Match Genes Linked to Phenotypes

This algorithm determines matches between the gene annotations of each variant and list of genes associated with a group of user-specified phenotypes.

Requirements

This algorithm requires first annotating and classifying variants using a gene annotation source.

After clicking OK you will be prompted to select a Gene Names field to be used for matching.

After clicking OK a second time you will be prompted to enter a delimited list of phenotypes to use for selecting a gene list.

Options

This dialog allows the user to specify the following options:

• New Field Name: Name to be used for the newly created field.
• Enhance with OMIM phenotypes: Specifies that OMIM terms may be used.
• Gene Association: Determines how many nodes may be traversed in the ontology to reach a gene.
  • HPO gene association The matched genes must be directly related to the term in the HPO ontology
  • HPO +1 hop in GO Genes will be matched if they share a neighbor with one of the entered phenotype terms in the ontology. This allows for genes indirectly related through GO terms to be included in the gene list.
• Linked Genes: The computed set of gene names to match.

Output

A boolean column indicating whether the gene annotation for each variant matches at least one of the genes.