Introducing the NIAGADS Alzheimer's GenomicsDB API: A toolkit for remote exploration of Alzheimer's disease genetics. (1st February 2022)

• Record Type: Journal Article
• Authors: Greenfest‐Allen, Emily; Klamann, Conor; Mlynarski, Elizabeth E.; Kuksa, Pavel P.; Gangadharan, Prabhakaran; Kuzma, Amanda B; Valladares, Otto; Leung, Yuk Yee; Stoeckert, Christian J; Wang, Li‐San
• Is Part Of: Alzheimer's & dementia. Volume 17(2021)Supplement 3
• Page Start: n/a
• Page End: n/a
• Publication Date: 2022-02-01
• 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.053963
• Languages: English
• ISSNs: 1552-5260

Abstract

Abstract: Background: The Alzheimer's Genomics Database (NIAGADS GenomicsDB) provides public access to GWAS summary statistics datasets deposited at the NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS). The NIAGADS GenomicsDB makes available 69 summary statistics datasets and reports >150 million annotated variants from 23 GWAS studies of Alzheimer's disease and related dementias (AD/ADRD). Programmatic access to the database is essential for many bioinformatics applications dealing with AD/ADRD genetics. Method: The NIAGADS GenomicsDB is powered by a big data optimized relational database system. It uses ontologies to consistently annotate datasets, facilitating data harmonization and efficient real‐time data mining. AD/ADRD‐risk associated variants from GWAS datasets are annotated using the Alzheimer's Disease Sequencing Project's (ADSP) annotation pipeline (Butkiewicz et al. 2018). Variants are also mapped to proximal and co‐located genes and regulatory regions using the NIAGADS FILER functional genomics data repository (https://lisanwanglab.org/FILER). We have created a RESTful Application Programming Interface (API) that facilitates the integration of NIAGADS GenomicsDB datasets and annotations into software applications. The web service supports queries that return annotated GenomicsDB entries (genes, variants, genomic loci) and GWAS summary statistics results in the form of JSON documents. Results may contain functional annotations, genetic evidence for AD/ADRD risk, and/or sequence information associated with an entry. Calls to the API are based on simple URLs that specify the entry type and data required. The API also provides endpoints for querying variant linkage disequilibrium blocks, variant tracks (annotations and summary statistics) compatible with the IGV.js genome browser (https://github.com/igvteam/igv.js/), and LocusZoom.js (https://github.com/statgen/locuszoom/) renderings of the GWAS summary statistics datasets. Result: The NIAGADS GenomicsDB API establishes a simple framework that enables sharing and integration of annotated NIAGADS GenomicsDB entries and datasets. Use of the API requires only a HTTPS library and JSON parser, permitting large‐scale programmatic access and analysis of AD/ADRD‐linked variants independent of any specific programming language. Conclusion: The NIAGADS GenomicsDB API enables the easy retrieval of a wide range of genetic evidence for AD/ADRD, promoting data sharing and reuse among the AD/ADRD research community. Information about accessing the REST API as it becomes available can be found on the NIAGADS GenomicsDB website (https://www.niagads.org/genomics).