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Updated: Jan 13, 2026

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

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

Published on: July 5, 2019

EcDNA-borne structural variants drive oncogenic fusion transcript amplification.

Hyerim Yi¹, Shu Zhang¹, Jason Swinderman²

¹RNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.

|January 8, 2026

Summary

This summary is machine-generated.

Extrachromosomal DNA (ecDNA) amplifications drive cancer by creating oncogene fusions. These ecDNA fusions, particularly involving PVT1 and MYC, enhance cancer cell survival and transcription.

Keywords:

PVT1 RNA fusion RNA stability SRSF1 cancer ecDNA extrachromosomal DNA oncogene

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Last Updated: Jan 13, 2026

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

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Published on: July 5, 2019

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Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors

Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors

Published on: September 20, 2016

Area of Science:

Oncology
Genetics
Molecular Biology

Background:

Extrachromosomal DNA (ecDNA) amplifications are recognized drivers of human cancers.
Understanding the role of ecDNA in cancer development is crucial for therapeutic advancements.

Purpose of the Study:

To investigate the role of ecDNA in generating and amplifying oncogene fusion transcripts across various cancer types.
To identify the mechanisms by which ecDNA fusions contribute to cancer progression.

Main Methods:

Integrated analysis of whole-genome and transcriptome sequencing data from diverse tumor samples and cancer cell lines.
Comparative analysis of oncogene fusion event rates across different copy-number alterations.

Main Results:

ecDNAs exhibit the highest rate of oncogene fusion events among all copy-number alterations.
Fusion of the PVT1 gene with various 3' partners on ecDNA increases RNA stability and enhances MYC-dependent transcription.
This mechanism promotes cancer cell survival.

Conclusions:

ecDNA acts as a significant platform for oncogene fusion formation in cancer.
ecDNA contributes to genome instability and drives cancer progression through fusion events.