3.12.4. Annotate Fusions

This algorithm annotates against gene fusions in the selected source. This algorithm identifies complex rearrangements with breakends whose overlapping genes match those of fusions in the annotation source.

Requirements

An annotation source to use for annotating the fusions.

Options

The user may specify the following options:

  • Field of the 5’ gene identifier: Field of the 5’ gene ID in the annotation source

  • Field of the 3’ gene identifier: Field of the 3’ gene ID in the annotation source

  • Require both genes to be present in the annotated feature: Matching fusion is selected only if both genes match the genes of the annotated rearrangement

Output

The output includes columns for the selected source. If multiple features match, the results will be joined together in a list for each field. If a rearrangement does not have an matching feature, the fields will be filled in with missing values.

The following additional fields are also included in the output:

  • 5’ Gene IDs: The set of Entrez gene identifiers overlapping the 5’ mate pair

  • 3’ Gene IDs: The set of Entrez gene identifiers overlapping the right mate pair

  • Fusion Namess: Name of fusions to match.

  • # Matched: The number of annotation features matching this rearrangement.