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FusionMap specifications


Unique identifier OMICS_00316
Name FusionMap
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Windows
Programming languages C#
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for FusionMap

FusionMap citations


Importance of Comprehensive Molecular Profiling for Clinical Outcome in Children With Recurrent Cancer

PMCID: 5920151
PMID: 29732366
DOI: 10.3389/fped.2018.00114

[…] genuity Variant Analysis. RNA sequencing was performed using Illumina's TruSeq Stranded Total RNA Library Prep Kit and paired-end sequencing was performed to gain an average output of 50–100 M reads. FusionMap was used for the screening of fusion transcripts [], and if positive, validation was carried out by Sanger sequencing. Sequencing data can be found in ENA under accession number PRJEB23819. […]


Genomic profiling of dedifferentiated liposarcoma compared to matched well differentiated liposarcoma reveals higher genomic complexity and a common origin

PMCID: 5880260
PMID: 29610390
DOI: 10.1101/mcs.a002386

[…] To reduce false positives (), we applied an integrative analysis of multiple fusion detection methods. We first applied four tools—TopHat-Fusion (), MapSplice (), FusionMap (), and PRADA ()—to detect putative fusions in our nine pairs of frozen WD/DD samples. Then, fusions with at least one junction read and at least two supporting mate pair reads that mapped t […]


Integrated Molecular Characterization of Gastrointestinal Stromal Tumors (GIST) Harboring the Rare D842V Mutation in PDGFRA Gene

Int J Mol Sci
PMCID: 5877593
PMID: 29510530
DOI: 10.3390/ijms19030732

[…] ine for the presence of any chromosomal rearrangements leading to gene fusions. For this purpose, four different tools were adopted: TopHat-Fusion v.2.0.9 [], Defuse v0.6.2 [], ChimeraScan v0.4.5 [], FusionMap v2015 []. In order to increase the specificity, a predicted gene fusion was considered for further investigation if it was detected at least by two of four predictors. Gene expression profil […]


Unforeseen clonal evolution of tumor cell population in recurrent and metastatic dermatofibrosarcoma protuberans

PLoS One
PMCID: 5627939
PMID: 28977029
DOI: 10.1371/journal.pone.0185826
call_split See protocol

[…] wiki/Bam_read_count) was used to count unique reads (MAPQ ≥ 20) at a gene level and the gene expression levels were normalized by reads per kilobase per million (RPKM). Fusion events were detected by FusionMap (http://www.arrayserver.com/wiki/index.php?title=FusionMap) []. […]


Involvement of DPP9 in gene fusions in serous ovarian carcinoma

BMC Cancer
PMCID: 5594496
PMID: 28893231
DOI: 10.1186/s12885-017-3625-6

[…] h were sequenced. The RNA-seq files gave on average 32 million read pairs per sample (range: 24–42 million). The FASTQC software was used for quality control of the raw sequence data []. The software FusionMap [] (release date 2012–04-16; paired-end utility using default parameters) and the associated pre-built Human B37 and RefGene from the FusionMap website were used for discovery of fusion tran […]


Investigating the mechanisms of papillary thyroid carcinoma using transcriptome analysis

PMCID: 5865774
PMID: 28849102
DOI: 10.3892/mmr.2017.7346

[…] The potential gene fusion events were predicted using FusionMap software (http://www.omicsoft.com/fusionmap/) (), and then visualized using Circos software (http://www.circos.ca/) (). The Gene Ontology (GO; www.geneontology.org/) database describes cellu […]


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FusionMap institution(s)
Research and Development Informatics, Amgen Inc; One Amgen Center Drive, Thousand Oaks, CA, USA

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