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Alzheimer's disease variant portal (ADVP): a catalog of genetic findings for Alzheimer's disease

By Pavel P. Kuksa, Chia-Lun Liu, Wei Fu, Liming Qu, Yi Zhao, Zivadin Katanic, Amanda B Kuzma, Pei-Chuan Ho, Kai-Teh Tzeng, Otto Valladares, Shin-Yi Chou, Adam C Naj, Gerard D. Schellenberg, Li-San Wang, Yuk Yee Leung

Posted 30 Sep 2020
medRxiv DOI: 10.1101/2020.09.29.20203950

BackgroundAlzheimers disease (AD) genetic findings span progressively larger genome-wide association studies (GWASs) for various outcomes and populations. These genetic findings are obtained from a single GWAS, joint- or meta-analyses of multiple GWAS datasets. However, no single resource provides harmonized and searchable information on all AD genetic associations obtained from these analyses, nor linking the identified genetic variants and reported genes with other supporting functional genomic evidence. MethodsWe created the Alzheimers Disease Variant Portal (ADVP), which provides unified access to a uniquely extensive collection of high-quality GWAS association results for AD. Records in ADVP are curated from the genome-wide significant and suggestive loci reported in AD genetics literature. ADVP contains curated results from all AD GWAS publications by Alzheimers Disease Genetics Consortium (ADGC) since 2009 and AD GWAS publications identified from other public catalogs (GWAS catalog). Genetic association information was systematically extracted from these publications, harmonized, and organized into three types of tables. These tables included structured publication, variant, and association categories to ensure consistent representation of all AD genetic findings. All extracted AD genetic associations were further annotated and integrated with NIAGADS Alzheimers Genomics DB in order to provide extensive biological and functional genomics annotations. ResultsCurrently, ADVP contains 6,990 AD-association records curated from >200 AD GWAS publications corresponding to >900 unique genomic loci and >1,800 unique genetic variants. The ADVP collection contains genetic findings from >80 cohorts and across various populations, including Caucasians, Hispanics, African-Americans, and Asians. Of all the association records, 46% are disease-risk, 13% are related to expression quantitative trait analyses, and 27% are related to AD endophenotypes and neuropathology. ADVP web interface allows accessing AD association records by individual variants, genes, publications, genomic regions of interest, and genome-wide interactive variant views. ADVP is integrated with the NIAGADS Alzheimers Genomics Database. Researchers can explore additional biological annotations at the genetic variant or gene level and view cross-reference functional genomics evidence provided by other public resources. ConclusionsADVP is the largest, most up-to-date, and comprehensive literature-derived collection of AD genetic associations. All records have been systematically curated, harmonized, and comprehensively annotated. ADVP is freely accessible at https://advp.niagads.org/.

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