Alzheimer's disease variant portal (ADVP): Harmonized genetics data and evidence collection for Alzheimer's disease: Genetics/genetic factors of Alzheimer's disease. (7th December 2020)

• Record Type: Journal Article
• Authors: Leung, Yuk Yee; Kuksa, Pavel; Qu, Liming; Zhao, Yi; Katanic, Zivadin; Kuzma, Amanda B.; Fu, Wei; Liu, Chia‐Lun; Tzeng, Kai‐Teh; Valladares, Otto; Chou, Shin‐Yi; Naj, Adam C.; Schellenberg, Gerard D.; Wang, Li‐San
• Is Part Of: Alzheimer's & dementia. Volume 16(2020)Supplement 2
• Page Start: n/a
• Page End: n/a
• Publication Date: 2020-12-07
• Subjects: Alzheimer's disease -- Periodicals; Alzheimer Disease -- Periodicals; Dementia -- Periodicals; Démence; Maladie d'Alzheimer; Périodique électronique (Descripteur de forme); Ressource Internet (Descripteur de forme); 616.83
• DOI: 10.1002/alz.044090
• Languages: English
• ISSNs: 1552-5260

Abstract

Abstract: Background: Alzheimer's disease (AD) genetic findings span progressively large genome‐wide association studies (GWASs) and meta‐analyses, with no single resource providing unified, searchable information on identified genetic variants and genes and supporting functional genomic evidence. We developed ADVP (Alzheimer's Disease Variant Portal), a curated and harmonized interactive platform that provides unified access and visualization of a uniquely extensive up‐to‐date collection of GWAS data for AD. Methods: The contents of ADVP database are curated from high quality genome‐wide significant loci reported in literature. We included all AD GWAS publications by Alzheimer's Disease Genetics Consortium (ADGC) over the last ten years as a starting point and all other AD studies in GWAS catalog/GWAS central (MeSH D000544). For each publication, we systematically recorded all the association results reported in the main text. To facilitate curation, we developed a minimal set of information (meta‐data schema) to ensure all findings are annotated with the same information, including publication, association (variant rsID, genomic position, gene, association test results (p‐value, beta, odds ratio), effect allele, etc), phenotype, study design, target population, GWAS characteristics (size, number of cases/controls) among others. Collected data were organized into publication, variant, association, and evidence (functional genomics) database tables. Results: ADVP web interface provides multiple views of underlying data allowing browsing individual variants, genes, studies, genomic regions, genome‐wide/chromosome variant maps (interactive ideograms), and genome browser views incorporating functional genomics data. ADVP is also integrated with National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) GenomicsDB, a database that provides genetic and functional evidence for AD, to allow researchers cross‐reference other public resources (e.g., dbSNP, ClinVAR, ENCODE, Roadmap), and view functional evidence available for each genetic variant or gene. Conclusions: ADVP is the largest collection of systematically curated, harmonized and comprehensively annotated literature‐derived AD‐associated genetic variants. This current ADVP collection contains genetic findings from more than 60 cohorts and >200 studies across a variety of populations including Caucasians, Hispanics, African‐Americans, and Asians. Currently, ADVP contains ∼7, 000 AD‐association records corresponding to over 913 unique loci, 1803 unique genetic variants and 951 associations published in multiple studies. ADVP is freely accessible at http://advp.niagads.org .