Genetic Association Database (GAD)

Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract The Genetic Association Database (GAD) is an archive of human genetic association studies of complex diseases and disorders.

The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature.

GAD is intended for use primarily by medical scientists and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine.

The data is from published scientific papers. Study data is recorded in the context of official human gene nomenclature with additional molecular reference numbers and links.

It is gene centered. That is, each record is a record of a gene or marker. If a study investigated 6 genes for a particular disorder, there will be 6 records.

Anyone may view this database and anyone may submit records. You do Not have to be an author on the original study to submit a record. All submitted records will be reviewed before inclusion into GAD.

There are three (3) main components of GAD: 1) A web interface; 2) PERL Modules; and 3) the database which uses the Oracle Relational DataBase Management System (RDBMS).

The database has three (3) layers; gene and disease are organized into a large fact table in a middle layer with dimensional views on the top layer. The bottom layer contains the tools for adding, editing, batch loading, and downloading data to and from the database.

The manufacturer identifies data fields common to genetic association studies such as disease phenotypes, sample sizes, significance values, population information and allele descriptions.

These fields are grouped into seven (7) views relevant to disease phenotypes, (Disease View), gene-based molecular data (Gene View), chromosomal and mutation information (CH-SNP-HapMap View), Reference View, Environmental Factor View, Gene Interaction View, and All View.

Query tools include keyword-search functions that permit field-specific searches, advanced combinatorial queries and pull-down selections of controlled vocabularies. Batch searches are done against an aggregate table, allowing the user to input a list of genes (300) at once.

New Features of GAD as of the October 2007 update -- The main emphasis of this update has been an increase in data content, quality, and integration with outside genomic data sources.

The number of database records has increased ~3.5 fold from ~8,000 records to over 28,000 records.

This is from a major contribution of core information from the CDC database via HuGE Navigator (version 1.3) - An integrated, searchable knowledge base of genetic associations and human genome epidemiology.

The CDC database is a component of the Human Genome Epidemiology Network, or HuGENet™.

The manufacturer has added a Gene-Gene Interaction-Environmental Factors View. This is built from the starting flag information from the CDC database.

In many cases, the manufacturer has stripped out the specific genes and alleles that are thought to be involved in gene-gene interactions and whether that interaction is dependent upon an environmental factor.

This information is relatively primitive at this time. As the manufacturer develops the gene-gene interaction view with added information and useful ways to represent this data, this area should take greater value.

Over time, the manufacturer hopes to assign replicated interacting gene relationships to biological pathways, genetic networks, and allow use of gene-gene interactions for applications in complex genetic disease.

Expansion of the Disease Class categories to include: Pharmacogenomic, Hematological, Neurological, Mitochondrial, Renal, and Vision.

In addition to official HUGO gene symbols, the Batch Search function now supports high-throughput searching with human UNIGENE numbers and human ENTREZ GENE numbers (the old locus link numbers).

In addition, in collaboration with the UCSC Genome Browser (see G6G Abstract Number 20197) the manufacturer has developed a UCSC track, called GADview, which places the entire GAD database on the UCSC browser system.

This allows integration of large-scale genetic disease data with molecular annotation such as SNPs, RNA splicing, CpG islands, QTLs, etc. as well as integration with the genomes of model organisms.

New Fields in GAD --

DNA end (bp): This adds the genomic nucleotide stop position in addition to the start position.

OMIM gene links: Added links from each GAD official HUGO genes to OMIM genes.

RS (Reference SNP) number: This is the dbSNP rs#. There are very few rs numbers in the database. However this information is of very high value. It allows integration with modern molecular databases.

UCSC Genome Browser gene link -- The UCSC Genome Browser is a major resource for comparative genomics and genetics.

Each HUGO official gene record links to the UCSC browser to allow cross comparison with numerous molecular and genomic data tracks within the UCSC browser system.

LSDB link: LSDBs are Locus Specific Databases. They are gene or gene family specific databases that collect mutation information related to specific genes or specific disorders.

The information from the GAD results page is 'very extensive', the following list is the 'GAD Link Information' to other databases that is displayed as part of the results page when you click on 'view' --

PubMed - The URL of the single PubMed abstract for this study;

GeneCards (see G6G Abstract Number 20170) - GeneCards URL for this gene; Pathway search - Pathway database;

NCBI SNP - A link to NCBI SNP database for that gene;

PubMed + Gene + Disease - Pre-set PubMed search for this Gene and this Disease;

PubMed + Gene + polymorphism - Pre-set PubMed search for this Gene and Polymorphism;

Map View - Link to NCBI map view; Ensembl - Link to Ensembl Genome Browser;

Entrez Gene Link - Entrez Gene extensive info for this gene;

NCBI AceView - NCBI AceView extensive info for this gene; Locus Specific Database - Access to this database for this gene;

CNV - Access to Database of Genomic Variants; HapMap - Access to the HapMap database;

Rep seq - Link to the NCBI Sequence Viewer; CDC GDPInfo Link - Link to HuGE Navigator Genopedia for this gene;

Comparative Toxicogenomics Database - Link to the Comparative Toxicogenomics Database for this gene;

ASAP Link - Link to the Alternative Splicing Annotation Project for this gene; SNPPER Link - Requires registration and password to access.

System Requirements



Manufacturer Web Site Genetic Association Database (GAD)

Price Contact manufacturer.

G6G Abstract Number 20314

G6G Manufacturer Number 101831