Autism Genetic Database (AGD): a Comprehensive Database Including Autism Susceptibility Gene-CNVs Integrated with Known Noncoding RNAs and Fragile Sites

Background: Autism belongs to a broad-spectrum of conditions known as autism spectrum disorders (ASD). To date, numerous susceptibility genes and genomic copy number variations (CNVs) have been reported in association with autism. However, in most cases the underlying causative genetic mechanisms are not fully understood. Recent developments in molecular genetic technologies and knowledge have introduced new avenues to be explored, in particular, for complex disorders. A good example is gene regulatory factors such as noncoding RNAs (ncRNAs) which are highly expressed in the nervous system. More recently, a study conducted by our group (Talebizadeh et al., 2008) and a report by Abu-Elneel et al. (2008) suggested that microRNAs, a group of ncRNAs, should be evaluated in the etiology of autism.

Objectives: In an effort to make all reported genomic features associated with ASD (i.e., susceptibility genes and CNVs) and their potential relationship with other genomic features impacting on human disease (e.g., ncRNAs and fragile sites) accessible to the scientific community, our research group designed the Autism Genetic Database, an open source database.

Methods: The Autism Genetic Database (AGD) system is installed on an Ubuntu Linux server and employs MySQL as a relational database management system (RDBMS) and Apache 2.0 as a web server platform. In AGD, data are searchable and displayed in either a genome browser or tabular format.

Results: Currently, a total of 145 and 473 autism susceptibility genes and CNVs respectively, plus 904 ncRNAs (i.e., microRNAs and snoRNAs) and 120 fragile sites (i.e., rare or common) grouped and organized by feature type are stored in AGD. This resource will be routinely updated and upgraded as new information relating to ASD becomes available. The existence of a comprehensive repository for the genomic information pertaining to ASD is crucial for the advancement of computational research into the field. The web interface provided by AGD will enable researchers, for example, to quickly identify specific ncRNAs within or close to reported autism candidate genes or CNVs in autistic subjects. Furthermore, the availability of such an integrated and comprehensive database will provide a valuable opportunity to explore and test autism genetic models.

Conclusions: While databases to maintain both autism susceptibility genes [AutDB (Basu et al., 2008)] and CNVs [Autism Chromosome Rearrangement Database (Marshall et al., 2008)] have been recently developed, the function of these available resources is to catalogue the relevant subset of autism related genomic data. While this information is useful to the research community, these currently available tools have a limited functionality with regards to the type of cross-talk search for which AGD has been designed.