FusionMap – detecting fusion genes from next-generation sequencing data at base-pair resolution

A novel method, FusionMap, is presented which aligns fusion reads directly to the genome without prior knowledge of potential fusion regions. FusionMap can detect fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq studies and characterize fusion junctions at base-pair resolution.

FusionMap achieved high sensitivity and specificity in fusion detection on two simulated RNA-Seq datasets which contained 75nt paired-end reads. FusionMap achieved substantially higher sensitivity and specificity than the paired-end approach when the inner distance between read pairs was small. Using FusionMap to characterize fusion genes in K562 chronic myeloid leukemia cell line, its accuracy was further demonstrated in fusion detection in both single-end RNA-Seq and gDNA-Seq datasets. These combined results show that FusionMap provides an accurate and systematic solution to detecting fusion events through junction-spanning reads.

AVAILABILITY: FusionMap includes reference indexing, read filtering, fusion alignment and reporting in one package. The software is free for non-commercial use at (http://www.omicsoft.com/fusionmap). CONTACT: ge@amgen.com SUPPLEMENTARY INFORMATION: Supplementary data are available at the journal’s web site.

  • Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W (2011) FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics [Epub ahead of print]. [abstract]