TopHat-Fusion

Overview

TopHat-Fusion is an extension of the TopHat RNA-seq aligner that detects gene fusions by identifying reads that span fusion junctions. It aligns reads to the genome, then searches for split-read evidence where portions of a read map to different genomic loci, indicative of a chimeric transcript.

Used by

  • Applied in ICGC PedBrain pilocytic astrocytoma study (n=73 cases with matched RNA-seq) alongside defuse for fusion gene discovery; identified novel NTRK2 fusions (QKI:NTRK2, NACC2:NTRK2) and novel BRAF fusion partners (RNF130, CLCN6, MKRN1, GNAI1) PMID:23817572
  • Applied to 80 rhabdomyosarcoma RNA-seq samples (Illumina HiSeq2000 100 bp PE) for fusion transcript detection; identified PAX3-NCOA1, PAX3-INO80D, and other cryptic rearrangements in histologically fusion-negative ARMS tumors PMID:24436047
  • TopHat (with Cufflinks) used for RNA-seq alignment and expression quantification in 25 TETs; fusion detection performed using FusionMap and DeFuse; 7 of 25 tumors had fusion transcripts identified PMID:24974848
  • Tophat2 with –fusion-search and Tophat-Post-Fusion used to detect 4,122 chimeras (mean 15 fusions/tumor) in 150 mCRPC transcriptomes, identifying recurrent ETS fusions in 56% of cases and actionable RAF/PI3K fusions. PMID:26000489
  • TopHat-Fusion used for fusion-transcript discovery in RNA-seq data from 17 ACC tumors; identified MYB-NFIB and novel NFIB fusion transcripts including RIMS1-NFIB and MYBL1-NFIB PMID:26862087
  • Applied TopHat-Fusion to detect gene fusion transcripts from RNA-seq data PMID:28373299

Notes

  • Corpus-grown slug; not found in cBioPortal canonical gene panel ontology.
  • Predecessor approach to STAR-Fusion and Arriba; used in TCGA-era fusion detection pipelines.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:24436047

This page was processed by crosslinker on 2026-05-14. - PMID:24974848

This page was processed by crosslinker on 2026-05-14. - PMID:26000489

This page was processed by crosslinker on 2026-05-14. - PMID:26862087

This page was processed by wiki-cli on 2026-05-14. - PMID:28373299

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