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Fusion table and cards

Fusion Table

This section describes the fusion annotation results presented in the fusion table. The table includes details such as fusion gene partners, gene breakpoint coordinates and strand orientation, JaxCKB tier, OncoKB annotations, associated transcripts, and the functional domains involved in each fusion event.


Fusion table content

Rows contain the identified fusions, and columns contain core annotations for each fusion (Fusion Genes, Gene1 and Gene 2 breakpoints and strand, Reading frame, Spanning read support, Split read support at the junction and Confidence). However, none of the columns are mandatory - you can choose which ones will be displayed with the "Show/hide columns" icon . The length of each column on the variant table can be adjusted by dragging the sides of the column headers.

The column order in the variant table is user-specific, meaning each user can set up a custom order and visibility of columns.

Table columns:
  • Fusion genes: Displays the gene partners involved in the fusion (Gene 1 and Gene 2).
  • Gene 1 breakpoint: Displays the genomic coordinates of the Gene 1 breakpoint, including strand orientation.
  • Gene 2 breakpoint: Displays the genomic coordinates of the Gene 2 breakpoint, including strand orientation.
  • User manual classification: Displays a user-defined classification for fusion events. Custom classifications are linked to specific fusions and will be reused across other analyses within the same group when the same variant is detected.
  • Reading frame: Indicates whether the fusion is in-frame or out-of-frame, when this information is available in the input TSV file.
  • JaxCKB highest tier: Displays the highest AMP tier assigned to the fusion by JaxCKB.
  • OncoKB annotation: Displays the strength of clinical evidence linking the fusion to cancer diagnosis, prognosis, or therapeutic actionability.
  • OncoKB mutation effect: Displays the functional impact of the fusion at the biological level, independent of its clinical actionability.
  • COSMIC sample global / exact match: Displays the total number of affected samples reported in databases aggregated by Cancer Aggregator (COSMIC), including both global matches (fusions involving the same gene pair without known breakpoints) and exact matches (fusions with known breakpoints).
  • Functional domains (Gene 1 / Gene 2): Displays the retained PFAM functional domains for Gene 1 and Gene 2. Functional domain information is not available when breakpoint coordinates are unknown.
  • Gene 1 transcript: it displays the Gene 1 MANE transcript
  • Transcript position (exon number) Gene 1: it displays the exon number within the transcript at which the breakpoint occurs.
  • Gene 2 transcript: it displays the Gene 2 MANE transcript
  • Transcript position (exon number) Gene 2: it displays the exon number within the transcript at which the breakpoint occurs.
  • Spanning read support: it displays the number of spanning reads supporting the fusion
  • Split reads at the junction: it displays the number of split reads supporting the fusion 

  • Confidence: it displays the level of confidence supporting the fusion, when this is available in the TSV/CSV input file.

When the fusion event involves more than 2 gene partners, the fusion is split in 2 lines and displayed in two different lines.

Moreover, if both DNA and RNA analyses were performed, the DNA results can be accessed via a link that redirects to the corresponding DNA analysis for the same sample.

 

Fusion Cards

This section covers the available fusion cards and the information each card provides on consolidated fusion-related biological and clinical relevance from JaxCKB, OncoKB, and Cosmic.

Fusion details

The Fusion Details card displays the gene symbols of the fusion partners along with the breakpoint coordinates for each gene. When breakpoint information is available, a graphical representation of the fusion is also provided. This visualization illustrates the breakpoint positions within the chromosomes, their locations within each transcript, and the resulting fused product.

OncoKB

The OncoKB card provides a summarized view of clinically relevant information for a selected fusion. The card displays the OncoKB title, a variant summary icon, and key annotations including Oncogenicity, Mutation Effect, and the Therapeutic, Diagnostic, and Prognostic levels of evidence.

By clicking on the card, users can access the detailed OncoKB component, which mirrors the layout and content of the OncoKB website for the selected fusion.

OncoKB Component Details

Within the expanded OncoKB component, users can view:

  • Fusion name (e.g., ABL1/BCR-ABL1)
  • Oncogenicity (label and icon)
  • Mutation effect (label and icon, with a link to supporting bibliography)
    Therapeutic, Diagnostic, Prognostic, and FDA-recognized levels of evidence (labels and icons)
  • Short variant description
  • Mutation effect prediction
Evidence Tables

The OncoKB component includes a table organized into four tabs:

- Therapeutic:

  • Level (Therapeutic icons)
  • Alterations
    Level-associated cancer types
  • Drugs (with hoverable icons displaying drug descriptions)
  • Publications

- Diagnostic:

  • Level (Diagnostic icons)
  • Alterations
  • Level-associated cancer types
  • Publications

- Prognostic:

  • Level (Prognostic icons)
  • Alterations
    Level-associated cancer types
  • Publications

- FDA-Recognized Content:

  • FDA level of evidence (FDA icons)
  • Alteration
  • Cancer types

Cancer Knowledge Base (CKB)

CKB is a dynamic digital resource for interpreting complex cancer genomic profiles in the context of protein impact, therapies, and clinical trials.

When the CKB card is opened, the CKB component displays:

  • Fusion variant description
  • Impact (always reported as Fusion)
  • Evidence type
  • Variant
  • Extended evidence
  • Evidence count
  • Somatic classification tier
  • Protein effect
  • Evidence results
  • Extended evidence results

Fusion annotations are displayed for the relevant fusion (e.g., BCR-ABL1),or whenever a gene is involved regardless of the fusion partner (ABL1 fusions).

COSMIC

The Catalogue Of Somatic Mutations In Cancer (COSMIC), is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. Cosmic allows users to inspect gene fusions that are manually curated from peer reviewed publications by expert COSMIC curators. Importantly, COSMIC includes information on fusions involved in solid tumours and leukaemias.

The Cosmic card contains the gene level match with the Primary histologies frequency based on the total number of tested samples. Below this graph, a table is displayed with  the MutationIds in rows, and columns including i.e the gene partners,  the mRNA breakpoint position in each gene (inferred breakpoint), number of mutations and mutation frequency observed for each mutationID.

At the bottom of the table, the total number of publications is reported. Clicking this value opens a new window displaying the list of relevant publications.

When available, users can view Exact Match information, which corresponds to fusions with matching breakpoint coordinates.

The following details are displayed:

  • Genomic Mutation ID
  • Inferred Breakpoint 1
  • Inferred Breakpoint 2
  • Number of samples

Below these information a Sample table is displayed containing the following information:

  • Cosmic Sample ID
  • Primary tissue
  • Sub-tissue
  • Histology
  • Sub-histology
  • Sample type (e.g., tumour sample)
  • Age
  • Sex
  • Publications