The IBsquare Toolbox for Oligogenic Analysis comprises three tools that assist researchers and doctors in the identification of genetic diseases. These three tools are closely intertwined as the data contained in the DIDA database was used to train the VarCopp predictor, which in turn is part of the pipeline for ORVAL.
DIDA (Digenic Diseases Database) is a database that provides detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance. The original DIDA database is transferred to a new repository named OLIDA (Oligogenic Diseases Database), which offers new features and adds support for new types of variants and combinations (from digenic to oligogenic) to the database.
VarCoPP (Variant Combination Pathogenicity Predictor) predicts the potential pathogenicity of variant combinations in gene pairs. It is based on digenic data present in DIDA and it was trained against variants from the 1000 Genomes Project. VarCoPP consists of an ensemble of 500 individual Random Forest predictors.
ORVAL (Oligogenic Resource for Variant Analysis) is a platform for the prediction and exploration of candidate disease-causing oligogenic variant combinations.
The tools are developed by the Interuniversity Institute of Bioinformatics in Brussels (IBsquare) which groups bioinformaticians and computational biologists from the VUB and ULB.