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Updated: Dec 26, 2025

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
09:49

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing

Published on: July 5, 2019

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Pan-Cancer Analysis Reveals the Diverse Landscape of Novel Sense and Antisense Fusion Transcripts

Neetha Nanoth Vellichirammal1, Abrar Albahrani1, Jasjit K Banwait2

  • 1Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA.

Molecular Therapy. Nucleic Acids
|March 13, 2020
PubMed

Insights

Researchers discovered novel gene fusions in cancer, with non-canonical fusions being more common and variable across cancer types. These findings offer new cancer biomarkers and drug targets for further investigation.

Area of Science:

  • Oncology
  • Genomics
  • Bioinformatics

Background:

  • Gene fusions are implicated in cancer development and can serve as biomarkers and drug targets.
  • Understanding the landscape of fusion transcripts is crucial for cancer research.

Purpose of the Study:

  • To investigate the nature and distribution of gene fusions across various cancer types.
  • To identify novel fusion transcripts as potential biomarkers and therapeutic targets.

Main Methods:

  • Analyzed transcriptome data from ~9,000 primary tumors (The Cancer Genome Atlas) and cell lines (Cancer Cell Line Encyclopedia).
  • Utilized ChimeRScope, a novel algorithm, for detecting sense (canonical) and antisense (non-canonical) fusion transcripts.
  • Validated a subset of fusions using whole-genome sequencing and Sanger sequencing.

Main Results:

  • Identified recurrent fusions across cancers, with 61% being non-canonical (antisense) and 39% canonical (sense).
  • Discovered a high proportion (70%) of novel recurrent fusions, with significant variability in profiles across cancer types.
  • Observed notable differences in fusion profiles between primary tumors and cell lines.

Conclusions:

  • Recurrent non-canonical gene fusions represent a largely unexplored area in cancer biology.
  • Identified fusion genes hold promise for drug repurposing and mechanistic studies in oncology.
  • The study highlights the potential of fusion transcript analysis for cancer biomarker discovery.
Keywords:
CCLEChimeRScopeTCGAantisense fusioncancerfusion transcriptspan-cancer analysisprimary tumor-cell line comparisonrecurrent fusionstherapeutic targets

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