SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of...

Area of Science:

• Genomics
• Bioinformatics
• Oncology

Background:

• Detecting gene fusions is crucial for cancer diagnosis and treatment.
• Next-generation sequencing (NGS) technologies have advanced gene fusion detection.
• Targeted PCR-based NGS assays offer improved accuracy for clinical applications.

Purpose of the Study:

• To develop a computationally efficient and accurate bioinformatics pipeline for detecting gene fusions.
• To address the limitations of existing methods in analyzing targeted PCR-based NGS data.
• To introduce SeekFusion as a novel solution for gene fusion identification.

Main Methods:

• Developed SeekFusion, a pipeline specifically designed for PCR-based NGS chemistries.
• Utilized biological samples processed with the QIAseq RNAscan assay.
• Employed in-silico simulated data for comprehensive evaluation.

Main Results:

• SeekFusion demonstrated superior accuracy in gene fusion detection compared to STAR-Fusion, TOPHAT-Fusion, and JAFFA-hybrid.
• The pipeline showed high computational efficiency.
• Analysis of 4,484 patient samples identified novel fusions in neurological tumors and sarcoma.

Conclusions:

• SeekFusion is a highly accurate and efficient tool for identifying gene fusions from targeted PCR-based NGS data.
• The pipeline outperforms existing methods and has potential for clinical utility in cancer diagnostics.
• SeekFusion facilitates the discovery of novel gene fusions in various cancer types.