What support does VarElect have for WGS?

VarElect allows phenotype interpretation for non-coding variants sequenced by Whole Genome Sequencing (WGS). This functionality is implemented by leveraging GeneHancer - the regulatory elements (promoters and enhancers) database of the GeneCards Suite (more details in the GeneHancer paper and the GeneCards Guide). In addition to gene symbols, VarElect input can include variant-containing regulatory elements (called GeneHancers), relate them to target genes and include those genes in the VarElect analysis along with variant-containing genes.

After mapping variants of interest to GeneHancers, GeneHancer identifiers (GHids) can be specified in the Gene/GeneHancer input box. In the interpretation results page, genes inferred via GeneHancers are annotated with all genes, marked by the relevant GeneHancer identifier (symbol::GHid).

When analyzing GeneHancers, the phenotype score is calculated as follows. Each gene-GeneHancer association has a total score, calculated by multiplying the GeneHancer confidence score by the GeneHancer–Gene association score. Total scores are normalized to a range of 0.05-0.8, and each gene-phenotype score of the GeneHancer gene target is multiplied by the normalized GeneHancer total score.