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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

Fusion Gene Detection in Driver Mutation-Negative Melanomas Using RNA-Based Anchored Multiplex Polymerase Chain

Tokimasa Hida¹, Masashi Idogawa², Sayuri Sato¹

¹Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan.

Pigment Cell & Melanoma Research

|October 1, 2025

Summary

Fusion genes were identified in Japanese melanomas lacking common mutations, offering new therapeutic targets. This RNA-based approach detects actionable gene fusions in driver-negative melanoma.

Keywords:

CIC protein RNA gene fusion melanoma proto‐oncogene proteins B‐raf

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Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

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Published on: August 14, 2018

Area of Science:

Oncology
Genetics
Molecular Biology

Background:

Advanced melanoma treatment relies on immune checkpoint inhibitors (ICIs) and targeted therapies.
Efficacy of current treatments is limited in acral and mucosal melanomas, common in non-White populations.
These melanoma subtypes often lack major driver mutations like BRAF, necessitating alternative therapeutic strategies.

Purpose of the Study:

To detect fusion genes in Japanese melanomas that lack common driver mutations (BRAF, RAS, NF1, KIT).
To evaluate the utility of RNA-based anchored multiplex polymerase chain reaction (AMP) for identifying fusion genes in clinical samples.

Main Methods:

Analysis of RNA from 14 Japanese melanoma tumors, mostly formalin-fixed paraffin-embedded.
Utilized a custom Archer FUSIONPlex panel for RNA-based fusion detection.
Developed and validated an anchored multiplex PCR (AMP) workflow, including quality control.

Main Results:

Successfully generated libraries from 80% of analyzed samples.
Identified two in-frame fusion genes: MAD1L1::BRAF and CIC::MEGF8 (17% of cases).
MAD1L1::BRAF retains the BRAF kinase domain, suggesting potential MEK inhibitor targeting. CIC::MEGF8 is a novel fusion potentially causing transcriptional dysregulation.

Conclusions:

RNA-based fusion detection is a valuable method for driver-negative melanomas.
Fusion genes represent promising actionable therapeutic targets for specific melanoma subtypes.
The described AMP workflow is applicable to clinical samples for fusion gene identification.