Refine Fusion Genes

This tool has been deprecated and will be retired in a future version of the software. It has been moved to the Legacy Tools (Image legacy_tools) folder of the Toolbox, and its name has "(legacy)" appended to it. If you have concerns about the future retirement of this tool, please contact QIAGEN Bioinformatics Support team at

Refine Fusion Genes takes as input the fusions identified by the Detect Fusion Genes tool, and re-counts the number of fusion crossing reads as well as the wildtype supporting reads using the RNA-Seq mapping against the wild type and fusion references. The fusion reference is an artificial reference sequence that "assumes" the detected fusions by generating new chromosomes corresponding to each fusion in addition to the original chromosomes (figure 27.1).

Image refinefusion
Figure 27.4: An artificial chromosome is created consisting of the vicinity of both ends of the fusion.

The RNA-Seq Analysis tool is used to re-map the reads to the artificial reference, with the expectation that reads that were used to detect the fusion will now map to the fusion transcript with a spliced read. In addition, some reads that did not originally map at all will now map to the artifical reference sequence, increasing evidence for the fusion event. The tool then calculates the "refined" Z-score and p-value using the same binomial model as the Detect Fusion Genes tool.

Refine Fusion Genes can be found in the Toolbox at:

        Tools | QIAseq Panel Expert Tools (Image qiaseq_expert_folder_closed_16_n_p) | QIAseq RNAscan Panel Expert Tools (Image fusion_gene_detection_folder_closed_16_n_p) | Refine Fusion Genes (Image refine_fusion_16_n_p)

It takes a fusion track as input (figure 27.2).

Image refinefusion1
Figure 27.5: Select a fusion track.

The next dialog allows you to configure the following parameters (figure 27.3):

Image refinefusion2
Figure 27.6: Set the parameters for the Refine Fusion Genes tool.

The Refined fusion gene report

The principal output of Refine Fusion Genes is a report listing only those fusions with FILTER=PASS. Each Fusion Gene is described by two tables and a fusion plot (figure 27.4).

Image refinefusionreport
Figure 27.7: A report section for a fusion gene.

The first table contains an overview of the most supported fusion for the fusion gene. Values in this table include:

The second table lists values for all supported fusion breakpoints in the fusion gene, sorted by read count. Therefore the first row in the table recapitulates some of the values from the first table. Additional rows show evidence for other fusions between the same two genes. At most 10 rows are shown.

The fusion plot visualizes all fusions between the reported transcripts.

Another output is a fusion track, described in the next section.

Fusion tracks

The fusion track has a table view containing the following information:

The main differences in the fusion tracks produced by Refine Fusion Genes when compared to those produced by Detect Fusion Genes are: