Translating Alzheimer’s disease-associated polymorphisms into functional candidates: a survey of IGAP genes and SNPs
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The International Genomics of Alzheimer's Project (IGAP) is a consortium for characterizing the genetic landscape of Alzheimer's disease (AD). The identified and/or confirmed 19 single-nucleotide polymorphisms (SNPs) associated with AD are located on non-coding DNA regions, and their functional impacts on AD are as yet poorly understood. We evaluated the roles of the IGAP SNPs by integrating data from many resources, based on whether the IGAP SNP was (1) a proxy for a coding SNP or (2) associated with altered mRNA transcript levels. For (1), we confirmed that 12 AD-associated coding common SNPs and five nonsynonymous rare variants are in linkage disequilibrium with the IGAP SNPs. For (2), the IGAP SNPs in CELF1 and MS4A6A were associated with expression of their neighboring genes, MYBPC3 and MS4A6A, respectively, in blood. The IGAP SNP in DSG2 was an expression quantitative trait loci (eQTL) for DLGAP1 and NETO1 in the human frontal cortex. The IGAP SNPs in ABCA7, CD2AP, and CD33 each acted as eQTL for AD-associated genes in brain. Our approach for identifying proxies and examining eQTL highlighted potentially impactful, novel gene regulatory phenomena pertinent to the AD phenotype.
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Several studies have performed targeted analysis of the impact of identified AD SNPs on brain-specific gene expression.
“Several studies have performed targeted analysis of the impact of identified AD SNPs on brain-specific gene expression [200–202].”
From Genetic architecture of Alzheimer's disease (2020) · cites this paper as [201]
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Retracted
- Authors
- Katsumata, Y., Nelson, P. T., Estus, S., & Fardo, D. W.
- Affiliations
- University of Kentucky (US)
- Corresponding author
- Katsumata, Yuriko
- Venue
- Neurobiology of Aging
- Publisher
- Elsevier BV
- Published
- 2019-02
- Volume
- 74
- Pages
- 135-146
- ISSN
- 0197-4580 (ISSN-L)
- PMC
- PMC6331247
- OpenAlex
- W2896335844
- Cited by
- 30
- References
- 80
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 3 · 2023: 6 · 2022: 7 · 2021: 4 · 2020: 4 · 2019: 3
- FWCI
- 1.89
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Neurobiology of Aging (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Cell Repository for Alzheimer's Disease (U24 AG21886)
- National Institute on Aging (K25 AG043546, UL1TR000117, UK-ADC P30 AG028383, R01 AG045775, R01 AG057187)
- Topics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Keywords
- Alzheimer's disease, single nucleotide polymorphisms, non-coding variants, linkage disequilibrium, expression quantitative trait loci, gene expression regulation, CELF1, MS4A6A, MYBPC3, desmoglein 2, DLGAP1, Neto1, ABCA7, CD2AP, CD33, blood gene expression
- MeSH terms
- CELF1 Protein, SAP90-PSD95 Associated Proteins, Myosin Binding Protein C, Aged, Aged, 80 and over, Alzheimer Disease, Carrier Proteins, Female, Humans, Male, Membrane Proteins, RNA, Messenger, Transcription, Genetic, Linkage Disequilibrium, Receptors, N-Methyl-D-Aspartate, Polymorphism, Single Nucleotide, RNA, Untranslated, Quantitative Trait Loci, Desmoglein 2, Genetic Association Studies
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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