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

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Published on: July 5, 2019

Development of detection method for novel fusion gene using GeneChip exon array.

Yusaku Wada¹, Masaaki Matsuura, Minoru Sugawara

¹Genome Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan. ywada@fasmac.co.jp.

Journal of Clinical Bioinformatics

|February 19, 2014

Summary

A new method combining Exon Array and TAIL-PCR efficiently detects novel fusion genes, crucial in cancer development. This approach identified three new fusion genes in breast and pancreatic cancer cell lines.

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Area of Science:

Genomics
Molecular Biology
Oncology

Background:

Fusion genes are critical drivers of oncogenesis.
Existing genome-wide fusion gene detection methods require improvement for efficiency.

Purpose of the Study:

To develop and validate a novel, efficient method for detecting novel fusion genes.
To identify fusion genes in T-cell acute lymphocytic leukemia (T-ALL), breast, and pancreatic cancer cell lines.

Main Methods:

Utilized GeneChip Exon Array for whole-genome exon expression analysis.
Developed a computational program to screen for abnormal exon expression profiles.
Employed TAIL-PCR (Trans-PCR-based Amplification of Insert Ends) to confirm fusion partners.

Main Results:

The computational program successfully identified known fusion partner genes in T-ALL cell lines.
Applied to cancer cell lines, the method yielded 20 candidate genes in breast cancer and 23 in pancreatic cancer.
Three novel fusion genes were identified in breast and pancreatic cancer samples using TAIL-PCR.

Conclusions:

The developed Exon Array and TAIL-PCR based method is effective for novel fusion gene detection.
This method holds promise for identifying fusion genes in larger sample sets for cancer research.