Fusion Match Classes

An important step in interpreting gene fusion events involves matching detected gene fusions against genomic knowledgebases to extract relevant clinical evidence. FUSOR’s FusionMatcher class performs this operation, returning and classifying different kinds of matches along with their associated clinical evidence statements.

For more information on how to run the FusionMatcher, please visit Fusion Matching API

The list of potential match types is described below.

Exact Match

MatchType.EXACT

This occurs when the gene partner, transcript accession, exon number, exon offset, and genomic breakpoint for both the 5’ and 3’ partners are equivalent between the queried fusion and comparator fusion. This also occurs when the queried and comparator linker sequences are equivalent, if present.

Shared Genes, 5’ Exact

MatchType.SHARED_GENES_FIVE_PRIME_EXACT

This occurs when both the 5’ and 3’ gene partners of the queried fusion match those of the comparator fusion. Additionally, the transcript, exon number, exon offset, and genomic breakpoint for the 5’ partner are equivalent. However, at least one of these attributes is not equivalent for the 3’ partner.

Shared Genes, 3’ Exact

MatchType.SHARED_GENES_THREE_PRIME_EXACT

This occurs when both the 5’ and 3’ gene partners of the queried fusion match those of the comparator fusion. Additionally, the transcript, exon number, exon offset, and genomic breakpoint for the 3’ partner are equivalent. However, at least one of these attributes is not equivalent for the 5’ partner.

Shared Genes

MatchType.SHARED_GENES

This occurs when only the 5’ and 3’ gene partners of the queried fusion match those of the comparator fusion. The other transcript and exon data for the partners is either not equivalent or not present.

5’ Exact

MatchType.FIVE_PRIME_EXACT

This occurs when the 5’ partner of the queried fusion and comparator fusion have equivalent gene partners, transcript accessions, exon numbers, exon offsets, and genomic breakpoints. The 3’ partner of the queried fusion is unequal to the 3’ partner of the comparator fusion or is not available.

3’ Exact

MatchType.THREE_PRIME_EXACT

This occurs when the 3’ partner of the queried fusion and comparator fusion have equivalent gene partners, transcript accessions, exon numbers, exon offsets, and genomic breakpoints. The 5’ partner of the queried fusion is unequal to the 5’ partner of the comparator fusion or is not available.

5’ Gene

MatchType.FIVE_PRIME_GENE

This occurs when the 5’ partner of the queried fusion and comparator fusion have equivalent gene partners, but have missing or unequal transcript and breakpoint data. The 3’ partner of the queried fusion is unequal to the 3’ partner of the comparator fusion or is not available.

3’ Gene

MatchType.THREE_PRIME_GENE

This occurs when the 3’ partner of the queried fusion and comparator fusion have equivalent gene partners, but have missing or unequal transcript and breakpoint data. The 5’ partner of the queried fusion is unequal to the 5’ partner of the comparator fusion or is not available.

Fusion Matching Criteria and Example

A visualization describing the match criteria is shown below (A). An example assayed to categorical fusion match is also shown, where the assayed fusion describes joining of exon 13 of EML4 with exon 20 of ALK, and the categorical fusion describes the joining of exon 20 of EML4 with exon 20 of ALK (B).

In this example, both fusions have the same gene partners, there is an exact match for the 3’ partner, but the 5’ exon and 5’ junction location are unequal, resulting in a SHARED_GENES_THREE_PRIME_EXACT match being returned.