Key Features:

• Users can examine the variations in one genome, in a group of genomes, or in "computed" genomes, e.g. real-time subtraction of a germ-line genome from a cancer genome.

• User can view, through a tabbed interface, variations data at the level of base-pairs, genes and/or pathways, both in tables and in maps.

• Users can "filter" variations dynamically, to allow focus on features of biological interest. For example, filter out all variations present in dbSNP, or only show variations that alter protein function, or only show variations in genes found in the COSMIC cancer gene database, or in a subset of COSMIC by cancer type, or in a subset of the Gene Ontology, or in a subset of pathways from the NCI/Nature pathway set, or any combination of these. Each filtering operations takes a second or less.

• Variations can also be filtered by gene expression (i.e. only show genes present in a tissue, according to Affymetrix data) by uploading an Affymetrix data file; or filtered by any up-loaded gene set, e.g. genes hypothesized in a new paper to act as drivers for a particular cancer.

• Gene sets, created by any of the above mentioned methods, can be expanded using protein-protein interaction information, e.g. filter using an uploaded breast tumor gene expression set, filter by "Cell death" pathways, then expand to all the genes that have protein products that interact with the products of the resulting set.

• Users can also examine structural variants, and filter those based on the properties of the genes involved, e.g. show all tandem repeats involving a COSMIC gene.

• The results of these genomic analyses and any additional clinical data, serve as input to a rules engine, followed by a report generator. The report contains findings, notes and recommendations and can be edited before sign-off. Both the rule set and the report template can be tailored to the institution or even the department.