Much prior emphasis in research on Alzheimer's disease (AD) has been on genetic studies, which have uncovered the fundamental involvement of the APP, APOE and PS1 genes. But with the exception of polymorphisms in APOE, known coding variants in these genes are quite rare, and the existing data do not fully account for the heritability of late-onset AD (LOAD) in the general population. Additional chromosomal loci putatively influencing AD susceptibility have been uncovered by genome-wide association studies (GWAS) and related high-throughput genomic scans, but replication has been uneven and the causative or predisposing genes have not been clearly pinpointed. Further it has not been possible to gauge the importance of numerous sub-threshold statistical peaks in these scans. New approaches are needed to get through these roadblocks, and we believe that a combined strategy to first obtain lists of loci with sequence-dependent allele-specific methylation (ASM) and/or allele-specific mRNA expression (ASE) in human cerebral cortex, and then overlap this information with statistical peaks from GWAS, will help to solve this problem. We will screen for ASM/ASE in human cerebral cortex using microarray-based and sequencing-based methods. We will validate the strongest candidate loci for ASM/ASE using independent assays, and overlap the list of such loci with data from existing and ongoing GWAS in LOAD. Loci from the intersection of these 2 datasets will be subjected to highly focused and thus cost efficient genetic fine mapping in 3 independent well characterized cohorts of LOAD case and controls. Our reasoning is that sequence-dependent ASM/ASE in or near specific genes in the cerebral cortex will be a robust indicator for the presence of bona fide cis-acting regulatory polymorphisms (rSNPs, rCNPs) that confer inter-individual differences in the expression of specific genes in the human cerebral cortex, and that within this set of genes will be some that cause inter-individual differences in LOAD susceptibility. Reproducible signals from GWAS and related genome scans for LOAD that overlap with loci that show ASM and/or ASE will thus have a strong functional underpinning and warrant further intensive study as biological contributors and potential therapeutic targets in LOAD.

Public Health Relevance

Our project is a combined genetic and epigenetic approach to understand the pathogenesis of Alzheimer's disease (AD), a degenerative disorder of neurons that is the most common cause of age-related dementia. We will use microarray-based and sequencing-based methods to identify the set of genes with genetically determined inter-individual differences in DNA methylation and RNA expression in the human brain. We will overlay this list of genes with lists of AD susceptibility candidate genes that are now emerging from genome- wide association studies (GWAS), and we will carry out fine mapping of the genes and chromosomal regions that score positively in both types of data. By this strategy we expect to be able to more confidently identify genes that affect susceptibility to AD.

National Institute of Health (NIH)
National Institute on Aging (NIA)
Research Project (R01)
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Special Emphasis Panel (ZRG1-PSE-E (02))
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Miller, Marilyn
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Columbia University (N.Y.)
Schools of Medicine
New York
United States
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Nievergelt, Caroline M; Wineinger, Nathan E; Libiger, Ondrej et al. (2014) Chip-based direct genotyping of coding variants in genome wide association studies: utility, issues and prospects. Gene 540:104-9
Peng, Qian; Gizer, Ian R; Libiger, Ondrej et al. (2014) Association and ancestry analysis of sequence variants in ADH and ALDH using alcohol-related phenotypes in a Native American community sample. Am J Med Genet B Neuropsychiatr Genet 165B:673-83
Norden-Krichmar, Trina M; Gizer, Ian R; Libiger, Ondrej et al. (2014) Correlation analysis of genetic admixture and social identification with body mass index in a Native American community. Am J Hum Biol 26:347-60
Paliwal, Anupam; Temkin, Alexis M; Kerkel, Kristi et al. (2013) Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation. PLoS Genet 9:e1003622
(2012) Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans. Proc Natl Acad Sci U S A 109:3985-90
Tycko, Benjamin (2010) Allele-specific DNA methylation: beyond imprinting. Hum Mol Genet 19:R210-20