The NIAGADS GenomicsDB is a searchable annotation resource that provides access to publicly available NIAGADS summary statistics datasets for Alzheimer's Disease and related neuropathologies. These data are linked to AD-revelant variant and gene annotations and functional genomics datasets, allowing AD researchers to easily identify and interpret interesting genomic regions via interactive search strategies and the NIAGADS genome browser.

The GenomicsDB is a collaboration between the University of Pennsylvania's Computational Biology and Informatics Laboratory (CBIL) and NIAGADS.

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When citing the NIAGADS resource, please use:

NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS): 2016 Update. Alzhemeier's and Dementia, 12(7), Supplement:P855-P856.

The data in the NIAGADS GenomicsDB are provided by independent researchers. A full listing of the GWAS Summary Statistics datasets and other resources incorporated in the GenomicsDB is provided in the Resources section below. When using these data in a publication, please cite the data providers. Relevant manuscripts or data-use policies for each NIAGADS accession can be found by following the link associated with the accession.

An example acknowledgement statement is as follows:

The data used for the analyses described in this manuscript were obtained from the NIAGADS GenomicsDB on MM/DD/YY.

The NIAGADS GenomicsDB site is built using the Strategies-WDK system, a graphical search interface and web development kit for functional genomics databases.

NIAGADS Genomics is powered by the Genomics Unified Schema (GUS), a relational database system comprising a modular schema capturing sequence data, functional genomics data, rich descriptions of methodology and study design using ontologies, and network models. The NIAGADS Genomics site is using GUS v. 4.0 in PostgreSQL v.9.4.

The NIAGADS GenomicsDB genome browser is built on the GMOD:JBrowse framework, and allows users to browse tracks generated from NIAGADS GWAS summary statistics datasets and compare against personal data tracks or a set of reposited tracks, each relevant to Alzheimer's Disease

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Variant Effect Prediction performed by running snpEff version 4.3i (2016-12-15) with default options against all SNPs listed in dbSNP v. 147, with GRCh37.p13/hg19 as the reference genome.

Gene membership in pathways was determined by using custom scripts to parse KEGG Markup Languange (KGML) representations of pathway maps procured via the KEGG REST API and to map KEGG genes and orthologs to the Ensembl Gene reference.

Variants supported by a p-value ≤ 5 x 10^-8 were identified as having genome-wide significance in a NIAGADS GWAS summary statistics dataset. For exome array studies, a cutoff of p-value ≤ 1 x 10^-3 was used.

The region 1000bp upstream of the gene transcription start site was used as a proxy for the gene promoter region.

We used genomic co-location queries to find ChIP-Seq sites for transcription factor binding (from selected brain-relevant ENCODE tracks; see Resources) overlapping or contained within gene promoter regions.

We used genomic co-location queries to find FANTOM5 identified expressed enhancer sites (tissue-independent) proximal to gene transcription start sites.

The functional enrichment analysis tool uses a one-sided Fisher's Exact test to evaluate the enrichment of a GO term or pathway in a gene list.

The test is implemented using the statistical function library packaged with the Scientific Computing Tools for Python (SciPy) toolkit.

Multiple hypothesis testing corrections were performed using the python package statsmodel.