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SeqUIaSCOPE Documentation

Fusion Genes

The Fusion Genes module enables users to review, validate, and flag causal gene fusions for inclusion in the clinical report. It integrates supporting evidence from Arriba and STARFusion, IGV snapshots of fusion breakpoints, and Arriba visualisation reports directly within the table.

For general information about working with tables (sorting, filtering, column visibility, export, and flagging), see Working with Tables.

Background Pre-processing

Before the fusion table becomes available, the application runs a background pre-processing step that generates IGV snapshots of each fusion breakpoint and extracts images from Arriba reports. This runs in the background — you can explore other modules while it is in progress. The fusion table loads immediately and updates progressively as snapshots become available.

For more details on this step, see Upload Data — Fusion Pre-processing.

The Fusion Table

The table displays all detected fusions with columns from both Arriba and STARFusion callers. By default, the table is sorted by Arriba confidence (high first), then by whether Arriba and STARFusion both called the fusion.

Two additional columns are specific to the fusion table and are not part of the input file:

  • Visual check — use the ✔ and ✖ buttons to mark a fusion as true positive or false positive after reviewing the evidence. This helps track which fusions have been manually reviewed without committing to flagging them for the report.
  • Notes — a free-text field for adding case-specific observations, such as reasons for marking a fusion as false positive or notes about low coverage.

The filter menu provides column visibility control. There are no additional pre-set filters for fusion data — all fusions are shown on load.

Expanded Row Preview

Each row can be expanded to reveal a side-by-side view of the Arriba visualisation report and the IGV snapshot for that fusion. This allows quick assessment of whether a fusion is supported by sequencing evidence at both breakpoints.

The expanded row preview requires Arriba output files (.pdf + .tsv) for the Arriba report images, and BAM files for IGV snapshots. If these were not provided during upload, the expanded row will be empty or partially available.

Tip: Use the expanded row preview to quickly identify obvious false positives — for example, fusions where no signal is visible at one of the breakpoint positions in the IGV snapshot.

Flagging Fusions

Select fusions from the table and click Select fusion as causal to flag them for the report. Flagged fusions appear in the review panel below the table where you can also remove items from the selection.

Flagged fusions can be opened in the IGV viewer for detailed read-level inspection. Use the IGV dropdown to select one or more patients (up to 4) and click Go to IGV.

IGV requires BAM files. If no BAM files were provided during upload, the IGV dropdown will not be available.