deFuse protocols

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deFuse specifications

Information


Unique identifier OMICS_01345
Name deFuse
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format TSV
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Sohrab P. Shah <>

Additional information


https://sourceforge.net/projects/defuse

Publication for deFuse

deFuse in pipelines

 (3)
2017
PMCID: 5431906
PMID: 28232751
DOI: 10.1038/s41467-016-0008-7

[…] transfected sample. the nt3 sirna transfected sample was also compared to a vehicle lipofectamine 2000-treated sample as an additional control., cg discovery was carried out using a version of the defuse gene fusion detection software with the classifier modified by removing the est_breakseqs_percident and break-seqs_estislands_percident features. inclusion of these classifier features […]

2017
PMCID: 5522265
PMID: 28489570
DOI: 10.18632/oncotarget.17244

[…] ontology (go) and kegg pathway annotation and enrichment analyses. the significant threshold for enrichment was set as false discovery rate (fdr) < 0.05., fusion transcripts were identified by defuse []. the default filtering processes of defuse were carried out as previously described []. the results of defuse were further filtered to reduce false positives with the following criteria: 1) […]

2014
PMCID: 4282731
PMID: 25499959
DOI: 10.1186/s13000-014-0218-4

[…] according to bayes factors, psi values and confidence intervals (table ).table 3, many fusion genes were reported as the potential cause for tumorigenesis, including gastric cancer [,]. using defuse and tophat, 7 candidate fusion genes were identified with stringent filtering criteria. and finally 3 fusion genes were selected by tophat realignment and manual inspection (table , figure ). […]


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deFuse in publications

 (45)
PMCID: 5877593
PMID: 29510530
DOI: 10.3390/ijms19030732

[…] data analysis was performed to examine 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 […]

PMCID: 5826927
PMID: 29483503
DOI: 10.1038/s41467-018-03273-1

[…] which, unfortunately, only consider uniquely mapped reads and cannot identify alterations in repetitive dna. in fact, no available tool, even those designed to identify gene fusions only (e.g., defuse), aims to reconstruct the sequence content of a fusion between a gene and a highly similar pseudogene. additionally, no existing tool aims to infer variants from targeted capture sequencing […]

PMCID: 5711926
PMID: 29214215
DOI: 10.1038/s41523-017-0048-0

[…] ()., rna-sequencing (2 × 54 bp) was performed for all 17 mbcs included in this study using the standard illumina mrna library protocol on a genome analyzer ii (illumina) as previously described. defuse and chimerascan were used to identify mate-pairs supporting novel chimeric transcripts as previously described (). candidates that resulted in open reading frames were annotated using […]

PMCID: 5662567
PMID: 29084941
DOI: 10.1038/s41467-017-01178-z

[…] (20% of all), were considered true mutations., to detect fusion genes, rna-seq bam files were analyzed using the software tools fusioncatcher (http://biorxiv.org/content/early/2014/11/19/011650) and defuse. potential fusion genes were manually confirmed by reviewing the break point loci of each gene using igv v2.3., array cgh analysis was performed using the human genome cgh 4 × 180 k microarray […]

PMCID: 5638846
PMID: 29026114
DOI: 10.1038/s41467-017-01026-0

[…] were validated by definition at base-pair resolution. rna reads were searched for gene fusion using three different algorithms (tophat-fusion; star-fusion (github.com/star-fusion/star-fusion/wiki); defuse)., we used previously described methods to call driver events. in brief, drivers in recessive cancer genes were called if mutations truncated the gene footprint. in oncogenes, point mutations […]


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deFuse institution(s)
Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada; School of Computing Science, Simon Fraser University, Burnaby, BC, Canada; Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
deFuse funding source(s)
Supported by grants from the British Columbia Cancer Foundation and the Vancouver General Hospital Foundation, Genome Canada, the Michael Smith Foundation for Health Research, the Canadian Breast Cancer Foundation and the Canadian Institutes of Health Research’s Bioinformatics Training Program.

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