Identifying fusion genes from paired-end ribonucleic acid (rna) sequencing (rna-seq) data has the advantage that only expressed fusion genes will be found.

Whole genome sequencing data can also be used to search for gene fusions but it cannot tell which fusions are expressed and is less efficient at finding potentially oncogenic gene fusions.

Here, fusion gene detection is divided into two different use cases:

1) Full fusion gene search; identification of all gene fusions in a sample
2) Targeted fusion gene search: specific identification of only those gene fusions, in which one of the partner genes belongs to a short list of predefined genes. If the gene of interest is e.g. ABL1, this use case would identify all fusions XYZ-ABL1 and ABL1-XYZ, in which XYZ can be any gene other than ABL1 in the human genome

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