deFuse

Overview

deFuse is a computational tool for fusion gene discovery from RNA-seq data. It uses discordant reads and split reads to detect gene fusions, applying multiple statistical filters to reduce false positives. It operates on paired-end RNA-seq reads without requiring a known list of fusion genes.

Used by

  • Applied in ICGC PedBrain pilocytic astrocytoma study (n=73 cases with matched RNA-seq) alongside TopHat-Fusion for comprehensive fusion gene discovery; identified novel BRAF fusions (RNF130:BRAF, CLCN6:BRAF, MKRN1:BRAF, GNAI1:BRAF) and NTRK2 fusions (QKI:NTRK2, NACC2:NTRK2) PMID:23817572
  • Applied alongside tophat-fusion to 80 rhabdomyosarcoma RNA-seq samples for fusion transcript detection; complementary algorithm increased sensitivity for detecting PAX rearrangements and novel in-frame fusions including PAX3-INO80D PMID:24436047
  • DeFuse used alongside FusionMap for fusion transcript detection in 25 TETs; identified 7 tumors with 1–16 fusions per case, including the known BRD4-NUTM1 fusion in the TY82 thymic carcinoma cell line PMID:24974848
  • deFuse used for fusion-gene detection in periampullary tumor RNA-seq data; identified two non-recurrent fusions — SLC45A3–ELK4 and a LINE–MET fusion — among 160 periampullary tumors PMID:26804919
  • Used alongside PRADA for fusion-gene discovery across 649 diffuse glioma RNA-seq profiles in the TCGA pan-glioma study; fusions combined with mutations and CNAs for pathway-level alteration mapping PMID:26824661

Notes

  • Corpus-grown slug; not found in cBioPortal canonical gene panel ontology.
  • Typically used in tandem with TopHat-Fusion for complementary fusion-calling sensitivity.

Sources

This page was processed by crosslinker on 2026-05-09. - PMID:24436047

This page was processed by crosslinker on 2026-05-09. - PMID:24974848

This page was processed by wiki-cli on 2026-05-11. - PMID:26804919

This page was processed by wiki-cli on 2026-05-14. - PMID:26824661

This page was processed by wiki-cli on 2026-05-14.