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Related Experiment Video

Updated: Sep 28, 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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Rapid and highly sensitive approach for multiplexed somatic fusion detection.

Samuel Abbou1,2,3, Sarah Finstuen-Magro1, Brigit McDannell1

  • 1Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.

Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc
|March 29, 2022
PubMed
Summary

A new digital PCR assay detects multiple cancer gene fusions quickly and affordably. This method works with low-quality RNA and small samples, aiding diagnosis in resource-limited settings.

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Area of Science:

  • Molecular Biology
  • Oncology
  • Genetics

Background:

  • Somatic gene translocations are crucial diagnostic markers in cancers, particularly pediatric sarcomas.
  • Current molecular diagnostic methods for detecting these translocations are limited by cost, speed, and multiplexing capabilities.

Purpose of the Study:

  • To develop a novel, sensitive, and multiplexed digital PCR assay for detecting somatic gene fusions.
  • To overcome the limitations of existing diagnostic approaches, offering a faster and more cost-effective solution.

Main Methods:

  • Development of a highly sensitive, multiplexed digital PCR assay.
  • Validation of specificity using cell lines and synthetic DNA.
  • Optimization of sensitivity using a tiered amplification approach for low-input/degraded RNA.
  • Testing on FFPE tissues and liquid biopsies.

Main Results:

  • The assay accurately identified seven targeted fusion transcripts within 1-2 days.
  • Tiered amplification enabled fusion detection from as little as 1 pg of RNA.
  • Fusions were detected in FFPE tissue, circulating tumor cells, and liquid biopsies.

Conclusions:

  • This novel multiplexed digital PCR assay efficiently detects multiple somatic gene fusions in challenging samples.
  • The assay is rapid, cost-effective, and adaptable, making it suitable for various biopsy types and resource-limited settings.