IM-Fusion

IM-Fusion is a tool for identifying transposon insertion sites in insertional mutagenesis screens using single- and paired-end RNA-sequencing data. It essentially identifies insertion sites from gene-transposon fusions in the RNA-sequencing data, which represent splicing events between the transposon and endogeneous genes.

IM-Fusion also identifies candidate genes for a given screen using a statistical test (based on the Poisson distribution) that identifies Commonly Targeted Genes (CTGs) – genes that are more frequently affected by insertions than would be expected by chance. To further narrow down a list of CTGs, which may contain hundreds of genes, IM-Fusion also tests if insertions in a CTG have a significant effect on the expression of the gene, which is a strong indicator of them having an actual biological effect.

IM-Fusion has the following key features:

• It identifies transposon insertion sites from both single- and paired-end RNA-sequencing data, without having any special sequencing requirements.

• It uses a gene-centric approach – both for the identification of insertions and for testing of differential expression for identified candidate genes – which greatly reduces the number of false positive candidate genes.

• It implements several exon-level and gene-level differential expression tests, which provide detailed insight into the effects of insertions on the expression of their target gene(s). By providing both a group-wise and a single-sample version of the test, IM-Fusion can identify effects for a single insertion in a specific sample, or determine the general effect of insertions on a given gene within the tumor cohort.

For more details on the approach and a comparison with existing methods, please see our manuscript.

Documentation

IM-Fusion’s documentation is available at nki-ccb.github.io/imfusion.

References

de Ruiter J.R., Kas S.M. et al. “Identifying transposon insertions and their effects from RNA-sequencing data” Nucleic Acids Research 2017, in press.

License

This software is released under the MIT license.