Features and Results

System requisites
Java Runtime Environment of Sun Microsystems 1.6.0 (Oracle, Redwood City, CA, USA) or equivalent is required, since the system is written in Java language. We used MySQL database for storing and retrieving CNV data and GBrowse2 [12] for drawing regional information. Both are freely available from their distribution websites.
Since the main search pages are written in Java Server Page (JSP) language, Apache Tomcat is needed for the application server and Apache HTTP server is needed for Gbrowse2 viewer pages (Fig. 1).

Data
CNVs of our previous study were retrieved from the Affymetrix Genome-Wide Human SNP array 5.0 of 3,578 Korean individuals. A total of 4,003 CNVRs were defined, and 2,077 CNVRs (51.9%) were potentially novel. The annotation data for genes were collected based on the Human Mar. 2006 NCBI36/hg18 build, and reference structure variants were retrieved from DGV (hg18.v8.aut.2009).

Database and viewer
Our web-based database viewer can display previously discovered CNVs by their positions (Fig. 2). Users can also filter out CNVs based on the DGV overlapped regions, CNV type (Gain/Loss/Complex), or their frequencies. Each selected region could be diagnosed in detail by clicking on it. DGV and OMIM ID columns are linked with corresponding websites, and CNVR position columns are linked with the genome browser. The genome browser is integrated based on the open source project GBrowse2. Users can seek or zoom in/out of CNVs across the chromosome by entering positions or clicking zoom buttons. GBrowse2 can also display interesting areas by dragging the region bar without reloading the entire page. Gene information of the selected area is also displayed, and details will be given on separate pop-up page by clicking on it.