotype analysis for a short block of five SNPs across the gene using the ADNI whole genome sequencing dataset. The compilation of ADNI data with 1000 Genomes identified the APOE epsilon4 linked haplotypes, which appeared to be distant for the Asian, African and European populations. The common European epsilon4-bearing haplotype is associated with AD but not with MCI, and the Africans lack this haplotype. Haplotypic inference revealed alleles that may confer protection against AD. By assessing the DNA methylation profile of the APOE haplotypes, we found that the AD-associated haplotype features elevated APOE CpG content, implying that this locus can also be regulated by genetic-epigenetic interactions.
CONCLUSIONS: We showed that SNP frequency profiles within APOE locus are highly skewed to population-specific haplotypes, suggesting that the ancestral background within different sites at APOE gene may shape the disease phenotype. We propose that our results can be utilized for more specific risk assessment based on population descent of the individuals and on higher specificity of five site haplotypes associated with AD.
ADNI dataset, APOE, Alzheimer’s disease, DNA methylation, GWAS, Haplotype analysis, PCA, SNPs
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DOI of Published Version
BMC Neurosci. 2018 Apr 19;19(Suppl 1):16. doi: 10.1186/s12868-018-0413-4. Link to article on publisher's site
Babenko VN, Afonnikov DA, Ignatieva EV, Klimov AV, Gusev FE, Rogaev EI. (2018). Haplotype analysis of APOE intragenic SNPs. Open Access Articles. https://doi.org/10.1186/s12868-018-0413-4. Retrieved from https://escholarship.umassmed.edu/oapubs/3445
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This work is licensed under a Creative Commons Attribution 4.0 License.