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Updated: Dec 15, 2025

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

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Dysregulation of cancer genes by recurrent intergenic fusions

Jae Won Yun1,2,3, Lixing Yang4,5, Hye-Young Park6

  • 1Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea.

Genome Biology
|July 8, 2020
PubMed
Abstract

Insights

Intergenic gene fusions, previously overlooked, can create oncogenic transcripts and alter gene expression, significantly impacting cancer development. This study reveals their widespread role in tumorigenesis.

Area of Science:

  • Genomics
  • Cancer Biology
  • Molecular Oncology

Background:

  • Gene fusions are established drivers of cancer and therapeutic targets.
  • Intragenic breakpoints leading to chimeric mRNAs are well-documented.
  • The role of intergenic breakpoints in gene fusions remains largely unexplored.

Purpose of the Study:

  • To catalog gene-intergenic and intergenic-intergenic fusions.
  • To characterize the impact of these fusions on cancer genomes.
  • To investigate the mechanisms by which intergenic fusions contribute to tumorigenesis.

Main Methods:

  • Analysis of whole-genome sequencing data from 268 cancer patients.
  • Identification and cataloging of gene-intergenic and intergenic-intergenic fusion events.
  • Characterization of the functional impact of identified fusions.

Main Results:

  • Gene-intergenic fusions can generate chimeric oncogenic transcripts (e.g., ETV4, ERG, RSPO3, PIK3CA) via splicing.
  • Fusion-mediated repositioning of regulatory elements (enhancers) leading to gene overexpression is common.
  • Recurrent intergenic fusions were identified across various cancer types (breast, colon, prostate, thyroid).

Conclusions:

  • Intergenic fusions possess significant oncogenic potential.
  • Structural rearrangements involving intergenic regions have broad consequences in cancer.
  • This study highlights the importance of examining intergenic alterations in cancer genomics.
Keywords:
Chimeric transcriptsEnhancer hijackingStructural variationsWhole-genome sequencing

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